Merge branch 'amoeba' of github.com:lammps/lammps into amoeba
This commit is contained in:
Steve Plimpton
@ -0,0 +1,7 @@
|
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# Cij Matrix from post process computation
|
||||
3.36316 1.87373 1.87607 -0.00346 -0.00172 -0.00104
|
||||
1.87373 3.36170 1.87425 0.00443 0.00033 0.00014
|
||||
1.87607 1.87425 3.36573 0.00143 0.00155 0.00127
|
||||
-0.00346 0.00443 0.00143 1.87425 0.00127 0.00033
|
||||
-0.00172 0.00033 0.00155 0.00127 1.87607 -0.00346
|
||||
-0.00104 0.00014 0.00127 0.00033 -0.00346 1.87373
|
||||
118
examples/ELASTIC_T/BORN_MATRIX/Argon/Analytical/compute_born.py
Normal file
118
examples/ELASTIC_T/BORN_MATRIX/Argon/Analytical/compute_born.py
Normal file
@ -0,0 +1,118 @@
|
||||
#!/usr/bin/env python3
|
||||
# -*- coding: utf-8 -*-
|
||||
|
||||
import sys
|
||||
import numpy as np
|
||||
|
||||
def reduce_Born(Cf):
|
||||
C = np.zeros((6,6), dtype=np.float64)
|
||||
C[0,0] = Cf[0]
|
||||
C[1,1] = Cf[1]
|
||||
C[2,2] = Cf[2]
|
||||
C[3,3] = Cf[3]
|
||||
C[4,4] = Cf[4]
|
||||
C[5,5] = Cf[5]
|
||||
C[0,1] = Cf[6]
|
||||
C[0,2] = Cf[7]
|
||||
C[0,3] = Cf[8]
|
||||
C[0,4] = Cf[9]
|
||||
C[0,5] = Cf[10]
|
||||
C[1,2] = Cf[11]
|
||||
C[1,3] = Cf[12]
|
||||
C[1,4] = Cf[13]
|
||||
C[1,5] = Cf[14]
|
||||
C[2,3] = Cf[15]
|
||||
C[2,4] = Cf[16]
|
||||
C[2,5] = Cf[17]
|
||||
C[3,4] = Cf[18]
|
||||
C[3,5] = Cf[19]
|
||||
C[4,5] = Cf[20]
|
||||
C = np.where(C,C,C.T)
|
||||
return C
|
||||
|
||||
def compute_delta():
|
||||
D = np.zeros((3,3,3,3))
|
||||
for a in range(3):
|
||||
for b in range(3):
|
||||
for m in range(3):
|
||||
for n in range(3):
|
||||
D[a,b,m,n] = (a==m)*(b==n) + (a==n)*(b==m)
|
||||
d = np.zeros((6,6))
|
||||
d[0,0] = D[0,0,0,0]
|
||||
d[1,1] = D[1,1,1,1]
|
||||
d[2,2] = D[2,2,2,2]
|
||||
d[3,3] = D[1,2,1,2]
|
||||
d[4,4] = D[0,2,0,2]
|
||||
d[5,5] = D[0,1,0,1]
|
||||
d[0,1] = D[0,0,1,1]
|
||||
d[0,2] = D[0,0,2,2]
|
||||
d[0,3] = D[0,0,1,2]
|
||||
d[0,4] = D[0,0,0,2]
|
||||
d[0,5] = D[0,0,0,1]
|
||||
d[1,2] = D[1,1,2,2]
|
||||
d[1,3] = D[1,1,1,2]
|
||||
d[1,4] = D[1,1,0,2]
|
||||
d[1,5] = D[1,1,0,1]
|
||||
d[2,3] = D[2,2,1,2]
|
||||
d[2,4] = D[2,2,0,2]
|
||||
d[2,5] = D[2,2,0,1]
|
||||
d[3,4] = D[1,2,0,2]
|
||||
d[3,5] = D[1,2,0,1]
|
||||
d[4,5] = D[0,2,0,1]
|
||||
d = np.where(d,d,d.T)
|
||||
return d
|
||||
|
||||
|
||||
def write_matrix(C, filename):
|
||||
with open(filename, 'w') as f:
|
||||
f.write("# Cij Matrix from post process computation\n")
|
||||
for i in C:
|
||||
f.write("{:8.5f} {:8.5f} {:8.5f} {:8.5f} {:8.5f} {:8.5f}\n".format(
|
||||
i[0]*10**-9, i[1]*10**-9, i[2]*10**-9, i[3]*10**-9, i[4]*10**-9, i[5]*10**-9,
|
||||
)
|
||||
)
|
||||
return
|
||||
|
||||
def main():
|
||||
|
||||
N = 500
|
||||
vol = 27.047271**3 * 10**-30 # m^3
|
||||
T = 60 # K
|
||||
kb = 1.380649 * 10**-23 # J/K
|
||||
kbT = T*kb # J
|
||||
kcalmol2J = 4183.9954/(6.022*10**23)
|
||||
|
||||
born = np.loadtxt('born.out')
|
||||
stre = np.loadtxt('vir.out')
|
||||
stre[:, 1:] = -stre[:, 1:]*101325 # -> Pa
|
||||
try:
|
||||
mean_born = np.mean(born[:, 1:], axis=0)
|
||||
except IndexError:
|
||||
mean_born = born[1:]
|
||||
|
||||
CB = kcalmol2J/vol*reduce_Born(mean_born) # -> J/m^3=Pa
|
||||
Cs = vol/kbT*np.cov(stre[:,1:].T)
|
||||
Ct = N*kbT/vol * compute_delta()
|
||||
C = CB - Cs + Ct
|
||||
write_matrix(CB, 'born_matrix.out')
|
||||
write_matrix(Cs, 'stre_matrix.out')
|
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write_matrix(Ct, 'temp_matrix.out')
|
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write_matrix(C, 'full_matrix.out')
|
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C11 = np.mean([C[0,0], C[1,1], C[2,2]]) * 10**-9
|
||||
C12 = np.mean([C[0,1], C[0,2], C[1,2]]) * 10**-9
|
||||
C44 = np.mean([C[3,3], C[4,4], C[5,5]]) * 10**-9
|
||||
eC11 = np.std([C[0,0], C[1,1], C[2,2]]) * 10**-9
|
||||
eC12 = np.std([C[0,1], C[0,2], C[1,2]]) * 10**-9
|
||||
eC44 = np.std([C[3,3], C[4,4], C[5,5]]) * 10**-9
|
||||
print(C*10**-9)
|
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print("C11 = {:f} ± {:f}; C12 = {:f} ± {:f}; C44 = {:f} ± {:f}".format(C11, eC11, C12, eC12, C44, eC44))
|
||||
|
||||
return
|
||||
|
||||
|
||||
if __name__ == "__main__":
|
||||
try:
|
||||
main()
|
||||
except KeyboardInterrupt:
|
||||
raise SystemExit("User interruption.")
|
||||
|
||||
@ -0,0 +1,7 @@
|
||||
# Cij Matrix from post process computation
|
||||
2.18161 1.13726 1.16596 -0.01607 -0.02637 0.00291
|
||||
1.13726 2.20242 1.16714 0.00386 -0.05820 0.02644
|
||||
1.16596 1.16714 2.24704 -0.00354 -0.00368 0.02714
|
||||
-0.01607 0.00386 -0.00354 1.43706 0.00210 0.01003
|
||||
-0.02637 -0.05820 -0.00368 0.00210 1.37530 0.01401
|
||||
0.00291 0.02644 0.02714 0.01003 0.01401 1.42403
|
||||
154
examples/ELASTIC_T/BORN_MATRIX/Argon/Analytical/in.ljcov
Normal file
154
examples/ELASTIC_T/BORN_MATRIX/Argon/Analytical/in.ljcov
Normal file
@ -0,0 +1,154 @@
|
||||
# Analytical calculation
|
||||
# of Born matrix
|
||||
|
||||
# Note that because of cubic symmetry and central forces, we have:
|
||||
# C11, pure axial == positive mean value: 1,2,3
|
||||
# C44==C23, pure shear == positive mean value, exactly match in pairs: (4,12),(5,8),(6,7)
|
||||
# C14==C56, shear/axial(normal) == zero mean, exactly match in pairs: (9,21),(14,20),(18,19)
|
||||
# C15, shear/axial(in-plane) == zero mean: 10,11,13,15,16,17
|
||||
|
||||
# adjustable parameters
|
||||
|
||||
units real
|
||||
variable nsteps index 100000 # length of run
|
||||
variable nthermo index 1000 # thermo output interval
|
||||
variable nlat equal 5 # size of box
|
||||
variable T equal 60. # Temperature in K
|
||||
variable rho equal 5.405 # Lattice spacing in A
|
||||
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc ${rho}
|
||||
region box block 0 ${nlat} 0 ${nlat} 0 ${nlat}
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
|
||||
mass * 39.948
|
||||
|
||||
velocity all create ${T} 87287 loop geom
|
||||
velocity all zero linear
|
||||
|
||||
pair_style lj/cut 12.0
|
||||
pair_coeff 1 1 0.238067 3.405
|
||||
|
||||
neighbor 0.0 bin
|
||||
neigh_modify every 1 delay 0 check no
|
||||
|
||||
variable vol equal vol
|
||||
thermo 100
|
||||
fix aL all ave/time 1 1 1 v_vol ave running
|
||||
fix NPT all npt temp $T $T 100 aniso 1. 1. 1000 fixedpoint 0. 0. 0.
|
||||
|
||||
run 20000
|
||||
|
||||
unfix NPT
|
||||
|
||||
variable newL equal "f_aL^(1./3.)"
|
||||
change_box all x final 0 ${newL} y final 0. ${newL} z final 0. ${newL} remap units box
|
||||
|
||||
unfix aL
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
# Conversion variables
|
||||
variable kb equal 1.38065e-23 # J/K
|
||||
variable Myvol equal "vol*10^-30" # Volume in m^3
|
||||
variable kbt equal "v_kb*v_T"
|
||||
variable Nat equal atoms
|
||||
variable Rhokbt equal "v_kbt*v_Nat/v_Myvol"
|
||||
variable at2Pa equal 101325
|
||||
variable kcalmol2J equal "4183.9954/(6.022e23)"
|
||||
variable C1 equal "v_kcalmol2J/v_Myvol" # Convert Cb from energy to pressure units
|
||||
variable C2 equal "v_Myvol/v_kbt" # Factor for Cfl terms
|
||||
variable Pa2GPa equal 1e-9
|
||||
|
||||
# Born compute giving <C^b> terms
|
||||
compute born all born/matrix
|
||||
# The six virial stress component to compute <C^fl>
|
||||
compute VIR all pressure NULL virial
|
||||
variable s1 equal "-c_VIR[1]*v_at2Pa"
|
||||
variable s2 equal "-c_VIR[2]*v_at2Pa"
|
||||
variable s3 equal "-c_VIR[3]*v_at2Pa"
|
||||
variable s6 equal "-c_VIR[4]*v_at2Pa"
|
||||
variable s5 equal "-c_VIR[5]*v_at2Pa"
|
||||
variable s4 equal "-c_VIR[6]*v_at2Pa"
|
||||
variable press equal press
|
||||
|
||||
|
||||
# Average of Born term and vector to store stress
|
||||
# for post processing
|
||||
fix CB all ave/time 1 ${nthermo} ${nthermo} c_born[*] ave running file born.out overwrite
|
||||
fix CPR all ave/time 1 1 1 c_VIR[*] file vir.out
|
||||
fix APR all ave/time 1 1 1 v_press ave running
|
||||
fix VEC all vector 1 v_s1 v_s2 v_s3 v_s4 v_s5 v_s6
|
||||
|
||||
thermo ${nthermo}
|
||||
thermo_style custom step temp press f_APR c_born[1] f_CB[1] c_born[12] f_CB[12] c_born[4] f_CB[4]
