use mersenne twister rather than GSL for rng, and default to POSIX jn…

…/yn rather than GSL for Bessel functions (NanoComp#869)

configure.ac

@@ -20,6 +20,7 @@ AC_ENABLE_SHARED
 ##############################################################################
 
 # Check for mpiCC immediately after getting C++ compiler...
+AC_PROG_CC
 AC_PROG_CXX
 AC_LANG([C++])
 
@@ -569,6 +570,7 @@ AC_CONFIG_FILES([
 	Makefile
 	meep-pkgconfig
 	src/Makefile
+	src/support/Makefile
 	tests/Makefile
 ])
 

src/Makefile.am

@@ -19,6 +19,9 @@ sources.cpp step.cpp step_db.cpp stress.cpp structure.cpp structure_dump.cpp		\
 susceptibility.cpp time.cpp update_eh.cpp mpb.cpp update_pols.cpp 	\
 vec.cpp step_generic.cpp meepgeom.cpp GDSIIgeom.cpp $(HDRS) $(BUILT_SOURCES)
 
+SUBDIRS = support
+libmeep_la_LIBADD = support/libsupport.la
+
 libmeep_la_LDFLAGS = -version-info @SHARED_VERSION_INFO@
 
 PRELUDE = "/* This file was automatically generated --- DO NOT EDIT */"

src/initialize.cpp

@@ -36,10 +36,10 @@ namespace meep {
 
 #define J BesselJ
 double J(int m, double kr) {
-#if defined(HAVE_LIBGSL)
-  return gsl_sf_bessel_Jn(m, kr);
-#elif defined(HAVE_JN)
+#if defined(HAVE_JN)
   return jn(m, kr); // POSIX/BSD jn function
+#elif defined(HAVE_LIBGSL)
+  return gsl_sf_bessel_Jn(m, kr);
 #else
   abort("not compiled with GSL, required for Bessel functions");
   return 0;

src/near2far.cpp

@@ -157,9 +157,13 @@ void green3d(std::complex<double> *EH, const vec &x, double freq, double eps, do
     abort("unrecognized source type");
 }
 
-#ifdef HAVE_LIBGSL
-#include <gsl/gsl_sf_bessel.h>
 // hankel function J + iY
+#if defined(HAVE_JN)
+static std::complex<double> hankel(int n, double x) {
+  return std::complex<double>(jn(n, x), yn(n, x));
+}
+#elif defined(HAVE_LIBGSL)
+#include <gsl/gsl_sf_bessel.h>
 static std::complex<double> hankel(int n, double x) {
   return std::complex<double>(gsl_sf_bessel_Jn(n, x), gsl_sf_bessel_Yn(n, x));
 }

src/random.cpp

@@ -18,80 +18,52 @@
 #include "meep.hpp"
 #include "config.h"
 
-#ifdef HAVE_LIBGSL
-#include <gsl/gsl_randist.h>
-#else
-#include <stdlib.h>
-#endif
+#include "support/meep_mt.h"
 #include <time.h>
 
 using namespace std;
 
 namespace meep {
 
 static bool rand_inited = false;
-#ifdef HAVE_LIBGSL
-static gsl_rng *rng = NULL;
-#endif
 
 static void init_rand(void) {
   if (!rand_inited) {
-#ifdef HAVE_LIBGSL
-    if (rng) gsl_rng_free(rng);
-    rng = gsl_rng_alloc(gsl_rng_mt19937);
-#endif
     rand_inited = true; // no infinite loop since rand_inited == true
     set_random_seed(time(NULL) * (1 + my_global_rank()));
   }
 }
 
 void set_random_seed(unsigned long seed) {
   init_rand();
-  seed = ((unsigned long)broadcast(0, (int)seed)) + my_rank();
-#ifdef HAVE_LIBGSL
-  gsl_rng_set(rng, seed);
-#else
-  srand(seed);
-#endif
+  meep_mt_init_genrand(seed);
 }
 
 int random_int(int a, int b) {
   init_rand();
-#ifdef HAVE_LIBGSL
-  return ((int)gsl_rng_uniform_int(rng, b - a + 1)) + a;
-#else
-  return a + rand() % (b - a + 1);
-#endif
+  return a + meep_mt_genrand_int32() % (b - a + 1);
 }
 
 double uniform_random(double a, double b) {
   init_rand();
-#ifdef HAVE_LIBGSL
-  return a + gsl_rng_uniform(rng) * (b - a);
-#else
-  return a + rand() * (b - a) / RAND_MAX;
-#endif
+  return a + meep_mt_genrand_res53() * (b - a);
 }
 
