| /****************************************************************************** |
| * FILE: pgapack.h: This file contains all constant and structure |
| * definitions definitions for PGAPack as well as all |
| * function declarations. |
| * Authors: David M. Levine, Philip L. Hallstrom, David M. Noelle, |
| * Brian P. Walenz |
| ******************************************************************************/ |
| #include <stdio.h> |
| #include <stdlib.h> |
| #include <math.h> |
| #include <time.h> |
| #include <limits.h> |
| #include <float.h> |
| #include <string.h> |
| #include <ctype.h> |
| #include <mpi.h> |
| |
| |
| /* If OPTIMIZED, remove various sanity checks, and debug output. |
| * |
| * PGADebugEntered(a) - Print a debug message about entering "a" |
| * PGADebugExited(a) - Print a debug message about exiting "a" |
| * PGAFailIfNotSetup(a) - Fail fatally if PGASetUp has not been called |
| * PGAFailIfSetup(a) - Fail fatally if PGASetUp has been called |
| * PGACheckDataType(a, D) - Fail fatally if the datatype is not D |
| */ |
| #ifndef OPTIMIZE |
| #define OPTIMIZE 0 |
| #define PGADebugEntered(a) \ |
| PGADebugPrint(ctx, PGA_DEBUG_ENTERED, a, "Entered", PGA_VOID, NULL) |
| #define PGADebugExited(a) \ |
| PGADebugPrint(ctx, PGA_DEBUG_EXIT, a, "Exited", PGA_VOID, NULL) |
| #define PGAFailIfNotSetUp(Name) \ |
| if (ctx->sys.SetUpCalled == PGA_FALSE) \ |
| PGAError(ctx, "PGASetUp must be called before " Name, \ |
| PGA_FATAL, PGA_VOID, NULL) |
| #define PGAFailIfSetUp(Name) \ |
| if (ctx->sys.SetUpCalled == PGA_TRUE) \ |
| PGAError(ctx, Name " must be called before PGASetUp", PGA_FATAL, \ |
| PGA_VOID, NULL) |
| #define PGACheckDataType(Name, DataType) \ |
| if (ctx->ga.datatype != DataType) \ |
| PGAError(ctx, "DataType is incorrect for " Name,PGA_FATAL,PGA_VOID,NULL) |
| #else |
| #undef OPTIMIZE |
| #define OPTIMIZE 1 |
| #define PGADebugPrint(a,b,c,x,y,z) ; |
| #define PGADebugEntered(a) ; |
| #define PGADebugExited(a) ; |
| #define PGAFailIfNotSetUp(Name) ; |
| #define PGAFailIfSetUp(Name) ; |
| #define PGACheckDataType(Name, DataType) ; |
| #endif |
| |
| /***************************************** |
| * BINARY MACROS * |
| *****************************************/ |
| #ifndef WL |
| #error WL must be defined on the command line! |
| #endif |
| |
| #define ONEL ((PGABinary)1) |
| #define BIT(x,y) (y&(ONEL<<((WL-1)-(x)))) /* true if bit is 1, */ |
| #define SET(x,y) (y|=(ONEL<<((WL-1)-(x)))) /* set a bit to 1 */ |
| #define UNSET(x,y) (y&=(~(ONEL<<((WL-1)-(x)))))/* set a bit to 0, clear */ |
| #define TOGGLE(x,y) (y^=(ONEL<<((WL-1)-(x)))) /* complement a bits value */ |
| #define INDEX(ix,bx,bit,WL) ix=bit/WL;bx=bit%WL /* map global column (bit) */ |
| /* to word (ix) and bit (bx) */ |
| |
| /***************************************** |
| * ABSTRACT DATA TYPES * |
| *****************************************/ |
| #define PGA_DATATYPE_BINARY 1 /* Array of unsigned ints */ |
| /* parsed into bits : binary.c */ |
| #define PGA_DATATYPE_INTEGER 2 /* Array of ints : integer.c */ |
| #define PGA_DATATYPE_REAL 3 /* Array of doubles : real.c */ |
| #define PGA_DATATYPE_CHARACTER 4 /* Array of characters : character.c */ |
| #define PGA_DATATYPE_USER 5 /* --user defined-- */ |
| |
| #define PGABinary unsigned long |
| #define PGAInteger signed long int |
| #define PGAReal double |
| #define PGACharacter signed char |
| |
| #define PGA_INT 1 |
| #define PGA_DOUBLE 2 |
| #define PGA_CHAR 3 |
| #define PGA_VOID 4 |
| |
| |
| /***************************************** |
| * BOOLEANS * |
| *****************************************/ |
| #define PGA_TRUE 1 |
| #define PGA_FALSE 0 |
| |
| /***************************************** |
| * FLAGS * |
| *****************************************/ |
| #define PGA_FATAL 1 |
| #define PGA_WARNING 2 |
| |
| /***************************************** |
| * MISC CONSTANT * |
| *****************************************/ |
| #define PGA_TEMP1 -1138 |
| #define PGA_TEMP2 -4239 |
| |
| #define PGA_OLDPOP -6728 |
| #define PGA_NEWPOP -8376 |
| |
| #define PGA_UNINITIALIZED_INT -3827 |
| #define PGA_UNINITIALIZED_DOUBLE -968.3827 |
| |
| /***************************************** |
| * DEBUG LEVELS * |
| *****************************************/ |
| #define PGA_DEBUG_ENTERED 12 |
| #define PGA_DEBUG_EXIT 13 |
| #define PGA_DEBUG_MALLOC 80 |
| #define PGA_DEBUG_PRINTVAR 82 |
| #define PGA_DEBUG_SEND 22 |
| #define PGA_DEBUG_RECV 23 |
| #define PGA_DEBUG_MAXPGAPACKFUNCTIONS 300 |
| #define PGA_DEBUG_MAXFLAGS 1000 |
| |
| /***************************************** |
| * DIRECTION * |
| *****************************************/ |