|
||||
thermo_modify line multi
|
||||
|
||||
fix 1 all nvt temp $T $T 100
|
||||
|
||||
run ${nsteps}
|
||||
|
||||
# Compute vector averages
|
||||
# Note the indice switch.
|
||||
# LAMMPS convention is NOT the Voigt notation.
|
||||
variable aves1 equal "ave(f_VEC[1])"
|
||||
variable aves2 equal "ave(f_VEC[2])"
|
||||
variable aves3 equal "ave(f_VEC[3])"
|
||||
variable aves4 equal "ave(f_VEC[6])"
|
||||
variable aves5 equal "ave(f_VEC[5])"
|
||||
variable aves6 equal "ave(f_VEC[4])"
|
||||
|
||||
# Computing the covariance through the <s_{i}s_{j}>-<s_i><s_j>
|
||||
# is numerically instable. Here we go through the <(s-<s>)^2>
|
||||
# definition.
|
||||
|
||||
# Computing difference relative to average values
|
||||
variable ds1 vector "f_VEC[1]-v_aves1"
|
||||
variable ds2 vector "f_VEC[2]-v_aves2"
|
||||
variable ds3 vector "f_VEC[3]-v_aves3"
|
||||
variable ds4 vector "f_VEC[4]-v_aves4"
|
||||
variable ds5 vector "f_VEC[5]-v_aves5"
|
||||
variable ds6 vector "f_VEC[6]-v_aves6"
|
||||
|
||||
# Squaring and averaging
|
||||
variable dds1 vector "v_ds1*v_ds1"
|
||||
variable dds2 vector "v_ds2*v_ds2"
|
||||
variable dds3 vector "v_ds3*v_ds3"
|
||||
variable vars1 equal "ave(v_dds1)"
|
||||
variable vars2 equal "ave(v_dds2)"
|
||||
variable vars3 equal "ave(v_dds3)"
|
||||
variable C11 equal "v_Pa2GPa*(v_C1*f_CB[1] - v_C2*v_vars1 + 2*v_Rhokbt)"
|
||||
variable C22 equal "v_Pa2GPa*(v_C1*f_CB[2] - v_C2*v_vars2 + 2*v_Rhokbt)"
|
||||
variable C33 equal "v_Pa2GPa*(v_C1*f_CB[3] - v_C2*v_vars3 + 2*v_Rhokbt)"
|
||||
|
||||
variable dds12 vector "v_ds1*v_ds2"
|
||||
variable dds13 vector "v_ds1*v_ds3"
|
||||
variable dds23 vector "v_ds2*v_ds3"
|
||||
variable vars12 equal "ave(v_dds12)"
|
||||
variable vars13 equal "ave(v_dds13)"
|
||||
variable vars23 equal "ave(v_dds23)"
|
||||
variable C12 equal "v_Pa2GPa*(v_C1*f_CB[7] - v_C2*v_vars12)"
|
||||
variable C13 equal "v_Pa2GPa*(v_C1*f_CB[8] - v_C2*v_vars13)"
|
||||
variable C23 equal "v_Pa2GPa*(v_C1*f_CB[12] - v_C2*v_vars23)"
|
||||
|
||||
variable dds4 vector "v_ds4*v_ds4"
|
||||
variable dds5 vector "v_ds5*v_ds5"
|
||||
variable dds6 vector "v_ds6*v_ds6"
|
||||
variable vars4 equal "ave(v_dds4)"
|
||||
variable vars5 equal "ave(v_dds5)"
|
||||
variable vars6 equal "ave(v_dds6)"
|
||||
variable C44 equal "v_Pa2GPa*(v_C1*f_CB[4] - v_C2*v_vars4 + v_Rhokbt)"
|
||||
variable C55 equal "v_Pa2GPa*(v_C1*f_CB[5] - v_C2*v_vars5 + v_Rhokbt)"
|
||||
variable C66 equal "v_Pa2GPa*(v_C1*f_CB[6] - v_C2*v_vars6 + v_Rhokbt)"
|
||||
|
||||
variable aC11 equal "(v_C11 + v_C22 + v_C33)/3."
|
||||
variable aC12 equal "(v_C12 + v_C13 + v_C23)/3."
|
||||
variable aC44 equal "(v_C44 + v_C55 + v_C66)/3."
|
||||
|
||||
print """
|
||||
C11 = ${aC11}
|
||||
C12 = ${aC12}
|
||||
C44 = ${aC44}
|
||||
"""
|
||||
@ -0,0 +1,7 @@
|
||||
# Cij Matrix from post process computation
|
||||
1.22342 0.73647 0.71011 0.01261 0.02465 -0.00395
|
||||
0.73647 1.20115 0.70711 0.00057 0.05854 -0.02630
|
||||
0.71011 0.70711 1.16055 0.00497 0.00524 -0.02587
|
||||
0.01261 0.00057 0.00497 0.45813 -0.00083 -0.00969
|
||||
0.02465 0.05854 0.00524 -0.00083 0.52170 -0.01747
|
||||
-0.00395 -0.02630 -0.02587 -0.00969 -0.01747 0.47064
|
||||
@ -0,0 +1,7 @@
|
||||
# Cij Matrix from post process computation
|
||||
0.04187 0.00000 0.00000 0.00000 0.00000 0.00000
|
||||
0.00000 0.04187 0.00000 0.00000 0.00000 0.00000
|
||||
0.00000 0.00000 0.04187 0.00000 0.00000 0.00000
|
||||
0.00000 0.00000 0.00000 0.02093 0.00000 0.00000
|
||||
0.00000 0.00000 0.00000 0.00000 0.02093 0.00000
|
||||
0.00000 0.00000 0.00000 0.00000 0.00000 0.02093
|
||||
@ -0,0 +1,7 @@
|
||||
# Cij Matrix from post process computation
|
||||
3.35855 1.86892 1.87139 0.00233 0.00218 -0.00179
|
||||
1.86892 3.37104 1.87285 0.00112 0.00085 -0.00007
|
||||
1.87139 1.87285 3.37707 -0.00058 0.00038 -0.00057
|
||||
0.00233 0.00112 -0.00058 1.88326 -0.00039 0.00065
|
||||
0.00218 0.00085 0.00038 -0.00039 1.88229 0.00242
|
||||
-0.00179 -0.00007 -0.00057 0.00065 0.00242 1.87968
|
||||
118
examples/ELASTIC_T/BORN_MATRIX/Argon/Numdiff/compute_born.py
Normal file
118
examples/ELASTIC_T/BORN_MATRIX/Argon/Numdiff/compute_born.py
Normal file
@ -0,0 +1,118 @@
|
||||
#!/usr/bin/env python3
|
||||
# -*- coding: utf-8 -*-
|
||||
|
||||
import sys
|
||||
import numpy as np
|
||||
|
||||
def reduce_Born(Cf):
|
||||
C = np.zeros((6,6), dtype=np.float64)
|
||||
C[0,0] = Cf[0]
|
||||
C[1,1] = Cf[1]
|
||||
C[2,2] = Cf[2]
|
||||
C[3,3] = Cf[3]
|
||||
C[4,4] = Cf[4]
|
||||
C[5,5] = Cf[5]
|
||||
C[0,1] = Cf[6]
|
||||
C[0,2] = Cf[7]
|
||||
C[0,3] = Cf[8]
|
||||
C[0,4] = Cf[9]
|
||||
C[0,5] = Cf[10]
|
||||
C[1,2] = Cf[11]
|
||||
C[1,3] = Cf[12]
|
||||
C[1,4] = Cf[13]
|
||||
C[1,5] = Cf[14]
|
||||
C[2,3] = Cf[15]
|
||||
C[2,4] = Cf[16]
|
||||
C[2,5] = Cf[17]
|
||||
C[3,4] = Cf[18]
|
||||
C[3,5] = Cf[19]
|
||||
C[4,5] = Cf[20]
|
||||
C = np.where(C,C,C.T)
|
||||
return C
|
||||
|
||||
def compute_delta():
|
||||
D = np.zeros((3,3,3,3))
|
||||
for a in range(3):
|
||||
for b in range(3):
|
||||
for m in range(3):
|
||||
for n in range(3):
|
||||
D[a,b,m,n] = (a==m)*(b==n) + (a==n)*(b==m)
|
||||
d = np.zeros((6,6))
|
||||
d[0,0] = D[0,0,0,0]
|
||||
d[1,1] = D[1,1,1,1]
|
||||
d[2,2] = D[2,2,2,2]
|
||||
d[3,3] = D[1,2,1,2]
|
||||
d[4,4] = D[0,2,0,2]
|
||||
d[5,5] = D[0,1,0,1]
|
||||
d[0,1] = D[0,0,1,1]
|
||||
d[0,2] = D[0,0,2,2]
|
||||
d[0,3] = D[0,0,1,2]
|
||||
d[0,4] = D[0,0,0,2]
|
||||
d[0,5] = D[0,0,0,1]
|
||||
d[1,2] = D[1,1,2,2]
|
||||
d[1,3] = D[1,1,1,2]
|
||||
d[1,4] = D[1,1,0,2]
|
||||
d[1,5] = D[1,1,0,1]
|
||||
d[2,3] = D[2,2,1,2]
|
||||
d[2,4] = D[2,2,0,2]
|
||||
d[2,5] = D[2,2,0,1]
|
||||
d[3,4] = D[1,2,0,2]
|
||||
d[3,5] = D[1,2,0,1]
|
||||
d[4,5] = D[0,2,0,1]
|
||||
d = np.where(d,d,d.T)
|
||||
return d
|
||||
|
||||
|
||||
def write_matrix(C, filename):
|
||||
with open(filename, 'w') as f:
|
||||
f.write("# Cij Matrix from post process computation\n")
|
||||
for i in C:
|
||||
f.write("{:8.5f} {:8.5f} {:8.5f} {:8.5f} {:8.5f} {:8.5f}\n".format(
|
||||
i[0]*10**-9, i[1]*10**-9, i[2]*10**-9, i[3]*10**-9, i[4]*10**-9, i[5]*10**-9,
|
||||
)
|
||||
)
|
||||
return
|
||||
|
||||
def main():
|
||||
|
||||
N = 500
|
||||
vol = 27.047271**3 * 10**-30 # m^3
|
||||
T = 60 # K
|
||||
kb = 1.380649 * 10**-23 # J/K
|
||||
kbT = T*kb # J
|
||||
kcalmol2J = 4183.9954/(6.022*10**23)
|
||||
|
||||
born = np.loadtxt('born.out')
|
||||
stre = np.loadtxt('vir.out')
|
||||
stre[:, 1:] = -stre[:, 1:]*101325 # -> Pa
|
||||
try:
|
||||
mean_born = np.mean(born[:, 1:], axis=0)
|
||||
except IndexError:
|
||||
mean_born = born[1:]
|
||||
|
||||
CB = kcalmol2J/vol*reduce_Born(mean_born) # -> J/m^3=Pa
|
||||
Cs = vol/kbT*np.cov(stre[:,1:].T)
|
||||
Ct = N*kbT/vol * compute_delta()
|
||||
C = CB - Cs + Ct
|
||||
write_matrix(CB, 'born_matrix.out')
|
||||
write_matrix(Cs, 'stre_matrix.out')
|
||||
write_matrix(Ct, 'temp_matrix.out')
|
||||
write_matrix(C, 'full_matrix.out')
|
||||
C11 = np.mean([C[0,0], C[1,1], C[2,2]]) * 10**-9
|
||||
C12 = np.mean([C[0,1], C[0,2], C[1,2]]) * 10**-9
|
||||
C44 = np.mean([C[3,3], C[4,4], C[5,5]]) * 10**-9
|
||||
eC11 = np.std([C[0,0], C[1,1], C[2,2]]) * 10**-9
|
||||
eC12 = np.std([C[0,1], C[0,2], C[1,2]]) * 10**-9
|
||||
eC44 = np.std([C[3,3], C[4,4], C[5,5]]) * 10**-9
|
||||
print(C*10**-9)
|
||||
print("C11 = {:f} ± {:f}; C12 = {:f} ± {:f}; C44 = {:f} ± {:f}".format(C11, eC11, C12, eC12, C44, eC44))
|
||||
|
||||
return
|
||||
|
||||
|
||||
if __name__ == "__main__":
|
||||
try:
|
||||
main()
|
||||
except KeyboardInterrupt:
|
||||
raise SystemExit("User interruption.")