 double gaussian_random(double mean, double stddev) {
   init_rand();
-#ifdef HAVE_LIBGSL
-  return mean + gsl_ran_gaussian(rng, stddev);
-#else
   // Box-Muller algorithm to generate Gaussian from uniform
   // see Knuth vol II algorithm P, sec. 3.4.1
   double v1, v2, s;
   do {
-    v1 = uniform_random(-1, 1);
-    v2 = uniform_random(-1, 1);
+    v1 = 2*meep_mt_genrand_res53() - 1;
+    v2 = 2*meep_mt_genrand_res53() - 1;
     s = v1 * v1 + v2 * v2;
   } while (s >= 1.0);
   if (s == 0) {
     return mean;
   } else {
     return mean + v1 * sqrt(-2 * log(s) / s) * stddev;
   }
-#endif
 }
 
 } // namespace meep

src/support/Makefile.am

@@ -0,0 +1,3 @@
+noinst_LTLIBRARIES = libsupport.la
+
+libsupport_la_SOURCES = mt19937ar.c meep_mt.h

src/support/meep_mt.h

@@ -0,0 +1,21 @@
+#ifndef MEEP_MT_H
+#define MEEP_MT_H 1
+
+#ifdef __cplusplus
+extern "C" {
+#endif /* __cplusplus */
+
+void meep_mt_init_genrand(unsigned long s);
+void meep_mt_init_by_array(unsigned long init_key[], int key_length);
+unsigned long meep_mt_genrand_int32(void);
+long meep_mt_genrand_int31(void);
+double meep_mt_genrand_real1(void);
+double meep_mt_genrand_real2(void);
+double meep_mt_genrand_real3(void);
+double meep_mt_genrand_res53(void);
+
+#ifdef __cplusplus
+}
+#endif /* __cplusplus */
+
+#endif /* MEEP_MT_H */

src/support/mt19937ar.c

@@ -0,0 +1,196 @@
+/*
+   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)
+*/
+
+/* modified by SGJ for Meep: added meep_mt.h header and added meep_mt prefixes
+   to functions to avoid namespace pollution */
+
+#include <stdio.h>
+#include "meep_mt.h"
+
+/* 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 meep_mt_init_genrand(unsigned long s)
+{
+    mt[0]= s & 0xffffffffUL;
+    for (mti=1; mti<N; mti++) {
+        mt[mti] =
+	    (1812433253UL * (mt[mti-1] ^ (mt[mti-1] >> 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 meep_mt_init_by_array(unsigned long init_key[], int key_length)
+{
+    int i, j, k;
+    meep_mt_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 meep_mt_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, */
+            meep_mt_init_genrand(5489UL); /* a default initial seed is used */
+
+        for (kk=0;kk<N-M;kk++) {
+            y = (mt[kk]&UPPER_MASK)|(mt[kk+1]&LOWER_MASK);
+            mt[kk] = mt[kk+M] ^ (y >> 1) ^ mag01[y & 0x1UL];
+        }
+        for (;kk<N-1;kk++) {
+            y = (mt[kk]&UPPER_MASK)|(mt[kk+1]&LOWER_MASK);
+            mt[kk] = mt[kk+(M-N)] ^ (y >> 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 meep_mt_genrand_int31(void)
+{
+    return (long)(meep_mt_genrand_int32()>>1);
+}
+
+/* generates a random number on [0,1]-real-interval */
+double meep_mt_genrand_real1(void)
+{
+    return meep_mt_genrand_int32()*(1.0/4294967295.0);
+    /* divided by 2^32-1 */
+}
+
+/* generates a random number on [0,1)-real-interval */
+double meep_mt_genrand_real2(void)
+{
+    return meep_mt_genrand_int32()*(1.0/4294967296.0);
+    /* divided by 2^32 */
+}
+
+/* generates a random number on (0,1)-real-interval */
+double meep_mt_genrand_real3(void)
+{
+    return (((double)meep_mt_genrand_int32()) + 0.5)*(1.0/4294967296.0);
+    /* divided by 2^32 */
+}
+
+/* generates a random number on [0,1) with 53-bit resolution*/
+double meep_mt_genrand_res53(void)
+{
+    unsigned long a=meep_mt_genrand_int32()>>5, b=meep_mt_genrand_int32()>>6;
+    return(a*67108864.0+b)*(1.0/9007199254740992.0);
+}
+/* These real versions are due to Isaku Wada, 2002/01/09 added */
+
+#if 0
+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;
+}
+#endif