From 85a33507ea5c5f831d5bf0fcf961fa7de618215b Mon Sep 17 00:00:00 2001 From: Badi' Abdul-Wahid Date: Fri, 23 Nov 2012 03:38:13 +0100 Subject: [PATCH 1/4] Add GROMACS v4.5.5 --- .../molecular-dynamics/gromacs/4.5.5.nix | 26 ++++++++++++++++++ .../molecular-dynamics/gromacs/default.nix | 2 ++ .../molecular-dynamics/gromacs/meta.nix | 27 +++++++++++++++++++ pkgs/top-level/all-packages.nix | 15 +++++++++++ 4 files changed, 70 insertions(+) create mode 100644 pkgs/applications/science/molecular-dynamics/gromacs/4.5.5.nix create mode 100644 pkgs/applications/science/molecular-dynamics/gromacs/default.nix create mode 100644 pkgs/applications/science/molecular-dynamics/gromacs/meta.nix diff --git a/pkgs/applications/science/molecular-dynamics/gromacs/4.5.5.nix b/pkgs/applications/science/molecular-dynamics/gromacs/4.5.5.nix new file mode 100644 index 00000000000..0cb9b4c2c65 --- /dev/null +++ b/pkgs/applications/science/molecular-dynamics/gromacs/4.5.5.nix @@ -0,0 +1,26 @@ + +{ stdenv, fetchurl, cmake, + singlePrec ? true, + fftw +}: + + +let meta = import ./meta.nix; +in + +stdenv.mkDerivation { + name = "gromacs-4.5.5"; + + src = fetchurl { + url = "ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.5.tar.gz"; + md5 = "6a87e7cdfb25d81afa9fea073eb28468"; + }; + + buildInputs = [cmake fftw]; + + cmakeFlags = '' + ${if singlePrec then "-DGMX_DOUBLE=OFF" else "-DGMX_DOUBLE=ON -DGMX_DEFAULT_SUFFIX=OFF"} + ''; + + inherit meta; +} diff --git a/pkgs/applications/science/molecular-dynamics/gromacs/default.nix b/pkgs/applications/science/molecular-dynamics/gromacs/default.nix new file mode 100644 index 00000000000..ac5628bcdf8 --- /dev/null +++ b/pkgs/applications/science/molecular-dynamics/gromacs/default.nix @@ -0,0 +1,2 @@ + +import ./4.5.5.nix diff --git a/pkgs/applications/science/molecular-dynamics/gromacs/meta.nix b/pkgs/applications/science/molecular-dynamics/gromacs/meta.nix new file mode 100644 index 00000000000..fa6a041f719 --- /dev/null +++ b/pkgs/applications/science/molecular-dynamics/gromacs/meta.nix @@ -0,0 +1,27 @@ + + + +meta = { + homepage = "www.gromacs.org"; + licence = "GPLv2"; + description = "The GROMACS molecular dynamics software package"; + longDescription = '' + GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems + with hundreds to millions of particles. + + It is primarily designed for biochemical molecules like + proteins, lipids and nucleic acids that have a lot of + complicated bonded interactions, but since GROMACS is + extremely fast at calculating the nonbonded interactions (that + usually dominate simulations) many groups are also using it + for research on non-biological systems, e.g. polymers. + + GROMACS supports all the usual algorithms you expect from a + modern molecular dynamics implementation, (check the online + reference or manual for details), but there are also quite a + few features that make it stand out from the competition. + + See: www.gromacs.org/About_Gromacs + ''; +}; \ No newline at end of file diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index ede3e1eb175..97f3538d10d 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -8661,6 +8661,21 @@ let openblas = callPackage ../development/libraries/science/math/openblas { }; + + ### SCIENCE/MOLECULAR-DYNAMICS + + gromacs = callPackage ../applications/science/molecular-dynamics/gromacs { + singlePrec = true; + fftw = fftwSinglePrec; + cmake = cmakeCurses; + }; + + gromacsDouble = callPackage ../applications/science/molecular-dynamics/gromacs { + singlePrec = false; + fftw = fftw; + cmake = cmakeCurses; + }; + ### SCIENCE/LOGIC coq = callPackage ../applications/science/logic/coq { From 7bdcb521b27b460c3c1a8fac327bffae3f72be7a Mon Sep 17 00:00:00 2001 From: Badi' Abdul-Wahid Date: Fri, 23 Nov 2012 15:29:17 +0100 Subject: [PATCH 2/4] Update based on comments to pull request --- .../molecular-dynamics/gromacs/4.5.5.nix | 26 ---------- .../molecular-dynamics/gromacs/default.nix | 49 ++++++++++++++++++- .../molecular-dynamics/gromacs/meta.nix | 27 ---------- pkgs/top-level/all-packages.nix | 4 +- 4 files changed, 50 insertions(+), 56 deletions(-) delete mode 100644 pkgs/applications/science/molecular-dynamics/gromacs/4.5.5.nix delete mode 100644 pkgs/applications/science/molecular-dynamics/gromacs/meta.nix diff --git a/pkgs/applications/science/molecular-dynamics/gromacs/4.5.5.nix b/pkgs/applications/science/molecular-dynamics/gromacs/4.5.5.nix deleted file mode 100644 index 0cb9b4c2c65..00000000000 --- a/pkgs/applications/science/molecular-dynamics/gromacs/4.5.5.nix +++ /dev/null @@ -1,26 +0,0 @@ - -{ stdenv, fetchurl, cmake, - singlePrec ? true, - fftw -}: - - -let meta = import ./meta.nix; -in - -stdenv.mkDerivation { - name = "gromacs-4.5.5"; - - src = fetchurl { - url = "ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.5.tar.gz"; - md5 = "6a87e7cdfb25d81afa9fea073eb28468"; - }; - - buildInputs = [cmake fftw]; - - cmakeFlags = '' - ${if singlePrec then "-DGMX_DOUBLE=OFF" else "-DGMX_DOUBLE=ON -DGMX_DEFAULT_SUFFIX=OFF"} - ''; - - inherit meta; -} diff --git