| #define PGA_MAXIMIZE 1 /* specify direction for fitness calc */ |
| #define PGA_MINIMIZE 2 /* specify direction for fitness calc */ |
| |
| /***************************************** |
| * STOPPING CRITERIA * |
| *****************************************/ |
| #define PGA_STOP_MAXITER 1 /* Stop: for maximum iterations */ |
| #define PGA_STOP_NOCHANGE 2 /* Stop: no change in best string */ |
| #define PGA_STOP_TOOSIMILAR 4 /* Stop: homogeneous population */ |
| |
| /***************************************** |
| * CROSSOVER * |
| *****************************************/ |
| #define PGA_CROSSOVER_ONEPT 1 /* One point crossover */ |
| #define PGA_CROSSOVER_TWOPT 2 /* Two point crossover */ |
| #define PGA_CROSSOVER_UNIFORM 3 /* Uniform crossover */ |
| |
| /***************************************** |
| * SELECTION * |
| *****************************************/ |
| #define PGA_SELECT_PROPORTIONAL 1 /* proportional selection */ |
| #define PGA_SELECT_SUS 2 /* stochastic universal selection */ |
| #define PGA_SELECT_TOURNAMENT 3 /* tournament selection */ |
| #define PGA_SELECT_PTOURNAMENT 4 /* probabilistic tournament selection */ |
| |
| /***************************************** |
| * FITNESS * |
| *****************************************/ |
| #define PGA_FITNESS_RAW 1 /* use raw fitness (evaluation) */ |
| #define PGA_FITNESS_NORMAL 2 /* linear normalization fitness */ |
| #define PGA_FITNESS_RANKING 3 /* linear ranking fitness */ |
| |
| /***************************************** |
| * FITNESS (MINIMIZATION) * |
| *****************************************/ |
| #define PGA_FITNESSMIN_RECIPROCAL 1 /* reciprocal fitness */ |
| #define PGA_FITNESSMIN_CMAX 2 /* cmax fitness */ |
| |
| /***************************************** |
| * MUTATION * |
| *****************************************/ |
| #define PGA_MUTATION_CONSTANT 1 /* Real/Integer: Fixed value */ |
| #define PGA_MUTATION_RANGE 2 /* Real/Integer: Uniform range */ |
| #define PGA_MUTATION_UNIFORM 3 /* Real: +- Uniform random no. */ |
| #define PGA_MUTATION_GAUSSIAN 4 /* Real: +- Gaussian random no. */ |
| #define PGA_MUTATION_PERMUTE 5 /* Integer: Permutation (swap) */ |
| |
| /***************************************** |
| * POPULATION REPLACEMENT * |
| *****************************************/ |
| #define PGA_POPREPL_BEST 1 /* Select best string */ |
| #define PGA_POPREPL_RANDOM_NOREP 2 /* Select random string w/o replacement*/ |
| #define PGA_POPREPL_RANDOM_REP 3 /* Select random string w/ replacement*/ |
| |
| /**************************************** |
| * REPORT OPTIONS * |
| ****************************************/ |
| #define PGA_REPORT_ONLINE 1 /* Print the online analysis */ |
| #define PGA_REPORT_OFFLINE 2 /* Print the offline analysis */ |
| #define PGA_REPORT_HAMMING 4 /* Print the Hamming distance */ |
| #define PGA_REPORT_STRING 8 /* Print the string */ |
| #define PGA_REPORT_WORST 16 /* Print the worst individual */ |
| #define PGA_REPORT_AVERAGE 32 /* Print the average of the population */ |
| |
| /***************************************** |
| * RANDOMIZER * |
| *****************************************/ |
| #define PGA_RINIT_PERCENT 1 /* real percent offset */ |
| #define PGA_RINIT_RANGE 2 /* real range */ |
| #define PGA_IINIT_PERMUTE 1 /* integer permutation */ |
| #define PGA_IINIT_RANGE 2 /* integer range (nonunique) */ |
| #define PGA_CINIT_LOWER 1 /* all lowercase letters */ |
| #define PGA_CINIT_UPPER 2 /* all uppercase letters */ |
| #define PGA_CINIT_MIXED 3 /* both upper and lower case letters */ |
| |
| /***************************************** |
| * SET USER FUNCTION * |
| *****************************************/ |
| #define PGA_USERFUNCTION_CREATESTRING 1 |
| #define PGA_USERFUNCTION_MUTATION 2 |
| #define PGA_USERFUNCTION_CROSSOVER 3 |
| #define PGA_USERFUNCTION_PRINTSTRING 4 |
| #define PGA_USERFUNCTION_COPYSTRING 5 |
| #define PGA_USERFUNCTION_DUPLICATE 6 |
| #define PGA_USERFUNCTION_INITSTRING 7 |
| #define PGA_USERFUNCTION_BUILDDATATYPE 8 |
| #define PGA_USERFUNCTION_STOPCOND 9 |
| #define PGA_USERFUNCTION_ENDOFGEN 10 |
| #define PGA_NUM_USERFUNCTIONS 10 |
| |
| /***************************************** |
| * MPI SEND/RECV TAGS * |
| *****************************************/ |
| #define PGA_COMM_STRINGTOEVAL 1 /* MPI tag for sending string */ |
| #define PGA_COMM_EVALOFSTRING 2 /* MPI tag for returning evaluation */ |
| #define PGA_COMM_DONEWITHEVALS 3 /* MPI tag for ending parallel eval */ |
| |
| |
| |
| |
| /***************************************** |
| * INDIVIDUAL STRUTURE * |
| *****************************************/ |
| |
| typedef struct { /* primary population data structure */ |
