Add wrapper function curve_tyd, for use in GROMACS.

.gitignore

@@ -61,4 +61,5 @@ man/*.html
 # executables
 
 demo/*1
+demo/*2
 test/test_qr

CHANGELOG

@@ -1,4 +1,12 @@
-Changes in lmfit-5.3, released 24nov15:
+lmfit-6.0, released 24nov15:
+
+- API changes:
+  - a few more 'const' qualifiers in lmmin and lmcurve.
+- code cleanup:
+  - further unify code layout
+  - use temporary variable for readability in lmcurve (suggested by T. Klauser)
+
+lmfit-5.3, released 24nov15:
 
 - autotools:
   - set default optimization -O3
@@ -14,14 +22,14 @@ Changes in lmfit-5.3, released 24nov15:
 - testing:
   - new unit test directory test/, for development purposes only
 
-Changes in lmfit-5.2, released 23oct14:
+lmfit-5.2, released 23oct14:
 
 - bug fix:
   - correct man page (5.0 API change)
 - acceleration(?):
   - revert to just one malloc for all workspaces, now based on a char array
 
-Changes in lmfit-5.1, released 29aug13:
+lmfit-5.1, released 29aug13:
 
 - bug fix:
   - FILE** initialization from &stdout was not standard compliant
@@ -30,7 +38,7 @@ Changes in lmfit-5.1, released 29aug13:
 - code cleanup:
   - better wrapper for "extern C" declaration
 
-Changes in lmfit-5.0, released 9aug13:
+lmfit-5.0, released 9aug13:
 
 - API changes:
   - removed callback function for printout
@@ -48,7 +56,7 @@ Changes in lmfit-5.0, released 9aug13:
   - otherwise testsuite started as new project fittest
 - packaging: configure now supports pkg-config
 
-Changes in lmfit-4.0, released 16jul13:
+lmfit-4.0, released 16jul13:
 
 - binary library renamed: lmmin -> lmfit
 - API changes:
@@ -71,13 +79,13 @@ Changes in lmfit-4.0, released 16jul13:
   - new entry page (dokuwiki) instead of man page
   - man page split and largely rewritten: lmcurve(3), lmmin(3)
 
-Changes in lmfit-3.5, released 3feb13:
+lmfit-3.5, released 3feb13:
 
 - changed overall license to FreeBSD to facilitate inclusion in Linux
   distributions (request by M. Hroncok)
 - directory doc renamed man
 
-Changes in lmfit-3.4, released 21jan13:
+lmfit-3.4, released 21jan13:
 
 - only one malloc call to allocate all arrays (proposal by F. Polchow)
 - liblmmin_la_LDFLAGS += -lm (required by Ubuntu, report by J. M. Agosta)
@@ -86,25 +94,25 @@ Changes in lmfit-3.4, released 21jan13:
 - long message for degenerate case now suggests increasing epsilon
   (suggestion by Nghia Ho)
 
-Changes in lmfit-3.3, released 12sep12:
+lmfit-3.3, released 12sep12:
 
 - moved "int" declarations to top of lm_printout_std() and lmmin()
   (required by Visual Studio 2005: bug report M. Beek)
 - corrected typo 0.55 -> 0.5 (bug reports M. Kardas and D. Pescia)
 - man pages now produced by make; finally got rid of dmake
 - untabified code (hint by W. Pimenta)
 
-Changes in lmfit-3.2, released 28mar10 (preview 27mar10):
+lmfit-3.2, released 28mar10 (preview 27mar10):
 
 - shared library is given correct version number (set in configure.ac)
 - man page lmfit(3) is copied by dmake to lmmin(3) and lmcurve_fit(3)
 
-Changes in lmfit-3.1, released 12mar10:
+lmfit-3.1, released 12mar10:
 
 - debian directory not part of tgz distribution
 - temporarily removed lmmin.3 (was symlink -> lmfit.3)
 
-Changes in lmfit-3.0, released 2mar10 (preview 27feb10):
+lmfit-3.0, released 2mar10 (preview 27feb10):
 
 - for parameter close to zero, change step width for calculation of jabobian
 - outer iteration counter starting at zero (C style)
@@ -124,27 +132,27 @@ Changes in lmfit-3.0, released 2mar10 (preview 27feb10):
 - provide vector minimization demos
 - test for fnorm<=LM_DWARF, renumbered info values 0, 10, 11
 
