update kim_style command semantics as discussed in PR #1440

this also adds documentation of error messages in the kim_style header
This commit is contained in:
Axel Kohlmeyer
2019-05-30 21:51:13 -04:00
parent b3a01694b7
commit 24a63f0f31
7 changed files with 79 additions and 117 deletions

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@ -8,7 +8,7 @@ kim_style init Sim_LAMMPS_ReaxFF_ChenowethVanDuinPersson_2008_CHOV__SM_429148913
read_data data.VOH
kim_style define NULL H C O V
kim_style define H C O V
neighbor 2 bin
neigh_modify every 10 delay 0 check no

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@ -54,7 +54,7 @@ velocity all create ${thi} 5287286 mom yes rot yes dist gaussian
group del id 300
delete_atoms group del
kim_style define NULL Si
kim_style define Si
thermo 10

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@ -1,69 +0,0 @@
units metal
kim_style init ex_sim_model_Si_mod_tersoff
atom_style atomic
atom_modify map array
boundary p p p
# temperatures
variable tlo equal 1800.0
variable thi equal 2400.0
# coordination number cutoff
variable r equal 2.835
# minimization parameters
variable etol equal 1.0e-5
variable ftol equal 1.0e-5
variable maxiter equal 100
variable maxeval equal 100
variable dmax equal 1.0e-1
# diamond unit cell
variable a equal 5.431
lattice custom $a &
a1 1.0 0.0 0.0 &
a2 0.0 1.0 0.0 &
a3 0.0 0.0 1.0 &
basis 0.0 0.0 0.0 &
basis 0.0 0.5 0.5 &
basis 0.5 0.0 0.5 &
basis 0.5 0.5 0.0 &
basis 0.25 0.25 0.25 &
basis 0.25 0.75 0.75 &
basis 0.75 0.25 0.75 &
basis 0.75 0.75 0.25
region myreg block 0 4 &
0 4 &
0 4
create_box 1 myreg
create_atoms 1 region myreg
mass 1 28.06
group Si type 1
velocity all create ${thi} 5287286 mom yes rot yes dist gaussian
# make a vacancy
group del id 300
delete_atoms group del
kim_style define ex_sim_model_Si_mod_tersoff Si
thermo 10
fix 1 all nve
fix 2 all langevin ${thi} ${thi} 0.1 48278
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
run 100

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@ -18,6 +18,8 @@ units metal
atom_style atomic
newton on
kim_style init LennardJones_Ar
lattice fcc 4.4300
region box block 0 ${xx} 0 ${yy} 0 ${zz}
create_box 1 box
@ -26,7 +28,7 @@ create_atoms 1 box
#pair_style lj/cut 8.1500
#pair_coeff 1 1 0.0104 3.4000
kim_style define LennardJones_Ar Ar
kim_style define Ar
mass 1 39.95
velocity all create 200.0 232345 loop geom