GEM - Gyrokinetic Turbulence Code
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Description of input parameters

Input parameters: FLUX TUBE GEM
itube          :Always 1 for flux tube  
ibase          :No longer used in the flux tube code
iperi          :1, periodic boundary condition for potentials
                     0, fixed boundary condition
iperidf        :1, periodic boundary condition for particles
                      0, fixed boundary condition for particles
ibunit         :1, convert the GYRO rhostar and beta_e to gem rhostar and beta_e
                     **In this case the rhostar and beta_e in gem.in uses gyro definitions
                       0, no need to convert
                          **In this case the rhostar and beta_e in gem.in uses GEM definitions
mimp           :Mass ratio of ions with respect to to protons
mcmp         :Mass ratio of impurities with respect to to protons
chgi              :Charge of ions with respect to to electron charge
chgc             :Charge of impurity ions with respect to electron charge

R/a                        :Aspect ratio, ratio of major radius to minor radius
elongation        :Elongation, stretch up-down
selon                    :Radial variation of elongation
triangularity    :Triangularity: stretch radially outward
stria                    :Radial variation of triangularity
shift                    :Measure of Shafranov shift
q0                       :Safety factor   
shat0                :Shear    
teti                     :Ratio of electron temperature to ion temperature
tcti                     :Ratio of impurity temperature to ion temperature
rhoia                :rhos/a

R/Lni                   :Ion density gradient scale length normalized to major radius
R/Lti                     :Ion temperature gradient scale length normalized to major radius
R/Lne                  :Electron density gradient scale length normalized to major radius
R/Lte                   :Electron temperature gradient scale length normalized to major radius
R/Lnc                 :Impurity density gradient scale length normalized to major radius
R/Ltc                  :Impurity temperature gradient scale length normalized to major radius
nc/ne                :Measure of impurity concentration, ratio of impurity to electron density

imx                 :Number of grid points along x direction
jmx                :Number of grid points along y direction
kmx               :Number of grid points along z direction
mmx             :Maximum number of marker particles 
nmx              :Maximum number of time steps
nsmx            :Maximum number if impurity ions
modemx      :Maximum number of modes 
ntube             :The z direction is divided in to km grids. These grids are used for the primary domain decomposition. Particles in each z grid are then                  distributed among ntube processors so that,  total number of processors=kmx*ntube.  Also, the calculation of jm Fourier components of potentials               is equally distributed among the ntube processors.   Therefore, jmx/ntube must be an integer
      
icrs_sec    :Used in global codes to plot poloidal cross-section
             =1 when to get the plot
             =0 otherwise
ipg        :which snapshot to get   
isphi        :which potential to plot
               =0 for A_||
               =1 for phi


icrs_sec    :Used in global codes to plot poloidal cross-section
             =1 when to get the plot
             =0 otherwise
ipg        :which snapshot to get   
isphi        :which potential to plot
               =0 for A_||
               =1 for phi

lxa        :Radial box size, for fixed BC in linear runs
             radial box size for nonlinear simulation
             for periodic boundary condition linear runs, lxa is defined in equilf90 as 1/nq'
lymult         :No of wedges the whole tokamak is partitioned in to.
               Number of toroidal mode number in linear runs
              :delta n in nonlinear runs.

delra        :No longer used in the flux tube code

delri        :No longer used in the flux tube code
delre        :No longer used in the flux tube code
delrn           :No longer used in the flux tube code

nrst        :Sets the interval in time steps after which the coarse graining is to be invoked 
eprs        :The parameter for coarse graining   
nlow        :determines the lowest wave number in the NONLINEAR simulation in multiples of lymult
             for example, if nlow=1, lowest wave number in the simulation is lymult x nlow=lymult
dt         :Times steps in units of omega_u=eB/mp
nm        :Total no of times steps
nsm        :Number of ion species
xshape        :Gaussian filter used in nonlinear simulation along x
yshape        :Gaussian filter used in nonlinear simulation along y
shape        :Gaussian filter used in nonlinear simulation along z


kymode        :No longer used in the flux tube code
iput        :Save files for restart, iput=1 always
iget        :To retrieve saved stuff during a restart.
                 iget=0 for the first run
                 iget=1 for all restarts
ision        :Is in gem.f90
                 used in push_wrapper
                         grid1
                         ezamp
                         ezampL
                         drdt
                always 1
                calculates ion contributions to current and density
peritr        :Do not understand the use. Always set 0.
llk        :Always set 0, used only in yveck, picks the i=0 Fourier component in
mlk        :1 always to pick the m=1 Fourier component in y in the case of onemd=1 (linear runs)

