= Development Manual [http://www.lanseyilin.cn:8080/trac/wiki/code_page 开发手册]
== Matlab Code
Analysis files for ISSDE calculation
Categories: Input_setting, Analysis_Input, Analysis_Theory_&_Simulation, Analysis_Output, Script

Input_setting:
{{{
get_input_file.m
get_n_T_for_read_data.m
get_psirz_psidr_psidz.m
get_ripple_deltarz_deltar_deltaz.m
get_xyz_vxyz.m
manipulateGfile.m
readGfile.m
MHD_input_setting:
    R_z_from_psi.m
    poloidal_theta_calculation.m
MHD_trace_input_setting:
    R_phi_z_each_psi.m
    R_phi_z_pitch_energy_each_psi.m
    get_cartesian_coordinate_from_guiding_center_each_psi_mhd.m
Stellarator_input_setting:
    vmec_read.m
}}}

Analysis_Input
{{{
NBI_position_distribution.m
magnetic_line_psi.m
n_T_plot.m
particle_orbit_type.m
psi_distribution_fun.m
q_profile.m
ripple_delta_engineering.m
}}}

Analysis_Theory_&_Simulation:
{{{
magnetic_island_width_calculation.m
}}}

Analysis_Output:
{{{
poincare_map_plot.m
magnetic_trace.m
}}}

Script:
{{{
run_diff_E_alpha_mhd_phase_space.sh
}}}
== C++ Code
=== ISSDE flow chart
[[Image(htdocs:flow_chart_english.png,50%,title=ISSDE与拟牛顿法流程图)]]

=== ISSDE structure
[[Image(htdocs:ISSDE_different_scenarios.png,50%,title=ISSDE程序框架)]]

== Git branch

=== ISSDE Normalization
The normalization of the program is based on the mass of electron [[math(m_{e}=9.10938356\times10^{-31}\rm{kg})]], charge of electron [[math(q=1.602176565\times10^{-19}\rm{C})]], the speed of light [[math(c=3.0\times10^{8}\rm{m/s})]] and the vacuum dielectric constant [[math(\epsilon_0=8.854187817\times 10^{-12})]]. The physical normalized physics quantities are [[math(m_{e},e,c,\varepsilon_{0})]], the other quantities are as follow
||  variable  ||  symbols  ||  unit  ||
||  mass  ||  [[math(m)]]  ||  [[math(m_e)]]  ||
||  charge  ||  [[math(q)]]  ||  [[math(|e|)]]  ||  
||  velocity  ||  [[math(\bf{v})]]  ||  [[math(c)]]  || 
||  position  ||  [[math(\bf{x})]]  ||  [[math(\frac{e^2}{m_e c^2 \varepsilon_0})]]  ||
||  time  ||  [[math(t)]]  ||  [[math(\frac{e^2}{m_e c^3 \varepsilon_0})]]  ||
||  eletric field  ||  [[math(\bf{E})]]  ||  [[math(\frac{m_e ^2 e^4 \varepsilon_0}{|e|^3})]]  ||
||  magnetic field  ||  [[math(\bf{B})]]  ||  [[math(\frac{m_e ^2 e^3 \varepsilon_0}{|e|^3})]]  ||
||  magnetic flux  ||  [[math(\psi)]]  ||  [[math(\frac{|e|}{c\varepsilon_0})]]  ||
||  Derivative of magnetic flux  ||  [[math(\partial\psi/\partial R)]]  ||  [[math(m_ec)]]  ||


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