|
||||
|
||||
@ -0,0 +1,7 @@
|
||||
# Cij Matrix from post process computation
|
||||
2.29922 1.17439 1.20854 -0.01653 -0.01684 0.01188
|
||||
1.17439 2.20673 1.21718 -0.00781 -0.00753 0.00867
|
||||
1.20854 1.21718 2.30804 0.01535 -0.01596 0.00426
|
||||
-0.01653 -0.00781 0.01535 1.47647 -0.01355 -0.01601
|
||||
-0.01684 -0.00753 -0.01596 -0.01355 1.37905 0.01975
|
||||
0.01188 0.00867 0.00426 -0.01601 0.01975 1.40170
|
||||
154
examples/ELASTIC_T/BORN_MATRIX/Argon/Numdiff/in.ljcov
Normal file
154
examples/ELASTIC_T/BORN_MATRIX/Argon/Numdiff/in.ljcov
Normal file
@ -0,0 +1,154 @@
|
||||
# Numerical difference calculation
|
||||
# of Born matrix
|
||||
|
||||
# Note that because of cubic symmetry and central forces, we have:
|
||||
# C11, pure axial == positive mean value: 1,2,3
|
||||
# C44==C23, pure shear == positive mean value, exactly match in pairs: (4,12),(5,8),(6,7)
|
||||
# C14==C56, shear/axial(normal) == zero mean, exactly match in pairs: (9,21),(14,20),(18,19)
|
||||
# C15, shear/axial(in-plane) == zero mean: 10,11,13,15,16,17
|
||||
|
||||
# adjustable parameters
|
||||
|
||||
units real
|
||||
variable nsteps index 100000 # length of run
|
||||
variable nthermo index 1000 # thermo output interval
|
||||
variable nlat equal 5 # size of box
|
||||
variable T equal 60. # Temperature in K
|
||||
variable rho equal 5.405 # Lattice spacing in A
|
||||
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc ${rho}
|
||||
region box block 0 ${nlat} 0 ${nlat} 0 ${nlat}
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
|
||||
mass * 39.948
|
||||
|
||||
velocity all create ${T} 87287 loop geom
|
||||
velocity all zero linear
|
||||
|
||||
pair_style lj/cut 12.0
|
||||
pair_coeff 1 1 0.238067 3.405
|
||||
|
||||
neighbor 0.0 bin
|
||||
neigh_modify every 1 delay 0 check no
|
||||
|
||||
variable vol equal vol
|
||||
thermo 100
|
||||
fix aL all ave/time 1 1 1 v_vol ave running
|
||||
fix NPT all npt temp $T $T 100 aniso 1. 1. 1000 fixedpoint 0. 0. 0.
|
||||
|
||||
run 20000
|
||||
|
||||
unfix NPT
|
||||
|
||||
variable newL equal "f_aL^(1./3.)"
|
||||
change_box all x final 0 ${newL} y final 0. ${newL} z final 0. ${newL} remap units box
|
||||
|
||||
unfix aL
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
# Conversion variables
|
||||
variable kb equal 1.38065e-23 # J/K
|
||||
variable Myvol equal "vol*10^-30" # Volume in m^3
|
||||
variable kbt equal "v_kb*v_T"
|
||||
variable Nat equal atoms
|
||||
variable Rhokbt equal "v_kbt*v_Nat/v_Myvol"
|
||||
variable at2Pa equal 101325
|
||||
variable kcalmol2J equal "4183.9954/(6.022e23)"
|
||||
variable C1 equal "v_kcalmol2J/v_Myvol" # Convert Cb from energy to pressure units
|
||||
variable C2 equal "v_Myvol/v_kbt" # Factor for Cfl terms
|
||||
variable Pa2GPa equal 1e-9
|
||||
|
||||
# Born compute giving <C^b> terms
|
||||
# The six virial stress component to compute <C^fl>
|
||||
compute VIR all pressure NULL virial
|
||||
compute born all born/matrix numdiff 1e-6 VIR
|
||||
variable s1 equal "-c_VIR[1]*v_at2Pa"
|
||||
variable s2 equal "-c_VIR[2]*v_at2Pa"
|
||||
variable s3 equal "-c_VIR[3]*v_at2Pa"
|
||||
variable s6 equal "-c_VIR[4]*v_at2Pa"
|
||||
variable s5 equal "-c_VIR[5]*v_at2Pa"
|
||||
variable s4 equal "-c_VIR[6]*v_at2Pa"
|
||||
variable press equal press
|
||||
|
||||
|
||||
# Average of Born term and vector to store stress
|
||||
# for post processing
|
||||
fix CB all ave/time 1 ${nthermo} ${nthermo} c_born[*] ave running file born.out overwrite
|
||||
fix CPR all ave/time 1 1 1 c_VIR[*] file vir.out
|
||||
fix APR all ave/time 1 1 1 v_press ave running
|
||||
fix VEC all vector 1 v_s1 v_s2 v_s3 v_s4 v_s5 v_s6
|
||||
|
||||
thermo ${nthermo}
|
||||
thermo_style custom step temp press f_APR c_born[1] f_CB[1] c_born[12] f_CB[12] c_born[4] f_CB[4]
|
||||
thermo_modify line multi
|
||||
|
||||
fix 1 all nvt temp $T $T 100
|
||||
|
||||
run ${nsteps}
|
||||
|
||||
# Compute vector averages
|
||||
# Note the indice switch.
|
||||
# LAMMPS convention is NOT the Voigt notation.
|
||||
variable aves1 equal "ave(f_VEC[1])"
|
||||
variable aves2 equal "ave(f_VEC[2])"
|
||||
variable aves3 equal "ave(f_VEC[3])"
|
||||
variable aves4 equal "ave(f_VEC[6])"
|
||||
variable aves5 equal "ave(f_VEC[5])"
|
||||
variable aves6 equal "ave(f_VEC[4])"
|
||||
|
||||
# Computing the covariance through the <s_{i}s_{j}>-<s_i><s_j>
|
||||
# is numerically instable. Here we go through the <(s-<s>)^2>
|
||||
# definition.
|
||||
|
||||
# Computing difference relative to average values
|
||||
variable ds1 vector "f_VEC[1]-v_aves1"
|
||||
variable ds2 vector "f_VEC[2]-v_aves2"
|
||||
variable ds3 vector "f_VEC[3]-v_aves3"
|
||||
variable ds4 vector "f_VEC[4]-v_aves4"
|
||||
variable ds5 vector "f_VEC[5]-v_aves5"
|
||||
variable ds6 vector "f_VEC[6]-v_aves6"
|
||||
|
||||
# Squaring and averaging
|
||||
variable dds1 vector "v_ds1*v_ds1"
|
||||
variable dds2 vector "v_ds2*v_ds2"
|
||||
variable dds3 vector "v_ds3*v_ds3"
|
||||
variable vars1 equal "ave(v_dds1)"
|
||||
variable vars2 equal "ave(v_dds2)"
|
||||
variable vars3 equal "ave(v_dds3)"
|
||||
variable C11 equal "v_Pa2GPa*(v_C1*f_CB[1] - v_C2*v_vars1 + 2*v_Rhokbt)"
|
||||
variable C22 equal "v_Pa2GPa*(v_C1*f_CB[2] - v_C2*v_vars2 + 2*v_Rhokbt)"
|
||||
variable C33 equal "v_Pa2GPa*(v_C1*f_CB[3] - v_C2*v_vars3 + 2*v_Rhokbt)"
|
||||
|
||||
variable dds12 vector "v_ds1*v_ds2"
|
||||
variable dds13 vector "v_ds1*v_ds3"
|
||||
variable dds23 vector "v_ds2*v_ds3"
|
||||
variable vars12 equal "ave(v_dds12)"
|
||||
variable vars13 equal "ave(v_dds13)"
|
||||
variable vars23 equal "ave(v_dds23)"
|
||||
variable C12 equal "v_Pa2GPa*(v_C1*f_CB[7] - v_C2*v_vars12)"
|
||||
variable C13 equal "v_Pa2GPa*(v_C1*f_CB[8] - v_C2*v_vars13)"
|
||||
variable C23 equal "v_Pa2GPa*(v_C1*f_CB[12] - v_C2*v_vars23)"
|
||||
|
||||
variable dds4 vector "v_ds4*v_ds4"
|
||||
variable dds5 vector "v_ds5*v_ds5"
|
||||
variable dds6 vector "v_ds6*v_ds6"
|
||||
variable vars4 equal "ave(v_dds4)"
|
||||
variable vars5 equal "ave(v_dds5)"
|
||||
variable vars6 equal "ave(v_dds6)"
|
||||
variable C44 equal "v_Pa2GPa*(v_C1*f_CB[4] - v_C2*v_vars4 + v_Rhokbt)"
|
||||
variable C55 equal "v_Pa2GPa*(v_C1*f_CB[5] - v_C2*v_vars5 + v_Rhokbt)"
|
||||
variable C66 equal "v_Pa2GPa*(v_C1*f_CB[6] - v_C2*v_vars6 + v_Rhokbt)"
|
||||
|
||||
variable aC11 equal "(v_C11 + v_C22 + v_C33)/3."
|
||||
variable aC12 equal "(v_C12 + v_C13 + v_C23)/3."
|
||||
variable aC44 equal "(v_C44 + v_C55 + v_C66)/3."
|
||||
|
||||
print """
|
||||
C11 = ${aC11}
|
||||
C12 = ${aC12}
|
||||
C44 = ${aC44}
|
||||
"""
|
||||
@ -0,0 +1,7 @@
|
||||
# Cij Matrix from post process computation
|
||||
1.10120 0.69454 0.66285 0.01885 0.01902 -0.01367
|
||||
0.69454 1.20617 0.65567 0.00893 0.00839 -0.00873
|
||||
0.66285 0.65567 1.11090 -0.01593 0.01634 -0.00483
|
||||
0.01885 0.00893 -0.01593 0.42772 0.01316 0.01666
|
||||
0.01902 0.00839 0.01634 0.01316 0.52416 -0.01733
|
||||
-0.01367 -0.00873 -0.00483 0.01666 -0.01733 0.49891
|
||||
@ -0,0 +1,7 @@
|
||||
# Cij Matrix from post process computation
|
||||
0.04187 0.00000 0.00000 0.00000 0.00000 0.00000
|
||||
0.00000 0.04187 0.00000 0.00000 0.00000 0.00000
|
||||
0.00000 0.00000 0.04187 0.00000 0.00000 0.00000
|
||||
0.00000 0.00000 0.00000 0.02093 0.00000 0.00000
|
||||
0.00000 0.00000 0.00000 0.00000 0.02093 0.00000
|
||||
0.00000 0.00000 0.00000 0.00000 0.00000 0.02093
|
||||
13
examples/ELASTIC_T/BORN_MATRIX/Argon/README.md
Normal file
13
examples/ELASTIC_T/BORN_MATRIX/Argon/README.md
Normal file
@ -0,0 +1,13 @@
|
||||
This repository is a test case for the compute born/matrix. It provides short
|
||||
scripts creating argon fcc crystal and computing the Born term using the two
|
||||
methods described in the documentation.
|
||||
|
||||
In the __Analytical__ directory the terms are computed using the analytical
|
||||
derivation of the Born term for the lj/cut pair style.
|
||||
|
||||
In the __Numdiff__ directory, the Born term is evaluated through small
|
||||
numerical differences of the stress tensor. This method can be used with any
|
||||
interaction potential.
|
||||
|
||||
Both script show examples on how to compute the full Cij elastic stiffness
|
||||
tensor in LAMMPS.
|
||||
37
examples/ELASTIC_T/BORN_MATRIX/Silicon/README
Normal file
37
examples/ELASTIC_T/BORN_MATRIX/Silicon/README
Normal file
@ -0,0 +1,37 @@
|
||||
This directory shows how to use the `fix born` command
|
||||
to calculate the full matrix of elastic constants
|
||||
for cubic diamond at finite temperature
|
||||
running the Stillinger-Weber potential.
|
||||
|
||||
The input script `in.elastic` can be run
|
||||
directly from LAMMPS, or via a Python wrapper
|
||||
script.
|
||||
|
||||
to run directly from LAMMPS, use:
|
||||
|
||||
mpirun -np 4 lmp.exe -in in.elastic
|
||||
|
||||
This simulates an orthorhombic box with the cubic crystal axes
|
||||
aligned with x, y, and z.
|
||||
The default settings replicate the 1477~K benchmark of
|
||||
Kluge, Ray, and Rahman (1986) that is Ref.[15] in:
|
||||
Y. Zhen, C. Chu, Computer Physics Communications 183(2012) 261-265
|
||||
|
||||
The script contains many adjustable parameters that can be used
|
||||
to generate different crystal structures, supercell sizes,
|
||||
and sampling rates.