onemd        :defines whether to use one mode or multimode runs. For linear runs
                 onemd=1 to pick single mode.
izonal        :=0 to remove the zonal component from \phi and d\phi/dt
                 =1 to retain the zonal component in \phi and d\phi/dt
iflut        :1 always to keep the magnetic flutter component v_||delB/B in x and y component of velocity/drift   
kxz        :No longer used in the flux tube code

nplot           :The interval in time steps, at which the data are stored for contour plots and other
                  post-processing stuff
XNPLT           :The interval in time steps at which spec and dchi called to calculate potentials,
                 weight, fluxes and other stuff
modem           :Used in outd.f for hist.out. The maximum no of mode history plots
nzcrt           :The kx components to be removed from n=0 component. All i<nzcrt components are removed
npze            :Used to define critical value of electron toroidal canonical momentum pzcrite
npzi            :Used to define critical value of main ion toroidal canonical momentum pzcrite
npzc            :Used to define critical value of impurity ion toroidal canonical momentum pzcrite
npzb            :Used to define critical value of beam ion toroidal canonical momentum pzcrite

isft            :If isft=1, code calculates the real frequency
mynf            :Nfreq=kmx*mynf no of points in in Fourier transform
frmax           :Maximum range of frequency
ifskp           :Used in yveck1 and ftcamp,  nsize=nm/ifskp
iphbf           :=1, use blending function for phi
iapbf           :=1, use blending function for A_{||}
idpbf           :=1, use blending flunction for d\phi/dt
                 =0 always 

cut             :Used in restart, redefines weight as weight/cut
                 however in initialize, cut redefined if (cut.eq.0.) cut=1
                 always 1 in gem.in
amp(0.01)       :Amplitude of initial weight defined in loading (loadi and ldel)

                :Always set 0.01 in gem.in
                :Automatically set to 0 when iget=1, that is restarting
tor             :Always set 1 in gem.in.
                :???exact role is not understood, whether to take toroidal effect in to account or not
ishift          :No longer used in the flux tube code
fradi           :Adiabatic fraction of electrons; set equal to isg the split weight factor in the subroutine
                 init
kxcut           :Cut off value for kx
kxcut           :Cut off value for ky
bcut            :Cut off value for aruguments of Bessel function
                 =always set to 3000 in gem.in

r0a             :r0/a; center of the radial domain
width           :No longer used in the flux tube code
vpp             :No longer used in the flux tube code
vt0             :No longer used in the flux tube code
yd0             :No longer used in the flux tube code

c4              :Always 2 defined in gem.in, the power in the Gaussian filter that is epx(-b2^c4)  
ifluid          :Always 1, invokes kinetic electron
isg             :Split weigh factor, almost always 0.1
amie            :Proton to electron mass ratio
rneu            :Electron ion collision frequency
rneui           :Ion electron(?) collision frequency
vexbsw          :Switch for equilibrium EXB shear
                 =1, takes in to account the effect of EXB shear
                  with EXB shear, the boundary condition is always fixed
                =0, ignores EXB shear.
vparsw          :Switch for equilibrium parallel flow
mach            :Value with respect to ion sound speed, used to define flow (??)
gamma_E.a/cs    :EXB shearing rate, given in cs/a
   

beta            :ELECTRON beta
nonlin          :Switch for ion nonlinear terms
                        =0 for linear runs
                 =1 for nonlinear runs
nonline         :Switch for electron nonlinear terms
                 =0 for linear runs
                 =1 for nonlinear runs
ipara           :Switch to take in to parallel non-linearity(??)
                 =0 to exclude
                 =1 to include 
vwidth          :Used for uniform loading; No longer used in the flux tube code
vwidthe         :Used for uniform loading; No longer used in the flux tube code
vcut            :Always 4 in gem.in
                 used to reset electron weight when v_||/vthe>vcut, wght=0
                 used in subroutines grid1, jie, jpar0, and in setw
isuni           :0 always. Used earlier for uniform loading (??)
idg             :0 always, =1, writes various component to the output file run.out

mm              :Total no of marker particles per species
mbeam           :Mass of beam ions=2,
                 No longer used in the flux tube code
qbeam           :Charge of beam ions=1, N
                 No longer used in the flux tube code in the flux tube code
lr        :Is the number of points for gyro averaging.
                 =4 always in gem.in
iflr            :Always 1.
                 To include the finite Larmor radius effect of the ions; used in ppush, cpush, grid1, jie
iorb            :Always 1.
                 To include finite orbit width term (??). Multiplied to the magnetic drift terms
                 in ppush an cpush


---------------------------------------------------------------
Length in rho_u, time in inverse omega_u, velocity in v_u mass is in mp



Input parameters: GLOBAL GEM

itube          :Always 1   
ibase          :=1, use analytical equilibrium
                 =0, otherwise
iperi             :0 always, fixed boundary condition
ixgc            :2 Iterdb;
                :3 Miller from Fluxgrid (??)
                :4 Miller from Matlab full (??)
                :5 General geometry from Matlab full (??)



