run.in.ch4_ionized

# PREREQUISITES:
#   system_ch4_ionized.data, system_ch4_ionized.in.init, system.in.settings
# Generate these files using:
#   cd moltemplate_files/
#   moltemplate.sh -atomstyle electron system_ch4_ionized.lt

# WARNING: As of 2014-3-12, the "pair_style eff/cut 5000.0 0 0" command
#          located in "orig_files/in.ch4_ionized.dynamics" (as well as the
#          files "moltemplate_files/ch4_ionized.lt" and "system.in.settings",
#          which are both derived from it) causes LAMMPS to hang.
#          Running LAMMPS on Andres' original eFF example has the same behavior.
#          This appears to be an eFF/LAMMPS issue, not a moltemplate issue.
#          The "pair_style eff/cut 100" command works, so
#          try reducing the cutoff (or ask Andres Jaramillo-Botero for help).
#          Please let me know if you solve this issue (jewett.aij -at- g mail )


variable	sname index ch4
log		${sname}.nve.log


boundary        f f f
include         system_${sname}.in.init


read_data  	system_${sname}.data


include         system_${sname}.in.settings



# Minimize

min_style       cg
min_modify      line quadratic 
minimize        0 1.0e-6 10000 100000



# Dynamics

compute		effTemp all temp/eff

thermo		100
thermo_style	custom step etotal pe ke temp press
thermo_modify	temp effTemp

# Equilibrate
timestep 	0.001
fix 		1 all nvt/eff temp 300.0 300.0 0.1
 
# the custom dump includes the radii
compute         1 all property/atom spin eradius
dump            1 all custom 100 ${sname}.nvt.lammpstrj id type x y z c_1[1] c_1[2]
dump		2 all xyz 100 ${sname}.nvt.xyz 

run 		1000000

fix		2 all nve/eff

run		1000000