| double evalfunc; /* evaluation function value */ |
| double fitness; /* fitness function value */ |
| int evaluptodate; /* flag whether evalfunc is current */ |
| void *chrom; /* pointer to the GA string */ |
| } PGAIndividual; |
| |
| |
| /***************************************** |
| * GA ALGORITHM STRUCTURE * |
| *****************************************/ |
| typedef struct { |
| int datatype; /* data type: binary, integer, or real */ |
| int optdir; /* direction of optimization */ |
| int tw; /* total number of words, full + partial */ |
| int fw; /* number of full (WL length) words */ |
| int eb; /* number of extra bits in last NOT full word*/ |
| int PopSize; /* Number of strings to use */ |
| int StringLen; /* string lengths */ |
| int StoppingRule; /* Termination Criteria */ |
| int MaxIter; /* Maximum number of iterations to run */ |
| int MaxNoChange; /* # of iters with no change before stopping */ |
| int MaxSimilarity; /* % of pop the same before stopping */ |
| int NumReplace; /* Number of string to replace each gen */ |
| int PopReplace; /* Method of choosing ind.s to copy to newpop*/ |
| int iter; /* iteration (generation) counter */ |
| int ItersOfSame; /* # iters with no change in best */ |
| int PercentSame; /* % of pop that is homogeneous */ |
| int NoDuplicates; /* Don't allow duplicate strings */ |
| int CrossoverType; /* Type of crossover for genetic algorithm */ |
| int SelectType; /* Type of selection for genetic algorithm */ |
| int SelectIndex; /* index of Select for next two individuals */ |
| int FitnessType; /* Type of fitness transformation used */ |
| int FitnessMinType; /* Transformation for minimization problems */ |
| int MutateOnlyNoCross; /* Mutate only strings not from crossover */ |
| int MutationType; /* Type of mutation used */ |
| int MutateIntegerValue; /* Multiplier to mutate Integer strings with */ |
| int MutateBoundedFlag; /* Confine integer alleles to given range */ |
| double MutateRealValue; /* Multiplier to mutate Real strings with */ |
| double MutationProb; /* Starting mutation probability */ |
| double CrossoverProb; /* Crossover probability */ |
| double UniformCrossProb; /* Prob of bit select in uniform crossover */ |
| double PTournamentProb; /* Prob of selection in Prob. Tournament */ |
| double FitnessRankMax; /* MAX value for use in ranking */ |
| double FitnessCmaxValue; /* Cmax value used to convert minimizations */ |
| double restartAlleleProb;/* prob of changing an allele in a restart */ |
| int restart; /* whether to use the restart operator */ |
| int restartFreq; /* frequency with which to restart */ |
| int *selected; /* array of indices for selection */ |
| int *sorted; /* array of sorted individual indices */ |
| PGAIndividual *oldpop; /* pointer to population (old) */ |
| PGAIndividual *newpop; /* pointer to population (new) */ |
| } PGAAlgorithm; |
| |
| |
| |
| /***************************************** |
| * OPERATIONS STRUCTURES * |
| *****************************************/ |
| typedef struct PGAContext PGAContext; |
| typedef struct { |
| void (*CreateString)(PGAContext *, int, int, int); |
| int (*Mutation)(PGAContext *, int, int, double); |
| void (*Crossover)(PGAContext *, int, int, int, int, int, int); |
| void (*PrintString)(PGAContext *, FILE *, int, int); |
| void (*CopyString)(PGAContext *, int, int, int, int); |
| int (*Duplicate)(PGAContext *, int, int, int, int); |
| void (*InitString)(PGAContext *, int, int); |
| MPI_Datatype (*BuildDatatype)(PGAContext *, int, int); |
| int (*StopCond)(PGAContext *); |
| void (*EndOfGen)(PGAContext *); |
| } PGACOperations; |
| |
| typedef struct { |
| int (*Mutation)(void *, void *, void *, void *); |
| void (*Crossover)(void *, void *, void *, void *, void *, void *, void *); |
| void (*PrintString)(void *, void *, void *, void *); |
| void (*CopyString)(void *, void *, void *, void *, void *); |
| int (*Duplicate)(void *, void *, void *, void *, void *); |
| void (*InitString)(void *, void *, void *); |
| int (*StopCond)(void *); |
| void (*EndOfGen)(void *); |
| } PGAFortranOperations; |
| |
| /***************************************** |
| * PARALLEL STRUCTURE * |
| *****************************************/ |
| typedef struct { |
| int MPIAlreadyInit; /* Flag whether MPI was previously initialized*/ |
| int NumIslands; /* Number of islands in island model */ |
| int NumDemes; /* Number of demes in neighborhood model */ |
| MPI_Comm DefaultComm; /* Default communicator for PGARun */ |
| int MPIStubLibrary; /* Boolean: real or stub version of MPI */ |
| } PGAParallel; |
| |
| /***************************************** |
