Initial import of new "mcsim" package:

Monte Carlo Simulation software

5 files changed, 363 insertions, 0 deletions

diff --git a/math/mcsim/patches/patch-aa b/math/mcsim/patches/patch-aa
new file mode 100644
index 00000000000..ac1dbf1b05f
--- /dev/null
+++ b/math/mcsim/patches/patch-aa
@@ -0,0 +1,20 @@
+$NetBSD: patch-aa,v 1.1.1.1 2000/11/26 23:02:38 jtb Exp $
+
+--- doc/mcsim.texinfo.orig	Sat Nov 15 02:14:40 1997
++++ doc/mcsim.texinfo
+@@ -1,10 +1,14 @@
+ \input texinfo @c -*-texinfo-*-
+ @comment %**start of header (This is for running Texinfo on a region.)
+-@setfilename mcsimdoc
++@setfilename mcsim
+ @settitle MCSim User' Manual
+ @setchapternewpage odd
+ @comment %**end of header (This is for running Texinfo on a region.)
+ 
++@dircategory Monte Carlo Simulation
++@direntry
++* MCSim: (mcsim).		A Monte Carlo Simulation Program.
++@end direntry
+ 
+ @comment  the following is just for the texinfo file
+ @ifinfo
diff --git a/math/mcsim/patches/patch-ab b/math/mcsim/patches/patch-ab
new file mode 100644
index 00000000000..bc111757bbe
--- /dev/null
+++ b/math/mcsim/patches/patch-ab
@@ -0,0 +1,31 @@
+$NetBSD: patch-ab,v 1.1.1.1 2000/11/26 23:02:38 jtb Exp $
+
+--- mod/Makefile.orig	Wed Nov 22 22:39:24 2000
++++ mod/Makefile
+@@ -97,8 +97,8 @@
+ #
+ #>>>>  Define the COMPILER name and LINKER name here only.
+ 
+-CC = gcc
+-LINK = gcc
++#CC =
++LINK = $(CC)
+ 
+ #>>>>  Define PATHS
+ #	The include path should be a directory containing header
+@@ -137,13 +137,13 @@
+ #>>>> To compile with OPTIMIZATION uncomment the following lines
+ #
+ DEBUG_SYMBOLS = -DNDEBUG
+-C_OPTIM_FLAG = -O
++C_OPTIM_FLAG = -O2
+ L_OPTIM_FLAG =
+ 
+ #
+ #>>>> Include any special warning flags 
+ #
+-WARNINGS = -Wall
++WARNINGS = -ansi
+ 
+ #--------------------
+ #****  You shouldn't need to change these lines.  They are dependent
diff --git a/math/mcsim/patches/patch-ac b/math/mcsim/patches/patch-ac
new file mode 100644
index 00000000000..a9533bf83c1
--- /dev/null
+++ b/math/mcsim/patches/patch-ac
@@ -0,0 +1,31 @@
+$NetBSD: patch-ac,v 1.1.1.1 2000/11/26 23:02:39 jtb Exp $
+
+--- sim/Makefile.orig	Wed Nov 22 22:41:05 2000
++++ sim/Makefile
+@@ -62,8 +62,8 @@
+ #
+ #>>>>  Define the COMPILER name and LINKER name here only.
