[Tomato] Added preliminary Autotools-based build system

tomato/.gitignore

+Makefile.in
+aclocal.m4
+autom4te.cache
+/config/gnu
+config.h.in
+configure
+libtool.m4
+ltoptions.m4
+ltsugar.m4
+ltversion.m4
+lt~obsolete.m4

tomato/INSTALL

+Installation Instructions
+*************************
+
+Copyright (C) 1994-1996, 1999-2002, 2004-2013 Free Software Foundation,
+Inc.
+
+   Copying and distribution of this file, with or without modification,
+are permitted in any medium without royalty provided the copyright
+notice and this notice are preserved.  This file is offered as-is,
+without warranty of any kind.
+
+Basic Installation
+==================
+
+   Briefly, the shell command `./configure && make && make install'
+should configure, build, and install this package.  The following
+more-detailed instructions are generic; see the `README' file for
+instructions specific to this package.  Some packages provide this
+`INSTALL' file but do not implement all of the features documented
+below.  The lack of an optional feature in a given package is not
+necessarily a bug.  More recommendations for GNU packages can be found
+in *note Makefile Conventions: (standards)Makefile Conventions.
+
+   The `configure' shell script attempts to guess correct values for
+various system-dependent variables used during compilation.  It uses
+those values to create a `Makefile' in each directory of the package.
+It may also create one or more `.h' files containing system-dependent
+definitions.  Finally, it creates a shell script `config.status' that
+you can run in the future to recreate the current configuration, and a
+file `config.log' containing compiler output (useful mainly for
+debugging `configure').
+
+   It can also use an optional file (typically called `config.cache'
+and enabled with `--cache-file=config.cache' or simply `-C') that saves
+the results of its tests to speed up reconfiguring.  Caching is
+disabled by default to prevent problems with accidental use of stale
+cache files.
+
+   If you need to do unusual things to compile the package, please try
+to figure out how `configure' could check whether to do them, and mail
+diffs or instructions to the address given in the `README' so they can
+be considered for the next release.  If you are using the cache, and at
+some point `config.cache' contains results you don't want to keep, you
+may remove or edit it.
+
+   The file `configure.ac' (or `configure.in') is used to create
+`configure' by a program called `autoconf'.  You need `configure.ac' if
+you want to change it or regenerate `configure' using a newer version
+of `autoconf'.
+
+   The simplest way to compile this package is:
+
+  1. `cd' to the directory containing the package's source code and type
+     `./configure' to configure the package for your system.
+
+     Running `configure' might take a while.  While running, it prints
+     some messages telling which features it is checking for.
+
+  2. Type `make' to compile the package.
+
+  3. Optionally, type `make check' to run any self-tests that come with
+     the package, generally using the just-built uninstalled binaries.
+
+  4. Type `make install' to install the programs and any data files and
+     documentation.  When installing into a prefix owned by root, it is
+     recommended that the package be configured and built as a regular
+     user, and only the `make install' phase executed with root
+     privileges.
+
+  5. Optionally, type `make installcheck' to repeat any self-tests, but
+     this time using the binaries in their final installed location.
+     This target does not install anything.  Running this target as a
+     regular user, particularly if the prior `make install' required
+     root privileges, verifies that the installation completed
+     correctly.
+
+  6. You can remove the program binaries and object files from the
+     source code directory by typing `make clean'.  To also remove the
+     files that `configure' created (so you can compile the package for
+     a different kind of computer), type `make distclean'.  There is
+     also a `make maintainer-clean' target, but that is intended mainly
+     for the package's developers.  If you use it, you may have to get
+     all sorts of other programs in order to regenerate files that came
+     with the distribution.
+
+  7. Often, you can also type `make uninstall' to remove the installed
+     files again.  In practice, not all packages have tested that
+     uninstallation works correctly, even though it is required by the
+     GNU Coding Standards.
+
+  8. Some packages, particularly those that use Automake, provide `make
+     distcheck', which can by used by developers to test that all other
+     targets like `make install' and `make uninstall' work correctly.
+     This target is generally not run by end users.
+
+Compilers and Options
+=====================
+
+   Some systems require unusual options for compilation or linking that
+the `configure' script does not know about.  Run `./configure --help'
+for details on some of the pertinent environment variables.
+
+   You can give `configure' initial values for configuration parameters
+by setting variables in the command line or in the environment.  Here
+is an example:
+
+     ./configure CC=c99 CFLAGS=-g LIBS=-lposix
+
+   *Note Defining Variables::, for more details.
+
+Compiling For Multiple Architectures
+====================================
