Initial addition of dSFMT files and documentation.

README

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+Chemical Metabolism Simulator
+=============================
+
+Chemical Metabolism Simulator is a work in progress.  
+
+Dependencies
+============
+
+This project uses code developed by the Qt, Qwt, and SFMT projects. 
+
+To build this program, you will need to install the development tools for 
+Qt 4 (version 4.3 or later, available from www.trolltech.com) and the Qwt 
+libraries (available from qwt.sourceforge.net).  The SFMT libraries have
+been modified and are included with the source code, but the project page
+can be found at http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/SFMT ).
+
+Compilation Instructions
+========================
+This program uses the standard Qt build process run from the src directory:
+
+  cd src
+  qmake
+  make
+

dSFMT/CHANGE-LOG.txt

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+ver 1.2.1
+-------
+add #include <altivec.h> to dSFMT.c
+
+ver 1.2
+-------
+The precision specifier of printf was too large in test.c
+CAUTION! *.out.txt is changed.
+add dSFMT-params216091.h
+gcc compile option changed form -O9 to -O3.
+add AltiVec parameter format for systems which are not OSX.
+change Makefile for systems which are not OSX and support AltiVec.
+change sample2 of howto-compile for Free BSD.
+change period certification code more smart.
+change source files for BORLANDC and Visual Studio.
+
+ver 1.1.1
+-------
+BUG in dSFMT-sse2.h is fixed.
+This bug didn't change the result.
+Change test.c
+
+ver 1.1
+-------
+add dSFMT-params132049.h
+fix bug in period_certification. It's a bug but result is the same for 
+all parameter files.
+change macro definition names and global variables. Thank you, Adam Piatyszek.
+remove L suffix from floating point constants. It's Saito's misunderstanding.
+fix bug of sfmt_idxof definition for BIG ENDIAN machine.
+
+ver 1.0.1
+-------
+change name dSFMT-alti.c to SFMT-alti.h
+change name dSFMT-sse2.c to SFMT-sse2.h
+This version is not released.
+
+ver 1.0
+-------
+The first version.

dSFMT/FILES.txt

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+This archive contails following directories and files.
+
+TOP DIRECTORY
+FILES.txt:		This file.
+CHANGE-LOG.txt		change log.
+LICENSE.txt:		License file.
+Makefile:		Makefile for test programs.
+dSFMT.h:		Header file.
+dSFMT-params.h:		parameter file control for various Mersenne expornent
+dSFMT-params607.h:	parameters for period of 2^{607}-1
+dSFMT-params1279.h:	parameters for period of 2^{1279}-1
+dSFMT-params2281.h:	parameters for period of 2^{2281}-1
+dSFMT-params4423.h:	parameters for period of 2^{4423}-1
+dSFMT-params11213.h:	parameters for period of 2^{11213}-1
+dSFMT-params19937.h:	parameters for period of 2^{19937}-1
+dSFMT-params44497.h:	parameters for period of 2^{44497}-1
+dSFMT-params86243.h:	parameters for period of 2^{86243}-1
+dSFMT-params132049.h:	parameters for period of 2^{132049}-1
+dSFMT-params216091.h:	parameters for period of 2^{216091}-1
+dSFMT-ref.c:		simple reference C code.
+dSFMT.c:		C code for standard C (c99) and unix like systems.
+dSFMT-alti.h:		C code optimized for PowerPC AltiVec.
+dSFMT-sse2.h:		C code optimized for intel SSE2.
+test.c:			Test driver for standard C.
+check.sh:		Test shell script.
+dSFMT.607.out.txt:	correct output of dSFMT MEXP=607
+dSFMT.1279.out.txt:	correct output of dSFMT MEXP=1279
+dSFMT.2281.out.txt:	correct output of dSFMT MEXP=2281
+dSFMT.4423.out.txt:	correct output of dSFMT MEXP=4423
+dSFMT.11213.out.txt:	correct output of dSFMT MEXP=11213
+dSFMT.19937.out.txt:	correct output of dSFMT MEXP=19937
+dSFMT.44497.out.txt:	correct output of dSFMT MEXP=44497
+dSFMT.86243.out.txt:	correct output of dSFMT MEXP=86243
+dSFMT.132049.out.txt:	correct output of dSFMT MEXP=132049
+dSFMT.216091.out.txt:	correct output of dSFMT MEXP=216091
+
+html DIRECTORY:		The documents generated by doxygen.