+ 
+-CC = gcc
+-LINK = gcc
++#CC = gcc
++LINK = $(CC)
+ 
+ #>>>>  Define PATHS
+ #	The include path should be a directory containing header
+@@ -101,13 +101,13 @@
+ #>>>> To compile with OPTIMIZATION uncomment the following lines
+ #
+ DEBUG_SYMBOLS = -DNDEBUG
+-C_OPTIM_FLAG = -O
++C_OPTIM_FLAG = -O2
+ L_OPTIM_FLAG =
+ 
+ #
+ #>>>> Include any special warning flags 
+ #
+-WARNINGS = -Wall -ansi
++WARNINGS = -ansi
+ 
+ #--------------------
+ #****  You shouldn't need to change the next 2 lines.  They are dependent
diff --git a/math/mcsim/patches/patch-ad b/math/mcsim/patches/patch-ad
new file mode 100644
index 00000000000..53a7bbfe82f
--- /dev/null
+++ b/math/mcsim/patches/patch-ad
@@ -0,0 +1,22 @@
+$NetBSD: patch-ad,v 1.1.1.1 2000/11/26 23:02:39 jtb Exp $
+
+--- sim/sim.c.orig	Wed Nov 22 22:45:45 2000
++++ sim/sim.c
+@@ -653,7 +653,7 @@
+   scanf ("%[^:\f\r\v\n]", *pszFileIn);
+   getchar();
+ #else
+-  gets (*pszFileIn);
++  fgets (*pszFileIn, sizeof(*pszFileIn), stdin);
+   *pszFileIn = strtok (*pszFileIn, " \t");
+ #endif
+ 
+@@ -665,7 +665,7 @@
+ #ifdef _MACOSLEVEL1_
+     scanf ("%[^:\f\r\v\n]", *pszFileOut);
+ #else
+-    gets (*pszFileOut);
++    fgets (*pszFileOut, sizeof(pszFileOut), stdin);
+     *pszFileOut = strtok (*pszFileOut, " \t");
+ #endif
+   }
diff --git a/math/mcsim/patches/patch-ae b/math/mcsim/patches/patch-ae
new file mode 100644
index 00000000000..8aa82a6ce26
--- /dev/null
+++ b/math/mcsim/patches/patch-ae
@@ -0,0 +1,259 @@
+$NetBSD: patch-ae,v 1.1.1.1 2000/11/26 23:02:41 jtb Exp $
+
+--- sim/Test_mcsim.orig	Fri Nov 14 15:45:56 1997
++++ sim/Test_mcsim
+@@ -1,147 +1,147 @@
+ # Run diagnostic tests on several features of the program.
+ # results are compared to prepared files.
+-one:	
+-	@echo
+-	@echo ----------
+-	@echo
+-	@echo '* Testing MCSim: this could take a few minutes.'
+-	@echo '* Creating logfile mcsim.log'
+-	@touch mcsim.log
+-	@date >> mcsim.log
+-#
+-	@echo
+-	@echo ----------
+-	@echo
+-	@echo Testing with the tetrachloroethylene model
+-	@mod perc.model
+-	@gcc -I . -Wall -ansi -c model.c -o model.o  > /dev/null
+-	@gcc -o mcsim *.o -lm
+-	@echo
++#one:	
++	echo
++	echo ----------
++	echo
++	echo '* Testing MCSim: this could take a few minutes.'
++	echo '* Creating logfile mcsim.log'
++	touch mcsim.log
++	date >> mcsim.log
++#
++	echo
++	echo ----------
++	echo
++	echo Testing with the tetrachloroethylene model
++	../mod/mod perc.model
++	cc -I . -Wall -ansi -c model.c -o model.o  > /dev/null
++	cc -o mcsim *.o -lm
++	echo
+ #
+ # perc.lsodes.in    
+-	@echo Testing Lsodes with perc.lsodes.in ...
+-	@chmod -w perc.lsodes.in perc.lsodes.out 
+-	@mcsim perc.lsodes.in sim.out >> mcsim.log
+-	@(diff sim.out perc.lsodes.out > .tmp) && echo '-PASSED-'
++	echo Testing Lsodes with perc.lsodes.in ...
++	chmod -w perc.lsodes.in perc.lsodes.out 
++	./mcsim perc.lsodes.in sim.out >> mcsim.log
++	(diff sim.out perc.lsodes.out > .tmp) && echo '-PASSED-'
+ #
+ # perc.ndoses.in
+-	@echo Testing NDoses with perc.ndoses.in ...
+-	@chmod -w perc.ndoses.in perc.ndoses.out 
+-	@mcsim perc.ndoses.in sim.out >> mcsim.log
+-	@(diff sim.out perc.ndoses.out > .tmp) && echo '-PASSED-'
++	echo Testing NDoses with perc.ndoses.in ...
++	chmod -w perc.ndoses.in perc.ndoses.out 
++	./mcsim perc.ndoses.in sim.out >> mcsim.log
++	(diff sim.out perc.ndoses.out > .tmp) && echo '-PASSED-'
+ #
+ # perc.mtc.in
+-	@echo Testing Monte Carlo with perc.mtc.in ...