+
+   You can compile the package for more than one kind of computer at the
+same time, by placing the object files for each architecture in their
+own directory.  To do this, you can use GNU `make'.  `cd' to the
+directory where you want the object files and executables to go and run
+the `configure' script.  `configure' automatically checks for the
+source code in the directory that `configure' is in and in `..'.  This
+is known as a "VPATH" build.
+
+   With a non-GNU `make', it is safer to compile the package for one
+architecture at a time in the source code directory.  After you have
+installed the package for one architecture, use `make distclean' before
+reconfiguring for another architecture.
+
+   On MacOS X 10.5 and later systems, you can create libraries and
+executables that work on multiple system types--known as "fat" or
+"universal" binaries--by specifying multiple `-arch' options to the
+compiler but only a single `-arch' option to the preprocessor.  Like
+this:
+
+     ./configure CC="gcc -arch i386 -arch x86_64 -arch ppc -arch ppc64" \
+                 CXX="g++ -arch i386 -arch x86_64 -arch ppc -arch ppc64" \
+                 CPP="gcc -E" CXXCPP="g++ -E"
+
+   This is not guaranteed to produce working output in all cases, you
+may have to build one architecture at a time and combine the results
+using the `lipo' tool if you have problems.
+
+Installation Names
+==================
+
+   By default, `make install' installs the package's commands under
+`/usr/local/bin', include files under `/usr/local/include', etc.  You
+can specify an installation prefix other than `/usr/local' by giving
+`configure' the option `--prefix=PREFIX', where PREFIX must be an
+absolute file name.
+
+   You can specify separate installation prefixes for
+architecture-specific files and architecture-independent files.  If you
+pass the option `--exec-prefix=PREFIX' to `configure', the package uses
+PREFIX as the prefix for installing programs and libraries.
+Documentation and other data files still use the regular prefix.
+
+   In addition, if you use an unusual directory layout you can give
+options like `--bindir=DIR' to specify different values for particular
+kinds of files.  Run `configure --help' for a list of the directories
+you can set and what kinds of files go in them.  In general, the
+default for these options is expressed in terms of `${prefix}', so that
+specifying just `--prefix' will affect all of the other directory
+specifications that were not explicitly provided.
+
+   The most portable way to affect installation locations is to pass the
+correct locations to `configure'; however, many packages provide one or
+both of the following shortcuts of passing variable assignments to the
+`make install' command line to change installation locations without
+having to reconfigure or recompile.
+
+   The first method involves providing an override variable for each
+affected directory.  For example, `make install
+prefix=/alternate/directory' will choose an alternate location for all
+directory configuration variables that were expressed in terms of
+`${prefix}'.  Any directories that were specified during `configure',
+but not in terms of `${prefix}', must each be overridden at install
+time for the entire installation to be relocated.  The approach of
+makefile variable overrides for each directory variable is required by
+the GNU Coding Standards, and ideally causes no recompilation.
+However, some platforms have known limitations with the semantics of
+shared libraries that end up requiring recompilation when using this
+method, particularly noticeable in packages that use GNU Libtool.
+
+   The second method involves providing the `DESTDIR' variable.  For
+example, `make install DESTDIR=/alternate/directory' will prepend
+`/alternate/directory' before all installation names.  The approach of
+`DESTDIR' overrides is not required by the GNU Coding Standards, and
+does not work on platforms that have drive letters.  On the other hand,
+it does better at avoiding recompilation issues, and works well even
+when some directory options were not specified in terms of `${prefix}'
+at `configure' time.
+
+Optional Features
+=================
+
+   If the package supports it, you can cause programs to be installed
+with an extra prefix or suffix on their names by giving `configure' the
+option `--program-prefix=PREFIX' or `--program-suffix=SUFFIX'.
+
+   Some packages pay attention to `--enable-FEATURE' options to
+`configure', where FEATURE indicates an optional part of the package.
+They may also pay attention to `--with-PACKAGE' options, where PACKAGE
+is something like `gnu-as' or `x' (for the X Window System).  The
+`README' should mention any `--enable-' and `--with-' options that the
+package recognizes.
+
+   For packages that use the X Window System, `configure' can usually
+find the X include and library files automatically, but if it doesn't,
+you can use the `configure' options `--x-includes=DIR' and
+`--x-libraries=DIR' to specify their locations.
+
+   Some packages offer the ability to configure how verbose the
+execution of `make' will be.  For these packages, running `./configure
+--enable-silent-rules' sets the default to minimal output, which can be
+overridden with `make V=1'; while running `./configure
+--disable-silent-rules' sets the default to verbose, which can be
+overridden with `make V=0'.
+
+Particular systems
