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| − | == Prerequisites ==
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| − | In this guide, it is assumed that readers have a basic knowledge of Unix. In the following, most works will be done in the command-line interface of Unix. For the installation of SALMON, following packages are required.
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| − |
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| − | * Fortran90/C compiler with MPI support. Our package assumes users have one of the following compilers:
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| − | ** GCC (Gnu Compiler Collection)
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| − | ** Intel Fortran/C Compiler
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| − | ** Fujitsu Compiler (at FX100 / K-Computer)
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| − |
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| − | * One of the following library packages for linear algebra:
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| − | ** BLAS/LAPACK
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| − | ** Intel Math Kernel Library (MKL)
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| − | ** Fujitsu Scientific Subroutine Library 2 (SSL-II)
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| − |
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| − | * One of the following build tools.
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| − | ** CMake
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| − | ** Gnu Make
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| − |
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| − | If you use other compilers, you may need to change build scripts (CMake, Makefile). If no numerical library is installed on your computer system, you may need to install BLAS/LAPACK by yourself. See Tips for Installation.
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| − | See [[Troubleshooting of the Installation Process]].
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| − |
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| − | == Download ==
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| − |
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| − | The newest version of the SALMON can be downloaded from [[Download]].
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| − | To extract files from the downloaded file ''salmon-<VERSION>.tar.gz'', type the following command in the command-line,
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| − |
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| − | $ tar –zxvf ./salmon-<VERSION>.tar.gz
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| − |
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| − | After the extraction, the following directories will be created.
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| − |
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| − | SALMON
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| − | |- ARTED Source codes related to periodic systems
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| − | |- GCEED Source codes related to isolated systems
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| − | |- src Source codes of core modules
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| − | |- main Source codes of the main routines
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| − | |- example Samples
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| − | |- Makefile Files related to building
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| − |
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| − | == Build ==
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| − |
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| − | To compile SALMON to create executable binary files, two options are prepared, CMake and Gnu Make.
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| − | If CMake works in your environment, we recommend to use it.
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| − | If CMake fails in your environment, consider using Gnu Make.
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| − |
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| − | === Build using CMake ===
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| − |
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| − | First, examine whether CMake is usable in your environment or not.
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| − | Type the following in Unix command-line:
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| − |
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| − | $ cmake --version
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| − |
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| − | If CMake is not installed in your system, an error message such as <code>cmake: command not found</code> will appear.
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| − | If CMake is installed on your system, the version number will be shown.
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| − | To build SALMON, CMake of version 3.0.2 or later is required.
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| − | If CMake is not installed or CMake of the older version is installed in your system, you need to install the new version by yourself.
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| − |
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| − | The installation of the CMake is simple.
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| − | A detailed description of the installation is given in [[Tips_for_Installation#Installation_of_CMake | Installation of CMake]].
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| − | Here we describe a simple method to use the binary distribution of CMake.
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| − | First, download the '''binary distribution file''' appropriate for your system from https://cmake.org/download/.
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| − | The filename of the downloaded file will be ''cmake-<VERSION_PLATFORM>.tar.gz''.
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| − | In standard Unix environment, files for the platform of Linux x86_64 will be appropriate.
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| − | Next extract the binary executable file of CMake, typing in the command-line as
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| − |
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| − | $ tar xvfz cmake-<VERSION_PLATFORM>.tar.gz
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| − |
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| − | Then you will have the cmake binary file in ''bin'' directory.
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| − | For the CMake binary file to be usable, you need to modify the Unix environmental variable ''$PATH'' appropriately.
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| − |
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| − | '''''Description how to modify the $PATH should come here'''''
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| − | To confirm that CMake of the new version is usable in your environment, type <code>cmake --version</code> in the command-line.
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| − |
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| − | ==== Build using CMake specifying archtechture ====
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| − |
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| − | Confirming that CMake of version 3.0.2 or later can be usable on your system, proceed the following steps.
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| − | We assume that you are in the directory SALMON.
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| − | * Create a new temporary directory ''build'' and move to the directory,
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| − |
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| − | $ mkdir build
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| − | $ cd build
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| − |
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| − | * Execute the python script ''configure.py'' and then make,
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| − |
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| − | $ python ../configure.py –arch=ARCHTECTURE
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| − | $ make
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| − | Here ''ARCHITECTURE'' specifies the architecture of the CPU in your computer system such as ''intel-avx''.