+-	@chmod -w perc.mtc.in perc.mtc.out 
+-	@mcsim perc.mtc.in sim.out >> mcsim.log
+-	@(diff sim.out perc.mtc.out > .tmp) && echo '-PASSED-'
++	echo Testing Monte Carlo with perc.mtc.in ...
++	chmod -w perc.mtc.in perc.mtc.out 
++	./mcsim perc.mtc.in sim.out >> mcsim.log
++	(diff sim.out perc.mtc.out > .tmp) && echo '-PASSED-'
+ #
+ # perc.setpoint.in
+-	@echo Testing Set Point run with perc.setpoint.in ...
+-	@chmod -w perc.setpoint.dat perc.setpoint.in perc.setpoint.out 
+-	@mcsim perc.setpoint.in sim.out >> mcsim.log
+-	@(diff sim.out perc.setpoint.out > .tmp) && echo '-PASSED-'
+-#
+-	@echo
+-	@echo ----------
+-	@echo
+-	@echo Testing with the 1 compartment model
+-	@mod 1cpt.model
+-	@gcc -I . -Wall -ansi -c model.c -o model.o  > /dev/null
+-	@gcc -o mcsim *.o -lm
+-	@echo
++	echo Testing Set Point run with perc.setpoint.in ...
++	chmod -w perc.setpoint.dat perc.setpoint.in perc.setpoint.out 
++	./mcsim perc.setpoint.in sim.out >> mcsim.log
++	(diff sim.out perc.setpoint.out > .tmp) && echo '-PASSED-'
++#
++	echo
++	echo ----------
++	echo
++	echo Testing with the 1 compartment model
++	../mod/mod 1cpt.model
++	cc -I . -Wall -ansi -c model.c -o model.o  > /dev/null
++	cc -o mcsim *.o -lm
++	echo
+ #
+ # 1cpt_no_noise.in
+-	@echo Testing Lsodes non random output with 1cpt_no_noise.in ...
+-	@chmod -w 1cpt_no_noise.in 1cpt_no_noise.out
+-	@mcsim 1cpt_no_noise.in sim.out >> mcsim.log
+-	@(diff sim.out 1cpt_no_noise.out > .tmp) && echo '-PASSED-'
++	echo Testing Lsodes non random output with 1cpt_no_noise.in ...
++	chmod -w 1cpt_no_noise.in 1cpt_no_noise.out
++	./mcsim 1cpt_no_noise.in sim.out >> mcsim.log
++	(diff sim.out 1cpt_no_noise.out > .tmp) && echo '-PASSED-'
+ #
+ # 1cpt_w._noise.in
+-	@echo Testing Lsodes randomized output with 1cpt_w._noise.in ...
+-	@chmod -w 1cpt_w._noise.in 1cpt_w._noise.out
+-	@mcsim 1cpt_w._noise.in sim.out >> mcsim.log
+-	@(diff sim.out 1cpt_w._noise.out > .tmp) && echo '-PASSED-'
++	echo Testing Lsodes randomized output with 1cpt_w._noise.in ...
++	chmod -w 1cpt_w._noise.in 1cpt_w._noise.out
++	./mcsim 1cpt_w._noise.in sim.out >> mcsim.log
++	(diff sim.out 1cpt_w._noise.out > .tmp) && echo '-PASSED-'
+ #
+ # 1cpt.MCMC1.in
+-	@echo Testing MCMC set uncertainties with 1cpt.MCMC1.in ...
+-	@chmod -w 1cpt.MCMC1.in 1cpt.MCMC1.out
+-	@mcsim 1cpt.MCMC1.in sim.out >> mcsim.log
+-	@(diff sim.out 1cpt.MCMC1.out > .tmp) && echo '-PASSED-'
++	echo Testing MCMC set uncertainties with 1cpt.MCMC1.in ...