| * REPORT STRUCTURE * |
| *****************************************/ |
| typedef struct { |
| int PrintFreq; /* How often to print statistics reports*/ |
| int PrintOptions; |
| double Offline; |
| double Online; |
| double Average; |
| double Best; |
| time_t starttime; |
| } PGAReport; |
| |
| |
| /***************************************** |
| * SYSTEM STRUCTURE * |
| *****************************************/ |
| typedef struct { |
| int UserFortran; /* user routines in Fortran or C? */ |
| int SetUpCalled; /* has PGASetUp been called? */ |
| int PGAMaxInt; /* largest int of machine */ |
| int PGAMinInt; /* smallest int of machine */ |
| double PGAMaxDouble; /* largest double of machine */ |
| double PGAMinDouble; /* smallest double of machine */ |
| } PGASystem; |
| |
| |
| /***************************************** |
| * DEBUG STRUCTURE * |
| *****************************************/ |
| typedef struct { |
| int PGADebugFlags[PGA_DEBUG_MAXFLAGS]; |
| } PGADebug; |
| |
| /***************************************** |
| * INITIALIZATION STRUCTURE * |
| *****************************************/ |
| typedef struct { |
| int RandomInit; /* flag whether to randomize strings */ |
| double BinaryProbability; /* probability that a Bit will be 1 */ |
| int RealType; /* type of real initialization */ |
| int IntegerType; /* type of integer initialization */ |
| int CharacterType; /* type of character initialization */ |
| int *IntegerMin; /* minimum of range of integers */ |
| int *IntegerMax; /* maximum of range of integers */ |
| double *RealMin; /* minimum of range of reals */ |
| double *RealMax; /* maximum of range of reals */ |
| int RandomSeed; /* integer to seed random numbers with */ |
| } PGAInitialize; |
| |
| /***************************************** |
| * SCRATCH DATA STRUCTURES * |
| *****************************************/ |
| typedef struct { |
| int *intscratch; /* integer-scratch space */ |
| double *dblscratch; /* double- scratch space */ |
| } PGAScratch; |
| |
| /***************************************** |
| * CONTEXT STRUCTURE * |
| *****************************************/ |
| struct PGAContext { |
| PGAAlgorithm ga; |
| PGACOperations cops; |
| PGAFortranOperations fops; |
| PGAParallel par; |
| PGAReport rep; |
| PGASystem sys; |
| PGADebug debug; |
| PGAInitialize init; |
| PGAScratch scratch; |
| }; |
| |
| /***************************************** |
| * binary.c |
| *****************************************/ |
| |
| void PGASetBinaryAllele ( PGAContext *ctx, int p, int pop, int i, int val ); |
| int PGAGetBinaryAllele ( PGAContext *ctx, int p, int pop, int i ); |
| void PGASetBinaryInitProb ( PGAContext *ctx, double probability ); |
| double PGAGetBinaryInitProb (PGAContext *ctx); |
| void PGABinaryCreateString(PGAContext *ctx, int p, int pop, int initflag); |
| int PGABinaryMutation( PGAContext *ctx, int p, int pop, double mr ); |
| void PGABinaryOneptCrossover(PGAContext *ctx, int p1, int p2, int pop1, int c1, |
| int c2, int pop2); |
| void PGABinaryTwoptCrossover(PGAContext *ctx, int p1, int p2, int pop1, int c1, |
| int c2, int pop2); |
| void PGABinaryUniformCrossover(PGAContext *ctx, int p1, int p2, int pop1, |
| int c1, int c2, int pop2); |
| void PGABinaryPrintString( PGAContext *ctx, FILE *fp, int p, int pop ); |
| void PGABinaryCopyString (PGAContext *ctx, int p1, int pop1, int p2, int pop2); |
| int PGABinaryDuplicate( PGAContext *ctx, int p1, int pop1, int p2, int pop2); |
| void PGABinaryInitString(PGAContext *ctx, int p, int pop); |
| MPI_Datatype PGABinaryBuildDatatype(PGAContext *ctx, int p, int pop); |
| int PGABinaryHammingDistance ( PGAContext *ctx, PGABinary *s1, PGABinary *s2 ); |
| void PGABinaryPrint( PGAContext *ctx, FILE *fp, PGABinary *chrom, int nb ); |
| |
| /***************************************** |
| * char.c |
| *****************************************/ |
| |
| void PGASetCharacterAllele (PGAContext *ctx, int p, int pop, int i, char value); |
| char PGAGetCharacterAllele (PGAContext *ctx, int p, int pop, int i); |
| void PGASetCharacterInitType(PGAContext *ctx, int value); |
| void PGACharacterCreateString (PGAContext *ctx, int p, int pop, int InitFlag); |
| int PGACharacterMutation( PGAContext *ctx, int p, int pop, double mr ); |
| void PGACharacterOneptCrossover(PGAContext *ctx, int p1, int p2, int pop1, |
| int c1, int c2, int pop2); |
| void PGACharacterTwoptCrossover( PGAContext *ctx, int p1, int p2, int pop1, |
| int c1, int c2, int pop2); |
| void PGACharacterUniformCrossover(PGAContext *ctx, int p1, int p2, int pop1, |
| int c1, int c2, int pop2); |