+==================
+
+   On HP-UX, the default C compiler is not ANSI C compatible.  If GNU
+CC is not installed, it is recommended to use the following options in
+order to use an ANSI C compiler:
+
+     ./configure CC="cc -Ae -D_XOPEN_SOURCE=500"
+
+and if that doesn't work, install pre-built binaries of GCC for HP-UX.
+
+   HP-UX `make' updates targets which have the same time stamps as
+their prerequisites, which makes it generally unusable when shipped
+generated files such as `configure' are involved.  Use GNU `make'
+instead.
+
+   On OSF/1 a.k.a. Tru64, some versions of the default C compiler cannot
+parse its `<wchar.h>' header file.  The option `-nodtk' can be used as
+a workaround.  If GNU CC is not installed, it is therefore recommended
+to try
+
+     ./configure CC="cc"
+
+and if that doesn't work, try
+
+     ./configure CC="cc -nodtk"
+
+   On Solaris, don't put `/usr/ucb' early in your `PATH'.  This
+directory contains several dysfunctional programs; working variants of
+these programs are available in `/usr/bin'.  So, if you need `/usr/ucb'
+in your `PATH', put it _after_ `/usr/bin'.
+
+   On Haiku, software installed for all users goes in `/boot/common',
+not `/usr/local'.  It is recommended to use the following options:
+
+     ./configure --prefix=/boot/common
+
+Specifying the System Type
+==========================
+
+   There may be some features `configure' cannot figure out
+automatically, but needs to determine by the type of machine the package
+will run on.  Usually, assuming the package is built to be run on the
+_same_ architectures, `configure' can figure that out, but if it prints
+a message saying it cannot guess the machine type, give it the
+`--build=TYPE' option.  TYPE can either be a short name for the system
+type, such as `sun4', or a canonical name which has the form:
+
+     CPU-COMPANY-SYSTEM
+
+where SYSTEM can have one of these forms:
+
+     OS
+     KERNEL-OS
+
+   See the file `config.sub' for the possible values of each field.  If
+`config.sub' isn't included in this package, then this package doesn't
+need to know the machine type.
+
+   If you are _building_ compiler tools for cross-compiling, you should
+use the option `--target=TYPE' to select the type of system they will
+produce code for.
+
+   If you want to _use_ a cross compiler, that generates code for a
+platform different from the build platform, you should specify the
+"host" platform (i.e., that on which the generated programs will
+eventually be run) with `--host=TYPE'.
+
+Sharing Defaults
+================
+
+   If you want to set default values for `configure' scripts to share,
+you can create a site shell script called `config.site' that gives
+default values for variables like `CC', `cache_file', and `prefix'.
+`configure' looks for `PREFIX/share/config.site' if it exists, then
+`PREFIX/etc/config.site' if it exists.  Or, you can set the
+`CONFIG_SITE' environment variable to the location of the site script.
+A warning: not all `configure' scripts look for a site script.
+
+Defining Variables
+==================
+
+   Variables not defined in a site shell script can be set in the
+environment passed to `configure'.  However, some packages may run
+configure again during the build, and the customized values of these
+variables may be lost.  In order to avoid this problem, you should set
+them in the `configure' command line, using `VAR=value'.  For example:
+
+     ./configure CC=/usr/local2/bin/gcc
+
+causes the specified `gcc' to be used as the C compiler (unless it is
+overridden in the site shell script).
+
+Unfortunately, this technique does not work for `CONFIG_SHELL' due to
+an Autoconf limitation.  Until the limitation is lifted, you can use
+this workaround:
+
+     CONFIG_SHELL=/bin/bash ./configure CONFIG_SHELL=/bin/bash
+
+`configure' Invocation
+======================
+
+   `configure' recognizes the following options to control how it
+operates.
+
+`--help'
+`-h'
+     Print a summary of all of the options to `configure', and exit.
+
+`--help=short'
+`--help=recursive'
+     Print a summary of the options unique to this package's
+     `configure', and exit.  The `short' variant lists options used
+     only in the top level, while the `recursive' variant lists options
+     also present in any nested packages.
+
+`--version'
+`-V'
+     Print the version of Autoconf used to generate the `configure'
+     script, and exit.
+
+`--cache-file=FILE'
+     Enable the cache: use and save the results of the tests in FILE,
+     traditionally `config.cache'.  FILE defaults to `/dev/null' to
+     disable caching.
+
+`--config-cache'
+`-C'
+     Alias for `--cache-file=config.cache'.
+
+`--quiet'
+`--silent'
+`-q'
+     Do not print messages saying which checks are being made.  To
+     suppress all normal output, redirect it to `/dev/null' (any error
+     messages will still be shown).
+
+`--srcdir=DIR'
+     Look for the package's source code in directory DIR.  Usually
+     `configure' can determine that directory automatically.
+
+`--prefix=DIR'
+     Use DIR as the installation prefix.  *note Installation Names::
+     for more details, including other options available for fine-tuning
+     the installation locations.
+
+`--no-create'
+`-n'
+     Run the configure checks, but stop before creating any output
+     files.
+
+`configure' also accepts some other, not widely useful, options.  Run
+`configure --help' for more details.