++	chmod -w 1cpt.MCMC1.in 1cpt.MCMC1.out
++	./mcsim 1cpt.MCMC1.in sim.out >> mcsim.log
++	(diff sim.out 1cpt.MCMC1.out > .tmp) && echo '-PASSED-'
+ #
+ # 1cpt.MCMC2.in
+-	@echo Testing MCMC estimated uncertainties with 1cpt.MCMC2.in ...
+-	@chmod -w 1cpt.MCMC2.in 1cpt.MCMC2.out
+-	@mcsim 1cpt.MCMC2.in sim.out >> mcsim.log
+-	@(diff sim.out 1cpt.MCMC2.out > .tmp) && echo '-PASSED-'
++	echo Testing MCMC estimated uncertainties with 1cpt.MCMC2.in ...
++	chmod -w 1cpt.MCMC2.in 1cpt.MCMC2.out
++	./mcsim 1cpt.MCMC2.in sim.out >> mcsim.log
++	(diff sim.out 1cpt.MCMC2.out > .tmp) && echo '-PASSED-'
+ #
+ # 1cpt.MCMC3.in
+-	@echo Testing MCMC print every 2 iterations with 1cpt.MCMC3.in ...
+-	@chmod -w 1cpt.MCMC3.in 1cpt.MCMC3.out
+-	@mcsim 1cpt.MCMC3.in sim.out >> mcsim.log
+-	@(diff sim.out 1cpt.MCMC3.out > .tmp) && echo '-PASSED-'
++	echo Testing MCMC print every 2 iterations with 1cpt.MCMC3.in ...
++	chmod -w 1cpt.MCMC3.in 1cpt.MCMC3.out
++	./mcsim 1cpt.MCMC3.in sim.out >> mcsim.log
++	(diff sim.out 1cpt.MCMC3.out > .tmp) && echo '-PASSED-'
+ #
+ # 1cpt.MCMC4.in
+-	@echo Testing MCMC estimated bounds on F with 1cpt.MCMC4.in ...
+-	@chmod -w 1cpt.MCMC4.in 1cpt.MCMC4.out
+-	@mcsim 1cpt.MCMC4.in sim.out >> mcsim.log
+-	@(diff sim.out 1cpt.MCMC4.out > .tmp) && echo '-PASSED-'
++	echo Testing MCMC estimated bounds on F with 1cpt.MCMC4.in ...
++	chmod -w 1cpt.MCMC4.in 1cpt.MCMC4.out
++	./mcsim 1cpt.MCMC4.in sim.out >> mcsim.log
++	(diff sim.out 1cpt.MCMC4.out > .tmp) && echo '-PASSED-'
+ #
+ # 1cpt.MCMC5.in
+-	@echo Testing MCMC model-computed SDs with 1cpt.MCMC5.in ...
+-	@chmod -w 1cpt.MCMC5.in 1cpt.MCMC5.out
+-	@mcsim 1cpt.MCMC5.in sim.out >> mcsim.log
+-	@(diff sim.out 1cpt.MCMC5.out > .tmp) && echo '-PASSED-'
+-#
+-	@echo
+-	@echo ----------
+-	@echo
+-	@echo Testing with the linear model
+-	@mod linear.model
+-	@gcc -I . -Wall -ansi -c model.c -o model.o  > /dev/null
+-	@gcc -o mcsim *.o -lm
+-	@echo
++	echo Testing MCMC model-computed SDs with 1cpt.MCMC5.in ...
++	chmod -w 1cpt.MCMC5.in 1cpt.MCMC5.out
++	./mcsim 1cpt.MCMC5.in sim.out >> mcsim.log
++	(diff sim.out 1cpt.MCMC5.out > .tmp) && echo '-PASSED-'
++#
++	echo
++	echo ----------
++	echo
++	echo Testing with the linear model
++	../mod/mod linear.model
++	cc -I . -Wall -ansi -c model.c -o model.o  > /dev/null
++	cc -o mcsim *.o -lm
++	echo
+ #
+ # linear.in
+-	@echo Testing Lsodes with linear.in ...
+-	@chmod -w linear.in linear.out 
+-	@mcsim linear.in sim.out >> mcsim.log
+-	@(diff sim.out linear.out > .tmp) && echo '-PASSED-'
++	echo Testing Lsodes with linear.in ...