|
||||
|
||||
to run via the Python wrapper, use:
|
||||
|
||||
mpirun -np 4 python elastic.py
|
||||
|
||||
This will first run the orthorhombic supercell as before,
|
||||
follows by an equivalent simulation using a triclinic structure.
|
||||
The script shows how the standard triclinic primitive cell for cubic diamond
|
||||
can be rotated in to the LAMMPS upper triangular frame. The resultant
|
||||
elastic constant matrix does not exhibit the standard symmetries of cubic crystals.
|
||||
However, the matrix is then rotated back to the standard orientation
|
||||
to recover the cubic symmetry form of the elastic matrix,
|
||||
resulting in elastic constants that are the same for both
|
||||
simulations, modulo statistical uncertainty.
|
||||
|
||||
1
examples/ELASTIC_T/BORN_MATRIX/Silicon/Si.sw
Symbolic link
1
examples/ELASTIC_T/BORN_MATRIX/Silicon/Si.sw
Symbolic link
@ -0,0 +1 @@
|
||||
../../../../potentials/Si.sw
|
||||
114
examples/ELASTIC_T/BORN_MATRIX/Silicon/elastic.py
Executable file
114
examples/ELASTIC_T/BORN_MATRIX/Silicon/elastic.py
Executable file
@ -0,0 +1,114 @@
|
||||
#!/usr/bin/env python -i
|
||||
# preceding line should have path for Python on your machine
|
||||
|
||||
# elastic.py
|
||||
# Purpose: demonstrate elastic constant calculation for
|
||||
# two different crystal supercells, one with non-standard orientation
|
||||
#
|
||||
# Syntax: elastic.py
|
||||
# uses in.elastic as LAMMPS input script
|
||||
|
||||
from __future__ import print_function
|
||||
from elastic_utils import *
|
||||
|
||||
np.set_printoptions(precision = 3, suppress=True)
|
||||
|
||||
# get MPI settings from LAMMPS
|
||||
|
||||
lmp = lammps()
|
||||
me = lmp.extract_setting("world_rank")
|
||||
nprocs = lmp.extract_setting("world_size")
|
||||
|
||||
# cubic diamond lattice constants
|
||||
|
||||
alat = 5.457
|
||||
|
||||
# define the cubic diamond orthorhombic supercell
|
||||
# with 8 atoms
|
||||
|
||||
basisstring = ""
|
||||
origin = np.zeros(3)
|
||||
bond = np.ones(3)*0.25
|
||||
b = origin
|
||||
basisstring += "basis %g %g %g " % (b[0],b[1],b[2])
|
||||
b = bond
|
||||
basisstring += "basis %g %g %g " % (b[0],b[1],b[2])
|
||||
|
||||
for i in range(3):
|
||||
b = 2*bond
|
||||
b[i] = 0
|
||||
basisstring += "basis %g %g %g " % (b[0],b[1],b[2])
|
||||
b += bond
|
||||
basisstring += "basis %g %g %g " % (b[0],b[1],b[2])
|
||||
|
||||
hmat = np.eye(3)
|
||||
|
||||
varlist = {
|
||||
"logsuffix":"ortho",
|
||||
"a":alat,
|
||||
"a1x":hmat[0,0],
|
||||
"a2x":hmat[0,1],
|
||||
"a2y":hmat[1,1],
|
||||
"a3x":hmat[0,2],
|
||||
"a3y":hmat[1,2],
|
||||
"a3z":hmat[2,2],
|
||||
"l":alat,
|
||||
"basis":basisstring,
|
||||
"nlat":3,
|
||||
}
|
||||
|
||||
cmdargs = gen_varargs(varlist)
|
||||
cij_ortho = calculate_cij(cmdargs)
|
||||
|
||||
# define the cubic diamond triclinic primitive cell
|
||||
# with 2 atoms
|
||||
|
||||
basisstring = ""
|
||||
origin = np.zeros(3)
|
||||
bond = np.ones(3)*0.25
|
||||
b = origin
|
||||
basisstring += "basis %g %g %g " % (b[0],b[1],b[2])
|
||||
b = bond
|
||||
basisstring += "basis %g %g %g " % (b[0],b[1],b[2])
|
||||
|
||||
hmat1 = np.array([[1, 1, 0], [0, 1, 1], [1, 0, 1]]).T/np.sqrt(2)
|
||||
|
||||
# rotate primitive cell to LAMMPS orientation
|
||||
# (upper triangular)
|
||||
|
||||
qmat, rmat = np.linalg.qr(hmat1)
|
||||
ss = np.diagflat(np.sign(np.diag(rmat)))
|
||||
rot = ss @ qmat.T
|
||||
hmat2 = ss @ rmat
|
||||
|
||||
varlist = {
|
||||
"logsuffix":"tri",
|
||||
"a":alat,
|
||||
"a1x":hmat2[0,0],
|
||||
"a2x":hmat2[0,1],
|
||||
"a2y":hmat2[1,1],
|
||||
"a3x":hmat2[0,2],
|
||||
"a3y":hmat2[1,2],
|
||||
"a3z":hmat2[2,2],
|
||||
"l":alat/2**0.5,
|
||||
"basis":basisstring,
|
||||
"nlat":5,
|
||||
}
|
||||
|
||||
cmdargs = gen_varargs(varlist)
|
||||
cij_tri = calculate_cij(cmdargs)
|
||||
|
||||
if me == 0:
|
||||
print("\nPython output:")
|
||||
print("C_ortho = \n",cij_ortho)
|
||||
print()
|
||||
print("C_tri = \n",cij_tri)
|
||||
print()
|
||||
|
||||
cij_tri_rot = rotate_cij(cij_tri, rot.T)
|
||||
|
||||
print("C_tri(rotated back) = \n",cij_tri_rot)
|
||||
print()
|
||||
|
||||
print("C_ortho-C_tri = \n", cij_ortho-cij_tri_rot)
|
||||
print()
|
||||
110
examples/ELASTIC_T/BORN_MATRIX/Silicon/elastic_utils.py
Normal file
110
examples/ELASTIC_T/BORN_MATRIX/Silicon/elastic_utils.py
Normal file
@ -0,0 +1,110 @@
|
||||
import numpy as np
|
||||
from lammps import lammps, LAMMPS_INT, LMP_STYLE_GLOBAL, LMP_VAR_EQUAL, LMP_VAR_ATOM
|
||||
|
||||
# method for rotating elastic constants
|
||||
|
||||
def rotate_cij(cij, r):
|
||||
|
||||
# K_1
|
||||
# R_11^2 R_12^2 R_13^2
|
||||
# R_21^2 R_22^2 R_23^2
|
||||
# R_31^2 R_32^2 R_33^2
|
||||
|
||||
k1 = r*r
|
||||
|
||||
# K_2
|
||||
# R_12.R_13 R_13.R_11 R_11.R_12
|
||||
# R_22.R_23 R_23.R_21 R_21.R_22
|
||||
# R_32.R_33 R_33.R_31 R_31.R_32
|
||||
|
||||
k2 = np.array([
|
||||
[r[0][1]*r[0][2], r[0][2]*r[0][0], r[0][0]*r[0][1]],
|
||||
[r[1][1]*r[1][2], r[1][2]*r[1][0], r[1][0]*r[1][1]],
|
||||
[r[2][1]*r[2][2], r[2][2]*r[2][0], r[2][0]*r[2][1]],
|
||||
])
|
||||
|
||||
# K_3
|
||||
# R_21.R_31 R_22.R_32 R_23.R_33
|
||||
# R_31.R_11 R_32.R_12 R_33.R_13
|
||||
# R_11.R_21 R_12.R_22 R_13.R_23
|
||||
|
||||
k3 = np.array([
|
||||
[r[1][0]*r[2][0], r[1][1]*r[2][1], r[1][2]*r[2][2]],
|
||||
[r[2][0]*r[0][0], r[2][1]*r[0][1], r[2][2]*r[0][2]],
|
||||
[r[0][0]*r[1][0], r[0][1]*r[1][1], r[0][2]*r[1][2]],
|
||||
])
|
||||
|
||||
# K_4a
|
||||
# R_22.R_33 R_23.R_31 R_21.R_32
|
||||
# R_32.R_13 R_33.R_11 R_31.R_12
|
||||
# R_12.R_23 R_13.R_21 R_11.R_22
|
||||
|
||||
k4a = np.array([
|
||||
[r[1][1]*r[2][2], r[1][2]*r[2][0], r[1][0]*r[2][1]],
|
||||
[r[2][1]*r[0][2], r[2][2]*r[0][0], r[2][0]*r[0][1]],
|
||||
[r[0][1]*r[1][2], r[0][2]*r[1][0], r[0][0]*r[1][1]],
|
||||
])
|
||||
|
||||
# K_4b
|
||||
# R_23.R_32 R_21.R_33 R_22.R_31
|
||||
# R_33.R_12 R_31.R_13 R_32.R_11
|
||||
# R_13.R_22 R_11.R_23 R_12.R_21
|
||||
|
||||
k4b = np.array([
|
||||
[r[1][2]*r[2][1], r[1][0]*r[2][2], r[1][1]*r[2][0]],
|
||||
[r[2][2]*r[0][1], r[2][0]*r[0][2], r[2][1]*r[0][0]],
|
||||
[r[0][2]*r[1][1], r[0][0]*r[1][2], r[0][1]*r[1][0]],
|
||||
])
|
||||
|
||||
k = np.block([[k1, 2*k2],[k3, k4a+k4b]])
|
||||
cijrot = k.dot(cij.dot(k.T))
|
||||
return cijrot
|
||||
|
||||
def calculate_cij(cmdargs):
|
||||
lmp = lammps(cmdargs=cmdargs)
|
||||
lmp.file("in.elastic")
|
||||
|
||||
C11 = lmp.extract_variable("C11",None, LMP_VAR_EQUAL)
|
||||
C22 = lmp.extract_variable("C22",None, LMP_VAR_EQUAL)
|
||||
C33 = lmp.extract_variable("C33",None, LMP_VAR_EQUAL)
|
||||
C44 = lmp.extract_variable("C44",None, LMP_VAR_EQUAL)
|
||||
C55 = lmp.extract_variable("C55",None, LMP_VAR_EQUAL)
|
||||
C66 = lmp.extract_variable("C66",None, LMP_VAR_EQUAL)
|
||||
|
||||
C12 = lmp.extract_variable("C12",None, LMP_VAR_EQUAL)
|
||||
C13 = lmp.extract_variable("C13",None, LMP_VAR_EQUAL)
|
||||
C14 = lmp.extract_variable("C14",None, LMP_VAR_EQUAL)
|
||||
C15 = lmp.extract_variable("C15",None, LMP_VAR_EQUAL)
|
||||
C16 = lmp.extract_variable("C16",None, LMP_VAR_EQUAL)
|
||||
|
||||
C23 = lmp.extract_variable("C23",None, LMP_VAR_EQUAL)
|
||||
C24 = lmp.extract_variable("C24",None, LMP_VAR_EQUAL)
|
||||
C25 = lmp.extract_variable("C25",None, LMP_VAR_EQUAL)
|
||||
C26 = lmp.extract_variable("C26",None, LMP_VAR_EQUAL)
|
||||
|
||||
C34 = lmp.extract_variable("C34",None, LMP_VAR_EQUAL)
|
||||
