= Users' Document

== Introduction
ISSDE is a parallel program that is compiled and run on the Linux platform.

== Install

=== Install Requirement
* gcc-7.5.0
* openmpi-4.1.1
* gsl lib
* Eigen lib

=== gcc-7.5.0 Install
{{{
sudo apt install gcc-7.5.0
}}}

=== openmpi-4.1.1 Install
* Download openmpi[https://download.open-mpi.org/release/open-mpi/v4.1/openmpi-4.1.1.tar.gz Install package]
* Decompress, compile, install
{{{
tar -zxvf openmpi-4.1.1
cd openmpi-4.1.1
./configure --prefix=/opt/openmpi-4.1.1 --enable-mpi-cxx --enable-mpi-cxx-seek --enable-debug
make
make install
}}}

=== openmpi-4.1.1 configuration
{{{
vim ~/.bashrc
}}}
* Add contents to the end of .bashrc
{{{
export PATH=$PATH:/opt/openmpi-4.1.1/bin
export C_PATH=$C_PATH:/opt/openmpi-4.1.1/include
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/openmpi-4.1.1/lib
export LIBRARY_PATH=/$LIBRARY_PATH:/opt/openmpi-4.1.1/lib
export INCLUDE=$INCLUDE:/opt/openmpi-4.1.1/include
}}}
* Update the configuration
{{{
source ~/.bashrc
}}}

=== gsl lib install and configuration
* Download gsl lib[https://mirror.ibcp.fr/pub/gnu/gsl/gsl-latest.tar.gz Install package]
* Decompress, compile, install
{{{
tar -zxvf gsl-lastest.tar.gz
cd gsl-2.7.1
./configure --prefix=/opt/gsl-2.7.1
make
make install
}}}

=== Eigen lib install and configuration
* Download Eigen lib[https://gitlab.com/libeigen/eigen/-/archive/3.4.0/eigen-3.4.0.tar.gz Install Package]
* Cecompress and mv to lib
{{{
tar -zxvf eigen-3.4.0.tar.gz
cp -r Eigen path_of_lib
}}}


== ISSDE compile, run, function and parameter setting

=== ISSDE Obtain
Contact Us
{{{
Email:yifeng.zheng@ipp.ac.cn
}}}

=== Program compile
{{{
cd src
make
}}}

=== Program run
{{{
cd bin
mpirun -np 4 ./a.out
}}}

=== Code structure
* bin Binary run files
* src Source code files
* include Head files and input files
* lib lib files
* configure configure files

=== Source code strctures
* Main function stochastic_process_uniform_field_mpi.cpp
* Input interview function read_data.cpp
* Newton Method function newton_raphason_general.cpp
* Runge-Kutta Method runge_kutta_general.cpp
* Extern function ext_fun.cpp

=== Parameter Setting
* Major paramters
{{{
    int store_size=10;  //store size
    int DATA_NUBEAM=2;  //0 single particle, 1 multi-particles, 2 source from NUBEAM
    int CO_CTR_TANG_PERP=2;     //Numbers of beam
    int A0BEAM=0;   //0 for beam 1，1 for beam 2
    int CLOCKWISE=1;    //Direction of longitudinal magnetic field, 1 for counterclockwise ,-1 for clockwise
    int CHECKPOINT=0;   //checkpoint, 1 use checkpoint data, 0 use initial data
    int RIP=0;      //Ripple setting, 0 no ripple, 1 analysis solution of ripple, 2 EAST Engineering ripple data, 3 Fish-tail ripple(DEVICE=4), 4 BEST Engineering ripple for 3.6m case(DEVICE=5), 5 CFETR Engineering data for 7.2m case (DEVICE=4)
    int NORMALIZATION=1;       //Normalization
    int SPLITTING=1;    //Splitting method
    int DEVICE=7;           //Devices, 0 for EAST discharge #93910, 1 for BEST 3.3m case with Q=1, 2 for BEST 3.3m case with Q=5, 3 for BEST 3.3m with Q=1, 4 for CFETR steady-state case with alpha particles, 5 for BEST 3.6m with alpha particle and Q=, 6 for BEST 3.6m with Q=5, 7 for EAST discharge #101735
    int ICRF=1;             //When DEVICE=7, ICRF-NBI fast ion with different minority concentration, 0 for only NBI, 1 for 1% H, 2 for 5% H and 3 for 10% H
    int COLLISION=0;    //0 no collision, 1 collision with electron， 2 collision with D, 3 collision with T, 4 collision with electron and D, 5 collision with electron and T, 6 collision with D and t 7 collision with electron, D and T.
    int BC=1;           //0 for LCFS boundary, 1 for first wall
    int MHD=1;          //0 no MHD, 1 with MHD perturbation field
    int MHD_OVERLAP=0;  //0 no MHD overleaping，1 for overlaping of MHD (2,1) and (3,2)
}}}

* Major output files
{{{
v_para_dis_NBI_1_ICRF_EAST_mhd_one_particle_D_Limiter_g_nor_mi_e_i_t_f_mpi.txt;    //Parallel velocity distribution of particles
v_perp_dis_NBI_1_ICRF_EAST_mhd_one_particle_D_Limiter_g_nor_mi_e_i_t_f_mpi.txt;    //Perpendecular velocity distribution of particles
v_x_dis_NBI_1_ICRF_EAST_mhd_one_particle_D_Limiter_g_nor_mi_e_i_t_f_mpi.txt;    //Velocity distribution in x direction
v_y_dis_NBI_1_ICRF_EAST_mhd_one_particle_D_Limiter_g_nor_mi_e_i_t_f_mpi.txt;    //Velocity distribution in y direction
v_z_dis_NBI_1_ICRF_EAST_mhd_one_particle_D_Limiter_g_nor_mi_e_i_t_f_mpi.txt;    //Velocity distribution in z direction
x_dis_NBI_1_ICRF_EAST_mhd_one_particle_D_Limiter_g_nor_mi_e_i_t_f_mpi.txt;    //Position distribution in x direction
y_dis_NBI_1_ICRF_EAST_mhd_one_particle_D_Limiter_g_nor_mi_e_i_t_f_mpi.txt;    //Position distribution in y direction
z_dis_NBI_1_ICRF_EAST_mhd_one_particle_D_Limiter_g_nor_mi_e_i_t_f_mpi.txt;    //Position distribution in z direction
}}}

=== Results
* The agreement between the results of ISSDE code and the analytical solution of FP equation
[[Image(htdocs:slowing_down_velocity_no_field_e_i_benckmark.png,50%,align=middle)]]
* The agreement between the results of ISSDE code and the physical process
[[Image(htdocs:slowing_down_thermal_e_e_maxwellian.png,50%,align=middle)]]
* Comparison of long-term stability between splitting method and stochastic Runge-Kutta method  
[[Image(htdocs:relative_energy_error_of_splitting_method.png,50%,align=middle)]]
* Fast ion trajectory compared with the results of PTC
[[Image(htdocs:Fig.1.png,50%,align=middle)]]
* Fast ion loss in EAST
[[Image(htdocs:heat_NBI_H001_new_rip_3d_limiter_10ms.png,50%,align=middle)]]

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