tomato/Makefile.am

+# -*- Automake -*-
+#
+# Makefile for the Tomato package
+#
+# Copyright (C) 2017 Yann Pouillon
+#
+# This file is part of the Tomato software package. For license information,
+# please see the COPYING file in the top-level directory of the source
+# distribution.
+#
+
+                    # ------------------------------------ #
+
+# Autotools parameters
+ACLOCAL_AMFLAGS = -I config/m4
+AM_DISTCHECK_CONFIGURE_FLAGS = --with-msw="@with_msw@"
+
+# Subdirectories containing makefiles
+SUBDIRS = src
+
+# Support for pkg-config (see http://pkg-config.freedesktop.org/wiki/)
+pkgconfigdir = $(prefix)/lib/pkgconfig
+pkgconfig_DATA = config/data/tomato.pc
+
+# Files to explicitly distribute in the source package
+EXTRA_DIST = \
+  config/data/tomato.pc.in \
+  config/data/tomato-config.yaml.in \
+  config/scripts/markdown
+
+# Custom targets
+distclean-local:
+	rm -f $(distdir).tar.bz2 $(distdir).tar.gz $(distdir).tar.xz

tomato/autogen.sh

+#!/bin/sh
+#
+# Copyright (C) 2017 Yann Pouillon <notifications@materialsevolution.es>
+#
+# This file is part of Tomato.
+#
+# Tomato is free software: you can redistribute it and/or modify it under the
+# terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation, version 3 of the License, or (at your option) any later
+# version.
+#
+# Tomato is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
+# A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with Tomato.  If not, see <http://www.gnu.org/licenses/> or write to the
+# Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA
+# 02110-1301  USA.
+
+# Stop at first error encountered
+set -e
+
+# Check that we are in the right directory
+if test ! -s "./configure.ac" -o ! -s "src/tomato_TB.F90"; then
+  echo "This is not a Tomato source tree - aborting now"
+  exit 1
+fi
+
+# Create possibly missing directories
+mkdir -p config/gnu config/m4
+
+# Generate M4 macros
+#echo "Generating M4 macros..."
+#echo "done."
+
+# Generate makefiles
+#echo "Generating makefiles..."
+#echo "done."
+
+# Generate M4 includes
+echo "Generating aclocal.m4..."
+aclocal -I config/m4
+echo "done."
+
+# Generate configure auxiliary files
+echo "Generating config.h.in..."
+autoheader
+echo "done."
+
+# Generate configure
+echo "Generating configure script..."
+autoconf
+echo "done."
+
+# Generate libtool scripts
+echo "Generating libtool scripts..."
+my_libtoolize="libtoolize"
+${my_libtoolize} --version >/dev/null 2>&1
+if test "${?}" != "0"; then 
+  my_libtoolize="glibtoolize"
+fi
+${my_libtoolize} --version >/dev/null 2>&1
+if test "${?}" != "0"; then 
+  echo "Error: could not find a working version of libtoolize" >&2
+  exit 1
+fi
+${my_libtoolize} --automake --copy --force
+echo "done."
+
+# Generate makefile inputs
+# Do not use "automake --force-missing", as it overwrites the INSTALL file.
+echo "Generating Makefile.in for each directory..."
+automake --add-missing --copy
+echo "done."