C35 = lmp.extract_variable("C35",None, LMP_VAR_EQUAL)
|
||||
C36 = lmp.extract_variable("C36",None, LMP_VAR_EQUAL)
|
||||
|
||||
C45 = lmp.extract_variable("C45",None, LMP_VAR_EQUAL)
|
||||
C46 = lmp.extract_variable("C46",None, LMP_VAR_EQUAL)
|
||||
|
||||
C56 = lmp.extract_variable("C56",None, LMP_VAR_EQUAL)
|
||||
|
||||
cij = np.array([
|
||||
[C11, C12, C13, C14, C15, C16],
|
||||
[ 0, C22, C23, C24, C25, C26],
|
||||
[ 0, 0, C33, C34, C35, C36],
|
||||
[ 0, 0, 0, C44, C45, C46],
|
||||
[ 0, 0, 0, 0, C55, C56],
|
||||
[ 0, 0, 0, 0, 0, C66],
|
||||
])
|
||||
cij = np.triu(cij) + np.tril(cij.T, -1)
|
||||
|
||||
return cij
|
||||
|
||||
def gen_varargs(varlist):
|
||||
cmdargs = []
|
||||
for key in varlist:
|
||||
cmdargs += ["-var",key,str(varlist[key])]
|
||||
return cmdargs
|
||||
68
examples/ELASTIC_T/BORN_MATRIX/Silicon/final_output.in
Normal file
68
examples/ELASTIC_T/BORN_MATRIX/Silicon/final_output.in
Normal file
@ -0,0 +1,68 @@
|
||||
# Average moduli for cubic crystals
|
||||
|
||||
variable C11cubic equal (${C11}+${C22}+${C33})/3.0
|
||||
variable C12cubic equal (${C12}+${C13}+${C23})/3.0
|
||||
variable C44cubic equal (${C44}+${C55}+${C66})/3.0
|
||||
|
||||
variable bulkmodulus equal (${C11cubic}+2*${C12cubic})/3.0
|
||||
variable shearmodulus1 equal ${C44cubic}
|
||||
variable shearmodulus2 equal (${C11cubic}-${C12cubic})/2.0
|
||||
variable poissonratio equal 1.0/(1.0+${C11cubic}/${C12cubic})
|
||||
|
||||
# For Stillinger-Weber silicon, the analytical results
|
||||
# are known to be (E. R. Cowley, 1988):
|
||||
# C11 = 151.4 GPa
|
||||
# C12 = 76.4 GPa
|
||||
# C44 = 56.4 GPa
|
||||
|
||||
#print "========================================="
|
||||
#print "Components of the Elastic Constant Tensor"
|
||||
#print "========================================="
|
||||
|
||||
print "Elastic Constant C11 = ${C11} ${cunits}"
|
||||
print "Elastic Constant C22 = ${C22} ${cunits}"
|
||||
print "Elastic Constant C33 = ${C33} ${cunits}"
|
||||
|
||||
print "Elastic Constant C12 = ${C12} ${cunits}"
|
||||
print "Elastic Constant C13 = ${C13} ${cunits}"
|
||||
print "Elastic Constant C23 = ${C23} ${cunits}"
|
||||
|
||||
print "Elastic Constant C44 = ${C44} ${cunits}"
|
||||
print "Elastic Constant C55 = ${C55} ${cunits}"
|
||||
print "Elastic Constant C66 = ${C66} ${cunits}"
|
||||
|
||||
print "Elastic Constant C14 = ${C14} ${cunits}"
|
||||
print "Elastic Constant C15 = ${C15} ${cunits}"
|
||||
print "Elastic Constant C16 = ${C16} ${cunits}"
|
||||
|
||||
print "Elastic Constant C24 = ${C24} ${cunits}"
|
||||
print "Elastic Constant C25 = ${C25} ${cunits}"
|
||||
print "Elastic Constant C26 = ${C26} ${cunits}"
|
||||
|
||||
print "Elastic Constant C34 = ${C34} ${cunits}"
|
||||
print "Elastic Constant C35 = ${C35} ${cunits}"
|
||||
print "Elastic Constant C36 = ${C36} ${cunits}"
|
||||
|
||||
print "Elastic Constant C45 = ${C45} ${cunits}"
|
||||
print "Elastic Constant C46 = ${C46} ${cunits}"
|
||||
print "Elastic Constant C56 = ${C56} ${cunits}"
|
||||
|
||||
print "========================================="
|
||||
print "Average properties for a cubic crystal"
|
||||
print "========================================="
|
||||
|
||||
print "Bulk Modulus = ${bulkmodulus} ${cunits}"
|
||||
print "Shear Modulus 1 = ${shearmodulus1} ${cunits}"
|
||||
print "Shear Modulus 2 = ${shearmodulus2} ${cunits}"
|
||||
print "Poisson Ratio = ${poissonratio}"
|
||||
|
||||
# summarize sampling protocol
|
||||
|
||||
variable tmp equal atoms
|
||||
print "Number of atoms = ${tmp}"
|
||||
print "Stress sampling interval = ${nevery}"
|
||||
variable tmp equal ${nrun}/${nevery}
|
||||
print "Stress sample count = ${tmp}"
|
||||
print "Born sampling interval = ${neveryborn}"
|
||||
variable tmp equal ${nrun}/${neveryborn}
|
||||
print "Born sample count = ${tmp}"
|
||||
25
examples/ELASTIC_T/BORN_MATRIX/Silicon/in.elastic
Normal file
25
examples/ELASTIC_T/BORN_MATRIX/Silicon/in.elastic
Normal file
@ -0,0 +1,25 @@
|
||||
# Compute elastic constant tensor for a crystal at finite temperature
|
||||
# These settings replicate the 1477~K benchmark of
|
||||
# Kluge, Ray, and Rahman (1986) that is Ref.[15] in:
|
||||
# Y. Zhen, C. Chu, Computer Physics Communications 183(2012) 261-265
|
||||
|
||||
# here: Y. Zhen, C. Chu, Computer Physics Communications 183(2012) 261-265
|
||||
|
||||
include init.in
|
||||
|
||||
# Compute initial state
|
||||
|
||||
include potential.in
|
||||
thermo_style custom step temp pe press density
|
||||
run ${nequil}
|
||||
|
||||
# Run dynamics
|
||||
|
||||
include potential.in
|
||||
include output.in
|
||||
|
||||
run ${nrun}
|
||||
|
||||
# Output final values
|
||||
|
||||
include final_output.in
|
||||
79
examples/ELASTIC_T/BORN_MATRIX/Silicon/init.in
Normal file
79
examples/ELASTIC_T/BORN_MATRIX/Silicon/init.in
Normal file
@ -0,0 +1,79 @@
|
||||
# NOTE: This script can be modified for different atomic structures,
|
||||
# units, etc. See in.elastic for more info.
|
||||
#
|
||||
# Define MD parameters
|
||||
# These can be modified by the user
|
||||
# These settings replicate the 1477~K benchmark of
|
||||
# Kluge, Ray, and Rahman (1986) that is Ref.[15] in:
|
||||
# Y. Zhen, C. Chu, Computer Physics Communications 183(2012) 261-265
|
||||
|
||||
# set log file
|
||||
|
||||
variable logsuffix index ortho
|
||||
log log.elastic.${logsuffix}
|
||||
|
||||
# select temperature and pressure (lattice constant)
|
||||
|
||||
variable temp index 1477.0 # temperature of initial sample
|
||||
variable a index 5.457 # lattice constant
|
||||
|
||||
# select sampling parameters, important for speed/convergence
|
||||
|
||||
variable nthermo index 1500 # interval for thermo output
|
||||
variable nevery index 10 # stress sampling interval
|
||||
variable neveryborn index 100 # Born sampling interval
|
||||
variable timestep index 0.000766 # timestep
|
||||
variable nlat index 3 # number of lattice unit cells
|
||||
|
||||
# other settings
|
||||
|
||||
variable mass1 index 28.06 # mass
|
||||
variable tdamp index 0.01 # time constant for thermostat
|
||||
variable seed index 123457 # seed for thermostat
|
||||
variable thermostat index 1 # 0 if NVE, 1 if NVT
|
||||
variable delta index 1.0e-6 # Born numdiff strain magnitude
|
||||
|
||||
# hard-coded rules-of-thumb for run length, etc.
|
||||
|
||||
variable nfreq equal ${nthermo} # interval for averaging output
|
||||
variable nrepeat equal floor(${nfreq}/${nevery}) # number of samples
|
||||
variable nrepeatborn equal floor(${nfreq}/${neveryborn}) # number of samples
|
||||
variable nequil equal 10*${nthermo} # length of equilibration run
|
||||
variable nrun equal 100*${nthermo} # length of equilibrated run
|
||||
|
||||
# this generates a general triclinic cell
|
||||
# conforming to LAMMPS cell (upper triangular)
|
||||
|
||||
units metal
|
||||
box tilt large
|
||||
|
||||
# unit lattice vectors are
|
||||
# a1 = (a1x 0 0)
|
||||
# a2 = (a2x a2y 0)
|
||||
# a3 = (a3x a3y a3z)
|
||||
|
||||
variable a1x index 1
|
||||
variable a2x index 0
|
||||
variable a2y index 1
|
||||
variable a3x index 0
|
||||
variable a3y index 0
|
||||
variable a3z index 1
|
||||
variable atmp equal $a
|
||||
variable l index $a
|
||||
variable basis index "basis 0 0 0 basis 0.25 0.25 0.25 basis 0 0.5 0.5 basis 0.25 0.75 0.75 basis 0.5 0 0.5 basis 0.75 0.25 0.75 basis 0.5 0.5 0 basis 0.75 0.75 0.25"
