[packmol/f15] Initial import.

[Jussi Lehtola]

commit 7e6ef37baa4408b4e9f627816f2ed3e89e7bf967
Author: Jussi Lehtola <jussilehtola at fedoraproject.org>
Date:   Mon Jan 23 15:56:49 2012 +0200

    Initial import.

 packmol-CMakeLists.txt |   45 +++++++++++++++++++++++++++
 packmol.spec           |   79 ++++++++++++++++++++++++++++++++++++++++++++++++
 sources                |    1 +
 3 files changed, 125 insertions(+), 0 deletions(-)
---
diff --git a/packmol-CMakeLists.txt b/packmol-CMakeLists.txt
new file mode 100644
index 0000000..2571483
--- /dev/null
+++ b/packmol-CMakeLists.txt
@@ -0,0 +1,45 @@
+cmake_minimum_required(VERSION 2.6)
+enable_language (Fortran)
+project(packmol)
+
+# Build for release or debug purposes?
+SET(CMAKE_BUILD_TYPE release)
+#SET(CMAKE_BUILD_TYPE debug)
+
+# Default flags for release and debug
+set(CMAKE_Fortran_FLAGS_RELEASE "-Wall -O2")
+set(CMAKE_Fortran_FLAGS_DEBUG "-Werror -g -O2")
+
+
+# Common sources
+SET(srcall cenmass.f gencan.f initial.f io.f fgcommon.f packmolnew.f
+polartocart.f heuristics.f)
+# Common headers
+SET(headers sizes.i gencan.i molpa.i)
+# Serial-only sources
+SET(srcserial feasy.f geasy.f)
+# Parallel-only sources
+SET(srcparallel feasyparallel.f geasyparallel.f compindexes.f)
+
+
+# Compile SMP version?
+# Find_package doesn't currently support Fortran, so we need to do things by hand.
+#find_package( OpenMP )
+
+option(USE_OPENMP "Compile OpenMP enabled version?" OFF)
+if(USE_OPENMP)
+ # Determine necessary flags
+ if(CMAKE_Fortran_COMPILER_ID STREQUAL "GNU")
+  set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -fopenmp")
+ elseif(CMAKE_Fortran_COMPILER_ID STREQUAL "Intel")
+  set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -openmp")
+ else(CMAKE_Fortran_COMPILER_ID STREQUAL "GNU")
+  message(SEND_ERROR "Makefile does not support the chosen Fortran compiler \"${CMAKE_Fortran_COMPILER_NAME}\" using OpenMP.")
+ endif(CMAKE_Fortran_COMPILER_ID STREQUAL "GNU")
+
+ # Compile
+ add_executable(ppackmol ${srcall} ${srcparallel})
+else(USE_OPENMP)
+ # Build the serial executable.
+ add_executable(packmol ${srcall} ${srcserial})
+endif(USE_OPENMP)
diff --git a/packmol.spec b/packmol.spec
new file mode 100644
index 0000000..7c9f91a
--- /dev/null
+++ b/packmol.spec
@@ -0,0 +1,79 @@
+Name:		packmol
+Version:	1.1.2.023
+Release:	1%{?dist}
+Summary:	Packing optimization for molecular dynamics simulations
+Group:		Applications/Engineering
+License:	GPLv2+
+URL:		http://www.ime.unicamp.br/~martinez/packmol/
+Source0:	http://packmol.googlecode.com/files/packmol-%{version}.tar.gz
+# CMake file for compiling project, sent upstream.
+Source1:	packmol-CMakeLists.txt
+BuildRoot:	%(mktemp -ud %{_tmppath}/%{name}-%{version}-%{release}-XXXXXX)
+
+BuildRequires:	cmake
+BuildRequires:	gcc-gfortran
+
+%description
+Packmol creates an initial point for molecular dynamics simulations by
+packing molecules in defined regions of space. The packing guarantees
+that short range repulsive interactions do not disrupt the
+simulations.
+
+The great variety of types of spatial constraints that can be
+attributed to the molecules, or atoms within the molecules, makes it
+easy to create ordered systems, such as lamellar, spherical or tubular
+lipid layers.
+
+The user must provide only the coordinates of one molecule of each
+type, the number of molecules of each type and the spatial constraints
+that each type of molecule must satisfy.
+
+The package is compatible with input files of PDB, TINKER, XYZ and
+MOLDY formats.
+
+
+%prep
+%setup -q -n %{name}
+cp -a %{SOURCE1} CMakeLists.txt
+find . -name \*.o -delete
+
+%build
+export FC=gfortran
+
+mkdir ser;cd ser
+%cmake -DUSE_OPENMP=OFF .. 
+make %{?_smp_mflags}
+cd ..
+
+# Parallel version segfaults; reported upstream.
+#mkdir par; cd par
+#cmake -DUSE_OPENMP=ON .. 
+#make %{?_smp_mflags}
+#cd ..
+
+
+%install
+rm -rf %{buildroot}
+install -D -p -m 755 ser/packmol %{buildroot}%{_bindir}/packmol
+#install -D -p -m 755 par/ppackmol %{buildroot}%{_bindir}/ppackmol
+install -D -p -m 755 solvate.tcl %{buildroot}%{_bindir}/packmol_solvate
+
+%clean
+rm -rf %{buildroot}
+
+%files
+%defattr(-,root,root,-)
+%doc AUTHORS LICENSE COPYING
+%{_bindir}/packmol
+#%{_bindir}/ppackmol
+%{_bindir}/packmol_solvate
+
+%changelog
+* Mon Jan 23 2012 Jussi Lehtola <jussilehtola at fedoraproject.org> - 1.1.2.023-1
+- Update to 1.1.2.023.
+
+* Sat Jan 21 2012 Jussi Lehtola <jussilehtola at fedoraproject.org> - 1.1.2.017-1
+- Update to 1.1.2.017.
+
+* Tue Sep 27 2011 Jussi Lehtola <jussilehtola at fedoraproject.org> - 1.1.1.258-1
+- Initial release.
diff --git a/sources b/sources
index e69de29..e747790 100644
--- a/sources
+++ b/sources
@@ -0,0 +1 @@
+b210c114a2ea534493c061e65f282ab7  packmol-1.1.2.023.tar.gz