/dports/science/smoldyn/smoldyn-2.67/source/Smoldyn/ |
H A D | smoldynfuncs.h | 56 enum MolecState molstring2ms(char *string); 57 char *molms2string(enum MolecState ms,char *string); 63 int molismobile(simptr sim,int species,enum MolecState ms); 80 void molsetexist(simptr sim,int ident,enum MolecState ms,int exist); 81 int molcount(simptr sim,int i,int *index,enum MolecState ms,int max); 85 double MolCalcDifcSum(simptr sim,int i1,enum MolecState ms1,int i2,enum MolecState ms2); 153 int rxnisprod(simptr sim,int i,enum MolecState ms,int code); 230 int issurfprod(simptr sim,int i,enum MolecState ms); 231 …dex2tristate(enum MolecState ms3,enum PanelFace face,enum MolecState ms4,enum MolecState *msptr,en… 257 …rate(surfaceptr srf,int ident,const int *index,enum MolecState ms,enum MolecState ms1,enum MolecSt… [all …]
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H A D | smolmolec.c | 76 enum MolecState ans; in molstring2ms() 133 enum MolecState ms; in molstring2pattern() 863 else {mslo=(enum MolecState)(0);mshi=(enum MolecState)(MSMAX);} in molsetdifc() 892 else {mslo=(enum MolecState)(0);mshi=(enum MolecState)(MSMAX);} in molsetdifm() 929 else {mslo=(enum MolecState)(0);mshi=(enum MolecState)(MSMAX);} in molsetdrift() 964 else {mslo=(enum MolecState)(1);mshi=(enum MolecState)(MSMAX);} in molsetsurfdrift() 1015 else {mslo=(enum MolecState)(0);mshi=(enum MolecState)(MSMAX);} in molsetdisplaysize() 1064 for(ms1=(enum MolecState)0;ms1<(enum MolecState)MSMAX1;ms1=(enum MolecState)(ms1+1)) in molsetlistlookup() 1077 for(ms1=(enum MolecState)0;ms1<(enum MolecState)MSMAX1;ms1=(enum MolecState)(ms1+1)) in molsetlistlookup() 2564 for(ms4=(enum MolecState)0;ms4<(enum MolecState)MSMAX1;ms4=(enum MolecState)(ms4+1)) { in molgeneratespecies() [all …]
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H A D | libsmoldyn.h | 103 enum ErrorCode smolSetSpeciesMobility(simptr sim,const char *species,enum MolecState state,double d… 104 enum ErrorCode smolSetMoleculeColor(simptr sim, const char *species, enum MolecState state, double … 105 enum ErrorCode smolSetMoleculeSize(simptr sim, const char *species, enum MolecState state, double s… 112 enum ErrorCode smolSetMolList(simptr sim,const char *species,enum MolecState state,const char *moll… 116 enum ErrorCode smolAddSurfaceMolecules(simptr sim,const char *species,enum MolecState state,int num… 117 int smolGetMoleculeCount(simptr sim,const char *species,enum MolecState state); 118 enum ErrorCode smolSetMoleculeStyle(simptr sim,const char *species,enum MolecState state,double siz… 128 …r sim,const char *surface,enum PanelFace face,const char *species,enum MolecState state,enum SrfAc… 129 …sim,const char *surface,const char *species,enum MolecState state,enum MolecState state1,enum Mole… 152 …*reactant1,enum MolecState rstate1,const char *reactant2,enum MolecState rstate2,int nproduct,cons… [all …]
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H A D | smolrule.c | 482 enum MolecState *rctstate,*prdstate,ms; in RuleExpandRules() 563 ms=(enum MolecState) detailsi[0]; in RuleExpandRules() 569 ms=(enum MolecState) detailsi[0]; in RuleExpandRules() 575 ms=(enum MolecState) detailsi[0]; in RuleExpandRules() 581 ms=(enum MolecState) detailsi[0]; in RuleExpandRules() 587 ms=(enum MolecState) detailsi[0]; in RuleExpandRules() 593 ms=(enum MolecState) detailsi[0]; in RuleExpandRules() 599 ms=(enum MolecState) detailsi[0]; in RuleExpandRules() 605 ms=(enum MolecState) detailsi[0]; in RuleExpandRules() 612 ms=(enum MolecState) detailsi[0]; in RuleExpandRules() [all …]
