niedoida

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)

2. Download and unpack niedoida
3. Open Terminal window
4. Change directory to the niedoida source directory
5. 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

5. 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)

2. Download and unpack niedoida
3. Open Terminal window
4. Change directory to the niedoida source directory
5. 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

5. 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

2. Download and unpack niedoida
3. Open Developer Command Prompt for Visual Studio 15 2017 (64 bit mode)
4. Change directory to the niedoida source directory
5. 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 ..

3. 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 ..\..

4. 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 ..\..

5. 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

6. 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 ..\..

6. 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

6. 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