| void PGACharacterPrintString ( PGAContext *ctx, FILE *fp, int p, int pop); |
| void PGACharacterCopyString (PGAContext *ctx, int p1, int pop1, int p2, |
| int pop2); |
| int PGACharacterDuplicate( PGAContext *ctx, int p1, int pop1, int p2, int pop2); |
| void PGACharacterInitString(PGAContext *ctx, int p, int pop); |
| MPI_Datatype PGACharacterBuildDatatype(PGAContext *ctx, int p, int pop); |
| |
| /***************************************** |
| * cmdline.c |
| *****************************************/ |
| |
| void PGAReadCmdLine( PGAContext *ctx, int *argc, char **argv ); |
| void PGAParseDebugArg(PGAContext *ctx, char *st); |
| void PGAStripArgs(char **argv, int *argc, int *c, int num); |
| |
| /***************************************** |
| * create.c |
| *****************************************/ |
| |
| PGAContext *PGACreate ( int *argc, char **argv, |
| int datatype, int len, int maxormin ); |
| void PGASetUp ( PGAContext *ctx ); |
| void PGASetRandomInitFlag(PGAContext *ctx, int RandomBoolean); |
| int PGAGetRandomInitFlag (PGAContext *ctx); |
| void PGACreatePop (PGAContext *ctx, int pop); |
| void PGACreateIndividual (PGAContext *ctx, int p, int pop, int initflag); |
| |
| /***************************************** |
| * cross.c |
| *****************************************/ |
| |
| void PGACrossover ( PGAContext *ctx, int p1, int p2, int pop1, |
| int c1, int c2, int pop2 ); |
| int PGAGetCrossoverType (PGAContext *ctx); |
| double PGAGetCrossoverProb (PGAContext *ctx); |
| double PGAGetUniformCrossoverProb (PGAContext *ctx); |
| void PGASetCrossoverType (PGAContext *ctx, int crossover_type); |
| void PGASetCrossoverProb( PGAContext *ctx, double crossover_prob); |
| void PGASetUniformCrossoverProb( PGAContext *ctx, double uniform_cross_prob); |
| |
| /***************************************** |
| * debug.c |
| *****************************************/ |
| |
| void PGASortFuncNameIndex(PGAContext *ctx); |
| #if OPTIMIZE==0 |
| void PGADebugPrint( PGAContext *ctx, int level, char *funcname, |
| char *msg, int datatype, void *data ); |
| #endif |
| void PGASetDebugLevel(PGAContext *ctx, int level); |
| void PGAClearDebugLevel(PGAContext *ctx, int level); |
| void PGASetDebugLevelByName(PGAContext *ctx, char *funcname); |
| void PGAClearDebugLevelByName(PGAContext *ctx, char *funcname); |
| int PGAGetDebugLevelOfName(PGAContext *ctx, char *funcname); |
| int PGAGetDebugFlag(PGAContext *ctx, char *funcname); |
| void PGASetDebugFlag11(PGAContext *ctx, int Flag); |
| void PGASetDebugFlag20(PGAContext *ctx, int Flag); |
| void PGASetDebugFlag21(PGAContext *ctx, int Flag); |
| void PGASetDebugFlag30(PGAContext *ctx, int Flag); |
| void PGASetDebugFlag32(PGAContext *ctx, int Flag); |
| void PGASetDebugFlag34(PGAContext *ctx, int Flag); |
| void PGASetDebugFlag36(PGAContext *ctx, int Flag); |
| void PGASetDebugFlag40(PGAContext *ctx, int Flag); |
| void PGASetDebugFlag42(PGAContext *ctx, int Flag); |
| void PGASetDebugFlag44(PGAContext *ctx, int Flag); |
| void PGASetDebugFlag46(PGAContext *ctx, int Flag); |
| void PGASetDebugFlag48(PGAContext *ctx, int Flag); |
| void PGASetDebugFlag50(PGAContext *ctx, int Flag); |
| void PGASetDebugFlag52(PGAContext *ctx, int Flag); |
| void PGASetDebugFlag54(PGAContext *ctx, int Flag); |
| void PGASetDebugFlag56(PGAContext *ctx, int Flag); |
| void PGASetDebugFlag58(PGAContext *ctx, int Flag); |
| void PGASetDebugFlag60(PGAContext *ctx, int Flag); |
| void PGASetDebugFlag62(PGAContext *ctx, int Flag); |
| void PGASetDebugFlag64(PGAContext *ctx, int Flag); |
| void PGASetDebugFlag66(PGAContext *ctx, int Flag); |
| void PGAPrintDebugOptions(PGAContext *ctx); |
| |
| /***************************************** |
| * duplcate.c |
| *****************************************/ |
| |
| int PGADuplicate(PGAContext *ctx, int p, int pop1, int pop2, int n); |
| void PGAChange( PGAContext *ctx, int p, int pop ); |
| void PGASetNoDuplicatesFlag( PGAContext *ctx, int no_dup); |
| int PGAGetNoDuplicatesFlag (PGAContext *ctx); |
| |
| /***************************************** |
| * evaluate.c |
| *****************************************/ |
| |
| void PGASetEvaluation ( PGAContext *ctx, int p, int pop, double val ); |
| double PGAGetEvaluation ( PGAContext *ctx, int p, int pop ); |
| void PGASetEvaluationUpToDateFlag ( PGAContext *ctx, int p, int pop, |
| int status ); |
| int PGAGetEvaluationUpToDateFlag ( PGAContext *ctx, int p, int pop ); |
| double PGAGetRealFromBinary(PGAContext *ctx, int p, int pop, int start, |
| int end, double lower, double upper); |
| double PGAGetRealFromGrayCode(PGAContext *ctx, int p, int pop, int start, |
| int end, double lower, double upper); |
