From 0d6f42aee2797933d4fa6e62ddf0efbb0f131f54 Mon Sep 17 00:00:00 2001 From: Dariusz Murakowski Date: Fri, 5 Apr 2013 01:37:53 -0400 Subject: [PATCH] Add Mersenne Twister RNG library/header. Generalize to stream<< any std::map as CSV-like string. --- mt19937ar.h | 249 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ wf.cpp | 9 ++- 2 files changed, 255 insertions(+), 3 deletions(-) create mode 100644 mt19937ar.h diff --git a/mt19937ar.h b/mt19937ar.h new file mode 100644 index 0000000..8755c8f --- /dev/null +++ b/mt19937ar.h @@ -0,0 +1,249 @@ +// SOURCE DOWNLOADED FROM: http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/MT2002/CODES/mt19937ar.c +// MORE INFO: http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/MT2002/emt19937ar.html + +/* + A C-program for MT19937, with initialization improved 2002/1/26. + Coded by Takuji Nishimura and Makoto Matsumoto. + + Before using, initialize the state by using init_genrand(seed) + or init_by_array(init_key, key_length). + + Copyright (C) 1997 - 2002, Makoto Matsumoto and Takuji Nishimura, + All rights reserved. + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions and the following disclaimer in the + documentation and/or other materials provided with the distribution. + + 3. The names of its contributors may not be used to endorse or promote + products derived from this software without specific prior written + permission. + + THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS + "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT + LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR + A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR + CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, + EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, + PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR + PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF + LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING + NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + + Any feedback is very welcome. + http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/emt.html + email: m-mat @ math.sci.hiroshima-u.ac.jp (remove space) +*/ + +#include + +/* Period parameters */ +#define N 624 +#define M 397 +#define MATRIX_A 0x9908b0dfUL /* constant vector a */ +#define UPPER_MASK 0x80000000UL /* most significant w-r bits */ +#define LOWER_MASK 0x7fffffffUL /* least significant r bits */ + +static unsigned long mt[N]; /* the array for the state vector */ +static int mti=N+1; /* mti==N+1 means mt[N] is not initialized */ + +/* initializes mt[N] with a seed */ +void init_genrand(unsigned long s) +{ + mt[0]= s & 0xffffffffUL; + for (mti=1; mti> 30)) + mti); + /* See Knuth TAOCP Vol2. 3rd Ed. P.106 for multiplier. */ + /* In the previous versions, MSBs of the seed affect */ + /* only MSBs of the array mt[]. */ + /* 2002/01/09 modified by Makoto Matsumoto */ + mt[mti] &= 0xffffffffUL; + /* for >32 bit machines */ + } +} + +/* initialize by an array with array-length */ +/* init_key is the array for initializing keys */ +/* key_length is its length */ +/* slight change for C++, 2004/2/26 */ +void init_by_array(unsigned long init_key[], int key_length) +{ + int i, j, k; + init_genrand(19650218UL); + i=1; j=0; + k = (N>key_length ? N : key_length); + for (; k; k--) { + mt[i] = (mt[i] ^ ((mt[i-1] ^ (mt[i-1] >> 30)) * 1664525UL)) + + init_key[j] + j; /* non linear */ + mt[i] &= 0xffffffffUL; /* for WORDSIZE > 32 machines */ + i++; j++; + if (i>=N) { mt[0] = mt[N-1]; i=1; } + if (j>=key_length) j=0; + } + for (k=N-1; k; k--) { + mt[i] = (mt[i] ^ ((mt[i-1] ^ (mt[i-1] >> 30)) * 1566083941UL)) + - i; /* non linear */ + mt[i] &= 0xffffffffUL; /* for WORDSIZE > 32 machines */ + i++; + if (i>=N) { mt[0] = mt[N-1]; i=1; } + } + + mt[0] = 0x80000000UL; /* MSB is 1; assuring non-zero initial array */ +} + +/* generates a random number on [0,0xffffffff]-interval */ +unsigned long genrand_int32(void) +{ + unsigned long y; + static unsigned long mag01[2]={0x0UL, MATRIX_A}; + /* mag01[x] = x * MATRIX_A for x=0,1 */ + + if (mti >= N) { /* generate N words at one time */ + int kk; + + if (mti == N+1) /* if init_genrand() has not been called, */ + init_genrand(5489UL); /* a