dSFMT/LICENSE.txt

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+Copyright (c) 2007, Mutsuo Saito, Makoto Matsumoto and Hiroshima University.
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+    * Redistributions of source code must retain the above copyright
+      notice, this list of conditions and the following disclaimer.
+    * 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.
+    * Neither the name of the Hiroshima University nor the names of
+      its contributors may 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.

dSFMT/Makefile

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+# @file  Makefile
+# @brief Makefile
+#
+# @author Mutsuo Saito (Hiroshima University)
+# @author Makoto Matsumoto (Hiroshima University)
+#
+# Copyright (C) 2007 Mutsuo Saito, Makoto Matsumoto and Hiroshima
+# University. All rights reserved.
+#
+# The new BSD License is applied to this software.
+# see LICENSE.txt
+#
+# @note
+# We could comple test-sse2-Mxxx using gcc 3.4.4 of cygwin.
+# We could comple test-sse2-Mxxx using gcc 4.0.1 of Linux.
+# We coundn't comple test-sse2-Mxxx using gcc 3.3.2 of Linux.
+# We could comple test-alti-Mxxx using gcc 3.3 of osx.
+# We could comple test-alti-Mxxx using gcc 4.0 of osx.
+
+WARN = -Wmissing-prototypes -Wall #-Winline 
+#WARN = -Wmissing-prototypes -Wall -W
+OPTI = -O3 -finline-functions -fomit-frame-pointer -DNDEBUG \
+-fno-strict-aliasing --param max-inline-insns-single=1800 
+#--param inline-unit-growth=500 --param large-function-growth=900 #for gcc 4
+#STD =
+#STD = -std=c89 -pedantic
+#STD = -std=c99 -pedantic
+STD = -std=c99
+CC = gcc
+CCFLAGS = $(OPTI) $(WARN) $(STD)
+ALTIFLAGS = -mabi=altivec -maltivec -DHAVE_ALTIVEC
+OSXALTIFLAGS = -faltivec -maltivec -DHAVE_ALTIVEC
+SSE2FLAGS = -msse2 -DHAVE_SSE2
+STD_TARGET = test-std-M19937
+ALL_STD_TARGET = test-std-M607 test-std-M1279 test-std-M2281 test-std-M4423 \
+test-std-M11213 test-std-M19937 test-std-M44497 test-std-M86243 \
+test-std-M132049 test-std-M216091
+ALTI_TARGET = $(STD_TARGET) test-alti-M19937
+ALL_ALTI_TARGET = test-alti-M607 test-alti-M1279 test-alti-M2281 \
+test-alti-M4423 test-alti-M11213 test-alti-M19937 test-alti-M44497 \
+test-alti-M86243 test-alti-M132049 test-alti-M216091
+SSE2_TARGET = $(STD_TARGET) test-sse2-M19937
+ALL_SSE2_TARGET = test-sse2-M607 test-sse2-M1279 test-sse2-M2281 \
+test-sse2-M4423 test-sse2-M11213 test-sse2-M19937 test-sse2-M44497 \
+test-sse2-M86243 test-sse2-M132049 test-sse2-M216091
+# ==========================================================
+# comment out or EDIT following lines to get max performance
+# ==========================================================
+# --------------------
+# for gcc 4
+# --------------------
+#CCFLAGS += --param inline-unit-growth=500 \
+#--param large-function-growth=900
+# --------------------
+# for icl
+# --------------------
+#CC = icl /Wcheck /O3 /QxB /Qprefetch
+# -----------------
+# for PowerPC
+# -----------------
+#CCFLAGS += -arch ppc
+# -----------------
+# for Pentium M
+# -----------------
+#CCFLAGS += -march=prescott
+# -----------------
+# for Athlon 64
+# -----------------
+#CCFLAGS += -march=athlon64
+
+.PHONY: std-check sse2-check alti-check
+
+std: ${STD_TARGET}
+
+sse2: ${SSE2_TARGET}
+
+alti: ${ALTI_TARGET}
+
+osx-alti:
+	${MAKE} "ALTIFLAGS=${OSXALTIFLAGS}" alti
+