=====================================================
imx           :Maximum number of number of grid points along x direction
jmx           :Maximum number of number of grid points along y direction
kmx           :Maximum number of number of grid points along z direction
mmx           :Maximum number of marker particles 
nmx           :Maximum number of time steps
nsmx          :Maximum number if impurity ions
modemx        :Maximum number of modes 
ntube         :The z direction is divided in to km grids. These grids are used for the
                 primary domain decomposition. Particles in each z grid are then
                 distributed among ntube processors so that,                   
                 total number of processors=kmx*ntube.
                 Also, the calculation of jm Fourier components of potentials
                 is equally distributed among the ntube processors.
                 Therefore, jmx/ntube must be an integer
      
icrs_sec    :Used in global codes to plot poloidal cross-section
             =1 when to get the plot
             =0 otherwise
ipg        :which snapshot to get   
isphi        :which potential to plot
               =0 for A_||
               =1 for phi
im           :Number of grid points along x direction
jm           :Number of grid points along y direction
km           :Number of grid points along z direction
lxa        :Radial box size, for fixed BC in linear runs
             radial box size for nonlinear simulation
             for periodic boundary condition linear runs, lxa is defined in equilf90 as 1/nq'
lymult         :No of wedges the whole tokamak is partitioned in to.
               Number of toroidal mode number in linear runs
              :delta n in nonlinear runs.

delra        :No longer used
delri        :Smoothing in the ion temperature profile
                 smaller is the value lesser is the smoothing
delre        :Smoothing in the electron temperature profile
                 smaller is the value lesser is the smoothing
delrn           :Smoothing in the density profile
                 smaller is the value lesser is the smoothing

nrst        :Sets the interval in time steps after which the coarse graining is to be invoked 
eprs        :The parameter for coarse graining   
nlow        :determines the lowest wave number in the NONLINEAR simulation in multiples of lymult
             for example, if nlow=1, lowest wave number in the simulation is lymult x nlow=lymult
=================================================
dt         :Times steps in units of omega_u=eB/mp
nm        :Total no of times steps
nsm        :Number of ion species
xshape        :Gaussian filter used in nonlinear simulation along x
yshape        :Gaussian filter used in nonlinear simulation along y
zshape        :Gaussian filter used in nonlinear simulation along z

ipf             :No longer used
isham           :1 to incorporate fast ion current in ezamp
                :0 otherwise
ishgk           :Whether to use high energy ions
                :0 otherwise
=================================================

kymode        :No longer used
iput        :Save files for restart, iput=1 always
iget        :To retrieve saved stuff during a restart.
                 iget=0 for the first run
                 iget=1 for all restarts
ision        :Is in gem.f90
                 used in push_wrapper
                         grid1
                         ezamp
                         ezampL
                         drdt
                always 1
                calculates ion contributions to current and density
ish             :No longer used
peritr        :??Do not understand the use. Always set 0.
llk        :Always set 0, used only in yveck, picks the i=0 Fourier component in
mlk        :1 always to pick the m=1 Fourier component in y in the case of onemd=1 (linear runs)
onemd        :defines whether to use one mode or multimode runs. For linear runs
                 onemd=1 to pick single mode.
izonal        :=0 to remove the zonal component from \phi and d\phi/dt
                 =1 to retain the zonal component in \phi and d\phi/dt
iflut        :1 always to keep the magnetic flutter component v_||delB/B in x and y
                 component of velocity/drift   
kxz        :Used in the following expression, in the y velocity (??)
vp0 = vp0*(vt0+vpp*(r-lr0)+yd0*sin(kxz*(r+0.5*lx-lr0)*2*pi/lx))
=================================================