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H A D | smolreact.c | 44 enum MolecState rxnpackstate(int order,enum MolecState *mstate); 45 void rxnunpackstate(int order,enum MolecState mspack,enum MolecState *mstate); 249 enum MolecState rxnpackstate(int order,enum MolecState *mstate) { in rxnpackstate() 266 enum MolecState ms; in rxnallstates() 271 for(ms=(enum MolecState)0;ms<(enum MolecState)nms2o && rxn->permit[ms];ms=(enum MolecState)(ms+1)); in rxnallstates() 538 enum MolecState ms; in rxnalloc() 579 …for(ms=(enum MolecState)0;ms<(enum MolecState)nms2o;ms=(enum MolecState)(ms+1)) rxn->permit[ms]=0;… in rxnalloc() 784 for(ms=(enum MolecState)0;ms<nms2o;ms=(enum MolecState)(ms + 1)) { in rxnoutput() 963 for(ms=(enum MolecState)0;ms<MSMAX;ms=(enum MolecState)(ms+1)) in writereactions() 1323 for(ms1=(enum MolecState)0;ms1<MSMAX;ms1=(enum MolecState)(ms1+1)) in rxnsetrate() [all …]
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H A D | smolsurface.c | 48 int srfsamestate(enum MolecState ms1,enum PanelFace face1,enum MolecState ms2,enum MolecState *ms3p… 49 …erseaction(enum MolecState ms1,enum PanelFace face1,enum MolecState ms2,enum MolecState *ms3ptr,en… 50 …istate2index(enum MolecState ms,enum MolecState ms1,enum MolecState ms2,enum MolecState *ms3ptr,en… 581 int srfsamestate(enum MolecState ms1,enum PanelFace face1,enum MolecState ms2,enum MolecState *ms3p… in srfsamestate() 604 …erseaction(enum MolecState ms1,enum PanelFace face1,enum MolecState ms2,enum MolecState *ms3ptr,en… in srfreverseaction() 647 …istate2index(enum MolecState ms,enum MolecState ms1,enum MolecState ms2,enum MolecState *ms3ptr,en… in srftristate2index() 675 …dex2tristate(enum MolecState ms3,enum PanelFace face,enum MolecState ms4,enum MolecState *msptr,en… in srfindex2tristate() 1047 for(ms=(enum MolecState)0;ms<MSMAX;ms=(enum MolecState)(ms+1)) in surfacealloc() 1060 for(ms=(enum MolecState)0;ms<MSMAX;ms=(enum MolecState)(ms+1)) in surfacealloc() 1122 for(ms=(enum MolecState)0;ms<MSMAX;ms=(enum MolecState)(ms+1)) in surfacefree() [all …]
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H A D | smolbng.c | 123 enum MolecState *mslist; in bngalloc() 235 CHECKMEM(mslist=(enum MolecState *)calloc(newmax,sizeof(enum MolecState))); in bngalloc() 270 CHECKMEM(mslist=(enum MolecState *)calloc(newmax,sizeof(enum MolecState))); in bngalloc() 695 enum MolecState newstate; in bngaddmonomer() 880 enum MolecState ms,trialms; in bngmakedefaultstate() 911 enum MolecState ms; in bngmakedifc() 943 enum MolecState ms; in bngmakedisplaysize() 972 enum MolecState ms; in bngmakecolor() 1011 enum MolecState ms; in bngmakesurfaction() 1138 for(ms4=(enum MolecState)0;ms4<(enum MolecState)MSMAX1;ms4=(enum MolecState)(ms4+1)) { in bngparsespecies() [all …]
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H A D | smoldyn.h | 234 enum MolecState enum 272 enum MolecState mstate; // physical state of molecule (ms) 377 enum MolecState* rctstate; // list of reactant states [rct] 381 enum MolecState* prdstate; // list of product states [prd] 920 enum MolecState* monomerstate; // default monomer state [index] 929 enum MolecState* bspstate; // default species state [index]
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H A D | smolcmd.c | 500 enum MolecState ms; in cmdifno() 519 enum MolecState ms; in cmdifless() 541 enum MolecState ms; in cmdifmore() 563 enum MolecState ms; in cmdifincmpt() 612 enum MolecState ms; in cmdifchange() 668 enum MolecState ms; in cmdwarnescapee() 720 enum MolecState ms; in cmdwarnescapeecmpt() 908 enum MolecState ms; in fnmolcount() 944 enum MolecState ms; in fnmolcountonsurf() 1173 enum MolecState ms; in cmdmolcountincmpt2() [all …]