| void PGAEncodeRealAsBinary(PGAContext *ctx, int p, int pop, int start, |
| int end, double low, double high, double val); |
| void PGAEncodeRealAsGrayCode(PGAContext *ctx, int p, int pop, int start, |
| int end, double low, double high, double val); |
| int PGAGetIntegerFromBinary(PGAContext *ctx, int p, int pop, int start, |
| int end); |
| int PGAGetIntegerFromGrayCode(PGAContext *ctx, int p, int pop, int start, |
| int end); |
| void PGAEncodeIntegerAsBinary(PGAContext *ctx, int p, int pop, int start, |
| int end, int val); |
| void PGAEncodeIntegerAsGrayCode(PGAContext *ctx, int p, int pop, int start, |
| int end, int val); |
| double PGAMapIntegerToReal (PGAContext *ctx, int v, int a, int b, double l, |
| double u); |
| int PGAMapRealToInteger(PGAContext *ctx, double r, double l, double u, int a, |
| int b); |
| |
| /***************************************** |
| * fitness.c |
| *****************************************/ |
| |
| void PGAFitness ( PGAContext *ctx, int popindex ); |
| int PGARank( PGAContext *ctx, int p, int *order, int n ); |
| double PGAGetFitness ( PGAContext *ctx, int p, int pop ); |
| int PGAGetFitnessType (PGAContext *ctx); |
| int PGAGetFitnessMinType (PGAContext *ctx); |
| double PGAGetMaxFitnessRank (PGAContext *ctx); |
| void PGASetFitnessType( PGAContext *ctx, int fitness_type); |
| void PGASetFitnessMinType( PGAContext *ctx, int fitness_type); |
| void PGASetMaxFitnessRank( PGAContext *ctx, double fitness_rank_max); |
| void PGAFitnessLinearNormal ( PGAContext *ctx, PGAIndividual *pop ); |
| void PGAFitnessLinearRank ( PGAContext *ctx, PGAIndividual *pop ); |
| void PGAFitnessMinReciprocal ( PGAContext *ctx, PGAIndividual *pop ); |
| void PGAFitnessMinCmax ( PGAContext *ctx, PGAIndividual *pop ); |
| void PGASetFitnessCmaxValue( PGAContext *ctx, double val); |
| double PGAGetFitnessCmaxValue (PGAContext *ctx); |
| |
| /***************************************** |
| * hamming.c |
| *****************************************/ |
| |
| double PGAHammingDistance( PGAContext *ctx, int popindex); |
| |
| /***************************************** |
| * heap.c |
| *****************************************/ |
| |
| void PGADblHeapSort ( PGAContext *ctx, double *a, int *idx, int n ); |
| void PGAIntHeapSort ( PGAContext *ctx, int *a, int *idx, int n ); |
| |
| /***************************************** |
| * integer.c |
| *****************************************/ |
| |
| void PGASetIntegerAllele (PGAContext *ctx, int p, int pop, int i, int value); |
| int PGAGetIntegerAllele (PGAContext *ctx, int p, int pop, int i); |
| void PGASetIntegerInitPermute ( PGAContext *ctx, int min, int max); |
| void PGASetIntegerInitRange (PGAContext *ctx, int *min, int *max); |
| int PGAGetIntegerInitType (PGAContext *ctx); |
| int PGAGetMinIntegerInitValue (PGAContext *ctx, int i); |
| int PGAGetMaxIntegerInitValue (PGAContext *ctx, int i); |
| void PGAIntegerCreateString (PGAContext *ctx, int p, int pop, int InitFlag); |
| int PGAIntegerMutation( PGAContext *ctx, int p, int pop, double mr ); |
| void PGAIntegerOneptCrossover(PGAContext *ctx, int p1, int p2, int pop1, |
| int c1, int c2, int pop2); |
| void PGAIntegerTwoptCrossover( PGAContext *ctx, int p1, int p2, int pop1, |
| int c1, int c2, int pop2); |
| void PGAIntegerUniformCrossover(PGAContext *ctx, int p1, int p2, int pop1, |
| int c1, int c2, int pop2); |
| void PGAIntegerPrintString ( PGAContext *ctx, FILE *fp, int p, int pop); |
| void PGAIntegerCopyString (PGAContext *ctx, int p1, int pop1, int p2, int pop2); |
| int PGAIntegerDuplicate( PGAContext *ctx, int p1, int pop1, int p2, int pop2); |
| void PGAIntegerInitString(PGAContext *ctx, int p, int pop); |
| MPI_Datatype PGAIntegerBuildDatatype(PGAContext *ctx, int p, int pop); |
| |
| /***************************************** |
| * mpi_stub.c |
| *****************************************/ |
| |
| |
| /***************************************** |
| * mutation.c |
| *****************************************/ |
| |
| int PGAMutate(PGAContext *ctx, int p, int pop); |
| void PGASetMutationType( PGAContext *ctx, int mutation_type); |
| int PGAGetMutationType (PGAContext *ctx); |
| void PGASetMutationRealValue( PGAContext *ctx, double val); |
| double PGAGetMutationRealValue (PGAContext *ctx); |
| void PGASetMutationIntegerValue( PGAContext *ctx, int val); |
| int PGAGetMutationIntegerValue (PGAContext *ctx); |
| void PGASetMutationBoundedFlag(PGAContext *ctx, int val); |
| int PGAGetMutationBoundedFlag(PGAContext *ctx); |
| void PGASetMutationProb(PGAContext *ctx, double mutation_prob); |
| double PGAGetMutationProb (PGAContext *ctx); |
| |