tomato/config/data/tomato-config.yaml.in

+%YAML 1.1
+---
+timestamp: "@tom_timestamp@"
+
+target:
+    cpu: "@target_cpu@"
+    vendor: "@target_vendor@"
+    os: "@target_os@"
+
+compilers:
+    CPP: "@CPP@"
+    CPPFLAGS: "@CPPFLAGS@"
+    CC: "@CC@"
+    MPICC: "@MPICC@"
+    CFLAGS: "@CFLAGS@"
+    FC: "@FC@"
+    MPIFC: "@MPIFC@"
+    FCFLAGS: "@FCFLAGS@"
+    LDFLAGS: "@LDFLAGS@"
+    LIBS: "@LIBS@"
+
+defaults:
+    debug_enable: "@tom_debug_enable_def@"
+    randseed_enable: "@tom_randseed_enable_def@"
+    linalg_enable: "@tom_linalg_enable_def@"
+    mpi_enable: "@tom_mpi_enable_def@"
+    linalg_incs: "@tom_linalg_incs_def@"
+    linalg_libs: "@tom_linalg_libs_def@"
+    psp_enable: "@tom_psp_enable_def@"
+
+options:
+    enable_debug: "@enable_debug@"
+    enable_randseed: "@enable_randseed@"
+    with_linalg: "@with_linalg@"
+    with_mpi: "@with_mpi@"
+    with_psp: "@with_psp@"
+
+triggers:
+    debug_enable: "@tom_debug_enable@"
+    randseed_enable: "@tom_randseed_enable@"
+    linalg_enable: "@tom_linalg_enable@"
+    mpi_enable: "@tom_mpi_enable@"
+    psp_enable: "@tom_psp_enable@"
+
+inits:
+    debug: "@tom_debug_type@"
+    randseed: "@tom_randseed_type@"
+    linalg: "@tom_linalg_type@"
+    mpi: "@tom_mpi_type@"
+    psp: "@tom_psp_type@"
+
+deps:
+    linalg_incs: "@tom_linalg_incs@"
+    linalg_libs: "@tom_linalg_libs@"
+    mpi_incs: "@tom_mpi_incs@"
+    mpi_libs: "@tom_mpi_libs@"
+    psp_incs: "@tom_psp_incs@"
+    psp_libs: "@tom_psp_libs@"
+
+linalg_internals:
+    has_lapack: "@tom_linalg_has_lapack@"
+    has_scalapack: "@tom_linalg_has_lapack@"
+
+mpi_internals:
+    cc_set: "@tom_mpi_cc_set@"
+    cc_wrap: "@tom_mpi_cc_wrap@"
+    fc_set: "@tom_mpi_fc_set@"
+    fc_wrap: "@tom_mpi_fc_wrap@"
+    fc_wrap: "@tom_mpi_incs@"
+    fc_wrap: "@tom_mpi_libs@"
+

tomato/config/data/tomato.pc.in

+prefix=@prefix@
+exec_prefix=@exec_prefix@
+libdir=@libdir@
+includedir=@includedir@
+
+Name: tomato
+Description: Simple tight-binding program based on MatrixSwitch.
+Version: @VERSION@
+Libs: -L${libdir} -ltomato
+Cflags: -I${includedir}

tomato/config/m4/MatrixSwitch.m4

+# -*- Autoconf -*-
+#
+# M4 macros for Tomato
+#
+# Copyright (C) 2017 Yann Pouillon
+#
+# This file is part of the Tomato software package. For license information,
+# please see the COPYING file in the top-level directory of the Tomato source
+# distribution.
+#
+
+#
+# MatrixSwitch support
+#
+
+
+
+# TOM_MSW_DETECT()
+# -------------------
+#
+# Checks that the selected linear algebra libraries properly work.
+#
+AC_DEFUN([TOM_MSW_DETECT],[
+  dnl Init
+  tom_msw_ok="unknown"
+
+  dnl Prepare environment
+  saved_CPPFLAGS="${CPPFLAGS}"
+  saved_FCFLAGS="${FCFLAGS}"
+  saved_LIBS="${LIBS}"
+  CPPFLAGS="${CPPFLAGS} ${tom_msw_incs}"
+  FCFLAGS="${FCFLAGS} ${CPPFLAGS}"
+  LIBS="${tom_msw_libs} ${LIBS}"
+
+  dnl Check MatrixSwitch routine
+  AC_LANG_PUSH([Fortran])
+  AC_MSG_CHECKING([whether the MatrixSwitch library works])
+  AC_LINK_IFELSE([AC_LANG_PROGRAM([],
+    [[
+      use matrixswitch
+      character(3) :: m_operation
+      double precision :: x_min
+      type(matrix) :: HW, HWd
+      call m_add(HWd, 'c', HW, x_min, 1.0d0, m_operation)