nplot           :The interval in time steps, at which the data are stored for contour plots and other
                  post-processing stuff
XNPLT           :The interval in time steps at which spec and dchi called to calculate potentials,
                 weight, fluxes and other stuff
modem           :Used in outd.f for hist.out. The maximum no of mode history plots
nzcrt           :The kx components to be removed from n=0 component. All i<nzcrt components are removed
npze            :Used to define critical value of electron toroidal canonical momentum pzcrite
npzi            :Used to define critical value of main ion toroidal canonical momentum pzcrite
npzc            :Used to define critical value of impurity ion toroidal canonical momentum pzcrite
npzb            :Used to define critical value of beam ion toroidal canonical momentum pzcrite
swgradti        :No longer used
swgradte        :No longer used
swgradn         :No longer used
=================================================
isft            :If isft=1, code calculates the real frequency
mynf            :Nfreq=kmx*mynf no of points in in Fourier transform
frmax           :Maximum range of frequency
ifskp           :Used in yveck1 and ftcamp,  nsize=nm/ifskp
=================================================
iphbf           :=1, use blending function for phi
iapbf           :=1, use blending function for A_{||}
idpbf           :=1, use blending flunction for d\phi/dt
                 =0 always 

=================================================
cut             :Used in restart, redefines weight as weight/cut
                 however in initialize, cut redefined if (cut.eq.0.) cut=1
                 always 1 in gem.in
amp(0.01)       :Amplitude of initial weight defined in loading (loadi and ldel)
                :Always set 0.01 in gem.in
                :Automatically set to 0 when iget=1, that is restarting
tor             :Always set 1 in gem.in.
                :???exact role is not understood, whether to take toroidal effect in to account or not
ishift          :No longer used
fradi           :Adiabatic fraction of electrons; set equal to isg the split weight factor in the subroutine
                 init
kxcut           :Cut off value for kx
kxcut           :Cut off value for ky
bcut            :Cut off value for aruguments of Bessel function
                 =always set to 3000 in gem.in
=================================================
br0             :Set equal to rmaj0
r0a             :r0/a; center of the radial domain
q0              :No longer used
qp              :No longer used
width           :No longer used
vp0 = vp0*(vt0+vpp*(r-lr0)+yd0*sin(kxz*(r+0.5*lx-lr0)*2*pi/lx))
vpp             :No longer used
vt0             :No longer used
yd0             :No longer used
=================================================
c1              :coefficients to define q profile, also defined in equil.f90 as parameter   
c2              :coefficients to define q profile, also defined in equil.f90 as parameter   
c3              :Not used   
c4              :Always 2 defined in gem.in, the power in the Gaussian filter that is epx(-b2^c4)  
ifluid          :Always 1, invokes kinetic electron
isg             :Split weigh factor, almost always 0.1
amie            :Proton to electron mass ratio
rneu            :Electron ion collision frequency
rneui           :Ion electron(?) collision frequency
vexbsw          :Switch for equilibrium EXB shear
                 =1, takes in to account the effect of EXB shear
                  with EXB shear, the boundary condition is always fixed
                =0, ignores EXB shear.
vparsw          :Switch for equilibrium parallel flow
   
=================================================
betasw          :ELECTRON beta
nonlin          :Switch for ion nonlinear terms
                 =0 for linear runs
                 =1 for nonlinear runs
nonline         :Switch for electron nonlinear terms
                 =0 for linear runs
                 =1 for nonlinear runs
ipara           :Switch to take in to parallel non-linearity(??)
                 =0 to exclude
                 =1 to include 
vwidth          :Used for uniform loading; No longer used
vwidthe         :Used for uniform loading; No longer used
vcut            :Always 4 in gem.in
                 used to reset electron weight when v_||/vthe>vcut, wght=0
                 used in subroutines grid1, jie, jpar0, and in setw
isuni           :0 always. Used earlier for uniform loading (??)
idg             :0 always, =1, writes various component to the output file run.out
epa             :Not used
=================================================
mm              :Total no of marker particles per species
mion            :No longer used
qion            :No longer used
mimp            :No longer used
qimp            :No longer used
mbeam           :Mass of beam ions=2,
                 No longer used
qbeam           :Charge of beam ions=1, N
                 No longer used 
lr        :Is the number of points for gyro averaging.
                 =4 always in gem.in
=================================================
kappan 0.0022     
kappat 0.0069   
kapt
=================================================
nh    
lh     
ecpow     
ehmax      
ehmin   
teth 
iflr            :Always 1.
                 To include the finite Larmor radius effect of the ions; used in ppush, cpush, grid1, jie
iorb            :Always 1.
                 To include finite orbit width term (??). Multiplied to the magnetic drift terms
                 in ppush an cpush
iflrh