++	chmod -w linear.in linear.out 
++	./mcsim linear.in sim.out >> mcsim.log
++	(diff sim.out linear.out > .tmp) && echo '-PASSED-'
+ #
+ # linear.MCMC1.in
+-	@echo Testing MCMC 1 experiment with linear.MCMC1.in ...
+-	@chmod -w linear.MCMC1.in linear.MCMC1.out 
+-	@mcsim linear.MCMC1.in sim.out >> mcsim.log
+-	@(diff sim.out linear.MCMC1.out > .tmp) && echo '-PASSED-'
++	echo Testing MCMC 1 experiment with linear.MCMC1.in ...
++	chmod -w linear.MCMC1.in linear.MCMC1.out 
++	./mcsim linear.MCMC1.in sim.out >> mcsim.log
++	(diff sim.out linear.MCMC1.out > .tmp) && echo '-PASSED-'
+ #
+ # linear.MCMC2.in
+-	@echo Testing MCMC 1 repeated experiment with linear.MCMC2.in ...
+-	@chmod -w linear.MCMC2.in linear.MCMC2.out 
+-	@mcsim linear.MCMC2.in sim.out >> mcsim.log
+-	@(diff sim.out linear.MCMC2.out > .tmp) && echo '-PASSED-'
++	echo Testing MCMC 1 repeated experiment with linear.MCMC2.in ...
++	chmod -w linear.MCMC2.in linear.MCMC2.out 
++	./mcsim linear.MCMC2.in sim.out >> mcsim.log
++	(diff sim.out linear.MCMC2.out > .tmp) && echo '-PASSED-'
+ #
+ # linear.H.MCMC1.in
+-	@echo Testing MCMC hierarchical linear model, 10 exps with \
++	echo Testing MCMC hierarchical linear model, 10 exps with \
+          linear.H.MCMC1.in ...
+-	@chmod -w linear.H.MCMC1.in linear.H.MCMC1.out 
+-	@mcsim linear.H.MCMC1.in sim.out >> mcsim.log
+-	@(diff sim.out linear.H.MCMC1.out > .tmp) && echo '-PASSED-'
++	chmod -w linear.H.MCMC1.in linear.H.MCMC1.out 
++	./mcsim linear.H.MCMC1.in sim.out >> mcsim.log
++	(diff sim.out linear.H.MCMC1.out > .tmp) && echo '-PASSED-'
+ #
+ # linear.H.MCMC2.in
+-	@echo Testing MCMC hierarchical linear model, B1.1 set with \
++	echo Testing MCMC hierarchical linear model, B1.1 set with \
+          linear.H.MCMC2.in
+-	@chmod -w linear.H.MCMC2.in linear.H.MCMC2.out 
+-	@mcsim linear.H.MCMC2.in sim.out >> mcsim.log
+-	@(diff sim.out linear.H.MCMC2.out > .tmp) && echo '-PASSED-'
++	chmod -w linear.H.MCMC2.in linear.H.MCMC2.out 
++	./mcsim linear.H.MCMC2.in sim.out >> mcsim.log
++	(diff sim.out linear.H.MCMC2.out > .tmp) && echo '-PASSED-'
+ #
+ # linear.H.MCMC3.in
+-	@echo Testing MCMC hierarchical model, restart file with \
++	echo Testing MCMC hierarchical model, restart file with \
+          linear.H.MCMC3.in
+-	@chmod -w linear.H.MCMC3.in linear.H.MCMC3.out 
+-	@mcsim linear.H.MCMC3.in sim.out >> mcsim.log
+-	@(diff sim.out linear.H.MCMC3.out > .tmp) && echo '-PASSED-'
+-#
+-	@echo
+-	@echo Hourra!
+-	@echo MCSim passed all tests.
++	chmod -w linear.H.MCMC3.in linear.H.MCMC3.out 
++	./mcsim linear.H.MCMC3.in sim.out >> mcsim.log
++	(diff sim.out linear.H.MCMC3.out > .tmp) && echo '-PASSED-'
++#
++	echo
++	echo Hourra!
++	echo MCSim passed all tests.
+