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H A D | libsmoldyn.cpp | 885 enum MolecState ms; in smolGetSpecies() 900 for(ms=(enum MolecState)0;ms<(enum MolecState)MSMAX;ms=(enum MolecState)(ms+1)) { in smolGetSpecies() 1016 extern CSTRING enum ErrorCode smolSetMolList(simptr sim,const char *species,enum MolecState state,c… in smolSetMolList() 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() 1338 …sim,const char *surface,const char *species,enum MolecState state,enum MolecState state1,enum Mole… in smolSetSurfaceRate() 1774 …*reactant1,enum MolecState rstate1,const char *reactant2,enum MolecState rstate2,int nproduct,cons… in smolAddReaction() 1778 enum MolecState rctstate[MAXORDER]; in smolAddReaction() [all …]
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H A D | smoldynhybrid.c | 27 double evaluateSurfActionRate(simptr sim, surfactionptr actdetails, MolecState ms, double* pos, cha… in evaluateSurfActionRate()
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H A D | smolport.c | 418 int portgetmols(simptr sim,portptr port,int ident,enum MolecState ms,int remove) { in portgetmols() 436 int portgetmols2(simptr sim,portptr port,int ident,enum MolecState ms,int remove, double **position… in portgetmols2()
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H A D | smolgraphics.c | 567 enum MolecState ms; in graphicssettextitem() 1160 enum MolecState ms; in RenderMolecs() 1261 enum MolecState ms; in RenderText()
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H A D | smollattice.c | 702 enum MolecState ms; in latticereadstring()
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H A D | smolcomparts.c | 1224 enum MolecState ms; in comparttranslate()
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H A D | smolsim.cpp | 572 enum MolecState ms,rctstate[MAXORDER]; in simreadstring()
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/dports/science/smoldyn/smoldyn-2.67/source/python/ |
H A D | module.cpp | 161 .value("up", MolecState::MSup) in PYBIND11_MODULE() 712 MolecState state, in PYBIND11_MODULE() 798 MolecState state, in PYBIND11_MODULE() 826 MolecState state, in PYBIND11_MODULE() 835 MolecState state, in PYBIND11_MODULE() 852 MolecState state, in PYBIND11_MODULE() 909 MolecState state, in PYBIND11_MODULE() 930 MolecState state, in PYBIND11_MODULE() 931 MolecState state1, in PYBIND11_MODULE() 932 MolecState state2, in PYBIND11_MODULE() [all …]
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/dports/science/smoldyn/smoldyn-2.67/source/python/smoldyn/ |
H A D | smoldyn.py | 72 def _toMS(st: Union[str, _smoldyn.MolecState]) -> _smoldyn.MolecState: argument 81 return _smoldyn.MolecState.__members__[st] if isinstance(st, str) else st 136 if state not in _smoldyn.MolecState.__members__: 189 _smoldyn.MolecState.__members__[state] 247 size = {_smoldyn.MolecState.all: size} 251 _smoldyn.MolecState.__members__[state] 293 state = _smoldyn.MolecState.__members__["none"] 303 SpeciesState = Union[_smoldyn.MolecState, str] 828 sname, sstate = sp, _smoldyn.MolecState.soln 831 sstate = _smoldyn.MolecState.__members__[sstate]
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/dports/science/smoldyn/smoldyn-2.67/examples/S97_libsmoldyn/ |
H A D | test1.c | 29 enum MolecState states[1] = {MSsoln}; in main()
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/dports/science/smoldyn/smoldyn-2.67/tests/ |
H A D | test_libsmoldyn.py | 33 MS = CppApi.MolecState # enum MolcState
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/dports/science/smoldyn/smoldyn-2.67/examples/S97_libsmoldyn/testcode/ |
H A D | testcode.c | 31 enum MolecState prodstates[2]; in main()
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/dports/science/smoldyn/smoldyn-2.67/examples/S15_python/ |
H A D | DimensionalityEffect.py | 26 MS = S.MolecState
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