-Changes in lmfit-2.6, released 29sep09:
+lmfit-2.6, released 29sep09:
 
 - nfev incrementation even if printout=0 (bug report C. Tanner)
 - correct t->tvec, y->yvec in man page  (bug report C. Tanner)
 
-Changes in lmfit-2.5, released 20sep09:
+lmfit-2.5, released 20sep09:
 
 - malloc==NULL ? (suggestion R. Strickland)
 - allow printout=NULL (suggestion J. Lodewyck)
 - improve infmsg (correspondence B. McHoull)
 - eliminate some static variables (p25, p5, p75, ..)
 - eliminate function data types; they obscure more than they help
 
-Changes in lmfit-2.4, released 27jul08:
+lmfit-2.4, released 27jul08:
 
 - clearer file headers
 - clearer licence (everything has ever been in the public domain)
 - machine-dependent arithmetic constants from float.h (suggestion M. Bydder)
 - minor improvements of comments
 
-Changes in lmfit-2.3, released 5apr08:
+lmfit-2.3, released 5apr08:
 
 - fixed bug sf#1817631: replaced confusing variable names in lmmin.c:lm_qrsolv()
 - accepted feature request 1814970: inclusion protection in headers
@@ -155,7 +163,7 @@ Changes in lmfit-2.3, released 5apr08:
 - reverted comments in lmmin.c to pure C style
 - improved documentation of interfaces
 
-Changes up to lmfit-2.2, released 20sep07:
+lmfit-2.2, released 20sep07:
 
 - no change log has been maintained,
   there are just the sourceforge release notes

COPYING

@@ -3,7 +3,7 @@ The package lmfit is distributed under the FreeBSD License:
 --
   Copyright (c) 1980-1999 University of Chicago,
                           as operator of Argonne National Laboratory
-  Copyright (c) 2004-2016 Joachim Wuttke, Forschungszentrum Juelich GmbH
+  Copyright (c) 2004-2015 Joachim Wuttke, Forschungszentrum Juelich GmbH
 
   All rights reserved.
 

demo/Makefile.am

@@ -1,6 +1,7 @@
 AM_CFLAGS = -I$(srcdir)/../lib
-noinst_PROGRAMS = curve1 nonlin1 surface1
+noinst_PROGRAMS = curve1 curve2 nonlin1 surface1
 curve1_SOURCES = curve1.c
+curve2_SOURCES = curve2.c
 nonlin1_SOURCES = nonlin1.c
 surface1_SOURCES = surface1.c
 AM_LDFLAGS = -lm -L../lib -llmfit

demo/Makefile.in

@@ -88,7 +88,8 @@ PRE_UNINSTALL = :
 POST_UNINSTALL = :
 build_triplet = @build@
 host_triplet = @host@
-noinst_PROGRAMS = curve1$(EXEEXT) nonlin1$(EXEEXT) surface1$(EXEEXT)
+noinst_PROGRAMS = curve1$(EXEEXT) curve2$(EXEEXT) nonlin1$(EXEEXT) \
+	surface1$(EXEEXT)
 subdir = demo
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
 am__aclocal_m4_deps = $(top_srcdir)/m4/libtool.m4 \
@@ -110,6 +111,9 @@ AM_V_lt = $(am__v_lt_@AM_V@)
 am__v_lt_ = $(am__v_lt_@AM_DEFAULT_V@)
 am__v_lt_0 = --silent
 am__v_lt_1 = 
+am_curve2_OBJECTS = curve2.$(OBJEXT)
+curve2_OBJECTS = $(am_curve2_OBJECTS)
+curve2_LDADD = $(LDADD)
 am_nonlin1_OBJECTS = nonlin1.$(OBJEXT)
 nonlin1_OBJECTS = $(am_nonlin1_OBJECTS)
 nonlin1_LDADD = $(LDADD)
@@ -150,8 +154,9 @@ AM_V_CCLD = $(am__v_CCLD_@AM_V@)
 am__v_CCLD_ = $(am__v_CCLD_@AM_DEFAULT_V@)
 am__v_CCLD_0 = @echo "  CCLD    " $@;
 am__v_CCLD_1 = 
-SOURCES = $(curve1_SOURCES) $(nonlin1_SOURCES) $(surface1_SOURCES)
-DIST_SOURCES = $(curve1_SOURCES) $(nonlin1_SOURCES) \
+SOURCES = $(curve1_SOURCES) $(curve2_SOURCES) $(nonlin1_SOURCES) \
+	$(surface1_SOURCES)
+DIST_SOURCES = $(curve1_SOURCES) $(curve2_SOURCES) $(nonlin1_SOURCES) \
 	$(surface1_SOURCES)
 am__can_run_installinfo = \
   case $$AM_UPDATE_INFO_DIR in \
@@ -298,6 +303,7 @@ top_build_prefix = @top_build_prefix@
 top_builddir = @top_builddir@
 top_srcdir = @top_srcdir@
 curve1_SOURCES = curve1.c
+curve2_SOURCES = curve2.c
 nonlin1_SOURCES = nonlin1.c
 surface1_SOURCES = surface1.c
 AM_LDFLAGS = -lm -L../lib -llmfit
@@ -348,6 +354,10 @@ curve1$(EXEEXT): $(curve1_OBJECTS) $(curve1_DEPENDENCIES) $(EXTRA_curve1_DEPENDE
 	@rm -f curve1$(EXEEXT)
 	$(AM_V_CCLD)$(LINK) $(curve1_OBJECTS) $(curve1_LDADD) $(LIBS)
 