|
||||
lattice custom ${l} &
|
||||
a1 ${a1x} 0 0 &
|
||||
a2 ${a2x} ${a2y} 0 &
|
||||
a3 ${a3x} ${a3y} ${a3z} &
|
||||
${basis} &
|
||||
spacing 1 1 1
|
||||
|
||||
region box prism 0 ${a1x} 0 ${a2y} 0 ${a3z} ${a2x} ${a3x} ${a3y}
|
||||
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass 1 ${mass1}
|
||||
replicate ${nlat} ${nlat} ${nlat}
|
||||
velocity all create ${temp} 87287
|
||||
|
||||
|
||||
662
examples/ELASTIC_T/BORN_MATRIX/Silicon/log.16May22.ortho.g++.4
Normal file
662
examples/ELASTIC_T/BORN_MATRIX/Silicon/log.16May22.ortho.g++.4
Normal file
@ -0,0 +1,662 @@
|
||||
|
||||
# select temperature and pressure (lattice constant)
|
||||
|
||||
variable temp index 1477.0 # temperature of initial sample
|
||||
variable a index 5.457 # lattice constant
|
||||
|
||||
# select sampling parameters, important for speed/convergence
|
||||
|
||||
variable nthermo index 1500 # interval for thermo output
|
||||
variable nevery index 10 # stress sampling interval
|
||||
variable neveryborn index 100 # Born sampling interval
|
||||
variable timestep index 0.000766 # timestep
|
||||
variable nlat index 3 # number of lattice unit cells
|
||||
|
||||
# other settings
|
||||
|
||||
variable mass1 index 28.06 # mass
|
||||
variable tdamp index 0.01 # time constant for thermostat
|
||||
variable seed index 123457 # seed for thermostat
|
||||
variable thermostat index 1 # 0 if NVE, 1 if NVT
|
||||
variable delta index 1.0e-6 # Born numdiff strain magnitude
|
||||
|
||||
# hard-coded rules-of-thumb for run length, etc.
|
||||
|
||||
variable nfreq equal ${nthermo} # interval for averaging output
|
||||
variable nfreq equal 1500
|
||||
variable nrepeat equal floor(${nfreq}/${nevery}) # number of samples
|
||||
variable nrepeat equal floor(1500/${nevery})
|
||||
variable nrepeat equal floor(1500/10)
|
||||
variable nrepeatborn equal floor(${nfreq}/${neveryborn}) # number of samples
|
||||
variable nrepeatborn equal floor(1500/${neveryborn})
|
||||
variable nrepeatborn equal floor(1500/100)
|
||||
variable nequil equal 10*${nthermo} # length of equilibration run
|
||||
variable nequil equal 10*1500
|
||||
variable nrun equal 100*${nthermo} # length of equilibrated run
|
||||
variable nrun equal 100*1500
|
||||
|
||||
# this generates a general triclinic cell
|
||||
# conforming to LAMMPS cell (upper triangular)
|
||||
|
||||
units metal
|
||||
box tilt large
|
||||
|
||||
# unit lattice vectors are
|
||||
# a1 = (a1x 0 0)
|
||||
# a2 = (a2x a2y 0)
|
||||
# a3 = (a3x a3y a3z)
|
||||
|
||||
variable a1x index 1
|
||||
variable a2x index 0
|
||||
variable a2y index 1
|
||||
variable a3x index 0
|
||||
variable a3y index 0
|
||||
variable a3z index 1
|
||||
variable atmp equal $a
|
||||
variable atmp equal 5.457
|
||||
variable l index $a
|
||||
variable l index 5.457
|
||||
variable basis index "basis 0 0 0 basis 0.25 0.25 0.25 basis 0 0.5 0.5 basis 0.25 0.75 0.75 basis 0.5 0 0.5 basis 0.75 0.25 0.75 basis 0.5 0.5 0 basis 0.75 0.75 0.25"
|
||||
lattice custom ${l} a1 ${a1x} 0 0 a2 ${a2x} ${a2y} 0 a3 ${a3x} ${a3y} ${a3z} ${basis} spacing 1 1 1
|
||||
lattice custom 5.457 a1 ${a1x} 0 0 a2 ${a2x} ${a2y} 0 a3 ${a3x} ${a3y} ${a3z} ${basis} spacing 1 1 1
|
||||
lattice custom 5.457 a1 1.0 0 0 a2 ${a2x} ${a2y} 0 a3 ${a3x} ${a3y} ${a3z} ${basis} spacing 1 1 1
|
||||
lattice custom 5.457 a1 1.0 0 0 a2 0.0 ${a2y} 0 a3 ${a3x} ${a3y} ${a3z} ${basis} spacing 1 1 1
|
||||
lattice custom 5.457 a1 1.0 0 0 a2 0.0 1.0 0 a3 ${a3x} ${a3y} ${a3z} ${basis} spacing 1 1 1
|
||||
lattice custom 5.457 a1 1.0 0 0 a2 0.0 1.0 0 a3 0.0 ${a3y} ${a3z} ${basis} spacing 1 1 1
|
||||
lattice custom 5.457 a1 1.0 0 0 a2 0.0 1.0 0 a3 0.0 0.0 ${a3z} ${basis} spacing 1 1 1
|
||||
lattice custom 5.457 a1 1.0 0 0 a2 0.0 1.0 0 a3 0.0 0.0 1.0 ${basis} spacing 1 1 1
|
||||
lattice custom 5.457 a1 1.0 0 0 a2 0.0 1.0 0 a3 0.0 0.0 1.0 basis 0 0 0 basis 0.25 0.25 0.25 basis 0 0.5 0.5 basis 0.25 0.75 0.75 basis 0.5 0 0.5 basis 0.75 0.25 0.75 basis 0.5 0.5 0 basis 0.75 0.75 0.25 spacing 1 1 1
|
||||
Lattice spacing in x,y,z = 5.457 5.457 5.457
|
||||
|
||||
region box prism 0 ${a1x} 0 ${a2y} 0 ${a3z} ${a2x} ${a3x} ${a3y}
|
||||
region box prism 0 1.0 0 ${a2y} 0 ${a3z} ${a2x} ${a3x} ${a3y}
|
||||
region box prism 0 1.0 0 1.0 0 ${a3z} ${a2x} ${a3x} ${a3y}
|
||||
region box prism 0 1.0 0 1.0 0 1.0 ${a2x} ${a3x} ${a3y}
|
||||
region box prism 0 1.0 0 1.0 0 1.0 0.0 ${a3x} ${a3y}
|
||||
region box prism 0 1.0 0 1.0 0 1.0 0.0 0.0 ${a3y}
|
||||
region box prism 0 1.0 0 1.0 0 1.0 0.0 0.0 0.0
|
||||
|
||||
create_box 1 box
|
||||
Created triclinic box = (0 0 0) to (5.457 5.457 5.457) with tilt (0 0 0)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 8 atoms
|
||||
using lattice units in triclinic box = (0 0 0) to (5.457 5.457 5.457) with tilt (0 0 0)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
mass 1 ${mass1}
|
||||
mass 1 28.06
|
||||
replicate ${nlat} ${nlat} ${nlat}
|
||||
replicate 3 ${nlat} ${nlat}
|
||||
replicate 3 3 ${nlat}
|
||||
replicate 3 3 3
|
||||
Replicating atoms ...
|
||||
triclinic box = (0 0 0) to (16.371 16.371 16.371) with tilt (0 0 0)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
216 atoms
|
||||
replicate CPU = 0.001 seconds
|
||||
velocity all create ${temp} 87287
|
||||
velocity all create 1477.0 87287
|
||||
|
||||
|
||||
|
||||
# Compute initial state
|
||||
|
||||
include potential.in
|
||||
# NOTE: This script can be modified for different pair styles
|
||||
# See in.elastic for more info.
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
# Choose potential
|
||||
pair_style sw
|
||||
pair_coeff * * Si.sw Si
|
||||
Reading sw potential file Si.sw with DATE: 2007-06-11
|
||||
|
||||
# Setup neighbor style
|
||||
neighbor 1.0 nsq
|
||||
neigh_modify once no every 1 delay 0 check yes
|
||||
|
||||
# Setup MD
|
||||
|
||||
timestep ${timestep}
|
||||
timestep 0.000766
|
||||
fix 4 all nve
|
||||
if "${thermostat} == 1" then "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
|
||||
fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}
|
||||
fix 5 all langevin 1477.0 ${temp} ${tdamp} ${seed}
|
||||
fix 5 all langevin 1477.0 1477.0 ${tdamp} ${seed}
|
||||
fix 5 all langevin 1477.0 1477.0 0.01 ${seed}
|
||||
fix 5 all langevin 1477.0 1477.0 0.01 123457
|
||||
|
||||
|
||||
thermo_style custom step temp pe press density
|
||||
run ${nequil}
|
||||
run 15000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.77118
|
||||
ghost atom cutoff = 4.77118
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair sw, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/nsq
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.053 | 3.053 | 3.053 Mbytes
|
||||
Step Temp PotEng Press Density
|
||||
0 1477 -936.42473 -4264.7155 2.2938491
|
||||
15000 1409.2705 -887.74266 -595.80958 2.2938491
|
||||
Loop time of 1.46866 on 4 procs for 15000 steps with 216 atoms
|
||||
|
||||
Performance: 675.949 ns/day, 0.036 hours/ns, 10213.420 timesteps/s
|
||||
99.9% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.1178 | 1.1422 | 1.167 | 1.8 | 77.77
|
||||
Neigh | 0.015423 | 0.015665 | 0.015835 | 0.1 | 1.07
|
||||
Comm | 0.24267 | 0.26778 | 0.2925 | 3.8 | 18.23
|
||||
Output | 1.2863e-05 | 1.4971e-05 | 2.0888e-05 | 0.0 | 0.00
|
||||
Modify | 0.019642 | 0.020192 | 0.020638 | 0.3 | 1.37
|
||||
Other | | 0.02277 | | | 1.55
|
||||
|
||||
Nlocal: 54 ave 56 max 50 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||
Nghost: 353 ave 357 max 351 min
|
||||
Histogram: 2 0 0 1 0 0 0 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 1423.5 ave 1487 max 1324 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 0 2
|
||||
|
||||
Total # of neighbors = 5694
|
||||
Ave neighs/atom = 26.361111
|
||||
Neighbor list builds = 251
|
||||
Dangerous builds = 0
|
||||
|
||||
# Run dynamics
|
||||
|
||||
include potential.in
|
||||
# NOTE: This script can be modified for different pair styles
|
||||
# See in.elastic for more info.
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
# Choose potential
|
||||
pair_style sw
|
||||
pair_coeff * * Si.sw Si
|
||||
Reading sw potential file Si.sw with DATE: 2007-06-11
|
||||
|
||||
# Setup neighbor style
|
||||
neighbor 1.0 nsq
|
||||
neigh_modify once no every 1 delay 0 check yes
|
||||
|
||||
# Setup MD
|
||||
|
||||
timestep ${timestep}
|
||||
timestep 0.000766
|
||||
fix 4 all nve
|
||||
if "${thermostat} == 1" then "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
|
||||
fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}
|
||||
fix 5 all langevin 1477.0 ${temp} ${tdamp} ${seed}
|
||||
fix 5 all langevin 1477.0 1477.0 ${tdamp} ${seed}
|
||||
fix 5 all langevin 1477.0 1477.0 0.01 ${seed}
|
||||
fix 5 all langevin 1477.0 1477.0 0.01 123457
|
||||
|
||||
|
||||
include output.in
|
||||
# Setup output
|
||||
|
||||
# Stress fluctuation term F
|
||||
|
||||
compute stress all pressure thermo_temp
|
||||
variable s1 equal c_stress[1]
|
||||
variable s2 equal c_stress[2]
|
||||
variable s3 equal c_stress[3]
|
||||
variable s4 equal c_stress[6]
|
||||
variable s5 equal c_stress[5]
|
||||
variable s6 equal c_stress[4]
|
||||
|
||||
variable s11 equal v_s1*v_s1
|
||||
variable s22 equal v_s2*v_s2
|
||||
variable s33 equal v_s3*v_s3
|
||||
variable s44 equal v_s4*v_s4
|
||||
variable s55 equal v_s5*v_s5
|
||||
variable s66 equal v_s6*v_s6
|
||||
variable s33 equal v_s3*v_s3
|
||||
variable s12 equal v_s1*v_s2
|
||||
variable s13 equal v_s1*v_s3
|
||||
variable s14 equal v_s1*v_s4
|
||||
variable s15 equal v_s1*v_s5
|
||||
variable s16 equal v_s1*v_s6
|
||||
variable s23 equal v_s2*v_s3
|
||||
variable s24 equal v_s2*v_s4
|
||||
