176 	simptr sim;  in smolNewSim()  local
204 extern CSTRING enum ErrorCode smolUpdateSim(simptr sim) {  in smolUpdateSim()
217 extern CSTRING enum ErrorCode smolRunTimeStep(simptr sim) {  in smolRunTimeStep()
242 extern CSTRING enum ErrorCode smolRunSim(simptr sim) {  in smolRunSim()
274 extern CSTRING enum ErrorCode smolRunSimUntil(simptr sim,double breaktime) {  in smolRunSimUntil()
289 extern CSTRING enum ErrorCode smolFreeSim(simptr sim) {  in smolFreeSim()
295 extern CSTRING enum ErrorCode smolDisplaySim(simptr sim) {  in smolDisplaySim()
311 	simptr sim;  in smolPrepareSimFromFile()  local
338 	simptr sim;  in smolLoadSimFromFile()  local
362 extern CSTRING enum ErrorCode smolReadConfigString(simptr sim,const char *statement,char *parameter…  in smolReadConfigString()
382 extern CSTRING enum ErrorCode smolSetSimFlags(simptr sim,const char *flags) {  in smolSetSimFlags()
394 extern CSTRING enum ErrorCode smolSetSimTimes(simptr sim,double timestart,double timestop,double ti…  in smolSetSimTimes()
409 extern CSTRING enum ErrorCode smolSetTimeStart(simptr sim,double timestart) {  in smolSetTimeStart()
420 extern CSTRING enum ErrorCode smolSetTimeStop(simptr sim,double timestop) {  in smolSetTimeStop()
431 extern CSTRING enum ErrorCode smolSetTimeNow(simptr sim,double timenow) {  in smolSetTimeNow()
442 extern CSTRING enum ErrorCode smolSetTimeStep(simptr sim,double timestep) {  in smolSetTimeStep()
454 extern CSTRING enum ErrorCode smolSetRandomSeed(simptr sim,long int seed) {  in smolSetRandomSeed()
465 extern CSTRING enum ErrorCode smolSetPartitions(simptr sim,const char *method,double value) {  in smolSetPartitions()
485 extern CSTRING enum ErrorCode smolSetGraphicsParams(simptr sim,const char *method,int timesteps,int…  in smolSetGraphicsParams()
510 extern CSTRING enum ErrorCode smolSetTiffParams(simptr sim,int timesteps,const char *tiffname,int l…  in smolSetTiffParams()
535 extern CSTRING enum ErrorCode smolSetLightParams(simptr sim,int lightindex,double *ambient,double *…  in smolSetLightParams()
568 extern CSTRING enum ErrorCode smolSetBackgroundStyle(simptr sim,double *color) {  in smolSetBackgroundStyle()
584 extern CSTRING enum ErrorCode smolSetFrameStyle(simptr sim,double thickness,double *color) {  in smolSetFrameStyle()
603 extern CSTRING enum ErrorCode smolSetGridStyle(simptr sim,double thickness,double *color) {  in smolSetGridStyle()
622 extern CSTRING enum ErrorCode smolSetTextStyle(simptr sim,double *color) {  in smolSetTextStyle()
638 extern CSTRING enum ErrorCode smolAddTextDisplay(simptr sim,char *item) {  in smolAddTextDisplay()
657 extern CSTRING enum ErrorCode smolSetOutputPath(simptr sim,const char *path) {  in smolSetOutputPath()
671 extern CSTRING enum ErrorCode smolAddOutputFile(simptr sim,char *filename,int suffix,int append) {  in smolAddOutputFile()
690 extern CSTRING enum ErrorCode smolAddOutputData(simptr sim,char *dataname) {  in smolAddOutputData()
705 enum ErrorCode smolOpenOutputFiles(simptr sim, int overwrite = 0)  in smolOpenOutputFiles()
717 extern CSTRING enum ErrorCode smolAddCommand(simptr sim,char type,double on,double off,double step,…  in smolAddCommand()
732 extern CSTRING enum ErrorCode smolAddCommandFromString(simptr sim,char *string) {  in smolAddCommandFromString()
750 extern CSTRING enum ErrorCode smolGetOutputData(simptr sim,char *dataname,int *nrow,int *ncol,doubl…  in smolGetOutputData()
779 extern CSTRING enum ErrorCode smolRunCommand(simptr sim,const char *commandstring) {  in smolRunCommand()
804 extern CSTRING enum ErrorCode smolAddSpecies(simptr sim,const char *species,const char *mollist) {  in smolAddSpecies()
830 extern CSTRING int smolGetSpeciesIndex(simptr sim,const char *species) {  in smolGetSpeciesIndex()
