|
|
| Line 1: |
Line 1: |
| − | | + | [[SALMON Manual for Beginners]] |
| − | == Installation ==
| |
| − | | |
| − | === Prerequisites ===
| |
| − | | |
| − | In this guide, it is assumed that readers have a basic knowledge on 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.
| |
| − | | |
| − | * Fortran90/C compiler with MPI support. Our package assumes users have one of the following compilers:
| |
| − | ** GCC (Gnu Compiler Collection)
| |
| − | ** Intel Fortran/C Compiler
| |
| − | ** Fujitsu Compiler (at FX100 / K-Computer)
| |
| − | | |
| − | * One of the following library packages for linear algebra:
| |
| − | ** BLAS/LAPACK
| |
| − | ** Intel Math Kernel Library (MKL)
| |
| − | ** Fujitsu Scientific Subroutine Library 2 (SSL-II)
| |
| − | | |
| − | * One of the following build tools.
| |
| − | ** CMake
| |
| − | ** Gnu Make
| |
| − | | |
| − | If you use other compilers, you may need to change build scripts (CMake, Makefile).
| |
| − | If no numerical library is installed in your computer system, you may need to install BLAS/LAPACK by yourself.
| |
| − | See Installation of BLAS/LAPACK.
| |
| − | | |
| − | | |
| − | === Download ===
| |
| − | | |
| − | Newest version of the SALMON can be downloaded from [[Download]].
| |
| − | To extract files from the downloaded file <code>salmon-x.y.z.tar.gz</code>, type the following command in the command-line,
| |
| − | | |
| − | tar –zxvf ./salmon-xx.xx.xx.tar.gz
| |
| − | | |
| − | After the extraction, the following directories will be created.
| |
| − | | |
| − | SALMON
| |
| − | |- ARTED Source codes related to periodic systems
| |
| − | |- GCEED Source codes related to isolated systems
| |
| − | |- src Source codes of core modules
| |
| − | |- main Source codes of the main routines
| |
| − | |- example Samples
| |
| − | |- Makefile Files related to building
| |
| − | | |
| − | | |
| − | === Build ===
| |
| − | To compile SALMON to create executable binary files, two options are prepared, CMake and Gnu Make. If CMake works in your environment, we recommend to use it. If CMake fails in your environment, consider to use Gnu Make.
| |
| − | | |
| − | ==== Build using CMake ====
| |
| − | First examine whether CMake is usable in your environment or not.
| |
| − | If CMake is installed in your system, you can check the version of the CMake typing in the command-line as
| |
| − | | |
| − | $ cmake --version
| |
| − | | |
| − | If CMake is not installed in your system, error message such as <code>cmake: command not found</code> will appear.
| |
| − | If CMake is installed in your system, version number will be shown.
| |
| − | To build SALMON, CMake of version 3.0.2 or later is required.
| |
| − | If CMake is not installed or CMake of older version is installed in your system, you need to install the new version by yourself.
| |
| − | | |
| − | A detailed description how to install the CMake is given in [[Installation of CMake]].
| |
| − | We here describe a simple method to use the binary distribution of CMake.
| |
| − | First download the '''binary distribution file''' appropriate for your system from https://cmake.org/download/.
| |
| − | The filename of the downloaded file will be <code>cmake-<VERSION_PLATFORM>.tar.gz</code>.
| |
| − | In standard Unix environment, files for the platform of Linux x86_64 will be appropriate.
| |
| − | Next extract the binary executable file of CMake, typing in the command-line as
| |
| − | | |
| − | $ tar xvfz cmake-<VERSION_PLATFORM>.tar.gz
| |
| − | | |
| − | Then you will have the cmake binary file in <code>bin</code> directory.
| |
| − | For the cmake binary file to be usable, you need to modify the Unix environmental variable <code>$PATH</code>
| |
| − | appropriately.
| |
| − | | |
| − | '''Need to add how to modify the $PATH'''
| |
| − | | |
| − | To confirm that CMake of the new version is usable in your environment, type <code>cmake --version</code>
| |
| − | in the command-line.
| |
| − | | |
| − | ===== Build using CMake specifying archtechture =====
| |
| − | | |
| − | Confirming that CMake of version 3.0.2 or later can be usable in your system, proceed the following steps.
| |
| − | We assume that you are in the directory SALMON.
| |
| − | * Create a new temporary directory `build` and move to the directory,
| |
| − | | |
| − | $ mkdir build
| |
| − | $ cd build
| |
| − | | |
| − | * Execute the python script <code>configure.py</code> and then make,
| |
| − | | |
| − | $ python ../configure.py –arch=ARCHTECTURE
| |
| − | $ make
| |
| − | | |
| − | Here <code>ARCHTECTURE</code> specifies the architecture of the CPU in your computer system such as <code>intel-avx</code>. You need to choose <code>ARCHTECUTRE</code> from the following options:
| |
| − | | |
| − | {| class="wikitable"
| |
| − | | arch || Detail || Compiler || Numerical Library
| |
| − | |-
| |
| − | | intel-knl || Intel Knights Landing || Intel Compiler || Intel MKL
| |
| − | |-
| |
| − | | intel-knc || Intel Knights Corner || Intel Compiler || Intel MKL
| |
| − | |-
| |
| − | | intel-avx || Intel Processer (Ivy-, Sandy-Bridge) || Intel Compiler || Intel MKL
| |
| − | |-
| |
| − | | intel-avx2 || Intel Processer (Haswell, Broadwell ..) || Intel Compiler || Intel MKL
| |
| − | |-
| |
| − | | fujitsu-fx100 || FX100 Su || Fujitsu Compiler || SSL-II
| |
| − | |-
| |
| − | | fujitsu-k || Fujitsu FX100 / K-computer || Fujitsu Compiler || SSL-II
| |
| − | |}
| |
| − | | |
| − | If the build is successful, you will get a file <code>salmon.cpu</code> at the directory <code>./bin</code>. If you specify many-core archtechtures, <code>intel-knl</code> or <code>intel-knc</code>, you find a file <code>salmon.mic</code> or both files <code>salmon.cpu</code> and <code>salmon.mic</code>.
