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Octopus 5.0

    • Software:

      Octopus

    • Versão:

      5.0

    • Data:

      30/11/2015

    • Ambiente:

      Planck

    • Categoria:

      Simulações de dinâmica molecular DFT e ab initio

    • Descrição:

      Octopus does many things in many different ways. This is a summary of what are the features that are currently implemented (some of them are only available in the development version).

      Theory:Density Functional Theory for ground-state calculations, LDA, GGA, Meta-GGA, OEP functionals available through libxc andt ime-dependent DFT for response

      Systems Works in 1, 2, and 3, and 4 dimensions. Periodic boundary conditions in 1, 2, or 3 directions (only for ground-state calculations)

      Linear Response: Through time-propagation, Static polarizabilities, Absorption spectra (singlet, triplet), Mark Casida’s formulation of response, Electronic excitations, Sternheimer (frequency-dependent) linear-response formalism, Static and dynamic electric polarizabilities (including resonant response), Static and dynamic electric first hyperpolarizabilities (including resonant response), Static magnetic susceptibilities and Vibrational modes.

      Non-linear response – Dynamics: Ehrenfest dynamics for the nuclei, Real-time TDDFT propagation, Emission spectra, harmonic generation, Optimal control theory and Car-Parrinello Molecular Dynamics.

      Technical Norm-conserving pseudopotentials (most commonly used formats), Real-space grid discretization (no basis sets), Curvilinear coordinates, Parallelization in domains and in states and Runs both in single- and double-precision
      .

    • Local:

      home/sw/octopus/50/install/

    • Utilização:


#!/bin/bash
#PBS -M usuario@ifi.unicamp.br
### Mandar email no inicio e fim
#PBS -m abe
### Name do processo
#PBS -N octopus
### Arquivos de saida
#PBS -e o.err
#PBS -o o.out

### Definindo a fila e o número de processadores
## no caso, estamos solicitando para rodar na fila par120
## e solicitando 10 nodes e 12 cores em cada um, totalizando 120 cores
#PBS -q par12
#PBS -l nodes=1:ppn=12

 . /home/sw/intel/bin/compilervars.sh intel64
export PATH=/opt/sw/gcc-4.8.2/bin:$PATH
export LD_LIBRARY_PATH=/opt/sw/gcc-4.8.2/lib64/:/home/sw/octopus/50/install/gsl/lib:/home/sw/octopus/50/install/pfft/lib:$LD_LIBRARY_PATH

cd $PBS_O_WORKDIR
export MPI_GROUP_MAX=80000
export MPI_COMM_MAX=2000
cd /home/sw/octopus/50/install/octopus/example
## comando a ser executado, por exemplo a execução através do MPT (MPI da SGI):
mpiexec_mpt -n 12 /usr/bin/dplace -s 1 /home/sw/octopus/50/install/octopus/bin/octopus_mpi > saida.txt

  • Licença:

    GPL 2

  • Compilação:

    wget http://www.tddft.org/programs/octopus/down.php?file=5.0.0/octopus-5.0.0.tar.gz
    wget http://www.tddft.org/programs/octopus/wiki/index.php/Libxc_2.2.2
    . /home/sw/intel/bin/compilervars.sh intel64

    libxc

    export PATH=/opt/sw/gcc-4.8.2/bin:$PATH
    export LD_LIBRARY_PATH=/opt/sw/gcc-4.8.2/lib64/:$LD_LIBRARY_PATH
    . /home/sw/intel/bin/compilervars.sh intel64
    cd /home/sw/octopus/50/targz/libxc-2.2.2
    FC=ifort ./configure –prefix=/home/sw/octopus/50/install/libxc
    make -j 4
    make check
    make install

    pfft

    https://www-user.tu-chemnitz.de/~potts/workgroup/pippig/software/pfft-1.0.8-alpha.tar.gz
    cd /home/sw/octopus/50/targz/pfft-1.0.8-alpha
    FC=ifort ./configure –with-fftw3=/home/sw/octopus/50/install/fftw/fftw-3.3.4 –prefix=/home/sw/octopus/50/install/pfft
    make
    make install

    fftw
    https://www-user.tu-chemnitz.de/~potts/workgroup/pippig/software/install_fftw-3.3.4_gcc.sh
    ./script

    libgsl
    wget ftp://ftp.gnu.org/gnu/gsl/gsl-2.1.tar.gz
    FC=ifort ./configure –prefix=/home/sw/octopus/50/install/gsl
    make
    make check
    make install

    libgsl
    wget ftp://ftp.gnu.org/gnu/gsl/gsl-1.9.tar.gz
    FC=ifort ./configure –prefix=/home/sw/octopus/50/install/gsl
    make
    make check
    make install

    export MKL_DIR=/home/sw/intel/mkl/lib/intel64

    octopus
    FC=ifort ./configure –prefix=/home/sw/octopus/50/install/octopus –with-pfft-prefix=/home/sw/octopus/50/install/pfft –with-libxc-prefix=/home/sw/octopus/50/install/libxc –enable-mpi –with-blas=”-L/home/sw/intel/mkl/lib/intel64 -Wl,–start-group -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -Wl,–end-group -lpthread” –with-blacs=”/home/sw/intel/mkl/lib/intel64/libmkl_blacs_sgimpt_lp64.a” –with-scalapack=/home/sw/intel/mkl/lib/intel64/libmkl_scalapack_lp64.a –with-gsl-prefix=/home/sw/octopus/50/install/gsl –with-fft-lib=”/home/sw/octopus/50/install/fftw/fftw-3.3.4/lib/libfftw3_mpi.a -L/home/sw/octopus/50/install/fftw/fftw-3.3.4/lib/” –with-pfft-include=/home/sw/octopus/50/install/pfft/include