Difference between revisions of "SALMON Manual for Beginners-v0"

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Revision as of 09:09, 20 November 2017

Prerequisites

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.

• 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 on your computer system, you may need to install BLAS/LAPACK by yourself. See Tips for Installation. See Troubleshooting of the Installation Process.

Download

The newest version of the SALMON can be downloaded from Download. To extract files from the downloaded file salmon-<VERSION>.tar.gz, type the following command in the command-line,

$ tar –zxvf ./salmon-<VERSION>.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 using Gnu Make.

Build using CMake

First, examine whether CMake is usable in your environment or not. Type the following in Unix command-line:

$ cmake --version

If CMake is not installed in your system, an error message such as cmake: command not found will appear. If CMake is installed on your system, the 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 the older version is installed in your system, you need to install the new version by yourself.

The installation of the CMake is simple. A detailed description of the installation is given in Installation of CMake. Here we 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 cmake-<VERSION_PLATFORM>.tar.gz. 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 bin directory. For the CMake binary file to be usable, you need to modify the Unix environmental variable $PATH appropriately.

Description how to modify the $PATH should come here

To confirm that CMake of the new version is usable in your environment, type cmake --version in the command-line.

Build using CMake specifying archtechture

Confirming that CMake of version 3.0.2 or later can be usable on 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 configure.py and then make,

$ python ../configure.py –arch=ARCHTECTURE
$ make

Here ARCHITECTURE specifies the architecture of the CPU in your computer system such as intel-avx. You need to choose ARCHTECUTRE from the following options:

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 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.

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 SALMON/Makefile. 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 4 to 10

# This is a makefile for SALMON program.
# please select architecture by deleting “#”

#ARCH = gnu
ARCH = intel
#ARCH = intel-avx
#ARCH = intel-avx2
#ARCH = fujitsu
#ARCH = intel-knl
#ARCH = intel-knc

Then use make command in the command-line to build the executable file.

$ make

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 from 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. SALMON allows using several formats of pseudopotentials 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.

input file

SALMON describes electron dynamics in systems with both isolated and periodic boundary conditions. The boundary condition is specified by the variable iperiodic in the namelist &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 the namelist &calculation. For isolated systems, the ground state and the electron dynamics calculations should be carried out in two steps. First the ground state calculation is achieved specifying calc_mode = 'GS' . Then the real-time electron dynamics calculation is achieved specifying calc_mode = 'RT' . For periodic systems, two calculations should be carried out in one step specifying calc_mode = 'GS_RT' .

There are about 20 groups of namelists listed below. A list of variables in each namelist is provided in the file ??? included in the source-file distribution.

name of namelist	description
&calculation	specify calculation modes
&control	parameters related to general conditions for the calculation
&units	specify units of input and output files
&parallel	parameters related to parallelization
&system	information related to the system
&pseudo	information related to pseudopotentials
&functional	specify density functional to be used
&rgrid	parameters related to real space grid
&kgird	parameters related to k-points for periodic systems
&tgrid	parameters related to time evolution
&propagation	specify a choice of the propagation method
&scf	parameters related to ground state calculation
&emfield	parameters of electric fields applied to the system
&linear_response	magnitude of the distortion for linear response
&multiscale	parameters related to coupled multiscale calculations of electron dynamics and light propagations
&analysis	parameters related to output files
&hartree	parameters related to Hartree potential calculation of isolated systems
&ewald	parameters related to Ewald sum that appears in the ground state calculation of periodic systems
&atomic_coor	Atomic coordinates can be written here

In Samples, we prepare six samples that cover typical calculations feasible by using SALMON. We prepare explanations for the input files that will help to prepare input files of your own interests.

Here we briefly explain the format of the namelist.

&namelist1
  variable1 = int_value
  variable2 = 'char_value'
 /
&namelist2
  variable1 = real8_value
  variable2 = int_value1, int_value2, int_value3
/

A block 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 that 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 /. Input files constitute of several blocks of namelists. The blocks can appear in any order.

Run SALMON

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. In order to execute the calculation, for the single process environment, type the following command:

$ salmon.cpu < inputfile.inp > fileout.out

For the multiprocess environment, If the command to execute calculations using MPI is mpiexec', the calculation will start

$ mpiexec -n NPROC salmon.cpu < inputfile.inp > fileout.out

where NPROC is the number of MPI processes you want to use. For the many-core processor (e.g. intel-knl) environment, the execution command is

$ mpiexec.hydra -n NPROC salmon.mic < inputfile.inp > fileout.out

The execution command and the job submission procedure depends much on the local environment. We just summarize the general conditions to execute SALMON:

• salmon runs in parallel environment using MPI.
• executable files are prepared as /salmon/bin/salmon.cpu and/or /salmon/bin/salmon.mic in the standard build procedure.
• to start calculations, inputfile.inp should be read through stdin.

Output files

See Samples.