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niedoida

https://readthedocs.org/projects/niedoida/badge/?version=latest https://ci.appveyor.com/api/projects/status/ps5s0mq5yhgmpqfn?svg=true

Niedoida is a general-purpose quantum-chemical and microelectrostatic package. See http://www.niedoida.org for details.

License

Copyright © 2005-2018 Jagiellonian University

Niedoida is subject to the terms of the Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed with this file, you can obtain one at http://mozilla.org/MPL/2.0/.

Citation

When you publish results that were obtained using niedoida, you are required to include references to the program

niedoida 18.10, http://www.niedoida.org

and the following publication:

Grzegorz Mazur, Marcin Makowski, Development and Optimization of Computational Chemistry Algorithms, Computing and Informatics, 28 (2009) 115.

Installation from sources

Linux

  1. Prerequisites:
  1. GCC version 4.8 or newer
  2. Sphinx 1.6.7 or newer (optional, required for building documentation)
  1. Download and unpack niedoida
  2. Open Terminal window
  3. Change directory to the niedoida source directory
  4. Execute
./build_external_packages
mkdir build
cd build
../external_packages/bin/cmake -DCMAKE_BUILD_TYPE=Release [-DNIEDOIDA_ENABLE_USER_DOCS=On] [-DCMAKE_INSTALL_PREFIX=<installation path>] ..
make
  1. To install newly built binaries execute
make install

macOS

  1. Prerequisites:
  1. Xcode 10 or newer
  2. Sphinx 1.6.7 or newer (optional, required for building documentation)
  1. Download and unpack niedoida
  2. Open Terminal window
  3. Change directory to the niedoida source directory
  4. Execute
./build_external_packages
mkdir build
cd build
../external_packages/bin/cmake -DCMAKE_BUILD_TYPE=Release [-DNIEDOIDA_ENABLE_USER_DOCS=On] [-DCMAKE_INSTALL_PREFIX=<installation path>]..
make
  1. To install newly built binaries execute
make install

Microsoft Windows

  1. Prerequisites:
  1. Microsoft Visual Studio 15 2017
  2. MS MPI
  3. CMake version 3.12 or newer
  4. TortoiseSVN
  5. Cygwin version 2.10.0 or newer, with at least devel/make and python packages; /usr/bin/link.exe has to be renamed to /usr/bin/link-cygwin.exe
  6. Sphinx 1.6.7 or newer
  1. Download and unpack niedoida
  2. Open Developer Command Prompt for Visual Studio 15 2017 (64 bit mode)
  3. Change directory to the niedoida source directory
  4. Build third-party dependencies:
  1. Change directory to external_packages
  2. Install boost
  • Download and unpack boost_1_68_0.zip

  • Bootstrap the buildsystem

    cd boost_1_65_1\tools\build
    bootstrap.bat
    b2 --prefix=c:\Users\User\Documents\niedoida\external_packages install
    set PATH=c:\Users\User\Documents\niedoida\external_packages\bin;%PATH%
    cd ..\..
  • Create file tools\build\src\user-config.jam containing using mpi ;

  • Build and install the libraries

    b2 --prefix=c:\Users\User\Documents\niedoida\external_packages --layout=system toolset=msvc variant=release link=static threading=multi runtime-link=shared address-model=64 install
    cd ..
  1. Install yaml-cpp
  • Download and unpack yaml-cpp-yaml-cpp-0.6.2.zip

  • Build and install the library

    cd yaml-cpp-yaml-cpp-0.5.3
    mkdir build
    cd build
    cmake -DBUILD_SHARED_LIBS=OFF -DCMAKE_INSTALL_PREFIX=c:\Users\User\Documents\niedoida\external_packages -G "Visual Studio 15 2017 Win64" ..
    cmake --build . --config Release
    cmake --build . --config Release --target install
    cd ..\..
  1. Install hdf5
  • Download and unpack hdf5-1.10.1.zip

  • Build and install the library

    cd hdf5-1.10.1
    mkdir build
    cd build
    cmake -DCMAKE_INSTALL_PREFIX=c:\Users\User\Documents\niedoida\external_packages -DHDF5_BUILD_CPP_LIB=ON -G "Visual Studio 15 2017 Win64" ..
    cmake --build . --config Release
    cmake --build . --config Release --target install
    cd ..\..
  1. Install petsc
  • Download and unpack petsc-lite-3.9.2.tar.gz

