Merge branch 'master' into qmmm

.gitignore

@@ -7,3 +7,6 @@ autom4te.cache
 config.h.in
 config
 configure
+
+# hidden folders:
+/.*/

gromos++/INSTALL

@@ -1,11 +1,11 @@
-This is GROMOS++
-================
+GROMOS++ INSTALLATION INSTRUCTIONS
+==================================
 
 necessary compilation tools
 ***************************
 
 	ANSI C++ compatible compiler
-	(g++ >= 3.0; tested for gcc version up to 4.1.2)
+	(g++ >= 3.0; tested for gcc version up to 9.3)
 	(Intel C++ Compiler; tested with version 8.1)
 
 Required libraries
@@ -15,78 +15,94 @@ Required libraries
 	-----------------------------------------------------------
 
 	http://www.gnu.org/software/gsl/
-	compilation has been checked with version 
-	1.1, 1.2, 1.3, 1.4, 1.5 and 1.8
+	compilation has been checked with version 2.6. or lower
 
 	if the GSL is installed to the default location ./configure
 	will usually be able to find it.
-	Otherwise set the compilation flags accordingly:
+	Otherwise, when running configure in steps A 5. oder B 4. below, 
+        set the compilation flags accordingly:
 
-	--with-gsl=/path/to/gsl
+	e.g. ../configure --with-gsl=/path/to/gsl
 
+        FFTW Fast Fourier Transform Library (optional)
+        ----------------------------------------------
 
-installing from a tarball
-*************************
+        if the fftw3 installation directory is not in your standard search
+        path for header files and libraries, you can use
+
+        ../configure --with-fftw=/path/to/fftw3
+
+Case A) Installing from a tarball
+*********************************
 
 	1. tar zxvf gromos++-x.y.z.tar.gz
 	2. cd gromos++-x.y.z
-	3. ./configure
-	4. make
-	5. make check
-	6. make install
+	3. mkdir BUILD
+	4. cd BUILD
+	5. ../configure
+	6. make
+	7. make install
 
-	See ./configure --help for options.
-	step 5 and 6 are optional.
+	Info:
+	  .) See ./configure --help for options.
+          .) Step 7 is optional. It will place the programs in BUILD/bin, or in
+             the directory specified by --prefix in step 5.
+	  .) If you leave out step 7, programs will be in BUILD/program/
+             and BUILD/contrib
+	  .) You may choose any other name for the BUILD directory or do 
+             multiple builds by choosing different directory names by repeating 
+             from step 3.
 
-To compile and install the unconfigured source tree from cvs
-************************************************************
+Case B) To compile and install the unconfigured source tree from git
+********************************************************************
 
 	prerequisites:
 		GNU autotools:
-		    autoconf (GNU Autoconf) 2.58
-		    libtoolize (GNU libtool) 1.5
-		    automake (GNU automake) 1.7.9
-
-	1. mkdir -p config
-	2. aclocal
-	3. libtoolize --copy
-	4. autoconf
-	5. autoheader
-	6. automake --add-missing --copy
-	7. ./configure
-	8. make
-	9. make check
-       10. make install
-
-	See ./configure --help for options.
-
-	for convenience, the first five steps are in the Config.sh
-	script, so you only have to type:
+		    autoconf (GNU Autoconf) 2.58 or newer
+		    libtoolize (GNU libtool) 1.5 or newer
+		    automake (GNU automake) 1.7.9 or newer
 
 	1. ./Config.sh
-	2. mkdir ARCHITECTURE
-	3. cd ARCHITECTURE
+	2. mkdir BUILD
+	3. cd BUILD
 	4. ../configure
 	5. make
-	6. make check
-	7. make install
-
-installing the documentation
+        6. make install
+
+	Info:
+	  .) ./Config.sh is a wrapper of the following commands:
+		    1. mkdir -p config
+ 		    2. aclocal
+		    3. libtoolize --copy
+		    4. autoconf
+		    5. autoheader
+		    6. automake --add-missing --copy
+	  .) See ./configure --help for options.
+          .) Step 6 is optional. It will place the programs in BUILD/bin, or in
+             the directory specified by --prefix in step 4.
+	  .) If you leave out step 6, programs will be in BUILD/program/
+             and BUILD/contrib
+	  .) You may choose any other name for the BUILD directory or do 
+             multiple builds by choosing different directory names by repeating 
+             from step 3.
+
+
+installing online documentation
 ****************************
         1. make doc
         2. doxygen doc/gromos++.doxy
 
 optional libraries
 ******************
 
-	GromosXX MD library (optional)
+	MD++ library (optional)
 	------------------------------------------------------------
 
 	IGC: group for computational chemistry
 	W. F. van Gunsteren
 	Swiss Federal Institute of Technology
 
