Merge pull request #44752 from costrouc/costrouc/lammps-update

material science packages (init and update): lammps, python - ase, pymatgen-lammps, lammps-cython, dftfit

pkgs/applications/science/molecular-dynamics/lammps/default.nix

@@ -1,25 +1,37 @@
-{ stdenv, writeText, fetchurl,
-  libpng, fftw,
-  mpiSupport ? false, mpi ? null
+{ lib
+, bash
+, stdenv
+, writeText
+, fetchFromGitHub
+, libpng
+, gzip
+, fftw
+, openblas
+, mpiSupport ? false, mpi ? null
 }:
 
 assert mpiSupport -> mpi != null;
 
 stdenv.mkDerivation rec {
   # LAMMPS has weird versioning converted to ISO 8601 format
-  version = "2016-02-16";
+  version = "patch_2Aug2018";
   name = "lammps-${version}";
 
-  src = fetchurl {
-    url = "mirror://sourceforge/lammps/lammps-16Feb16.tar.gz";
-    sha256 = "1yzfbkxma3xa1288rnn66h4w0smbmjkwq1fx1y60pjiw0prmk105";
+  lammps_packages = "asphere body class2 colloid compress coreshell dipole granular kspace manybody mc misc molecule opt peri qeq replica rigid shock snap srd user-reaxc";
+  lammps_includes = "-DLAMMPS_EXCEPTIONS -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64";
+
+  src = fetchFromGitHub {
+    owner = "lammps";
+    repo = "lammps";
+    rev = "${version}";
+    sha256 = "1ph9pr7s11wgmspmnhxa55bh1pq2cyl8iimfi62lbpbpl9pr1ilc";
   };
 
   passthru = {
     inherit mpi;
   };
 
-  buildInputs = [ fftw libpng ]
+  buildInputs = [ fftw libpng openblas gzip bash ]
   ++ (stdenv.lib.optionals mpiSupport [ mpi ]);
 
   # Must do manual build due to LAMMPS requiring a seperate build for
@@ -27,13 +39,19 @@ stdenv.mkDerivation rec {
   builder = writeText "builder.sh" ''
     source $stdenv/setup
 
-    tar xzf $src
-    cd lammps-*/src
-    make mode=exe ${if mpiSupport then "mpi" else "serial"} SHELL=$SHELL LMP_INC="-DLAMMPS_GZIP -DLAMMPS_PNG" FFT_PATH=-DFFT_FFTW3 FFT_LIB=-lfftw3 JPG_LIB=-lpng
-    make mode=shlib ${if mpiSupport then "mpi" else "serial"} SHELL=$SHELL LMP_INC="-DLAMMPS_GZIP -DLAMMPS_PNG" FFT_PATH=-DFFT_FFTW3 FFT_LIB=-lfftw3 JPG_LIB=-lpng
+    mkdir lammps
+    cp -r $src/lib $src/src lammps
+    chmod -R 755 lammps/src/
+    cd lammps/src
+    for pack in ${lammps_packages}; do make "yes-$pack" SHELL=$SHELL; done
+    make mode=exe ${if mpiSupport then "mpi" else "serial"} SHELL=$SHELL LMP_INC="${lammps_includes}" FFT_PATH=-DFFT_FFTW3 FFT_LIB=-lfftw3 JPG_LIB=-lpng
+    make mode=shlib ${if mpiSupport then "mpi" else "serial"} SHELL=$SHELL LMP_INC="${lammps_includes}" FFT_PATH=-DFFT_FFTW3 FFT_LIB=-lfftw3 JPG_LIB=-lpng
 
     mkdir -p $out/bin
-    cp -v lmp_* $out/bin/lammps
+    cp -v lmp_* $out/bin/
+
+    mkdir -p $out/include
+    cp -v *.h $out/include/
 
     mkdir -p $out/lib
     cp -v liblammps* $out/lib/
@@ -51,5 +69,6 @@ stdenv.mkDerivation rec {
     homepage = http://lammps.sandia.gov;
     license = stdenv.lib.licenses.gpl2;
     platforms = stdenv.lib.platforms.linux;
+    maintainers = with lib.maintainers; [ costrouc ];
   };
 }