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| − | You need to choose ''ARCHTECUTRE'' from the following options:
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| − |
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| − | {| class="wikitable"
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| − | | arch || Detail || Compiler || Numerical Library
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| − | |-
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| − | | intel-knl || Intel Knights Landing || Intel Compiler || Intel MKL
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| − | |-
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| − | | intel-knc || Intel Knights Corner || Intel Compiler || Intel MKL
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| − | |-
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| − | | intel-avx || Intel Processer (Ivy-, Sandy-Bridge) || Intel Compiler || Intel MKL
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| − | |-
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| − | | intel-avx2 || Intel Processer (Haswell, Broadwell ..) || Intel Compiler || Intel MKL
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| − | |-
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| − | | fujitsu-fx100 || FX100 Su || Fujitsu Compiler || SSL-II
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| − | |-
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| − | | fujitsu-k || Fujitsu FX100 / K-computer || Fujitsu Compiler || SSL-II
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| − | |}
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| − |
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| − | If the build is successful, you will get a file ''salmon.cpu'' at the directory ''.salmon/bin''. If you specify many-core archtechtures, ''intel-knl'' or ''intel-knc'', you find a file ''salmon.mic'' or both files ''salmon.cpu'' and ''salmon.mic''.
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| − |
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| − | <!--
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| − | ===== Build using CMake manually =====
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| − |
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| − | In executing <code>configure.py</code>, you may manually specify compiler and environment variables instead of specifying the architecture, for example:
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| − |
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| − | $ python ../configure.py FC=mpiifort CC=mpiicc FFLAGS="-xAVX" CFLAGS="-restrict -xAVX"
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| − | $ make
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| − | A list of the environmental variables is given below:
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| − | (Table)
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| − | -->
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| − |
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| − | === Build using Gnu Make ===
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| − |
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| − | If CMake build fails in your environment, try Gnu Make for the build process.
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| − | Gnu Make utilize a file, ''Makefile'', which you can find at the directory ''SALMON/Makefile''.
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| − | First, you need to modify ''Makefile'' appropriately according to your environment.
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| − | Edit the ''Makefile'' using a text editor.
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| − | At least you need to change the line that choose the architecture of the system, from line 4 to 10
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| − |
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| − | # This is a makefile for SALMON program.
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| − | # please select architecture by deleting “#”
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| − |
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| − | #ARCH = gnu
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| − | ARCH = intel
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| − | #ARCH = intel-avx
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| − | #ARCH = intel-avx2
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| − | #ARCH = fujitsu
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| − | #ARCH = intel-knl
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| − | #ARCH = intel-knc
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| − |
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| − | Then use ''make'' command in the command-line to build the executable file.
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| − |
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| − | $ make
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| − |
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| − | == Files necessary to run SALMON ==
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| − | To run SALMON, at least two kinds of files are required for any calculations.
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| − | One is an input file, with the filename extension of ''*.inp*'', to be read from the standard input, ''stdin''.
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| − | It should be prepared in the Fortran90 namelist format.
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| − | Pseudopotential files of relevant elements are also required.
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| − | Depending on your purpose, some other files may also be necessary.
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| − | For example, coordinates of atomic positions of the target material may either be written in the input file or prepared as a separate file.
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| − |
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| − | === pseudopotentials ===
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| − |
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| − | SALMON utilizes norm-conserving pseudpotentials.
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| − | You may find pseudopotentials of some elements in [[Samples]].
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| − | SALMON allows using several formats of pseudopotentials that can be easily obtained from websites listed below.
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| − | {| class="wikitable"
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| − | | pseudopotential || website
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| − | |-
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| − | | Ab-init FHI || http://www.ab-init
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| − | |}
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| − | In the input file, you need to write the filename of the pseudopotential.
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| − | Use exactly the same filename as that downloaded from the website or that in the [[Samples]].
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| − |
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| − | === input file ===
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| − |
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| − | SALMON describes electron dynamics in systems with both isolated and periodic boundary conditions.
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| − | The boundary condition is specified by the variable ''iperiodic'' in the namelist ''&system''.
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| − | Calculations are achieved in two steps; first, the ground state calculation is carried out and then electron dynamics calculations in real time are achieved.
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| − | Choice of the calculation mode is specified by the variable ''calc_mode'' in the namelist ''&calculation''.
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| − | For isolated systems, the ground state and the electron dynamics calculations should be carried out in two steps.
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| − | First the ground state calculation is achieved specifying ''calc_mode = 'GS' ''.
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| − | Then the real-time electron dynamics calculation is achieved specifying ''calc_mode = 'RT' ''.
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| − | For periodic systems, two calculations can also be carried out in one step specifying ''calc_mode = 'GS_RT' ''.
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| − | For the isolated systems, ’GS-RT’ is not implemented. However, their calculations are done at once if
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| − | users prepare appropriate shell scripts.
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| − |
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| − | There are about 20 groups of main namelists listed below.