849 extern CSTRING int smolGetSpeciesIndexNT(simptr sim,const char *species) {  in smolGetSpeciesIndexNT()
868 extern CSTRING void smolGetSpeciesName(simptr sim,int speciesindex,char *species) {  in smolGetSpeciesName()
882 extern CSTRING int smolGetSpecies(simptr sim,int speciesindex,char *speciesname,double *difc,double…  in smolGetSpecies()
915 extern CSTRING enum ErrorCode smolSetSpeciesMobility(simptr sim,const char *species,enum MolecState…  in smolSetSpeciesMobility()
953 extern CSTRING enum ErrorCode smolAddMolList(simptr sim,const char *mollist) {  in smolAddMolList()
969 extern CSTRING int smolGetMolListIndex(simptr sim,const char *mollist) {  in smolGetMolListIndex()
985 extern CSTRING int smolGetMolListIndexNT(simptr sim,const char *mollist) {  in smolGetMolListIndexNT()
1001 extern CSTRING char *smolGetMolListName(simptr sim,int mollistindex,char *mollist) {  in smolGetMolListName()
1016 extern CSTRING enum ErrorCode smolSetMolList(simptr sim,const char *species,enum MolecState state,c…  in smolSetMolList()
1035 extern CSTRING enum ErrorCode smolSetMaxMolecules(simptr sim,int maxmolecules) {  in smolSetMaxMolecules()
1049 extern CSTRING enum ErrorCode smolAddSolutionMolecules(simptr sim,const char *species,int number,do…  in smolAddSolutionMolecules()
1077 extern CSTRING enum ErrorCode smolAddCompartmentMolecules(simptr sim,const char *species,int number…  in smolAddCompartmentMolecules()
1096 extern CSTRING enum ErrorCode smolAddSurfaceMolecules(simptr sim,const char *species,enum MolecStat…  in smolAddSurfaceMolecules()
1132 extern CSTRING int smolGetMoleculeCount(simptr sim,const char *species,enum MolecState state) {  in smolGetMoleculeCount()
1147     simptr sim, const char *species, enum MolecState state, double *color)  in smolSetMoleculeColor()
1174     simptr sim, const char *species, enum MolecState state, double size)  in smolSetMoleculeSize()
1196 extern CSTRING enum ErrorCode smolSetMoleculeStyle(simptr sim,const char *species,enum MolecState s…  in smolSetMoleculeStyle()
1222 extern CSTRING enum ErrorCode smolSetBoundaryType(simptr sim,int dimension,int highside,char type) {  in smolSetBoundaryType()
1238 extern CSTRING enum ErrorCode smolAddSurface(simptr sim,const char *surface) {  in smolAddSurface()
1256 extern CSTRING int smolGetSurfaceIndex(simptr sim,const char *surface) {  in smolGetSurfaceIndex()
1272 extern CSTRING int smolGetSurfaceIndexNT(simptr sim,const char *surface) {  in smolGetSurfaceIndexNT()
1288 extern CSTRING char *smolGetSurfaceName(simptr sim,int surfaceindex,char *surface) {  in smolGetSurfaceName()
1303 extern CSTRING enum ErrorCode smolSetSurfaceAction(simptr sim,const char *surface,enum PanelFace fa…  in smolSetSurfaceAction()
1338 extern CSTRING enum ErrorCode smolSetSurfaceRate(simptr sim,const char *surface,const char *species…  in smolSetSurfaceRate()
1377 extern CSTRING enum ErrorCode smolAddPanel(simptr sim,const char *surface,enum PanelShape panelshap…  in smolAddPanel()
1406 extern CSTRING int smolGetPanelIndex(simptr sim,const char *surface,enum PanelShape *panelshapeptr,…  in smolGetPanelIndex()
1442 extern CSTRING int smolGetPanelIndexNT(simptr sim,const char *surface,enum PanelShape *panelshapept…  in smolGetPanelIndexNT()
1476 extern CSTRING char *smolGetPanelName(simptr sim,const char *surface,enum PanelShape panelshape,int…  in smolGetPanelName()
1496 extern CSTRING enum ErrorCode smolSetPanelJump(simptr sim,const char *surface,const char *panel1,en…  in smolSetPanelJump()
1527 extern CSTRING enum ErrorCode smolAddSurfaceUnboundedEmitter(simptr sim,const char *surface,enum Pa…  in smolAddSurfaceUnboundedEmitter()
1549 extern CSTRING enum ErrorCode smolSetSurfaceSimParams(simptr sim,const char *parameter,double value…  in smolSetSurfaceSimParams()