pkgs/development/libraries/pagmo2/default.nix

@@ -0,0 +1,46 @@
+{ lib
+, fetchFromGitHub
+, stdenv
+, cmake
+, eigen
+, nlopt
+, ipopt
+, boost
+, writeText
+}:
+
+stdenv.mkDerivation rec {
+  name = "pagmo2-${version}";
+  version = "2.8";
+
+  src = fetchFromGitHub {
+     owner = "esa";
+     repo = "pagmo2";
+     rev = "v${version}";
+     sha256 = "1xwxamcn3fkwr62jn6bkanrwy0cvsksf75hfwx4fvl56awnbz41z";
+  };
+
+  buildInputs = [ cmake eigen nlopt ipopt boost ];
+
+  preBuild = ''
+    cp -r $src/* .
+  '';
+
+  cmakeFlags = [ "-DPAGMO_BUILD_TESTS=no"
+                 "-DPAGMO_WITH_EIGEN3=yes" "-DPAGMO_WITH_NLOPT=yes"
+                 "-DNLOPT_LIBRARY=${nlopt}/lib/libnlopt_cxx.so" "-DPAGMO_WITH_IPOPT=yes"
+                 "-DCMAKE_CXX_FLAGS='-fuse-ld=gold'" ];
+
+  checkPhase = ''
+    ctest
+  '';
+
+  # All but one test pass skip for now (tests also take about 30 min to compile)
+  doCheck = false;
+
+  meta = {
+    homepage = https://esa.github.io/pagmo2/;
+    description = "Scientific library for massively parallel optimization";
+    license = stdenv.lib.licenses.gpl3Plus;
+  };
+}

pkgs/development/python-modules/ase/default.nix

@@ -0,0 +1,36 @@
+{ lib
+, fetchurl
+, buildPythonPackage
+, numpy
+, scipy
+, matplotlib
+, flask
+, pillow
+, psycopg2
+}:
+
+buildPythonPackage rec {
+  version = "3.16.2";
+  pname = "ase";
+
+  src = fetchurl {
+     url = "https://gitlab.com/${pname}/${pname}/-/archive/${version}/${pname}-${version}.tar.gz";
+     sha256 = "171j3f4a261cfnqjq98px5fldxql65i3jgf60wc945xvh0mbc8ds";
+  };
+
+  propagatedBuildInputs = [ numpy scipy matplotlib flask pillow psycopg2 ];
+
+  checkPhase = ''
+    $out/bin/ase test
+  '';
+
+  # tests just hang most likely due to something with subprocesses and cli
+  doCheck = false;
+
+  meta = {
+    description = "Atomic Simulation Environment";
+    homepage = https://wiki.fysik.dtu.dk/ase/;
+    license = lib.licenses.lgpl21Plus;
+    maintainers = with lib.maintainers; [ costrouc ];
+  };
+}

pkgs/development/python-modules/dftfit/default.nix

@@ -0,0 +1,47 @@
+{ lib
+, fetchPypi
+, buildPythonPackage
+, pymatgen
+, marshmallow
+, pyyaml
+, pygmo
+, pandas
+, scipy
+, numpy
+, scikitlearn
+, lammps-cython
+, pymatgen-lammps
+, pytestrunner
+, pytest
+, pytestcov
+, pytest-benchmark
+, isPy3k
+, openssh
+}:
+
+buildPythonPackage rec {
+  pname = "dftfit";
+  version = "0.4.11";
+  disabled = (!isPy3k);
+
+  src = fetchPypi {
+     inherit pname version;
+     sha256 = "c6e36a793f9f94746bb8a04fb8316404aeacfa918704de07b15e1b4b8b62242d";
+  };
+
+  buildInputs = [ pytestrunner ];
+  checkInputs = [ pytest pytestcov pytest-benchmark openssh ];
+  propagatedBuildInputs = [ pymatgen marshmallow pyyaml pygmo
+                            pandas scipy numpy scikitlearn
+                            lammps-cython pymatgen-lammps ];
+
+  # tests require git lfs download. and is quite large so skip tests
+  doCheck = false;
+
+  meta = {
+    description = "Ab-Initio Molecular Dynamics Potential Development";
+    homepage = https://gitlab.com/costrouc/dftfit;
+    license = lib.licenses.mit;
+    maintainers = with lib.maintainers; [ costrouc ];
+  };
+}