+std-check: ${ALL_STD_TARGET}
+	./check.sh test-std
+
+sse2-check: ${ALL_SSE2_TARGET}
+	./check.sh test-sse2
+
+alti-check: ${ALL_ALTI_TARGET}
+	./check.sh test-alti
+
+osx-alti-check: 
+	make "ALTIFLAGS=${OSXALTIFLAGS}" alti-check
+
+test-std-M607: test.c dSFMT.c dSFMT.h
+	${CC} ${CCFLAGS} -DSFMT_MEXP=607 -o $@ test.c
+
+test-alti-M607: test.c dSFMT.c dSFMT.h
+	${CC} ${CCFLAGS} ${ALTIFLAGS} -DSFMT_MEXP=607 -o $@ test.c
+
+test-sse2-M607: test.c dSFMT.c dSFMT.h
+	${CC} ${CCFLAGS} ${SSE2FLAGS} -DSFMT_MEXP=607 -o $@ test.c
+
+test-std-M1279: test.c dSFMT.c dSFMT.h
+	${CC} ${CCFLAGS} -DSFMT_MEXP=1279 -o $@ test.c
+
+test-alti-M1279: test.c dSFMT.c dSFMT.h
+	${CC} ${CCFLAGS} ${ALTIFLAGS} -DSFMT_MEXP=1279 -o $@ test.c
+
+test-sse2-M1279: test.c dSFMT.c dSFMT.h
+	${CC} ${CCFLAGS} ${SSE2FLAGS} -DSFMT_MEXP=1279 -o $@ test.c
+
+test-std-M2281: test.c dSFMT.c dSFMT.h
+	${CC} ${CCFLAGS} -DSFMT_MEXP=2281 -o $@ test.c
+
+test-alti-M2281: test.c dSFMT.c dSFMT.h
+	${CC} ${CCFLAGS} ${ALTIFLAGS} -DSFMT_MEXP=2281 -o $@ test.c
+
+test-sse2-M2281: test.c dSFMT.c dSFMT.h
+	${CC} ${CCFLAGS} ${SSE2FLAGS} -DSFMT_MEXP=2281 -o $@ test.c
+
+test-std-M4423: test.c dSFMT.c dSFMT.h
+	${CC} ${CCFLAGS} -DSFMT_MEXP=4423 -o $@ test.c
+
+test-alti-M4423: test.c dSFMT.c dSFMT.h
+	${CC} ${CCFLAGS} ${ALTIFLAGS} -DSFMT_MEXP=4423 -o $@ test.c
+
+test-sse2-M4423: test.c dSFMT.c dSFMT.h
+	${CC} ${CCFLAGS} ${SSE2FLAGS} -DSFMT_MEXP=4423 -o $@ test.c
+
+test-std-M11213: test.c dSFMT.c dSFMT.h
+	${CC} ${CCFLAGS} -DSFMT_MEXP=11213 -o $@ test.c
+
+test-alti-M11213: test.c dSFMT.c dSFMT.h
+	${CC} ${CCFLAGS} ${ALTIFLAGS} -DSFMT_MEXP=11213 -o $@ test.c
+
+test-sse2-M11213: test.c dSFMT.c dSFMT.h
+	${CC} ${CCFLAGS} ${SSE2FLAGS} -DSFMT_MEXP=11213 -o $@ test.c
+
+test-std-M19937: test.c dSFMT.c dSFMT.h
+	${CC} ${CCFLAGS} -DSFMT_MEXP=19937 -o $@ test.c
+
+test-alti-M19937: test.c dSFMT.c dSFMT.h
+	${CC} ${CCFLAGS} ${ALTIFLAGS} -DSFMT_MEXP=19937 -o $@ test.c
+
+test-sse2-M19937: test.c dSFMT.c dSFMT.h
+	${CC} ${CCFLAGS} ${SSE2FLAGS} -DSFMT_MEXP=19937 -o $@ test.c
+
+test-std-M44497: test.c dSFMT.c dSFMT.h
+	${CC} ${CCFLAGS} -DSFMT_MEXP=44497 -o $@ test.c
+
+test-alti-M44497: test.c dSFMT.c dSFMT.h
+	${CC} ${CCFLAGS} ${ALTIFLAGS} -DSFMT_MEXP=44497 -o $@ test.c
+
+test-sse2-M44497: test.c dSFMT.c dSFMT.h
+	${CC} ${CCFLAGS} ${SSE2FLAGS} -DSFMT_MEXP=44497 -o $@ test.c
+
+test-std-M86243: test.c dSFMT.c dSFMT.h
+	${CC} ${CCFLAGS} -DSFMT_MEXP=86243 -o $@ test.c
+
+test-alti-M86243: test.c dSFMT.c dSFMT.h
+	${CC} ${CCFLAGS} ${ALTIFLAGS} -DSFMT_MEXP=86243 -o $@ test.c
+
+test-sse2-M86243: test.c dSFMT.c dSFMT.h
+	${CC} ${CCFLAGS} ${SSE2FLAGS} -DSFMT_MEXP=86243 -o $@ test.c
+
+test-std-M132049: test.c dSFMT.c dSFMT.h
+	${CC} ${CCFLAGS} -DSFMT_MEXP=132049 -o $@ test.c
+
+test-alti-M132049: test.c dSFMT.c dSFMT.h
+	${CC} ${CCFLAGS} ${ALTIFLAGS} -DSFMT_MEXP=132049 -o $@ test.c
+
+test-sse2-M132049: test.c dSFMT.c dSFMT.h
+	${CC} ${CCFLAGS} ${SSE2FLAGS} -DSFMT_MEXP=132049 -o $@ test.c
+
+test-std-M216091: test.c dSFMT.c dSFMT.h
+	${CC} ${CCFLAGS} -DSFMT_MEXP=216091 -o $@ test.c
+
+test-alti-M216091: test.c dSFMT.c dSFMT.h
+	${CC} ${CCFLAGS} ${ALTIFLAGS} -DSFMT_MEXP=216091 -o $@ test.c
+
+test-sse2-M216091: test.c dSFMT.c dSFMT.h
+	${CC} ${CCFLAGS} ${SSE2FLAGS} -DSFMT_MEXP=216091 -o $@ test.c
+
+.c.o:
+	${CC} ${CCFLAGS} -c $<
+
+clean:
+	rm -f *.o *~