  • Start Cygwin bash

    c:\cygwin64\bin\bash.exe --login
  • Build and install the library

    cd /cygdrive/c/Users/User/Documents/niedoida/external_packages/petsc-3.9.2
    ./configure --with-cc="win32fe cl" --with-cxx="win32fe cl" --with-fc=0 --download-f2cblaslapack --with-mpi-include="/cygdrive/c/Program Files (x86)/Microsoft SDKs/MPI/Include" --with-mpi-lib=["/cygdrive/c/Program Files (x86)/Microsoft SDKs/MPI/Lib/x64/msmpi.lib"] --with-mpi-exec="/cygdrive/c/Program Files/Microsoft MPI/Bin/mpiexec.exe" --with-debugging=0 -CFLAGS='-O2 -MD -wd4996' -CXXFLAGS='-O2 -MD -wd4996'
    make PETSC_DIR=/cygdrive/c/Users/User/Documents/niedoida/external_packages/petsc-3.9.2 PETSC_ARCH=arch-mswin-c-opt all
    cp -r include/* ../include
    cp arch-mswin-c-opt/lib/*.lib ../lib
    cp arch-mswin-c-opt/include/* ../include
    exit
  1. Install armadillo
  • Download and unpack armadillo-8.300.2.zip

  • In armadillo-8.300.2\cmake_aux\Modules\FindBLAS.cmake change

    SET(BLAS_NAMES ${BLAS_NAMES} blas)
    FIND_LIBRARY(BLAS_LIBRARY
      NAMES ${BLAS_NAMES}
      PATHS /usr/lib64/atlas /usr/lib/atlas /usr/lib64 /usr/lib /usr/local/lib64 /usr/local/lib
      )

    to

    SET(BLAS_NAMES ${BLAS_NAMES} libf2cblas)
    FIND_LIBRARY(BLAS_LIBRARY
      NAMES ${BLAS_NAMES}
      PATHS c:/Users/User/Documents/niedoida/external_packages/lib
      )
  • In armadillo-8.300.2\cmake_aux\Modules\FindLAPACK.cmake change

    SET(LAPACK_NAMES ${LAPACK_NAMES} lapack)
    FIND_LIBRARY(LAPACK_LIBRARY
      NAMES ${LAPACK_NAMES}
      PATHS /usr/lib64/atlas /usr/lib/atlas /usr/lib64 /usr/lib /usr/local/lib64 /usr/local/lib
      )

    to

    SET(LAPACK_NAMES ${LAPACK_NAMES} libf2clapack)
    FIND_LIBRARY(LAPACK_LIBRARY
      NAMES ${LAPACK_NAMES}
      PATHS c:/Users/User/Documents/niedoida/external_packages/lib
      )
  • Build and install the library

    cd armadillo-8.300.2
    mkdir build
    cd build
    cmake -DCMAKE_INSTALL_PREFIX=c:\Users\User\Documents\niedoida\external_packages -DDETECT_HDF5=Off -G "Visual Studio 15 2017 Win64" ..
    cmake --build . --config Release
    cmake --build . --config Release --target install
    cd ..\..
  1. Install yacas
  • Download and unpack yacas-1.6.1.zip

  • Build and install the program

    cd yacas-1.6.1
    mkdir build
    cd build
    cmake -DCMAKE_INSTALL_PREFIX=c:\Users\User\Documents\niedoida\external_packages -DCYACAS_ENABLE_GUI=OFF -DCYACAS_ENABLE_KERNEL=OFF -G "Visual Studio 15 2017 Win64" ..
    cmake --build . --config Release
    cmake --build . --config Release --target install
    cd ..\..
    editbin /stack:10000000 bin/yacas.exe
  1. Build and install niedoida
  • Execute

    mkdir build
    cd build
    cmake -G "Visual Studio 15 2017 Win64" [-DNIEDOIDA_ENABLE_USER_DOCS=On] [-DCMAKE_INSTALL_PREFIX=<installation path>] ..
    cmake --build . --config Release --target niedoida
  • To install newly built binaries execute

    cmake --build . --config Release --target install

Contributors

  • Grzegorz Mazur
  • Marcin Makowski
  • Witold Piskorz
  • Łukasz Ćwiklik
  • Mariusz Sterzel
  • Mariusz Radoń
  • Barbara Jagoda-Ćwiklik
  • Waldemar Kulig
  • Daniel Błażewicz
  • Jakub Sumera
  • Krzysztof Kowalczyk
  • Mateusz Brela
  • Roman Łazarski
  • Piotr Kuźniarowicz
  • Ewa Czajkowska
  • Mateusz Snamina
  • Michał Glanowski
  • Anna Styrcz
  • Alina Mreńca-Kolasińska
  • Krzysztof Kolasiński

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Niedoida is a general-purpose quantum-chemical and microelectrostatic package

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