| /***************************************** |
| * parallel.c |
| *****************************************/ |
| |
| void PGARunGM(PGAContext *ctx, double (*f)(PGAContext *, int, int), |
| MPI_Comm comm); |
| void PGAEvaluateSeq(PGAContext *ctx, int pop, |
| double (*f)(PGAContext *, int, int)); |
| void PGAEvaluateCoop(PGAContext *ctx, int pop, |
| double (*f)(PGAContext *, int, int), MPI_Comm comm); |
| void PGAEvaluateMS(PGAContext *ctx, int pop, |
| double (*f)(PGAContext *c, int p, int pop), MPI_Comm comm); |
| void PGAEvaluateSlave(PGAContext *ctx, int pop, |
| double (*f)(PGAContext *, int, int), MPI_Comm comm); |
| void PGAEvaluate(PGAContext *ctx, int pop, |
| double (*f)(PGAContext *, int, int), MPI_Comm comm); |
| MPI_Datatype PGABuildDatatype(PGAContext *ctx, int p, int pop); |
| void PGASendIndividual(PGAContext *ctx, int p, int pop, int dest, int tag, |
| MPI_Comm comm); |
| void PGAReceiveIndividual(PGAContext *ctx, int p, int pop, int source, int tag, |
| MPI_Comm comm, MPI_Status *status); |
| void PGASendReceiveIndividual(PGAContext *ctx, int send_p, int send_pop, |
| int dest, int send_tag, int recv_p, int recv_pop, |
| int source, int recv_tag, MPI_Comm comm, |
| MPI_Status *status); |
| void PGARunIM(PGAContext *ctx, double (*f)(PGAContext *c, int p, int pop), |
| MPI_Comm tcomm); |
| void PGARunNM(PGAContext *ctx, double (*f)(PGAContext *c, int p, int pop), |
| MPI_Comm tcomm); |
| int PGAGetRank (PGAContext *ctx, MPI_Comm comm); |
| int PGAGetNumProcs (PGAContext *ctx, MPI_Comm comm); |
| void PGASetNumIslands( PGAContext *ctx, int n); |
| int PGAGetNumIslands (PGAContext *ctx); |
| void PGASetNumDemes( PGAContext *ctx, int numdemes); |
| int PGAGetNumDemes (PGAContext *ctx); |
| void PGASetCommunicator( PGAContext *ctx, MPI_Comm comm); |
| MPI_Comm PGAGetCommunicator( PGAContext *ctx); |
| |
| /***************************************** |
| * pga.c |
| *****************************************/ |
| |
| void PGARun(PGAContext *ctx, double (*evaluate)(PGAContext *c, int p, int pop)); |
| void PGARunMutationAndCrossover (PGAContext *ctx, int oldpop, int newpop); |
| void PGARunMutationOrCrossover ( PGAContext *ctx, int oldpop, int newpop ); |
| void PGAUpdateGeneration(PGAContext *ctx, MPI_Comm comm); |
| int PGAGetDataType (PGAContext *ctx); |
| int PGAGetOptDirFlag (PGAContext *ctx); |
| int PGAGetStringLength (PGAContext *ctx); |
| int PGAGetVariableStringLength (PGAContext *ctx, int p, int pop); |
| int PGAGetGAIterValue (PGAContext *ctx); |
| void PGASetMutationOrCrossoverFlag( PGAContext *ctx, int flag); |
| void PGASetMutationAndCrossoverFlag( PGAContext *ctx, int flag); |
| int PGAGetMutationOrCrossoverFlag (PGAContext *ctx); |
| int PGAGetMutationAndCrossoverFlag (PGAContext *ctx); |
| |
| /***************************************** |
| * pop.c |
| *****************************************/ |
| |
| void PGASortPop ( PGAContext *ctx, int pop ); |
| int PGAGetPopSize (PGAContext *ctx); |
| int PGAGetNumReplaceValue (PGAContext *ctx); |
| int PGAGetPopReplaceType (PGAContext *ctx); |
| int PGAGetSortedPopIndex ( PGAContext *ctx, int n ); |
| void PGASetPopSize (PGAContext *ctx, int popsize); |
| void PGASetNumReplaceValue( PGAContext *ctx, int pop_replace); |
| void PGASetPopReplaceType( PGAContext *ctx, int pop_replace); |
| |
| /***************************************** |
| * random.c |
| *****************************************/ |
| |
| int PGARandomFlip ( PGAContext *ctx, double p ); |
| int PGARandomInterval( PGAContext *ctx, int start, int end); |
| double PGARandom01( PGAContext *ctx, int newseed ); |
| double PGARandomUniform( PGAContext *ctx, double start, double end); |
| double PGARandomGaussian( PGAContext *ctx, double mean, double sigma); |
| int PGAGetRandomSeed(PGAContext *ctx); |
| void PGASetRandomSeed(PGAContext *ctx, int seed); |
| |
| /***************************************** |
| * real.c |
| *****************************************/ |
| |
| void PGASetRealAllele (PGAContext *ctx, int p, int pop, int i, double value); |
| double PGAGetRealAllele (PGAContext *ctx, int p, int pop, int i); |
| void PGASetRealInitPercent ( PGAContext *ctx, double *median, double *percent); |
| void PGASetRealInitRange (PGAContext *ctx, double *min, double *max); |
| double PGAGetMinRealInitValue (PGAContext *ctx, int i); |
| double PGAGetMaxRealInitValue (PGAContext *ctx, int i); |
| int PGAGetRealInitType (PGAContext *ctx); |
| void PGARealCreateString (PGAContext *ctx, int p, int pop, int initflag); |
| int PGARealMutation( PGAContext *ctx, int p, int pop, double mr ); |
| void PGARealOneptCrossover( PGAContext *ctx, int p1, int p2, int pop1, |