-	--with-gromosxx=/path/to/gromosXX
+	--with-gromosxx=/path/to/md++
 
 
 ARCHITECTURE DEPENDENT DETAILS
@@ -95,37 +111,37 @@ ARCHITECTURE DEPENDENT DETAILS
 MacOS X (tested on V 10.3.3 Panther):
 ------------------------------------
 
-Panther ships with the so-called developertools (http://www.apple.com/macosx/developertools/),
-which include a port of the gcc 3.3. The developertools might not be installed by
-default though, so you should make sure that this is the case
-(e.g. type: 'which gcc'; if you dont get an answer it is not installed).
-
-Unfortunately, the MacOS version of the libtoolize program (and others) does
-sometimes not work with things you download from GNU and try to
-compile. Therefore, do this:
-
-1. Download the GNU autoconf, automake and libtool packages
-   and install them. By default they will be put under /usr/local
-   which is just fine.
-(As an alternative you might just want to install the binary
- packages from FINK (http://fink.sourceforge.net/), 
- i.e. the port of the Debian APT package tools.
- You will need to have FINK installed, though).
-2. Set the path to point to /usr/local/bin so that those versions
-   of automake/autoconf/libtool will be used.
-3. Build the distribution as written above.
-4. In case of linking errors when using the gcc port from Apple
-   build the distribution without support for shared libraries
-  (./configure --enable-shared=NO)
-   If you really need shared library support, it is possible to
-   first compile and install the regular GCC from the GNU tarball
-   and use that one to compile gromos++. This has been tested and
-   works.
+	Panther ships with the so-called developertools (http://www.apple.com/macosx/developertools/),
+	which include a port of the gcc 3.3. The developertools might not be installed by
+	default though, so you should make sure that this is the case
+	(e.g. type: 'which gcc'; if you dont get an answer it is not installed).
+
+	Unfortunately, the MacOS version of the libtoolize program (and others) does
+	sometimes not work with things you download from GNU and try to
+	compile. Therefore, do this:
+
+	1. Download the GNU autoconf, automake and libtool packages
+   	   and install them. By default they will be put under /usr/local
+   	   which is just fine.
+	   (As an alternative you might just want to install the binary
+	   packages from FINK (http://fink.sourceforge.net/), 
+	   i.e. the port of the Debian APT package tools.
+	   You will need to have FINK installed, though).
+	2. Set the path to point to /usr/local/bin so that those versions
+	   of automake/autoconf/libtool will be used.
+	3. Build the distribution as written above.
+	4. In case of linking errors when using the gcc port from Apple
+	   build the distribution without support for shared libraries
+	   (./configure --enable-shared=NO)
+   	   If you really need shared library support, it is possible to
+   	   first compile and install the regular GCC from the GNU tarball
+   	   and use that one to compile gromos++. This has been tested and
+   	   works.
 
 MacOS X (V. 10.4.10 Darwin) with gcc 4.0
 ----------------------------------------
-Similar as above.
+	Similar as above.
 
-Shared libraries can also be compiled by setting CC=g++ before the
-autoconf/automake/configure commands. (CC is used for linking).
+	Shared libraries can also be compiled by setting CC=g++ before the
+	iautoconf/automake/configure commands. (CC is used for linking).
 

gromos++/configure.ac

@@ -5,7 +5,7 @@ dnl 12/20/00
 
 AC_PREREQ(2.53)
 
-AC_INIT(gromos++, 1.5.0)
+AC_INIT([gromos++], [1.5.0], [biomos@igc.phys.chem.ethz.ch], [gromos++], [https//www.gromos.net])
 AC_CONFIG_AUX_DIR(config)
 AC_CONFIG_MACRO_DIR([m4])
 AC_CANONICAL_HOST
@@ -55,6 +55,10 @@ AC_ARG_ENABLE(gprof,
   [  --enable-gprof          compile with profiling on],
   , enable_gprof=no)
 
+AC_ARG_ENABLE(shared,
+[  --enable-shared          compile with shared libraries],
+    , enable_shared=no)
+
 
 AM_INIT_AUTOMAKE([no-define subdir-objects])
 AM_CONFIG_HEADER(config.h)

gromos++/contrib/Makefile.am

@@ -52,7 +52,9 @@ bin_PROGRAMS = \
     eds_mult_all\
     stat_ana\
     sphericity\
-	expand_ua
+	expand_ua\
+    fit_ener\
+    fit_ener_traj
 
 aggregates_SOURCES = aggregates.cc
 rottemp_SOURCES = rottemp.cc
@@ -102,6 +104,8 @@ eds_mult_all_SOURCES = eds_mult_all.cc
 stat_ana_SOURCES = stat_ana.cc
 sphericity_SOURCES = sphericity.cc
 expand_ua_SOURCES = expand_ua.cc
+fit_ener_SOURCES = fit_ener.cc
+fit_ener_traj_SOURCES = fit_ener_traj.cc
 
 LDADD = $(top_builddir)/src/libgromos.la