1576 extern CSTRING enum ErrorCode smolAddPanelNeighbor(simptr sim,const char *surface1,const char *pane…  in smolAddPanelNeighbor()
1607 extern CSTRING enum ErrorCode smolSetSurfaceStyle(simptr sim,const char *surface,enum PanelFace fac…  in smolSetSurfaceStyle()
1653 extern CSTRING enum ErrorCode smolAddCompartment(simptr sim,const char *compartment) {  in smolAddCompartment()
1671 extern CSTRING int smolGetCompartmentIndex(simptr sim,const char *compartment) {  in smolGetCompartmentIndex()
1687 extern CSTRING int smolGetCompartmentIndexNT(simptr sim,const char *compartment) {  in smolGetCompartmentIndexNT()
1703 extern CSTRING char *smolGetCompartmentName(simptr sim,int compartmentindex,char *compartment) {  in smolGetCompartmentName()
1718 extern CSTRING enum ErrorCode smolAddCompartmentSurface(simptr sim,const char *compartment,const ch…  in smolAddCompartmentSurface()
1735 extern CSTRING enum ErrorCode smolAddCompartmentPoint(simptr sim,const char *compartment,double *po…  in smolAddCompartmentPoint()
1751 extern CSTRING enum ErrorCode smolAddCompartmentLogic(simptr sim,const char *compartment,enum CmptL…  in smolAddCompartmentLogic()
1774 extern CSTRING enum ErrorCode smolAddReaction(simptr sim,const char *reaction,const char *reactant1…  in smolAddReaction()
1819 extern CSTRING int smolGetReactionIndex(simptr sim,int *orderptr,const char *reaction) {  in smolGetReactionIndex()
1844 extern CSTRING int smolGetReactionIndexNT(simptr sim,int *orderptr,const char *reaction) {  in smolGetReactionIndexNT()
1869 extern CSTRING char *smolGetReactionName(simptr sim,int order,int reactionindex,char *reaction) {  in smolGetReactionName()
1885 extern CSTRING enum ErrorCode smolSetReactionRate(simptr sim,const char *reaction,double rate,int i…  in smolSetReactionRate()
1909 extern CSTRING enum ErrorCode smolSetReactionRegion(simptr sim,const char *reaction,const char *com…  in smolSetReactionRegion()
1941     simptr sim, const char *reaction, int *rulelist)  in smolSetReactionIntersurface()
1986 extern CSTRING enum ErrorCode smolSetReactionProducts(simptr sim,const char *reaction,enum RevParam…  in smolSetReactionProducts()
2025 extern CSTRING enum ErrorCode smolAddPort(simptr sim,const char *port,const char *surface,enum Pane…  in smolAddPort()
2045 extern CSTRING int smolGetPortIndex(simptr sim,const char *port) {  in smolGetPortIndex()
2061 extern CSTRING int smolGetPortIndexNT(simptr sim,const char *port) {  in smolGetPortIndexNT()
2077 extern CSTRING char *smolGetPortName(simptr sim,int portindex,char *port) {  in smolGetPortName()
2092 extern CSTRING enum ErrorCode smolAddPortMolecules(simptr sim,const char *port,int nmolec,const cha…  in smolAddPortMolecules()
2117 extern CSTRING int smolGetPortMolecules(simptr sim,const char *port,const char *species,enum MolecS…  in smolGetPortMolecules()
2144 extern CSTRING enum ErrorCode smolAddLattice(simptr sim,const char *lattice,const double *min,const…  in smolAddLattice()
2163 extern CSTRING int smolGetLatticeIndex(simptr sim,const char *lattice) {  in smolGetLatticeIndex()
2179 extern CSTRING int smolGetLatticeIndexNT(simptr sim,const char *lattice) {  in smolGetLatticeIndexNT()
2195 extern CSTRING char *smolGetLatticeName(simptr sim,int latticeindex,char *lattice) {  in smolGetLatticeName()
2209 extern CSTRING enum ErrorCode smolAddLatticeMolecules(simptr sim,const char *lattice, const char *s…  in smolAddLatticeMolecules()
2239 extern CSTRING enum ErrorCode smolAddLatticePort(simptr sim, const char *lattice, const char *port)…  in smolAddLatticePort()
2259 extern CSTRING enum ErrorCode smolAddLatticeSpecies(simptr sim,const char *lattice, const char *spe…  in smolAddLatticeSpecies()
2277 extern CSTRING enum ErrorCode smolAddLatticeReaction(simptr sim,const char *lattice, const char *re…  in smolAddLatticeReaction()