a/pkgs/applications/science/molecular-dynamics/gromacs/default.nix b/pkgs/applications/science/molecular-dynamics/gromacs/default.nix index ac5628bcdf8..d6fe326a9d1 100644 --- a/pkgs/applications/science/molecular-dynamics/gromacs/default.nix +++ b/pkgs/applications/science/molecular-dynamics/gromacs/default.nix @@ -1,2 +1,49 @@ -import ./4.5.5.nix +{ stdenv, fetchurl, cmake, + singlePrec ? true, + fftw +}: + + +let meta = import ./meta.nix; +in + +stdenv.mkDerivation { + name = "gromacs-4.5.5"; + + src = fetchurl { + url = "ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.5.tar.gz"; + md5 = "6a87e7cdfb25d81afa9fea073eb28468"; + }; + + buildInputs = [cmake fftw]; + + cmakeFlags = '' + ${if singlePrec then "-DGMX_DOUBLE=OFF" else "-DGMX_DOUBLE=ON -DGMX_DEFAULT_SUFFIX=OFF"} + ''; + + meta = { + homepage = "http://www.gromacs.org"; + licence = "GPLv2"; + description = "The GROMACS molecular dynamics software package"; + longDescription = '' + GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems + with hundreds to millions of particles. + + It is primarily designed for biochemical molecules like + proteins, lipids and nucleic acids that have a lot of + complicated bonded interactions, but since GROMACS is + extremely fast at calculating the nonbonded interactions (that + usually dominate simulations) many groups are also using it + for research on non-biological systems, e.g. polymers. + + GROMACS supports all the usual algorithms you expect from a + modern molecular dynamics implementation, (check the online + reference or manual for details), but there are also quite a + few features that make it stand out from the competition. + + See: http://www.gromacs.org/About_Gromacs for details. + ''; + }; +} diff --git a/pkgs/applications/science/molecular-dynamics/gromacs/meta.nix b/pkgs/applications/science/molecular-dynamics/gromacs/meta.nix deleted file mode 100644 index fa6a041f719..00000000000 --- a/pkgs/applications/science/molecular-dynamics/gromacs/meta.nix +++ /dev/null @@ -1,27 +0,0 @@ - - - -meta = { - homepage = "www.gromacs.org"; - licence = "GPLv2"; - description = "The GROMACS molecular dynamics software package"; - longDescription = '' - GROMACS is a versatile package to perform molecular dynamics, - i.e. simulate the Newtonian equations of motion for systems - with hundreds to millions of particles. - - It is primarily designed for biochemical molecules like - proteins, lipids and nucleic acids that have a lot of - complicated bonded interactions, but since GROMACS is - extremely fast at calculating the nonbonded interactions (that - usually dominate simulations) many groups are also using it - for research on non-biological systems, e.g. polymers. - - GROMACS supports all the usual algorithms you expect from a - modern molecular dynamics implementation, (check the online - reference or manual for details), but there are also quite a - few features that make it stand out from the competition. - - See: www.gromacs.org/About_Gromacs - ''; -}; \ No newline at end of file diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index 78dc5c8776e..342b7e7af9c 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -8668,11 +8668,11 @@ let cmake = cmakeCurses; }; - gromacsDouble = callPackage ../applications/science/molecular-dynamics/gromacs { + gromacsDouble = lowPrio (callPackage ../applications/science/molecular-dynamics/gromacs { singlePrec = false; fftw = fftw; cmake = cmakeCurses; - }; + }); ### SCIENCE/LOGIC From cba15c96f6813c6c15961236602619fab67ca1ed Mon Sep 17 00:00:00 2001 From: Badi' Abdul-Wahid Date: Fri, 23 Nov 2012 15:45:19 +0100 Subject: [PATCH 3/4] fix skipped indentation --- .../applications/science/molecular-dynamics/gromacs/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/applications/science/molecular-dynamics/gromacs/default.nix b/pkgs/applications/science/molecular-dynamics/gromacs/default.nix index d6fe326a9d1..ea4855e26d7 100644 --- a/pkgs/applications/science/molecular-dynamics/gromacs/default.nix +++ b/pkgs/applications/science/molecular-dynamics/gromacs/default.nix @@ -43,7 +43,7 @@ stdenv.mkDerivation { reference or manual for details), but there are also quite a few features that make it stand out from the competition. - See: http://www.gromacs.org/About_Gromacs for details. + See: http://www.gromacs.org/About_Gromacs for details. ''; }; } From 06c522f7391df7ea8e8707f1f15af18300d287a1 Mon Sep 17 00:00:00 2001 From: Badi' Abdul-Wahid Date: Fri, 23 Nov 2012 15:46:49 +0100 Subject: [PATCH 4/4] remove reference to meta.nix --- .../science/molecular-dynamics/gromacs/default.nix | 3 --- 1 file changed, 3 deletions(-) diff --git a/pkgs/applications/science/molecular-dynamics/gromacs/default.nix b/pkgs/applications/science/molecular-dynamics/gromacs/default.nix index ea4855e26d7..c687fd5908c 100644 --- a/pkgs/applications/science/molecular-dynamics/gromacs/default.nix +++ b/pkgs/applications/science/molecular-dynamics/gromacs/default.nix @@ -5,9 +5,6 @@ }: -let meta = import ./meta.nix; -in - stdenv.mkDerivation { name = "gromacs-4.5.5";