default initial seed is used */ + + for (kk=0;kk> 1) ^ mag01[y & 0x1UL]; + } + for (;kk> 1) ^ mag01[y & 0x1UL]; + } + y = (mt[N-1]&UPPER_MASK)|(mt[0]&LOWER_MASK); + mt[N-1] = mt[M-1] ^ (y >> 1) ^ mag01[y & 0x1UL]; + + mti = 0; + } + + y = mt[mti++]; + + /* Tempering */ + y ^= (y >> 11); + y ^= (y << 7) & 0x9d2c5680UL; + y ^= (y << 15) & 0xefc60000UL; + y ^= (y >> 18); + + return y; +} + +/* generates a random number on [0,0x7fffffff]-interval */ +long genrand_int31(void) +{ + return (long)(genrand_int32()>>1); +} + +/* generates a random number on [0,1]-real-interval */ +double genrand_real1(void) +{ + return genrand_int32()*(1.0/4294967295.0); + /* divided by 2^32-1 */ +} + +/* generates a random number on [0,1)-real-interval */ +double genrand_real2(void) +{ + return genrand_int32()*(1.0/4294967296.0); + /* divided by 2^32 */ +} + +/* generates a random number on (0,1)-real-interval */ +double genrand_real3(void) +{ + return (((double)genrand_int32()) + 0.5)*(1.0/4294967296.0); + /* divided by 2^32 */ +} + +/* generates a random number on [0,1) with 53-bit resolution*/ +double genrand_res53(void) +{ + unsigned long a=genrand_int32()>>5, b=genrand_int32()>>6; + return(a*67108864.0+b)*(1.0/9007199254740992.0); +} +/* These real versions are due to Isaku Wada, 2002/01/09 added */ + +/* +int main(void) +{ + int i; + unsigned long init[4]={0x123, 0x234, 0x345, 0x456}, length=4; + init_by_array(init, length); + printf("1000 outputs of genrand_int32()\n"); + for (i=0; i<1000; i++) { + printf("%10lu ", genrand_int32()); + if (i%5==4) printf("\n"); + } + printf("\n1000 outputs of genrand_real2()\n"); + for (i=0; i<1000; i++) { + printf("%10.8f ", genrand_real2()); + if (i%5==4) printf("\n"); + } + return 0; +} +*/ +#undef N +#undef M +#undef MATRIX_A +#undef UPPER_MASK +#undef LOWER_MASK + + + +#define MT_RAND_MAX 0xffffffffUL /* 2**32 - 1 */ + +/* + * generate uniform 0 <= x < N, i.e. interval [0,N) + * int x = (int)((double)rand() / (((double)RAND_MAX + (double)1.0) / N)) + */ + +/* + * Returns a random integer in the range [0..limit) + * see http://stackoverflow.com/questions/2999075/generate-a-random-number-within-range/2999130#2999130 + * and http://stackoverflow.com/questions/10219355/does-n-rand-rand-max-make-a-skewed-random-number-distribution/10219422#10219422 + * alternate at http://stackoverflow.com/questions/11641629/generating-a-uniform-distribution-of-integers-in-c/11658168#11658168 + * also http://c-faq.com/lib/randrange.html + * and GSL source: http://bzr.savannah.gnu.org/lh/gsl/trunk/annotate/head:/rng/gsl_rng.h + */ +unsigned int rand_lim(unsigned int limit) { + unsigned int divisor = MT_RAND_MAX/limit; + unsigned int retval; + do { + retval = genrand_int32() / divisor; + } while (retval >= limit); + return retval; +} + +#undef MT_RAND_MAX + +/* generate a random number generator seed from /dev/urandom */ +// borrowed from SSC src/runtime/ssc_rts.c +static unsigned ising_sim_random_seed() { + unsigned random_seed; + FILE *rng = fopen("/dev/urandom", "r"); + if (rng == NULL) { + fprintf(stderr, + "error: cannot read /dev/urandom randomness generator\n"); + exit(1); + } + size_t num_random_read = fread(&random_seed, sizeof(random_seed), 1, rng); + if (num_random_read != 1) { + fprintf(stderr, + "error: cannot read /dev/urandom randomness generator\n"); + exit(1); + } + fclose(rng); + return random_seed; +} + diff --git a/wf.cpp b/wf.cpp index d0bbe04..dc0902f 100644 --- a/wf.cpp +++ b/wf.cpp @@ -7,16 +7,19 @@ #include // std::copy #include // std::ostream_iterator +#include "mt19937ar.h" + typedef unsigned int spin_t; typedef std::set mutset_t; // virus is defined by set of mutations typedef std::map pop_t; // number of each virus species /* - * print a set of mutations to stream as a CSV-like string + * print a set of mutations (or anything) to stream as a CSV-like string */ -std::ostream& operator<<(std::ostream& os, mutset_t v) +template +std::ostream& operator<<(std::ostream& os, const std::set &v) { - mutset_t::iterator i = v.begin(), end = v.end(); + typename std::set::iterator i = v.begin(), end = v.end(); os << *i; // print first element for (++i; i != end; ++i) // then with comma as prefix os << ',' << *i; -- 2.7.4