pkgs/development/python-modules/docutils/default.nix

@@ -0,0 +1,35 @@
+{ lib
+, fetchurl
+, buildPythonPackage
+, isPy3k
+, python
+}:
+
+buildPythonPackage rec {
+  pname = "docutils";
+  version = "0.14";
+
+  src = fetchurl {
+    url = "mirror://sourceforge/docutils/${pname}.tar.gz";
+    sha256 = "0x22fs3pdmr42kvz6c654756wja305qv6cx1zbhwlagvxgr4xrji";
+  };
+
+  checkPhase = if isPy3k then ''
+    ${python.interpreter} test3/alltests.py
+  '' else ''
+    ${python.interpreter} test/alltests.py
+  '';
+
+  # Create symlinks lacking a ".py" suffix, many programs depend on these names
+  postFixup = ''
+    (cd $out/bin && for f in *.py; do
+      ln -s $f $(echo $f | sed -e 's/\.py$//')
+    done)
+  '';
+
+  meta = {
+    description = "Docutils -- Python Documentation Utilities";
+    homepage = http://docutils.sourceforge.net/;
+    maintainers = with lib.maintainers; [ garbas AndersonTorres ];
+  };
+}

pkgs/development/python-modules/lammps-cython/default.nix

@@ -0,0 +1,53 @@
+{ lib
+, fetchurl
+, buildPythonPackage
+, lammps-mpi
+, mpi
+, mpi4py
+, numpy
+, cython
+, pymatgen
+, ase
+, pytestrunner
+, pytest
+, pytestcov
+, isPy3k
+, openssh
+}:
+
+buildPythonPackage rec {
+  pname = "lammps-cython";
+  version = "0.5.7";
+  disabled = (!isPy3k);
+
+  src = fetchurl {
+     url = "https://gitlab.com/costrouc/${pname}/-/archive/v${version}/${pname}-v${version}.tar.gz";
+     sha256 = "1wj9scmjdl00af13b5ihfccrjpikrdgkzd88ialam1nkxvxi42bl";
+  };
+
+  buildInputs = [ cython pytestrunner ];
+  checkInputs = [ pytest pytestcov openssh ];
+  propagatedBuildInputs = [ mpi4py pymatgen ase numpy ];
+
+  preBuild = ''
+    echo "Creating lammps.cfg file..."
+    cat << EOF > lammps.cfg
+    [lammps]
+    lammps_include_dir = ${lammps-mpi}/include
+    lammps_library_dir = ${lammps-mpi}/lib
+    lammps_library = lammps_mpi
+
+    [mpi]
+    mpi_include_dir = ${mpi}/include
+    mpi_library_dir = ${mpi}/lib
+    mpi_library     = mpi
+    EOF
+  '';
+
+  meta = {
+    description = "Pythonic Wrapper to LAMMPS using cython";
+    homepage = https://gitlab.com/costrouc/lammps-cython;
+    license = lib.licenses.mit;
+    maintainers = with lib.maintainers; [ costrouc ];
+  };
+}

pkgs/development/python-modules/pathlib/default.nix

@@ -0,0 +1,28 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, python
+, pythonAtLeast
+}:
+
+buildPythonPackage rec {
+  pname = "pathlib";
+  version = "1.0.1";
+  disabled = pythonAtLeast "3.4"; # Was added to std library in Python 3.4
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "17zajiw4mjbkkv6ahp3xf025qglkj0805m9s41c45zryzj6p2h39";
+  };
+
+  checkPhase = ''
+    ${python.interpreter} -m unittest discover
+  '';
+
+  meta = {
+    description = "Object-oriented filesystem paths";
+    homepage = https://pathlib.readthedocs.org/;
+    license = lib.licenses.mit;
+    maintainers = with lib.maintainers; [ costrouc ];
+  };
+}

