<commit_before>import numpy, os
import matplotlib.pyplot as plt
from labutil.plugins.lammps import lammps_run, parse_lammps_rdf, parse_lammps_thermo, get_rdf
from labutil.objects import File, Struc, Dir, ase2struc, ClassicalPotential
from ase.spacegroup import crystal
from ase.build import make_supercell

intemplate = """
    # ---------- Initialize simulation ---------------------
    units metal
    atom_style atomic
    dimension  3
    boundary   p p p
    newton off
    read_data /home/bond/Work/Lab4/AgI.data 

    pair_style mgpf
    pair_coeff * * /home/bond/Work/Lab4/AgI_FF.txt 47 53 yes yes

    velocity all create $TEMPERATURE 126342 dist gaussian rot yes mom yes

    group silvers type 1
    group iodines type 2

    # ---------- Describe computed properties------------------
    compute msdAg silvers msd com yes
    compute msdI iodines msd com yes
    compute rdfAg all rdf 1000 1 1
    compute rdfI all rdf 1000 2 2

    variable rdfAgFile string "$RDFFILE.Ag"
    variable rdfIFile string "RDFFILE.I"

    thermo_style custom step temp etotal press density c_msdAg[4] c_msdI[4]
    thermo $TOUTPUT 

    # record rdf
    fix 1 all ave/time 1 $RDFFRAME $RDFFRAME c_rdfAg[*] file ${rdfAgFile} mode vector
    fix 1 all ave/time 1 $RDFFRAME $RDFFRAME c_rdfI[*] file ${rdfIFile} mode vector

    # ---------- Specify ensemble  ---------------------
    fix 4 all npt temp $TEMPERATURE $TEMPERATURE $TDAMP tri 0.0 0.0 1.0

    # --------- Run -------------<commit_msg>updating rdf files for AgI<commit_after>import numpy, os
import matplotlib.pyplot as plt
from labutil.plugins.lammps import lammps_run, parse_lammps_rdf, parse_lammps_thermo, get_rdf
from labutil.objects import File, Struc, Dir, ase2struc, ClassicalPotential
from ase.spacegroup import crystal
from ase.build import make_supercell

intemplate = """
    # ---------- Initialize simulation ---------------------
    units metal
    atom_style atomic
    dimension  3
    boundary   p p p
    newton off
    read_data /home/bond/Work/Lab4/AgI.data 

    pair_style mgpf
    pair_coeff * * /home/bond/Work/Lab4/AgI_FF.txt 47 53 yes yes

    velocity all create $TEMPERATURE 126342 dist gaussian rot yes mom yes

    group silvers type 1
    group iodines type 2

    # ---------- Describe computed properties------------------
    compute msdAg silvers msd com yes
    compute msdI iodines msd com yes
    compute rdfAg all rdf 1000 1 1
    compute rdfI all rdf 1000 2 2

    variable rdfAgFile string "$RDFFILE.Ag"
    variable rdfIFile string "$RDFFILE.I"

    thermo_style custom step temp etotal press density c_msdAg[4] c_msdI[4]
    thermo $TOUTPUT 

    # record rdf
    fix 1 all ave/time 1 $RDFFRAME $RDFFRAME c_rdfAg[*] file ${rdfAgFile} mode vector
    fix 2 all ave/time 1 $RDFFRAME $RDFFRAME c_rdfI[*] file ${rdfIFile} mode vector

    # ---------- Specify ensemble  ---------------------
    fix 4 all npt temp $TEMPERATURE $TEMPERATURE $TDAMP tri 0.0 0.0 1.0

    # --------- Run -------------
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