Dear lammps users,
I have question about the below input using Green-Kubo relation for viscosity calculation
units real
variable T equal 200.0 # run temperature
variable Tinit equal 250.0 # equilibration temperature
variable V equal vol
variable dt equal 4.0
variable p equal 400 # correlation length
variable s equal 5 # sample interval
variable d equal $p*$s # dump interval
# convert from LAMMPS real units to SI
variable kB equal 1.3806504e-23 # [J/K] Boltzmann
variable atm2Pa equal 101325.0
variable A2m equal 1.0e-10
variable fs2s equal 1.0e-15
variable convert equal ${atm2Pa}*${atm2Pa}*${fs2s}*${A2m}*${A2m}*${A2m}
fix SS all ave/correlate $s $p $d &
v_pxy v_pxz v_pyz type auto file S0St.dat ave running
variable scale equal ${convert}/(${kB}*$T)*$V*$s*${dt}
variable v11 equal trap(f_SS[3])*${scale}
variable v22 equal trap(f_SS[4])*${scale}
variable v33 equal trap(f_SS[5])*${scale}
thermo_style custom step temp press v_pxy v_pxz v_pyz v_v11 v_v22 v_v33
my questions are listed below
(1) According to lammps manual, the global array that ave/correlate computes has 5 columns and the first column is time delta_t. However, the output of S0St.dat has six columns, and the first column is index and second column is delta_t. my question is if the index column is not considered when accessing the output of ave/correlate?
(2) I am not too sure how the trap function works after reading the manual. I think the The f_SS[3] represents correlation data (c1,c2,c3,c4…c400) which has 400 element. The trap(f_SS[3] ) function will return the data K=0.5*c1+c2+c3+c4+....+0.5c400 at time step d=400*5=2000. Is it right?
(3) The output v_v11 at time step d=400*5=2000 is v_v11=K*${scale}. Is it right
I will be grateful if someone can clarify those questions.
Thanks