+curve2$(EXEEXT): $(curve2_OBJECTS) $(curve2_DEPENDENCIES) $(EXTRA_curve2_DEPENDENCIES) 
+	@rm -f curve2$(EXEEXT)
+	$(AM_V_CCLD)$(LINK) $(curve2_OBJECTS) $(curve2_LDADD) $(LIBS)
+
 nonlin1$(EXEEXT): $(nonlin1_OBJECTS) $(nonlin1_DEPENDENCIES) $(EXTRA_nonlin1_DEPENDENCIES) 
 	@rm -f nonlin1$(EXEEXT)
 	$(AM_V_CCLD)$(LINK) $(nonlin1_OBJECTS) $(nonlin1_LDADD) $(LIBS)
@@ -363,6 +373,7 @@ distclean-compile:
 	-rm -f *.tab.c
 
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/curve1.Po@am__quote@
+@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/curve2.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/nonlin1.Po@am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/surface1.Po@am__quote@
 

demo/curve2.c

@@ -0,0 +1,63 @@
+/*
+ * Library:  lmfit (Levenberg-Marquardt least squares fitting)
+ *
+ * File:     demo/curve1.c
+ *
+ * Contents: Example for fitting data with error bars:
+ *           fit a data set (x,y+-dy) by a curve f(x;p).
+ *
+ * Author:   Joachim Wuttke <[email protected]> 2004-2013
+ *
+ * Licence:  see ../COPYING (FreeBSD)
+ *
+ * Homepage: apps.jcns.fz-juelich.de/lmfit
+ */
+
+#include "lmcurve.h"
+#include <stdio.h>
+
+/* model function: a parabola */
+
+double f( double t, const double *p )
+{
+    return p[0] + p[1]*t + p[2]*t*t;
+}
+
+int main()
+{
+    int n = 3; /* number of parameters in model function f */
+    double par[3] = { 100, 0, -10 }; /* really bad starting value */
+
+    /* data points: a slightly distorted standard parabola */
+    int m = 9;
+    int i;
+    double t[9] = { -4., -3., -2., -1.,  0., 1.,  2.,  3.,  4. };
+    double y[9] = { 16.6, 9.9, 4.4, 1.1, 0., 1.1, 4.2, 9.3, 16.4 };
+    double dy[9] = { 4, 3, 2, 1, 2, 3, 4, 5, 6 };
+
+    lm_control_struct control = lm_control_double;
+    lm_status_struct status;
+    control.verbosity = 1;
+
+    printf( "Fitting ...\n" );
+    /* now the call to lmfit */
+    lmcurve_tyd( n, par, m, t, y, dy, f, &control, &status );
+
+    printf( "Results:\n" );
+    printf( "status after %d function evaluations:\n  %s\n",
+            status.nfev, lm_infmsg[status.outcome] );
+
+    printf("obtained parameters:\n");
+    for ( i = 0; i < n; ++i)
+        printf("  par[%i] = %12g\n", i, par[i]);
+    printf("obtained norm:\n  %12g\n", status.fnorm );
+
+    printf("fitting data as follows:\n");
+    for ( i = 0; i < m; ++i)
+        printf(
+        "  t[%1d]=%2g y=%5.1f+-%4.1f fit=%8.5f residue=%8.4f weighed=%8.4f\n",
+        i, t[i], y[i], dy[i], f(t[i],par), y[i] - f(t[i],par),
+        (y[i] - f(t[i],par))/dy[i] );
+
+    return 0;
+}