pkgs/development/python-modules/py-cpuinfo/default.nix

@@ -0,0 +1,23 @@
+{ lib
+, fetchFromGitHub
+, buildPythonPackage
+}:
+
+buildPythonPackage rec {
+  pname = "py-cpuinfo";
+  version = "4.0.0";
+
+  src = fetchFromGitHub {
+     owner = "workhorsy";
+     repo = pname;
+     rev = "v${version}";
+     sha256 = "1pp561lj80jnvr2038nrzhmks2akxsbdqxvfrqa6n340x81981lm";
+  };
+
+  meta = {
+    description = "Get CPU info with pure Python 2 & 3";
+    homepage = https://github.com/workhorsy/py-cpuinfo;
+    license = lib.licenses.mit;
+    maintainers = with lib.maintainers; [ costrouc ];
+  };
+}

pkgs/development/python-modules/pygmo/default.nix

@@ -0,0 +1,48 @@
+{ lib
+, fetchFromGitHub
+, buildPythonPackage
+, cmake
+, eigen
+, nlopt
+, ipopt
+, boost
+, pagmo2
+, numpy
+, cloudpickle
+, ipyparallel
+, numba
+}:
+
+buildPythonPackage rec {
+  pname = "pygmo";
+  version = "2.8";
+
+  src = fetchFromGitHub {
+     owner = "esa";
+     repo = "pagmo2";
+     rev = "v${version}";
+     sha256 = "1xwxamcn3fkwr62jn6bkanrwy0cvsksf75hfwx4fvl56awnbz41z";
+  };
+
+  buildInputs = [ cmake eigen nlopt ipopt boost pagmo2 ];
+  propagatedBuildInputs = [ numpy cloudpickle ipyparallel numba ];
+
+  preBuild = ''
+    cp -v -r $src/* .
+    cmake -DCMAKE_INSTALL_PREFIX=$out -DPAGMO_BUILD_TESTS=no -DCMAKE_SYSTEM_NAME=Linux -DPagmo_DIR=${pagmo2} -DPAGMO_BUILD_PYGMO=yes -DPAGMO_BUILD_PAGMO=no -DPAGMO_WITH_EIGEN3=yes -DPAGMO_WITH_NLOPT=yes -DNLOPT_LIBRARY=${nlopt}/lib/libnlopt_cxx.so -DPAGMO_WITH_IPOPT=yes -DIPOPT=${ipopt}
+
+    make install
+    mv $out/lib/python*/site-packages/pygmo wheel
+    cd wheel
+  '';
+
+  # dont do tests
+  doCheck = false;
+
+  meta = {
+    description = "Parallel optimisation for Python";
+    homepage = https://esa.github.io/pagmo2/;
+    license = lib.licenses.gpl3Plus;
+    maintainers = with lib.maintainers; [ costrouc ];
+  };
+}

pkgs/development/python-modules/pymatgen-lammps/default.nix

@@ -0,0 +1,31 @@
+{ lib
+, fetchurl
+, buildPythonPackage
+, pymatgen
+, lammps
+, pytestrunner
+, pytest
+, isPy3k
+}:
+
+buildPythonPackage rec {
+  pname = "pymatgen-lammps";
+  version = "0.4.5";
+  disabled = (!isPy3k);
+
+  src = fetchurl {
+     url = "https://gitlab.com/costrouc/${pname}/-/archive/v${version}/${pname}-v${version}.tar.gz";
+     sha256 = "0shldl8is3195jmji7dr3zsh1bzxlahaqrmpr28niks7nnfj80fx";
+  };
+
+  buildInputs = [ pytestrunner ];
+  checkInputs = [ pytest ];
+  propagatedBuildInputs = [ pymatgen ];
+
+  meta = {
+    description = "A LAMMPS wrapper using pymatgen";
+    homepage = https://gitlab.com/costrouc/pymatgen-lammps;
+    license = lib.licenses.mit;
+    maintainers = with lib.maintainers; [ costrouc ];
+  };
+}