| |
| − | | |
| − | <!--
| |
| − | ===== Build using CMake manually =====
| |
| − | | |
| − | In executing <code>configure.py</code>, you may manually specify compiler and environment variables instead of specifying the architecture, for example:
| |
| − | | |
| − | $ python ../configure.py FC=mpiifort CC=mpiicc FFLAGS="-xAVX" CFLAGS="-restrict -xAVX"
| |
| − | $ make
| |
| − | | |
| − | A list of the environmental variables is given below:
| |
| − | (Table)
| |
| − | -->
| |
| − | | |
| − | ==== Build using Gnu Make ====
| |
| − | If CMake build fails in your environment, try Gnu Make for the build process. Gnu Make utilize a file, Makefile, which you can find at the directory <code>SALMON/Makefile</code>. First you need to modify Makefile appropriately according to your environment. Edit the Makefile using a text editor. At least you need to change the line that choose the architecture of the system, from line ?? to ??
| |
| − | | |
| − | # This is a makefile for SALMON program.
| |
| − | # please select architecture by deleting “#”
| |
| − | #ARCH = gnu
| |
| − | ARCH = intel
| |
| − | #ARCH = fujitsu
| |
| − | #ARCH = intel-knl
| |
| − | | |
| − | Then use make command in the command-line to build the executable file.
| |
| − | | |
| − | $ make
| |
| − | | |
| − | | |
| − | === Tips for installation ===
| |
| − | | |
| − | ==== Installation of CMake ====
| |
| − | Installation of CMake
| |
| − | When CMake is not available in your environment or the version of the installed CMake is former than version 3.0.2, you need to install the new version of CMake by yourself. It can be done as follows:
| |
| − | | |
| − | ==== Installation of BLAS/LAPACK ====
| |
| − | | |
| − | == Files necessary to run SALMON ==
| |
| − | To run SALMON, at least two kinds of files are required for any calculations. One is an input file, with the filename extension of *.inp*, to be read through the standard input, `stdin`. It should be prepared in the Fortran90 namelist format. Pseudopotential files of relevant elements are also required. Depending on your purpose, some other files may also be necessary. For example, coordinates of atomic positions of the target material may either be written in the input file or prepared as a separate file.
| |
| − | | |
| − | ==== pseudopotentials ====
| |
| − | SALMON utilizes norm-conserving pseudpotentials. You may find pseudopotentials of some elements in [Samples](http://www). SALMON allows to use several formats of pseudpotentials that can be easily obtained from websites listed below.
| |
| − | | |
| − | | pseudopotential | website |
| |
| − | |-----------------|---------|
| |
| − | | Ab-init FHI | http://www.ab-init |
| |
| − | | |
| − | In the input file, you need to write the filename of the pseudopotential. Use exactly the same filename as that downloaded from the website or that in the Samples.
| |
| − | | |
| − | # 2.2 input file
| |
| − | Input file should be written using Fortran90 namelist format such as
| |
| − | ```
| |
| − | &system
| |
| − | iperiodic = 0
| |
| − | al = 16d0, 16d0, 16d0
| |
| − | nstate = 5
| |
| − | nelem = 2
| |
| − | natom = 4
| |
| − | file_atom='coo.data'
| |
| − | /
| |
| − | ```
| |
| − | where the `system` in `&system` indicates the name of the namelist. In `iperiodic = 0`, `iperiodic` is the variable name and `0` is the value. A group of namelists starts with `&namelist` line and ends with `/` line. Between two lines, descriptions of variables and their values appear. Note that many variables have their default values, so it is not necessary to give values for all variables. The description of the variables may appear at any position if they are between `&namelist` and `/`.
| |
| − | Usually several groups of namelists are included in the input file. The order of the groups can be arbitrary.
| |
| − | | |
| − | SALMON describes electron dynamics in systems with both isolated and periodic boundary conditions. The boundary condition is specified by the variable `iperiodic` in `&system`. Calculations are achieved in two steps; first the ground state calculation is carried out and then electron dynamics calculations in real time are achieved. Choice of the calculation mode is specified by the variable `calc_mode` in `&calculation`. For isolated system, the ground state and the electron dynamics calculations should be carried out in two steps. For periodic system, two calculations should be carried out in one step. Therefore, we prepare three options in the `calc_mode`, 'GS', 'RT', and 'GS_RT'.
| |
| − | | |
| − | There are about 20 groups of namelists.
| |
| − | | |
| − | | name of namelist | description |
| |
| − | |----------------|-------------|
| |
| − | | &units | specify units of input and output files |
| |
| − | | &calculation | specify the type of calculation, GS (ground state), RT (real-time), and GS-RT (ground state and real time) |
| |
| − | | ¶llel | related to parallelization |
| |
| − | | &system | system information |
| |
| − | | &pseudo | specify pseudopotential |
| |
| − | | &rgrid | parameters related to real space grid |
| |
| − | | &scf | parameters related to ground state calculation |
| |
| − | | &hartree | construct Hartree potential |
| |
| − | | &group_fundamental | |
| |
| − | | &group_file | | |
| |
| − | | |
| − | In [Samples](http://), we prepare six samples that cover typical calculations by SALMON. We prepare explanation for the input files that will help to prepare input files of your own interests.
| |
| − | | |
| − | #3 Run SALMON
| |
| − | | |
| − | #4 Output files
| |