lib/lmcurve.c

@@ -15,27 +15,67 @@
 
 #include "lmmin.h"
 
+/******************************************************************************/
+/*  lmcurve                                                                   */
+/******************************************************************************/
+
 typedef struct {
     const double* t;
     const double* y;
     double (*f)(const double t, const double* par);
 } lmcurve_data_struct;
 
-void lmcurve_evaluate(const double* par, const int m_dat, const void* data,
-                      double* fvec, int* info)
+void lmcurve_evaluate(
+    const double* par, const int m_dat, const void* data, double* fvec,
+    int* info)
 {
     lmcurve_data_struct* D = (lmcurve_data_struct*)data;
     int i;
     for (i = 0; i < m_dat; i++)
         fvec[i] = D->y[i] - D->f(D->t[i], par);
 }
 
-void lmcurve(const int n_par, double* par, const int m_dat, const double* t,
-             const double* y, double (*f)(const double t, const double* par),
-             const lm_control_struct* control, lm_status_struct* status)
+void lmcurve(
+    const int n_par, double* par, const int m_dat,
+    const double* t, const double* y,
+    double (*f)(const double t, const double* par),
+    const lm_control_struct* control, lm_status_struct* status)
 {
     lmcurve_data_struct data = { t, y, f };
 
-    lmmin(n_par, par, m_dat, (const void*)&data, lmcurve_evaluate, control,
-          status);
+    lmmin(n_par, par, m_dat, (const void*)&data, lmcurve_evaluate,
+          control, status);
+}
+
+/******************************************************************************/
+/*  lmcurve_tyd                                                               */
+/******************************************************************************/
+
+typedef struct {
+    const double* t;
+    const double* y;
+    const double* dy;
+    double (*f)(const double t, const double* par);
+} lmcurve_tyd_data_struct;
+
+void lmcurve_tyd_evaluate(
+    const double* par, const int m_dat, const void* data, double* fvec,
+    int* info)
+{
+    lmcurve_tyd_data_struct* D = (lmcurve_tyd_data_struct*)data;
+    int i;
+    for (i = 0; i < m_dat; i++)
+        fvec[i] = ( D->y[i] - D->f(D->t[i], par) ) / D->dy[i];
+}
+
+void lmcurve_tyd(
+    const int n_par, double* par, const int m_dat,
+    const double* t, const double* y, const double* dy,
+    double (*f)(const double t, const double* par),
+    const lm_control_struct* control, lm_status_struct* status)
+{
+    lmcurve_tyd_data_struct data = { t, y, dy, f };
+
+    lmmin(n_par, par, m_dat, (const void*)&data, lmcurve_tyd_evaluate,
+          control, status);
 }

lib/lmcurve.h

@@ -29,9 +29,17 @@
 
 __BEGIN_DECLS
 
-void lmcurve(const int n_par, double* par, const int m_dat, const double* t,
-             const double* y, double (*f)(double t, const double* par),
-             const lm_control_struct* control, lm_status_struct* status);
+void lmcurve(
+    const int n_par, double* par, const int m_dat,
+    const double* t, const double* y,
+    double (*f)(double t, const double* par),
+    const lm_control_struct* control, lm_status_struct* status);
+
+void lmcurve_tyd(
+    const int n_par, double* par, const int m_dat,
+    const double* t, const double* y, const double* dy,
+    double (*f)(double t, const double* par),
+    const lm_control_struct* control, lm_status_struct* status);
 
 __END_DECLS
 #endif /* LMCURVE_H */