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Addd born/matrix numdiff to example

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This commit is contained in:
Aidan Thompson
2022-02-19 17:07:21 -07:00
parent 563f98b898
commit 335fa2e742
6 changed files with 461 additions and 361 deletions
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67
examples/numdiff/in.numdiff
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@ -1,5 +1,5 @@
# Numerical difference calculation
# of error in forces and virial stress
# of error in forces, virial stress, and Born matrix
# adjustable parameters
@ -8,8 +8,10 @@ variable nthermo index 10 # thermo output interval
variable ndump index 500 # dump output interval
variable nlat index 3 # size of box
variable fdelta index 1.0e-4 # displacement size
variable vdelta index 1.0e-6 # strain size
variable vdelta index 1.0e-6 # strain size for numdiff/virial
variable bdelta index 1.0e-8 # strain size for numdiff Born matrix
variable temp index 10.0 # temperature
variable nugget equal 1.0e-6 # regularization for relerr
units metal
atom_style atomic
@ -23,8 +25,8 @@ mass 1 39.903
velocity all create ${temp} 2357 mom yes dist gaussian
pair_style lj/cubic
pair_coeff * * 0.0102701 3.42
pair_style lj/cut 5.0
pair_coeff 1 1 0.0102701 3.42
neighbor 0.0 bin
neigh_modify every 1 delay 0 check no
@ -42,7 +44,7 @@ variable ferrsq atom v_ferrx^2+v_ferry^2+v_ferrz^2
compute faverrsq all reduce ave v_ferrsq
variable fsq atom fx^2+fy^2+fz^2
compute favsq all reduce ave v_fsq
variable frelerr equal sqrt(c_faverrsq/c_favsq)
variable frelerr equal sqrt(c_faverrsq/(c_favsq+${nugget}))
dump errors all custom ${ndump} force_error.dump v_ferrx v_ferry v_ferrz
# define numerical virial stress tensor calculation
@ -67,8 +69,59 @@ variable vsq equal "c_myvirial[1]^2 + &
c_myvirial[4]^2 + &
c_myvirial[5]^2 + &
c_myvirial[6]^2"
variable vrelerr equal sqrt(v_verrsq/v_vsq)
variable vrelerr equal sqrt(v_verrsq/(v_vsq+${nugget}))
thermo_style custom step temp pe etotal press v_frelerr v_vrelerr
# define numerical Born matrix calculation
compute bornnum all born/matrix numdiff ${bdelta} myvirial
compute born all born/matrix
variable berr vector c_bornnum-c_born
variable berrsq equal "v_berr[1]^2 + &
v_berr[2]^2 + &
v_berr[3]^2 + &
v_berr[4]^2 + &
v_berr[5]^2 + &
v_berr[6]^2 + &
v_berr[7]^2 + &
v_berr[8]^2 + &
v_berr[9]^2 + &
v_berr[10]^2 + &
v_berr[11]^2 + &
v_berr[12]^2 + &
v_berr[13]^2 + &
v_berr[14]^2 + &
v_berr[15]^2 + &
v_berr[16]^2 + &
v_berr[17]^2 + &
v_berr[18]^2 + &
v_berr[19]^2 + &
v_berr[20]^2 + &
v_berr[21]^2"
variable bsq equal "c_born[1]^2 + &
c_born[2]^2 + &
c_born[3]^2 + &
c_born[4]^2 + &
c_born[5]^2 + &
c_born[6]^2 + &
c_born[7]^2 + &
c_born[8]^2 + &
c_born[9]^2 + &
c_born[10]^2 + &
c_born[11]^2 + &
c_born[12]^2 + &
c_born[13]^2 + &
c_born[14]^2 + &
c_born[15]^2 + &
c_born[16]^2 + &
c_born[17]^2 + &
c_born[18]^2 + &
c_born[19]^2 + &
c_born[20]^2 + &
c_born[21]^2"
variable brelerr equal sqrt(v_berrsq/(v_bsq+${nugget}))
thermo_style custom step temp pe etotal press v_frelerr v_vrelerr v_brelerr
thermo ${nthermo}
run ${nsteps}