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| − | A list of variables in each namelist is provided in the file ''???'' included in the source-file distribution.
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| − |
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| − | {| class="wikitable"
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| − | | name of namelist || description
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| − | |-
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| − | | &calculation || specify calculation modes
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| − | |-
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| − | | &control || parameters related to general conditions for the calculation
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| − | |-
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| − | | &units || specify units of input and output files
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| − | |-
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| − | | ¶llel || parameters related to parallelization
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| − | |-
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| − | | &system || information related to the system
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| − | |-
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| − | | &pseudo || information related to pseudopotentials
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| − | |-
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| − | | &functional || specify density functional to be used
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| − | |-
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| − | | &rgrid || parameters related to real space grid
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| − | |-
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| − | | &kgird || parameters related to k-points for periodic systems
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| − | |-
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| − | | &tgrid || parameters related to time evolution
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| − | |-
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| − | | &propagation || specify a choice of the propagation method
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| − | |-
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| − | | &scf || parameters related to ground state calculation
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| − | |-
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| − | | &emfield || parameters of electric fields applied to the system
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| − | |-
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| − | | &linear_response || magnitude of the distortion for linear response
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| − | |-
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| − | | &multiscale || parameters related to coupled multiscale calculations of electron dynamics and light propagations
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| − | |-
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| − | | &analysis || parameters related to output files
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| − | |-
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| − | | &hartree || parameters related to Hartree potential calculation of isolated systems
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| − | |-
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| − | | &ewald || parameters related to Ewald sum that appears in the ground state calculation of periodic systems
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| − | |-
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| − | | &atomic_coor || Atomic coordinates can be written here
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| − | |}
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| − |
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| − | There are 5 groups of additional namelists listed below. In a future version of SALMON,
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| − | variables in these namelists may be added to main namelists, be combined to them, and be removed.
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| − |
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| − | {| class="wikitable"
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| − | | name of namelist || description
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| − | |-
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| − | | &group_fundamental || parameters related to fundamental variables for the isolated systems
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| − | |-
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| − | | &group_parallel || parameters related to parallelization for the isolated systems
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| − | |-
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| − | | &group_hartree || parameters related to Hartree otential calculation of isolated systems
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| − | |-
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| − | | &group_file || parameters related to intermediate files for isolated systems
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| − | |-
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| − | | &group_others || other parameters for isolated systems
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| − | |}
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| − | In [[Samples]], we prepare six samples that cover typical calculations feasible by using SALMON.
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| − | We prepare explanations for the input files that will help to prepare input files of your own interests.
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| − | Here we briefly explain the format of the namelist.
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| − |
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| − | &namelist1
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| − | variable1 = int_value
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| − | variable2 = 'char_value'
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| − | /
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| − | &namelist2
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| − | variable1 = real8_value
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| − | variable2 = int_value1, int_value2, int_value3
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| − | /
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| − | A block of namelists starts with ''&namelist'' line and ends with ''/'' line.
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| − | Between two lines, descriptions of variables and their values appear.
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| − | Note that many variables have their default values so that it is not necessary to give values for all variables.
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| − | The description of the variables may appear at any position if they are between ''&namelist'' and ''/''.
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| − | Input files constitute of several blocks of namelists.
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| − | The blocks can appear in any order.
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| − | == Run SALMON ==
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| − | To run SALMON, the executable file of ''salmon.cpu'' (and ''salmon.mic'' if your system is the many-core machine) should be built from the source file of SALMON as described above. An input file ''inputfile.inp'' and pseudopotential files should also be prepared as mentioned above.
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| − | In order to execute the calculation, for the single process environment, type the following command:
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| − | $ salmon.cpu < inputfile.inp > fileout.out
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| − |
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| − | For the multiprocess environment, If the command to execute calculations using MPI is ''mpiexec', the calculation will start
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| − |
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| − | $ mpiexec -n NPROC salmon.cpu < inputfile.inp > fileout.out
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| − |
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| − | where NPROC is the number of MPI processes you want to use.
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| − | For the many-core processor (e.g. intel-knl) environment, the execution command is
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| − | $ mpiexec.hydra -n NPROC salmon.mic < inputfile.inp > fileout.out
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| − |
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| − | The execution command and the job submission procedure depends much on the local environment.
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| − | We just summarize the general conditions to execute SALMON:
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| − |
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| − | * salmon runs in parallel environment using MPI.
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| − | * executable files are prepared as ''/salmon/bin/salmon.cpu'' and/or ''/salmon/bin/salmon.mic'' in the standard build procedure.
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| − | * to start calculations, ''inputfile.inp'' should be read through ''stdin''.
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| − |
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| − | == Output files ==
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| − |
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| − | See [[Samples]].
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