=================================================


Input Parameters: Hybrid Code
=====================================================
imx           :Maximum number of number of grid points along x direction
jmx           :Maximum number of number of grid points along y direction
kmx           :Maximum number of number of grid points along z direction
mmx           :Maximum number of marker particles 
nmx           :Maximum number of time steps
nsmx          :Maximum number if impurity ions
modemx        :Maximum number of modes 
ntube         :The z direction is divided in to km grids. These grids are used for the
                 primary domain decomposition. Particles in each z grid are then
                 distributed among ntube processors so that,                   
                 total number of processors=kmx*ntube.
                 Also, the calculation of jm Fourier components of potentials
                 is equally distributed among the ntube processors.
                 Therefore, jmx/ntube must be an integer
       

icrs_sec    :Used in global codes to plot poloidal cross-section
             =1 when to get the plot
             =0 otherwise

ipg        :which snapshot to get   
isphi        :which potential to plot
               =0 for A_||
               =1 for phi

itrace     
isft            :If isft=1, code calculates the real frequency
irlk            :No longer used
qoffset         :??? used to define sf_ref in equil.f
=====================================================
im           :Number of grid points along x direction
jm           :Number of grid points along y direction
km           :Number of grid points along z direction
lxa        :Radial box size, for fixed BC in linear runs
             radial box size for nonlinear simulation
             for periodic boundary condition linear runs, lxa is defined in equilf90 as 1/nq'

lyfra         :No of wedges the whole tokamak is partitioned
in to.
 
               Value of the toroidal mode number in linear runs
               delta n in nonlinear runs.

nrst        :Sets the interval in time steps after which the coarse graining is to be invoked 
eprs        :The parameter for coarse graining   
epsnx        :Filtering/smoothing parameter for electron density in x   
epsny        :Filtering/smoothing parameter for electron density in y 
epsny        :Filtering/smoothing parameter for electron density in z 

epsax        :smoothing parameter for A_|| in x after Fourier filtering   
epsay        :smoothing parameter for A_|| in y after Fourier filtering
epsay        :smoothing parameter for A_|| in z  after Fourier filtering
=================================================
dt         :Times steps in units of omega_u=eB/mp
nm        :Total no of times steps
nsm        :Number of ion species
xshape        :Not used
yshape        :Not Used
zshape        :Not Used

ipf             :Not used
isham           :1 to incorporate fast ion current in ezamp
                 0 otherwise
ishgk           :Whether to use high energy ions
                 0 otherwise
icmprs          :??? did not understand
iez             :1 calculates parallel electric field
                 0 otherwise
isgkm           :1 or 0; whether to use split weight scheme or not
icncl           :???Whether to cancle (icncl=1) or retain (icncl=0) the FLR effect
ispre           :??? did not understand
isdte           :??? did not understand
=================================================
delra        :No longer used
delri        :Smoothing in the ion temperature profile
                 smaller is the value lesser is the smoothing
delre        :Smoothing in the electron temperature profile
                 smaller is the value lesser is the smoothing
delrn           :Smoothing in the density profile

                 smaller is the value lesser is the smoothing

nlow        :determines the lowest wave number in the NONLINEAR simulation in multiples of lymult
             for example, if nlow=1, lowest wave number in the simulation is lymult x nlow=lymult
=====================================================
kymode        :No longer used
iput        :Save files for restart, iput=1 always
iget        :To retrieve saved stuff during a restart.
                 iget=0 for the first run
                 iget=1 for all restarts
ision        :Is in gem.f90
                 used in push_wrapper
                         grid1

                         ezamp
                         ezampL
                         drdt
                always 1
                calculates ion contributions to current and density
ish             :No longer used
peritr        :??Do not understand the use. Always set 0.
llk        :Always set 0, used only in yveck, picks the i=0 Fourier component in
mlk        :1 always to pick the m=1 Fourier component in y in the case of onemd=1 (linear runs)
onemd        :defines whether to use one mode or multimode runs. For linear runs
                 onemd=1 to pick single mode.
izon        :=0 to remove the zonal component from \phi and d\phi/dt
                 =1 to retain the zonal component in \phi and d\phi/dt
kxz        :???Used in the following expression, in the y velocity
                 vp0 = vp0*(vt0+vpp*(r-lr0)+yd0*sin(kxz*(r+0.5*lx-lr0)*2*pi/lx))
oml             :Lower value of frequency used in the calculation of real frequency
omu             :Upper value of frequency used in the calculation of real frequency
nom             :No of points in Fourier transform while calculation real frequency
delom           :
=================================================
nplot           :The interval in time steps, at which the data are stored for contour plots and other
                  post-processing stuff
XNPLT           :The interval in time steps at which spec and dchi called to calculate potentials,
                 weight, fluxes and other stuff
modem           :Used in outd.f for hist.out. The maximum no of mode history plots
npzh
nenh
dtref
islow
mynf            :Nfreq=kmx*mynf no of points in in Fourier transform
frmax           :Maximum range of frequency
ifskp           :Used in yveck1 and ftcamp,  nsize=nm/ifskp