pkgs/development/python-modules/pytest-benchmark/default.nix

@@ -0,0 +1,31 @@
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, pytestrunner
+, pytest
+, py-cpuinfo
+, pythonOlder
+, pathlib
+, statistics
+}:
+
+buildPythonPackage rec {
+  pname = "pytest-benchmark";
+  version = "3.1.1";
+
+  src = fetchFromGitHub {
+    owner = "ionelmc";
+    repo = pname;
+    rev = "v${version}";
+    sha256 = "1ch079dlc6c9ag74dh4dg6plkmh0h8kn78ari3fgadc75bald71m";
+  };
+
+  propagatedBuildInputs = [ pytest py-cpuinfo ] ++ lib.optional (pythonOlder "3.4") [ pathlib statistics ];
+
+  meta = {
+    description = "Py.test fixture for benchmarking code";
+    homepage = https://github.com/ionelmc/pytest-benchmark;
+    license = lib.licenses.bsd2;
+    maintainers = with lib.maintainers; [ costrouc ];
+  };
+}

pkgs/development/python-modules/statistics/default.nix

@@ -0,0 +1,27 @@
+{ lib
+, fetchPypi
+, buildPythonPackage
+, docutils
+}:
+
+buildPythonPackage rec {
+  pname = "statistics";
+  version = "1.0.3.5";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "2dc379b80b07bf2ddd5488cad06b2b9531da4dd31edb04dc9ec0dc226486c138";
+  };
+
+  propagatedBuildInputs = [ docutils ];
+
+  # statistics package does not have any tests
+  doCheck = false;
+
+  meta = {
+    description = "A Python 2.* port of 3.4 Statistics Module";
+    homepage = https://github.com/digitalemagine/py-statistics;
+    license = lib.licenses.asl20;
+    maintainers = with lib.maintainers; [ costrouc ];
+  };
+}

pkgs/top-level/all-packages.nix

@@ -4444,6 +4444,8 @@ with pkgs;
 
   padthv1 = callPackage ../applications/audio/padthv1 { };
 
+  pagmo2 = callPackage ../development/libraries/pagmo2 { };
+
   pakcs = callPackage ../development/compilers/pakcs {};
 
   pal = callPackage ../tools/misc/pal { };

pkgs/top-level/python-packages.nix

@@ -182,6 +182,8 @@ in {
 
   asana = callPackage ../development/python-modules/asana { };
 
+  ase = callPackage ../development/python-modules/ase { };
+
   asn1crypto = callPackage ../development/python-modules/asn1crypto { };
 
   aspy-yaml = callPackage ../development/python-modules/aspy.yaml { };
@@ -268,6 +270,8 @@ in {
     dbus = pkgs.dbus;
   };
 
+  dftfit = callPackage ../development/python-modules/dftfit { };
+
   discid = callPackage ../development/python-modules/discid { };
 
   discordpy = callPackage ../development/python-modules/discordpy { };
@@ -278,6 +282,8 @@ in {
 
   distorm3 = callPackage ../development/python-modules/distorm3 { };
 
+  docutils = callPackage ../development/python-modules/docutils { };
+
   dogtail = callPackage ../development/python-modules/dogtail { };
 
   diff-match-patch = callPackage ../development/python-modules/diff-match-patch { };
@@ -310,6 +316,10 @@ in {
 
   jira = callPackage ../development/python-modules/jira { };
 
+  lammps-cython = callPackage ../development/python-modules/lammps-cython {
+    mpi = pkgs.openmpi;
+  };
+
   lmtpd = callPackage ../development/python-modules/lmtpd { };
 
   logster = callPackage ../development/python-modules/logster { };
@@ -348,6 +358,8 @@ in {
 
   palettable = callPackage ../development/python-modules/palettable { };
 
+  pathlib = callPackage ../development/python-modules/pathlib { };
+
   pdf2image = callPackage ../development/python-modules/pdf2image { };
 
   pdfminer = callPackage ../development/python-modules/pdfminer_six { };
@@ -392,6 +404,8 @@ in {
 