dSFMT/README.txt

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+ =================================================================
+ dSFMT ver. 1.2
+ 2007.08.22
+
+ double precision SIMD oriented Fast Mersenne Twister(dSFMT)
+ based on IEEE 754 floating point format.
+
+ Mutsuo Saito (Hiroshima University) and
+ Makoto Matsumoto (Hiroshima University)
+
+ Copyright (C) 2007 Mutsuo Saito, Makoto Matsumoto and Hiroshima
+ University. All rights reserved.
+
+ The (modified) BSD License is applied to this software, see
+ LICENSE.txt
+ =================================================================
+ This program only works on systems which have IEEE754 floating point
+ format.
+
+ To see documents, see html/index.html.
+
+ To make test program, see html/howto-compile.html.
+ If your CPU is BIG ENDIAN and your compiler is not gcc,
+ define BIG_ENDIAN preprocessor macro, please.
+
+ If you want to redistribute and/or change source files, see LICENSE.txt.
+
+ When you change these files and redistribute them, PLEASE write your
+ e-mail address in redistribution and write to contact YOU first if
+ users of your changed source encounter troubles.

dSFMT/check.sh

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+#!/bin/sh
+prefix=$1
+tmp=tmp.$$
+exps="607 1279 2281 4423 11213 19937 44497 86243 132049 216091"
+for mexp in $exps; do
+    compare=dSFMT.${mexp}.out.txt
+    command=${prefix}-M${mexp}
+    ./$command -v > $tmp
+    if diff -q -w $tmp $compare; then
+	echo $command output check OK
+	rm -f $tmp
+    else
+	echo $command output check NG!
+	rm -f $tmp
+	exit 1
+    fi
+done
+exit 0