| int c1, int c2, int pop2); |
| void PGARealTwoptCrossover( PGAContext *ctx, int p1, int p2, int pop1, |
| int c1, int c2, int pop2); |
| void PGARealUniformCrossover( PGAContext *ctx, int p1, int p2, int pop1, |
| int c1, int c2, int pop2); |
| void PGARealPrintString (PGAContext *ctx, FILE *fp, int p, int pop); |
| void PGARealCopyString ( PGAContext *ctx, int p1, int pop1, int p2, int pop2); |
| int PGARealDuplicate( PGAContext *ctx, int p1, int pop1, int p2, int pop2); |
| void PGARealInitString ( PGAContext *ctx, int p, int pop); |
| MPI_Datatype PGARealBuildDatatype(PGAContext *ctx, int p, int pop); |
| |
| /***************************************** |
| * report.c |
| *****************************************/ |
| |
| void PGAPrintReport(PGAContext *ctx, FILE *fp, int pop); |
| void PGASetPrintOptions (PGAContext *ctx, int option); |
| void PGASetPrintFrequencyValue( PGAContext *ctx, int print_freq); |
| int PGAGetPrintFrequencyValue (PGAContext *ctx); |
| void PGAPrintPopulation ( PGAContext *ctx, FILE *fp, int pop ); |
| void PGAPrintIndividual ( PGAContext *ctx, FILE *fp, int p, int pop ); |
| void PGAPrintString ( PGAContext *ctx, FILE *file, int p, int pop ); |
| void PGAPrintContextVariable ( PGAContext *ctx, FILE *fp ); |
| |
| /***************************************** |
| * restart.c |
| *****************************************/ |
| |
| void PGARestart(PGAContext *ctx, int source_pop, int dest_pop); |
| void PGASetRestartFlag(PGAContext *ctx, int val); |
| int PGAGetRestartFlag(PGAContext *ctx); |
| void PGASetRestartFrequencyValue(PGAContext *ctx, int numiter); |
| int PGAGetRestartFrequencyValue(PGAContext *ctx); |
| void PGASetRestartAlleleChangeProb(PGAContext *ctx, double prob); |
| double PGAGetRestartAlleleChangeProb(PGAContext *ctx); |
| |
| /***************************************** |
| * select.c |
| *****************************************/ |
| |
| void PGASelect( PGAContext *ctx, int popix ); |
| int PGASelectNextIndex ( PGAContext *ctx ); |
| void PGASetSelectType( PGAContext *ctx, int select_type); |
| int PGAGetSelectType (PGAContext *ctx); |
| void PGASetPTournamentProb(PGAContext *ctx, double ptournament_prob); |
| double PGAGetPTournamentProb(PGAContext *ctx); |
| int PGASelectProportional(PGAContext *ctx, PGAIndividual *pop); |
| void PGASelectSUS( PGAContext *ctx, PGAIndividual *pop ); |
| int PGASelectTournament( PGAContext *ctx, PGAIndividual *pop ); |
| int PGASelectPTournament( PGAContext *ctx, PGAIndividual *pop ); |
| |
| /***************************************** |
| * stop.c |
| *****************************************/ |
| |
| int PGADone(PGAContext *ctx, MPI_Comm comm); |
| int PGACheckStoppingConditions( PGAContext *ctx); |
| void PGASetStoppingRuleType (PGAContext *ctx, int stoprule); |
| int PGAGetStoppingRuleType (PGAContext *ctx); |
| void PGASetMaxGAIterValue(PGAContext *ctx, int maxiter); |
| int PGAGetMaxGAIterValue (PGAContext *ctx); |
| void PGASetMaxNoChangeValue(PGAContext *ctx, int max_no_change); |
| void PGASetMaxSimilarityValue(PGAContext *ctx, int max_similarity); |
| |
| /***************************************** |
| * system.c |
| *****************************************/ |
| |
| void PGAError( PGAContext *ctx, char *msg, |
| int level, int datatype, void *data ); |
| void PGADestroy (PGAContext *ctx); |
| int PGAGetMaxMachineIntValue (PGAContext *ctx); |
| int PGAGetMinMachineIntValue (PGAContext *ctx); |
| double PGAGetMaxMachineDoubleValue (PGAContext *ctx); |
| double PGAGetMinMachineDoubleValue (PGAContext *ctx); |
| void PGAUsage( PGAContext *ctx ); |
| void PGAPrintVersionNumber( PGAContext *ctx ); |
| |
| /***************************************** |
| * user.c |
| *****************************************/ |
| |
| void PGASetUserFunction(PGAContext *ctx, int constant, void *f); |
| |
| /***************************************** |
| * utility.c |
| *****************************************/ |
| |
| double PGAMean ( PGAContext *ctx, double *a, int n); |
| double PGAStddev ( PGAContext *ctx, double *a, int n, double mean); |
| int PGARound(PGAContext *ctx, double x); |
| void PGACopyIndividual( PGAContext *ctx, int p1, int pop1, int p2, int pop2); |
| int PGACheckSum(PGAContext *ctx, int p, int pop); |
| int PGAGetWorstIndex(PGAContext *ctx, int pop); |
| int PGAGetBestIndex(PGAContext *ctx, int pop); |
| PGAIndividual *PGAGetIndividual ( PGAContext *ctx, int p, int pop); |
| void PGAUpdateAverage(PGAContext *ctx, int pop); |
| void PGAUpdateOnline(PGAContext *ctx, int pop); |
| void PGAUpdateOffline(PGAContext *ctx, int pop); |
| int PGAComputeSimilarity(PGAContext *ctx, PGAIndividual *pop); |