   PyChromecast = callPackage ../development/python-modules/pychromecast { };
 
+  py-cpuinfo = callPackage ../development/python-modules/py-cpuinfo { };
+
   pydbus = callPackage ../development/python-modules/pydbus { };
 
   pydocstyle = callPackage ../development/python-modules/pydocstyle { };
@@ -408,6 +422,8 @@ in {
 
   pygame_sdl2 = callPackage ../development/python-modules/pygame_sdl2 { };
 
+  pygmo = callPackage ../development/python-modules/pygmo { };
+
   pygobject2 = callPackage ../development/python-modules/pygobject { };
 
   pygobject3 = callPackage ../development/python-modules/pygobject/3.nix { };
@@ -437,6 +453,8 @@ in {
 
   pymatgen = callPackage ../development/python-modules/pymatgen { };
 
+  pymatgen-lammps = callPackage ../development/python-modules/pymatgen-lammps { };
+
   pynisher = callPackage ../development/python-modules/pynisher { };
 
   pyparser = callPackage ../development/python-modules/pyparser { };
@@ -519,6 +537,8 @@ in {
 
   spglib = callPackage ../development/python-modules/spglib { };
 
+  statistics = callPackage ../development/python-modules/statistics { };
+
   sumo = callPackage ../development/python-modules/sumo { };
 
   supervise_api = callPackage ../development/python-modules/supervise_api { };
@@ -1845,6 +1865,8 @@ in {
 
   pytest-aiohttp = callPackage ../development/python-modules/pytest-aiohttp { };
 
+  pytest-benchmark = callPackage ../development/python-modules/pytest-benchmark { };
+
   pytestcache = callPackage ../development/python-modules/pytestcache { };
 
   pytest-catchlog = callPackage ../development/python-modules/pytest-catchlog { };
@@ -4987,37 +5009,6 @@ in {
     };
   };
 
-
-  docutils = buildPythonPackage rec {
-    name = "docutils-${version}";
-    version = "0.14";
-
-    src = pkgs.fetchurl {
-      url = "mirror://sourceforge/docutils/${name}.tar.gz";
-      sha256 = "0x22fs3pdmr42kvz6c654756wja305qv6cx1zbhwlagvxgr4xrji";
-    };
-
-    checkPhase = if isPy3k then ''
-      ${python.interpreter} test3/alltests.py
-    '' else ''
-      ${python.interpreter} test/alltests.py
-    '';
-
-    # Create symlinks lacking a ".py" suffix, many programs depend on these names
-    postFixup = ''
-      (cd $out/bin && for f in *.py; do
-        ln -s $f $(echo $f | sed -e 's/\.py$//')
-      done)
-    '';
-
-    meta = {
-      description = "An open-source text processing system for processing plaintext documentation into useful formats, such as HTML or LaTeX";
-      homepage = http://docutils.sourceforge.net/;
-      maintainers = with maintainers; [ garbas AndersonTorres ];
-    };
-  };
-
-
   dtopt = buildPythonPackage rec {
     name = "dtopt-0.1";
 
@@ -9441,27 +9432,6 @@ in {
 
   patator = callPackage ../development/python-modules/patator { };
 
-  pathlib = buildPythonPackage rec {
-    name = "pathlib-${version}";
-    version = "1.0.1";
-    disabled = pythonAtLeast "3.4"; # Was added to std library in Python 3.4
-
-    src = pkgs.fetchurl {
-      url = "mirror://pypi/p/pathlib/${name}.tar.gz";
-      sha256 = "17zajiw4mjbkkv6ahp3xf025qglkj0805m9s41c45zryzj6p2h39";
-    };
-
-    checkPhase = ''
-      ${python.interpreter} -m unittest discover
-    '';
-
-    meta = {
-      description = "Object-oriented filesystem paths";
-      homepage = "https://pathlib.readthedocs.org/";
-      license = licenses.mit;
-    };
-  };
-
   pathlib2 = callPackage ../development/python-modules/pathlib2 { };
 
   pathpy = callPackage ../development/python-modules/path.py { };