variable s25 equal v_s2*v_s5
|
||||
variable s26 equal v_s2*v_s6
|
||||
variable s34 equal v_s3*v_s4
|
||||
variable s35 equal v_s3*v_s5
|
||||
variable s36 equal v_s3*v_s6
|
||||
variable s45 equal v_s4*v_s5
|
||||
variable s46 equal v_s4*v_s6
|
||||
variable s56 equal v_s5*v_s6
|
||||
|
||||
variable mytemp equal temp
|
||||
variable mypress equal press
|
||||
variable mype equal pe/atoms
|
||||
fix avt all ave/time ${nevery} ${nrepeat} ${nfreq} v_mytemp ave running
|
||||
fix avt all ave/time 10 ${nrepeat} ${nfreq} v_mytemp ave running
|
||||
fix avt all ave/time 10 150 ${nfreq} v_mytemp ave running
|
||||
fix avt all ave/time 10 150 1500 v_mytemp ave running
|
||||
fix avp all ave/time ${nevery} ${nrepeat} ${nfreq} v_mypress ave running
|
||||
fix avp all ave/time 10 ${nrepeat} ${nfreq} v_mypress ave running
|
||||
fix avp all ave/time 10 150 ${nfreq} v_mypress ave running
|
||||
fix avp all ave/time 10 150 1500 v_mypress ave running
|
||||
fix avpe all ave/time ${nevery} ${nrepeat} ${nfreq} v_mype ave running
|
||||
fix avpe all ave/time 10 ${nrepeat} ${nfreq} v_mype ave running
|
||||
fix avpe all ave/time 10 150 ${nfreq} v_mype ave running
|
||||
fix avpe all ave/time 10 150 1500 v_mype ave running
|
||||
fix avs all ave/time ${nevery} ${nrepeat} ${nfreq} v_s1 v_s2 v_s3 v_s4 v_s5 v_s6 ave running
|
||||
fix avs all ave/time 10 ${nrepeat} ${nfreq} v_s1 v_s2 v_s3 v_s4 v_s5 v_s6 ave running
|
||||
fix avs all ave/time 10 150 ${nfreq} v_s1 v_s2 v_s3 v_s4 v_s5 v_s6 ave running
|
||||
fix avs all ave/time 10 150 1500 v_s1 v_s2 v_s3 v_s4 v_s5 v_s6 ave running
|
||||
fix avssq all ave/time ${nevery} ${nrepeat} ${nfreq} v_s11 v_s22 v_s33 v_s44 v_s55 v_s66 v_s12 v_s13 v_s14 v_s15 v_s16 v_s23 v_s24 v_s25 v_s26 v_s34 v_s35 v_s36 v_s45 v_s46 v_s56 ave running
|
||||
fix avssq all ave/time 10 ${nrepeat} ${nfreq} v_s11 v_s22 v_s33 v_s44 v_s55 v_s66 v_s12 v_s13 v_s14 v_s15 v_s16 v_s23 v_s24 v_s25 v_s26 v_s34 v_s35 v_s36 v_s45 v_s46 v_s56 ave running
|
||||
fix avssq all ave/time 10 150 ${nfreq} v_s11 v_s22 v_s33 v_s44 v_s55 v_s66 v_s12 v_s13 v_s14 v_s15 v_s16 v_s23 v_s24 v_s25 v_s26 v_s34 v_s35 v_s36 v_s45 v_s46 v_s56 ave running
|
||||
fix avssq all ave/time 10 150 1500 v_s11 v_s22 v_s33 v_s44 v_s55 v_s66 v_s12 v_s13 v_s14 v_s15 v_s16 v_s23 v_s24 v_s25 v_s26 v_s34 v_s35 v_s36 v_s45 v_s46 v_s56 ave running
|
||||
|
||||
# bar to GPa
|
||||
variable pconv equal 1.0e5/1.0e9
|
||||
variable cunits index GPa
|
||||
# metal unit constants from LAMMPS
|
||||
# force->nktv2p = 1.6021765e6;
|
||||
# force->boltz = 8.617343e-5;
|
||||
variable boltz equal 8.617343e-5
|
||||
variable nktv2p equal 1.6021765e6
|
||||
variable vkt equal vol/(${boltz}*${temp})/${nktv2p}
|
||||
variable vkt equal vol/(8.617343e-05*${temp})/${nktv2p}
|
||||
variable vkt equal vol/(8.617343e-05*1477.0)/${nktv2p}
|
||||
variable vkt equal vol/(8.617343e-05*1477.0)/1602176.5
|
||||
variable ffac equal ${pconv}*${vkt}
|
||||
variable ffac equal 0.0001*${vkt}
|
||||
variable ffac equal 0.0001*0.0215159929384811
|
||||
|
||||
variable F11 equal -(f_avssq[1]-f_avs[1]*f_avs[1])*${ffac}
|
||||
variable F11 equal -(f_avssq[1]-f_avs[1]*f_avs[1])*2.15159929384811e-06
|
||||
variable F22 equal -(f_avssq[2]-f_avs[2]*f_avs[2])*${ffac}
|
||||
variable F22 equal -(f_avssq[2]-f_avs[2]*f_avs[2])*2.15159929384811e-06
|
||||
variable F33 equal -(f_avssq[3]-f_avs[3]*f_avs[3])*${ffac}
|
||||
variable F33 equal -(f_avssq[3]-f_avs[3]*f_avs[3])*2.15159929384811e-06
|
||||
variable F44 equal -(f_avssq[4]-f_avs[4]*f_avs[4])*${ffac}
|
||||
variable F44 equal -(f_avssq[4]-f_avs[4]*f_avs[4])*2.15159929384811e-06
|
||||
variable F55 equal -(f_avssq[5]-f_avs[5]*f_avs[5])*${ffac}
|
||||
variable F55 equal -(f_avssq[5]-f_avs[5]*f_avs[5])*2.15159929384811e-06
|
||||
variable F66 equal -(f_avssq[6]-f_avs[6]*f_avs[6])*${ffac}
|
||||
variable F66 equal -(f_avssq[6]-f_avs[6]*f_avs[6])*2.15159929384811e-06
|
||||
|
||||
variable F12 equal -(f_avssq[7]-f_avs[1]*f_avs[2])*${ffac}
|
||||
variable F12 equal -(f_avssq[7]-f_avs[1]*f_avs[2])*2.15159929384811e-06
|
||||
variable F13 equal -(f_avssq[8]-f_avs[1]*f_avs[3])*${ffac}
|
||||
variable F13 equal -(f_avssq[8]-f_avs[1]*f_avs[3])*2.15159929384811e-06
|
||||
variable F14 equal -(f_avssq[9]-f_avs[1]*f_avs[4])*${ffac}
|
||||
variable F14 equal -(f_avssq[9]-f_avs[1]*f_avs[4])*2.15159929384811e-06
|
||||
variable F15 equal -(f_avssq[10]-f_avs[1]*f_avs[5])*${ffac}
|
||||
variable F15 equal -(f_avssq[10]-f_avs[1]*f_avs[5])*2.15159929384811e-06
|
||||
variable F16 equal -(f_avssq[11]-f_avs[1]*f_avs[6])*${ffac}
|
||||
variable F16 equal -(f_avssq[11]-f_avs[1]*f_avs[6])*2.15159929384811e-06
|
||||
|
||||
variable F23 equal -(f_avssq[12]-f_avs[2]*f_avs[3])*${ffac}
|
||||
variable F23 equal -(f_avssq[12]-f_avs[2]*f_avs[3])*2.15159929384811e-06
|
||||
variable F24 equal -(f_avssq[13]-f_avs[2]*f_avs[4])*${ffac}
|
||||
variable F24 equal -(f_avssq[13]-f_avs[2]*f_avs[4])*2.15159929384811e-06
|
||||
variable F25 equal -(f_avssq[14]-f_avs[2]*f_avs[5])*${ffac}
|
||||
variable F25 equal -(f_avssq[14]-f_avs[2]*f_avs[5])*2.15159929384811e-06
|
||||
variable F26 equal -(f_avssq[15]-f_avs[2]*f_avs[6])*${ffac}
|
||||
variable F26 equal -(f_avssq[15]-f_avs[2]*f_avs[6])*2.15159929384811e-06
|
||||
|
||||
variable F34 equal -(f_avssq[16]-f_avs[3]*f_avs[4])*${ffac}
|
||||
variable F34 equal -(f_avssq[16]-f_avs[3]*f_avs[4])*2.15159929384811e-06
|
||||
variable F35 equal -(f_avssq[17]-f_avs[3]*f_avs[5])*${ffac}
|
||||
variable F35 equal -(f_avssq[17]-f_avs[3]*f_avs[5])*2.15159929384811e-06
|
||||
variable F36 equal -(f_avssq[18]-f_avs[3]*f_avs[6])*${ffac}
|
||||
variable F36 equal -(f_avssq[18]-f_avs[3]*f_avs[6])*2.15159929384811e-06
|
||||
|
||||
variable F45 equal -(f_avssq[19]-f_avs[4]*f_avs[5])*${ffac}
|
||||
variable F45 equal -(f_avssq[19]-f_avs[4]*f_avs[5])*2.15159929384811e-06
|
||||
variable F46 equal -(f_avssq[20]-f_avs[4]*f_avs[6])*${ffac}
|
||||
variable F46 equal -(f_avssq[20]-f_avs[4]*f_avs[6])*2.15159929384811e-06
|
||||
|
||||
variable F56 equal -(f_avssq[21]-f_avs[5]*f_avs[6])*${ffac}
|
||||
variable F56 equal -(f_avssq[21]-f_avs[5]*f_avs[6])*2.15159929384811e-06
|
||||
|
||||
# Born term
|
||||
|
||||
compute virial all pressure NULL virial
|
||||
compute born all born/matrix numdiff ${delta} virial
|
||||
compute born all born/matrix numdiff 1.0e-6 virial
|
||||
fix avborn all ave/time ${neveryborn} ${nrepeatborn} ${nfreq} c_born[*] ave running
|
||||
fix avborn all ave/time 100 ${nrepeatborn} ${nfreq} c_born[*] ave running
|
||||
fix avborn all ave/time 100 15 ${nfreq} c_born[*] ave running
|
||||
fix avborn all ave/time 100 15 1500 c_born[*] ave running
|
||||
|
||||
variable bfac equal ${pconv}*${nktv2p}/vol
|
||||
variable bfac equal 0.0001*${nktv2p}/vol
|
||||
variable bfac equal 0.0001*1602176.5/vol
|
||||
variable B vector f_avborn*${bfac}
|
||||
variable B vector f_avborn*0.036516128938577
|
||||
|
||||
# Kinetic term
|
||||
|
||||
variable kfac equal ${pconv}*${nktv2p}*atoms*${boltz}*${temp}/vol
|
||||
variable kfac equal 0.0001*${nktv2p}*atoms*${boltz}*${temp}/vol
|
||||
variable kfac equal 0.0001*1602176.5*atoms*${boltz}*${temp}/vol
|
||||
variable kfac equal 0.0001*1602176.5*atoms*8.617343e-05*${temp}/vol
|
||||
variable kfac equal 0.0001*1602176.5*atoms*8.617343e-05*1477.0/vol
|
||||
variable K11 equal 4.0*${kfac}
|
||||
variable K11 equal 4.0*1.00390440086865
|
||||
variable K22 equal 4.0*${kfac}
|
||||
variable K22 equal 4.0*1.00390440086865
|
||||
variable K33 equal 4.0*${kfac}
|
||||
variable K33 equal 4.0*1.00390440086865
|
||||
variable K44 equal 2.0*${kfac}
|
||||
variable K44 equal 2.0*1.00390440086865
|
||||
variable K55 equal 2.0*${kfac}
|
||||
variable K55 equal 2.0*1.00390440086865
|
||||
variable K66 equal 2.0*${kfac}
|
||||
variable K66 equal 2.0*1.00390440086865
|
||||
|
||||
# Add F, K, and B together
|
||||
|
||||
variable C11 equal v_F11+v_B[1]+v_K11
|
||||
variable C22 equal v_F22+v_B[2]+v_K22
|
||||
variable C33 equal v_F33+v_B[3]+v_K33
|
||||
variable C44 equal v_F44+v_B[4]+v_K44
|
||||
variable C55 equal v_F55+v_B[5]+v_K55
|
||||
variable C66 equal v_F66+v_B[6]+v_K66
|
||||
|
||||
variable C12 equal v_F12+v_B[7]
|
||||
variable C13 equal v_F13+v_B[8]
|
||||
variable C14 equal v_F14+v_B[9]
|
||||
variable C15 equal v_F15+v_B[10]
|
||||
variable C16 equal v_F16+v_B[11]
|
||||
|
||||
variable C23 equal v_F23+v_B[12]
|
||||
variable C24 equal v_F24+v_B[13]
|
||||
variable C25 equal v_F25+v_B[14]
|
||||
variable C26 equal v_F26+v_B[15]
|
||||
|
||||
variable C34 equal v_F34+v_B[16]
|
||||
variable C35 equal v_F35+v_B[17]
|
||||
variable C36 equal v_F36+v_B[18]
|
||||
|
||||
variable C45 equal v_F45+v_B[19]
|
||||
variable C46 equal v_F46+v_B[20]
|
||||
|
||||
variable C56 equal v_F56+v_B[21]
|
||||
|
||||
thermo ${nthermo}
|
||||
thermo 1500
|
||||
thermo_style custom step temp pe press density f_avt f_avp f_avpe v_F11 v_F22 v_F33 v_F44 v_F55 v_F66 v_F12 v_F13 v_F23 v_B[*8] v_B[12]
|
||||
|
||||
thermo_modify norm no
|
||||
|
||||
run ${nrun}
|
||||
run 150000
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.803 | 3.803 | 3.803 Mbytes
|
||||
Step Temp PotEng Press Density f_avt f_avp f_avpe v_F11 v_F22 v_F33 v_F44 v_F55 v_F66 v_F12 v_F13 v_F23 v_B[1] v_B[2] v_B[3] v_B[4] v_B[5] v_B[6] v_B[7] v_B[8] v_B[12]
|
||||
0 1409.2705 -887.74266 -595.80958 2.2938491 0 0 0 -0 -0 -0 -0 -0 -0 -0 -0 -0 0 0 0 0 0 0 0 0 0
|
||||
1500 1543.955 -894.59564 829.29754 2.2938491 1479.8455 -272.48983 -4.1286994 -9.8546328 -7.6109829 -6.9399455 -42.917041 -50.311599 -54.999307 -2.1718852 -0.37897892 0.021065401 136.52661 136.57057 136.8112 99.817258 99.81304 99.70618 74.718855 74.984867 74.922489
