Difference between revisions of "SALMON Manual for Beginners"

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== Prerequisites ==
 
== Prerequisites ==
  
−
In this guide, it is assumed that readers have a basic knowledge on Unix.  
+
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.
−
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:
 
* Fortran90/C compiler with MPI support. Our package assumes users have one of the following compilers:
Line 19: Line 17:
 
** Gnu Make
 
** Gnu Make
  
−
If you use other compilers, you may need to change build scripts (CMake, Makefile).
+
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.
−
If no numerical library is installed in your computer system, you may need to install BLAS/LAPACK by yourself.
+
See [[Troubleshooting of the Installation Process]].
−
See [[Tips for Installation]].
 
−
 
 
  
 
== Download ==
 
== Download ==
  
−
Newest version of the SALMON can be downloaded from [[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,
 
To extract files from the downloaded file ''salmon-<VERSION>.tar.gz'', type the following command in the command-line,
  
Line 40: Line 36:
 
   |- example    Samples
 
   |- example    Samples
 
   |- Makefile  Files related to building
 
   |- Makefile  Files related to building
−
 
  
 
== Build ==
 
== Build ==
Line 46: Line 41:
 
To compile SALMON to create executable binary files, two options are prepared, CMake and Gnu Make.  
 
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 works in your environment, we recommend to use it.  
−
If CMake fails in your environment, consider to use Gnu Make.
+
If CMake fails in your environment, consider using Gnu Make.
  
 
=== Build using CMake ===
 
=== Build using CMake ===
  
−
First examine whether CMake is usable in your environment or not.
+
First, examine whether CMake is usable in your environment or not.
 
Type the following in Unix command-line:
 
Type the following in Unix command-line:
  
 
  $ cmake --version
 
  $ 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 not installed in your system, an error message such as <code>cmake: command not found</code> will appear.  
−
If CMake is installed in your system, version number will be shown.
+
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.  
 
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.  
+
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.
 
The installation of the CMake is simple.
−
A detailed description of the installation is given in [[Installation of CMake]].
+
A detailed description of the installation is given in [[Tips_for_Installation#Installation_of_CMake | Installation of CMake]].
 
Here we describe a simple method to use the binary distribution 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/.
+
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''.
 
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.
 
In standard Unix environment, files for the platform of Linux x86_64 will be appropriate.
Line 79: Line 74:
 
==== Build using CMake specifying archtechture ====
 
==== 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.  
+
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.
 
We assume that you are in the directory SALMON.
 
* Create a new temporary directory ''build'' and move to the directory,
 
* Create a new temporary directory ''build'' and move to the directory,
Line 91: Line 86:
 
  $ make
 
  $ make
  
−
Here ''ARCHTECTURE'' specifies the architecture of the CPU in your computer system such as ''intel-avx''.  
+
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:
 
You need to choose ''ARCHTECUTRE'' from the following options:
  
Line 128: Line 123:
 
If CMake build fails in your environment, try Gnu Make for the build process.  
 
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''.  
 
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.  
+
First, you need to modify ''Makefile'' appropriately according to your environment.  
 
Edit the ''Makefile'' using a text editor.  
 
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 ??
+
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.
 
  # This is a makefile for SALMON program.
 
  # please select architecture by deleting “#”
 
  # please select architecture by deleting “#”
 +
 
  #ARCH = gnu
 
  #ARCH = gnu
 
  ARCH = intel
 
  ARCH = intel
 +
#ARCH = intel-avx
 +
#ARCH = intel-avx2
 
  #ARCH = fujitsu
 
  #ARCH = fujitsu
 
  #ARCH = intel-knl
 
  #ARCH = intel-knl
 +
#ARCH = intel-knc
  
 
Then use ''make'' command in the command-line to build the executable file.
 
Then use ''make'' command in the command-line to build the executable file.
Line 146: Line 145:
  
 
To run SALMON, at least two kinds of files are required for any calculations.  
 
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''.  
+
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.  
 
It should be prepared in the Fortran90 namelist format.  
 
Pseudopotential files of relevant elements are also required.  
 
Pseudopotential files of relevant elements are also required.  
Line 156: Line 155:
 
SALMON utilizes norm-conserving pseudpotentials.  
 
SALMON utilizes norm-conserving pseudpotentials.  
 
You may find pseudopotentials of some elements in [[Samples]].  
 
You may find pseudopotentials of some elements in [[Samples]].  
−
SALMON allows to use several formats of pseudpotentials that can be easily obtained from websites listed below.
+
SALMON allows using several formats of pseudopotentials that can be easily obtained from websites listed below.
 +
 
  
 
{| class="wikitable"
 
{| class="wikitable"
Line 171: Line 171:
 
SALMON describes electron dynamics in systems with both isolated and periodic boundary conditions.  
 
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''.  
 
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.  
+
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''.  
 
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.
 
For isolated systems, the ground state and the electron dynamics calculations should be carried out in two steps.
Line 186: Line 186:
 
| &calculation || specify calculation modes
 
| &calculation || specify calculation modes
 
|-
 
|-
−
| control  || parameters related to general conditions for the calculation
+
| &control  || parameters related to general conditions for the calculation
 
|-
 
|-
 
| &units        || specify units of input and output files  
 
| &units        || specify units of input and output files  
Line 220: Line 220:
 
| &ewald  || parameters related to Ewald sum that appears in the ground state calculation of periodic systems
 
| &ewald  || parameters related to Ewald sum that appears in the ground state calculation of periodic systems
 
|-
 
|-
−
| &atomic_positions || Atomic positions can be written here
+
| &atomic_coor || Atomic coordinates can be written here
−
|-
 
−
| &group_fundamental ||   
 
−
|-
 
−
| &group_file    ||     
 
 
|}
 
|}
  
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== Run SALMON ==
 
== 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 in [[Installation]].
+
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
  
−
an input file ''inputfile.inp'' and pseudopotential files should be prepared as mentioned above.
+
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
  
−
is prepared at ''/salmon/bin/''.  
+
where NPROC is the number of MPI processes you want to use.
−
If the command to execute calculations using MPI is ''mpirun'',
+
For the many-core processor (e.g. intel-knl)  environment, the execution command is
−
the calculation starts by
 
  
−
  $ mpirun salmon.cpu < inputfile.inp > stdout
+
  $ mpiexec.hydra -n NPROC salmon.mic < inputfile.inp > fileout.out
  
−
The execution command and job submission system depends much on the local environment.
+
The execution command and the job submission procedure depends much on the local environment.
−
We just summarize the general conditions:
+
We just summarize the general conditions to execute SALMON:
  
 
* salmon runs in parallel environment using MPI.
 
* salmon runs in parallel environment using MPI.
−
* executable files are prepared in ''/salmon/bin/salmon.cpu'' and/or ''/salmon/bin/salmon.mic'' in the standard build procedure.
+
* 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''.
 
* to start calculations, ''inputfile.inp'' should be read through ''stdin''.
  
 
== Output files ==
 
== Output files ==
  
−
See [[Samples]]. There are several examples.
+
See [[Samples]].

Latest revision as of 09:12, 30 July 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.

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