=================================================
cut             :Used in restart, redefines weight as weight/cut
                 however in initialize, cut redefined if (cut.eq.0.) cut=1
                 always 1 in gem.in
amp(0.01)       :Amplitude of initial weight defined in loading (loadi and ldel)
                :Always set 0.01 in gem.in
                :Automatically set to 0 when iget=1, that is restarting
tor             :Always set 1 in gem.in.
                :???exact role is not understood, whether to take toroidal effect in to account or not
ishift          :No longer used
fradi           :Adiabatic fraction of electrons; set equal to isg the split weight factor in the subroutine
                 init
kxcut           :Cut off value for kx
kxcut           :Cut off value for ky
bcut            :Cut off value for aruguments of Bessel function
                 =always set to 3000 in gem.in
epspx
epspz
etaohm
=================================================

br0             :Set equal to rmaj0
lr0             :r0/a; center of the radial domain
q0              :No longer used
qp              :No longer used
width           :No longer used
vpp             :No longer used
vt0             :No longer used
yd0             :No longer used
vp0 = vp0*(vt0+vpp*(r-lr0)+yd0*sin(kxz*(r+0.5*lx-lr0)*2*pi/lx))
=================================================
c1              :coefficients to define q profile, also defined in equil.f90 as parameter   
c2              :coefficients to define q profile, also defined in equil.f90 as parameter   
c3              :Not used   
c4              :Always 2 defined in gem.in, the power in the Gaussian filter that is epx(-b2^c4)  
ifluid          :Always 1, invokes kinetic electron
isg             :Split weigh factor, almost always 0.1
amie            :Proton to electron mass ratio
rneu            :Electron ion collision frequency
gamion
gambm
gamdne
gamphi
gamapa
gamte
=================================================
vexbsw          :Switch for equilibrium EXB shear
                 =1, takes in to account the effect of EXB shear
                  with EXB shear, the boundary condition is always fixed
                =0, ignores EXB shear.
vparsw          :Switch for equilibrium parallel flow
   
=================================================
beta          :ELECTRON beta

nonlin          :Switch for ion nonlinear terms
                 =0 for linear runs
                 =1 for nonlinear runs
nonline         :Switch for electron nonlinear terms
                 =0 for linear runs
                 =1 for nonlinear runs
nonlinh
ipara           :Switch to take in to parallel non-linearity(??)
                 =0 to exclude
                 =1 to include 
iparah          :Switch to take in to parallel non-linearity(??) for hot ions
                 =0 to exclude
                 =1 to include

nonlint         :Switch for tracer(?) ion nonlinear terms
                 =0 for linear runs
                 =1 for nonlinear runs

iparat          ::Switch to take in to parallel non-linearity(??) for tracer(?) ions
                 =0 to exclude
                 =1 to include


vwidth          :Used for uniform loading; No longer used
vwidthe         :Used for uniform loading; No longer used
vcut            :Always 4 in gem.in
                 used to reset electron weight when v_||/vthe>vcut, wght=0
                 used in subroutines grid1, jie, jpar0, and in setw
isuni           :0 always. Used earlier for uniform loading (??)
idg             :0 always, =1, writes various component to the
output file run.out
=================================================
mm              :Total no of marker particles per species
tets            :Ratio of electron temperature to impurity temperature
mims            :Ratio of ion mass to impurity mass
q               : Charge of ion
lr        :Is the number of points for gyro averaging.
                 =4 always in gem.in
=================================================
kappan 0.0022     
kappat 0.0069   
kapt
=================================================
talpha        :
betah         :
lh            :
delth         :
vc            :
vi            :
vmin
iflr            :Always 1.
                 To include the finite Larmor radius effect of the ions; used in ppush, cpush, grid1, jie
iorb            :Always 1.
                 To include finite orbit width term (??). Multiplied to the magnetic drift terms
                 in ppush an cpush
iflrh

=================================================