mala/examples/in.numdiff at 0b9829ee4cdf4d9438be7bae70b2f7eb5dfdec6c · RandomDefaultUser/mala · GitHub

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# example with unique grid type

variable         nfreq equal 1 # how frequently to run fix (should be every step)
variable         ngridx equal 18 # how many grid points
variable         ngridy equal 18 # how many grid points
variable         ngridz equal 27 # how many grid points
variable         nthermo equal 1 #frequency for printing thermodynamic data
variable         nrep index 3 # number of repeated unit cells for Ca
variable         a index 4.1 # fake lattice constant
variable         fdelta equal 5.0e-7
variable         fdeltam equal -1.0e-6

units            metal
atom_modify      map hash


boundary         p p p
#boundary         f f f

read_data        Be_snapshot1.data
#make a fictitious system to test grid force calculations
mass             1 9.0


pair_style       zero 6.0
pair_coeff       * *

group            acegroup type 1
group            first id 1
group            second id 2
variable         rcutfac equal 6.0 # define rcutfac for pairstyle_zero (must be bigger than radial cutoffs in coupling_coefficients_Be.yace

variable         ace_options string "coupling_coefficients_Be.yace ugridtype 1"

pair_style       zero ${rcutfac}
pair_coeff       * *
#
timestep         0.5e-3
neighbor         0.3 bin
neigh_modify     every 1 delay 0 check yes

compute          mygrid all pace/grid  grid ${ngridx} ${ngridy} ${ngridz} ${ace_options}

#define lammps python command
python           pre_force_callback file mala_betas.py
#python          pre_force_callback file dummy_betas.py

fix             4 all python/acegridforce ${nfreq} pre_force pre_force_callback grid ${ngridx} ${ngridy} ${ngridz} ${ace_options}

thermo          ${nthermo}
variable        fsq atom fx^2+fy^2+fz^2
compute         favsq all reduce ave v_fsq

thermo_style    custom step temp pe etotal press c_favsq


dump            1 all custom 1 dump.*.mala id type x y z fx fy fz
run             0

displace_atoms  first move ${fdelta} 0.0 0.0 units box
undump 1
reset_timestep  1
dump 1 all custom 1 dump.*.mala id type x y z fx fy fz
run             0
displace_atoms  first move ${fdeltam} 0.0 0.0 units box
undump 1
reset_timestep  2
dump 1 all custom 1 dump.*.mala id type x y z fx fy fz
run             0
displace_atoms  first move ${fdelta} ${fdelta} 0.0 units box
undump 1
reset_timestep  3
dump 1 all custom 1 dump.*.mala id type x y z fx fy fz
run             0
displace_atoms  first move 0.0 ${fdeltam} 0.0 units box
undump 1
reset_timestep  4
dump 1 all custom 1 dump.*.mala id type x y z fx fy fz
run             0
displace_atoms  first move 0.0 ${fdelta} ${fdelta} units box
undump 1
reset_timestep  5
dump 1 all custom 1 dump.*.mala id type x y z fx fy fz
run             0
displace_atoms  first move 0.0 0.0 ${fdeltam} units box
undump 1
reset_timestep  6
dump 1 all custom 1 dump.*.mala id type x y z fx fy fz
run             0