|
||||
3000 1533.4697 -891.05441 1291.5832 2.2938491 1482.4036 -135.16653 -4.130281 -8.5756153 -7.6746515 -7.0427547 -50.764257 -49.209172 -60.778328 -1.3700831 -0.4568356 0.20721573 136.58667 136.70561 136.69409 99.903478 99.76887 99.847801 74.700603 74.769035 74.913031
|
||||
4500 1559.2333 -895.95898 -169.5185 2.2938491 1481.5554 110.86891 -4.1325482 -8.0338125 -7.6953586 -7.3762168 -53.430221 -48.29504 -54.657257 -1.3016296 -1.0260182 -0.045906996 136.84569 136.91821 136.90927 100.0598 99.901964 100.07314 74.813284 74.723978 74.90986
|
||||
6000 1417.6434 -891.85991 84.448937 2.2938491 1480.5364 -26.042555 -4.130823 -8.2176554 -7.6691593 -7.5195046 -54.897719 -45.58593 -53.146497 -1.1159385 -0.4148108 -0.34277881 136.73272 136.74579 136.70656 99.899987 99.788575 99.91922 74.858104 74.751356 74.877807
|
||||
7500 1521.8549 -890.45085 -1986.131 2.2938491 1478.7883 -63.188659 -4.131248 -7.9884217 -7.5621903 -7.6827376 -53.505647 -51.167165 -54.069643 -1.0788226 -0.72907125 -0.40595255 136.65015 136.58541 136.66316 99.849936 99.770641 99.833465 74.762105 74.749673 74.793725
|
||||
9000 1481.1098 -893.58876 -302.11196 2.2938491 1480.8996 -86.706608 -4.1308352 -7.8504102 -7.4016325 -7.7875364 -52.129057 -50.748636 -55.590171 -1.0423024 -1.0411667 -0.42332136 136.61748 136.54744 136.63721 99.806859 99.750078 99.824904 74.793868 74.742871 74.75755
|
||||
10500 1602.1539 -891.59953 -120.50983 2.2938491 1481.8078 -58.72234 -4.1309965 -7.979615 -7.4378227 -7.6187667 -51.499039 -50.360191 -52.483908 -0.79006562 -0.97184735 -0.42288111 136.62376 136.57134 136.65198 99.809774 99.788741 99.818781 74.780283 74.754346 74.752685
|
||||
12000 1419.1584 -891.48511 -357.00507 2.2938491 1482.0565 -52.541967 -4.1307476 -7.8017302 -7.3965439 -7.5326968 -51.907957 -50.643325 -53.453282 -0.84401937 -1.0517326 -0.54021711 136.58968 136.54882 136.65563 99.810907 99.792391 99.770152 74.770444 74.788526 74.767629
|
||||
13500 1349.3981 -893.65888 15.31558 2.2938491 1481.1263 -55.35676 -4.1307105 -7.5797633 -7.3093859 -7.5484467 -52.298219 -49.804373 -54.555982 -0.8242492 -1.0633311 -0.58879705 136.59553 136.58666 136.66121 99.806084 99.807326 99.79773 74.783157 74.799104 74.776677
|
||||
15000 1572.7545 -888.05032 -1167.1259 2.2938491 1481.1845 -44.051939 -4.1307308 -7.4870604 -7.3959358 -7.7984973 -53.846519 -49.850023 -54.449806 -0.80437631 -0.98162577 -0.67631044 136.6089 136.60586 136.63322 99.804941 99.816756 99.807316 74.799246 74.79994 74.774964
|
||||
16500 1476.3559 -894.13606 -141.71585 2.2938491 1481.9977 -57.149347 -4.1305532 -7.3563308 -7.7377027 -7.7801895 -55.418093 -50.432917 -55.092322 -0.75882435 -0.91155917 -0.8012947 136.60588 136.59648 136.64052 99.783788 99.813543 99.811844 74.796195 74.795566 74.759748
|
||||
18000 1385.3464 -894.17196 -453.51135 2.2938491 1482.2841 -41.202526 -4.1305936 -7.4001985 -7.9100844 -7.7977726 -55.828868 -51.190641 -56.146338 -0.80951377 -0.88498405 -0.95870035 136.60877 136.58913 136.64391 99.807809 99.807278 99.804971 74.795414 74.787039 74.770228
|
||||
19500 1459.0464 -891.56293 -583.43289 2.2938491 1481.6087 -80.19681 -4.1305727 -7.503849 -7.832224 -8.0680015 -55.621765 -52.943951 -55.834411 -0.84395931 -0.92355108 -1.0598691 136.57225 136.54527 136.59315 99.781928 99.757893 99.808931 74.802468 74.747248 74.742414
|
||||
21000 1425.7724 -893.96346 -2476.1354 2.2938491 1480.7898 -80.510469 -4.1307098 -7.5517651 -7.7540688 -8.1263923 -55.676836 -51.985142 -57.190698 -0.79979707 -0.82062764 -0.96974038 136.62238 136.56316 136.58301 99.770462 99.774612 99.833221 74.817335 74.767434 74.729171
|
||||
22500 1478.3908 -893.03263 356.73894 2.2938491 1481.8216 -56.608103 -4.1307548 -7.5171851 -7.7473191 -8.1531481 -55.174277 -52.991179 -56.943478 -0.83236889 -0.86233325 -0.84237825 136.63109 136.54755 136.58015 99.768999 99.789091 99.834769 74.805682 74.762367 74.709251
|
||||
24000 1559.2834 -895.0061 408.35518 2.2938491 1481.7034 -50.365601 -4.1310012 -7.4371076 -7.6686437 -8.0973363 -55.391365 -53.957438 -56.758804 -0.75624259 -0.7712068 -0.79151732 136.63369 136.569 136.62933 99.801995 99.811857 99.834171 74.784642 74.764728 74.726548
|
||||
25500 1418.8679 -900.05172 1038.8634 2.2938491 1481.7117 -34.795555 -4.1311417 -7.3525995 -7.6549985 -8.0932453 -55.209186 -54.850159 -56.555154 -0.76945854 -0.80520239 -0.87729866 136.65191 136.56496 136.6234 99.797985 99.83181 99.845733 74.777288 74.761405 74.70467
|
||||
27000 1337.6729 -892.54371 -1223.1078 2.2938491 1481.7999 -6.868253 -4.1314105 -7.4344069 -7.670465 -8.0748588 -55.642919 -54.694351 -56.043818 -0.84229089 -0.85050448 -0.8848331 136.69353 136.58737 136.65353 99.816588 99.854571 99.87065 74.779124 74.767968 74.713918
|
||||
28500 1428.3391 -890.39992 1637.2396 2.2938491 1481.456 -5.7648513 -4.1315226 -7.401319 -7.6104928 -8.0522046 -55.924803 -54.963031 -55.354755 -0.80198132 -0.78513105 -0.89948604 136.66669 136.57056 136.6591 99.824707 99.851902 99.853954 74.769147 74.764532 74.720065
|
||||
30000 1610.749 -892.10736 579.88182 2.2938491 1480.9008 6.256216 -4.1316122 -7.4537451 -7.5486694 -7.9515037 -56.204342 -55.065875 -55.139775 -0.83945753 -0.80897524 -0.84944598 136.67155 136.59361 136.64942 99.830699 99.848762 99.869963 74.777778 74.755753 74.718528
|
||||
31500 1424.0387 -892.82589 -1088.8668 2.2938491 1480.8612 27.560648 -4.1318123 -7.4239872 -7.5434979 -7.8962752 -56.813306 -55.891849 -55.592699 -0.90786211 -0.78634826 -0.89364109 136.67764 136.59992 136.66244 99.844569 99.867062 99.872844 74.758315 74.7448 74.710189
|
||||
33000 1608.6242 -892.4438 2546.9882 2.2938491 1481.6562 47.051547 -4.1316992 -7.4646486 -7.5038235 -7.8961468 -57.865394 -55.375621 -56.027867 -0.8910679 -0.84053561 -0.89582173 136.68768 136.59732 136.67152 99.846034 99.880097 99.867468 74.752249 74.751739 74.710642
|
||||
34500 1459.0403 -892.25499 551.36057 2.2938491 1482.1308 44.660322 -4.1317055 -7.4352078 -7.5237108 -7.8649773 -58.468947 -55.357512 -55.779494 -0.84115908 -0.77476537 -0.87458546 136.66595 136.59551 136.65084 99.839323 99.866733 99.8611 74.741493 74.738738 74.709871
|
||||
36000 1421.5526 -896.28506 -29.316911 2.2938491 1481.789 47.541032 -4.1318408 -7.3733107 -7.5190295 -7.8143454 -57.929804 -55.418333 -55.785571 -0.83611043 -0.73869976 -0.86057781 136.67194 136.61145 136.66484 99.85524 99.874475 99.868689 74.735031 74.73536 74.716839
|
||||
37500 1420.8916 -891.82782 -124.77618 2.2938491 1481.4989 50.677557 -4.1319034 -7.351484 -7.4418106 -7.8130188 -57.428955 -55.290755 -55.728856 -0.79501628 -0.76420281 -0.87517695 136.6581 136.61188 136.65931 99.8659 99.870608 99.861288 74.723088 74.734658 74.717
|
||||
39000 1419.8533 -891.85187 775.65186 2.2938491 1481.3759 61.485208 -4.1320474 -7.3143703 -7.3968445 -7.781877 -57.264431 -55.699481 -55.805103 -0.76748846 -0.78919404 -0.83311458 136.66482 136.61272 136.64292 99.859449 99.871369 99.879933 74.724309 74.716924 74.690243
|
||||
40500 1618.5121 -891.22453 478.34407 2.2938491 1481.7031 51.968148 -4.1319722 -7.2819086 -7.5511556 -7.7257743 -57.306557 -55.743925 -56.312823 -0.83338334 -0.78815013 -0.80988519 136.65567 136.58905 136.64007 99.843268 99.870939 99.865104 74.716829 74.725634 74.69278
|
||||
42000 1532.044 -890.39164 1505.0844 2.2938491 1482.0334 59.439461 -4.1318795 -7.2758088 -7.601243 -7.6989373 -57.29647 -55.736173 -55.983442 -0.84537078 -0.77684239 -0.7910269 136.65858 136.5908 136.64401 99.845607 99.869513 99.867281 74.724164 74.732279 74.699567
|
||||
43500 1390.2967 -890.21856 1078.0917 2.2938491 1482.3754 56.694555 -4.1317225 -7.2485872 -7.568553 -7.7195095 -57.819566 -55.528042 -55.848214 -0.82149712 -0.82258095 -0.75292757 136.66772 136.57379 136.65372 99.83762 99.882723 99.854263 74.72191 74.747558 74.704137
|
||||
45000 1427.5782 -892.18995 -564.57357 2.2938491 1482.0054 64.751105 -4.1319259 -7.2234655 -7.5860705 -7.6146702 -57.745852 -56.095471 -55.618665 -0.77244466 -0.77811125 -0.75729958 136.66838 136.59611 136.6615 99.853922 99.886483 99.864469 74.715773 74.736269 74.702744
|
||||
46500 1457.907 -890.87371 1296.2125 2.2938491 1481.9658 74.963993 -4.1319725 -7.2288448 -7.5807903 -7.6640053 -57.821382 -55.848166 -55.521503 -0.80230061 -0.78832769 -0.77589289 136.69039 136.61343 136.68259 99.862454 99.896917 99.881487 74.726406 74.741295 74.710053
|
||||
48000 1526.0771 -895.53336 951.53234 2.2938491 1481.7295 84.065637 -4.1320813 -7.2137393 -7.545201 -7.6839878 -57.914627 -55.591336 -55.900718 -0.79496608 -0.78179316 -0.79496022 136.6987 136.62461 136.70778 99.879775 99.908913 99.883958 74.71782 74.746229 74.714358
|
||||
49500 1657.943 -890.09268 424.53616 2.2938491 1481.5972 95.06808 -4.1322261 -7.2312162 -7.5609924 -7.6933969 -58.460164 -55.614895 -55.68435 -0.7539777 -0.78036417 -0.84398343 136.70672 136.6326 136.70523 99.887231 99.910615 99.890981 74.711921 74.735306 74.70572
|
||||
51000 1517.8791 -894.6926 1412.5634 2.2938491 1481.8411 91.241557 -4.1321301 -7.2856849 -7.554417 -7.6852066 -58.824904 -55.906732 -55.722124 -0.72652169 -0.74459334 -0.824857 136.70149 136.63447 136.70155 99.892122 99.901377 99.890263 74.713234 74.73149 74.710717
|
||||
52500 1546.6245 -895.29958 181.50897 2.2938491 1482.1091 82.209025 -4.132121 -7.2711566 -7.5656939 -7.6600316 -58.75721 -55.971266 -55.724274 -0.72068642 -0.74174146 -0.81673789 136.68292 136.62513 136.69226 99.883717 99.900635 99.877994 74.704983 74.724386 74.708085
|
||||
54000 1432.5143 -892.33522 -1007.7153 2.2938491 1481.7799 82.064986 -4.1320527 -7.2297435 -7.5532463 -7.5873553 -58.769531 -56.753962 -55.320358 -0.69093494 -0.71376103 -0.8266532 136.66681 136.62772 136.68861 99.880916 99.890283 99.87535 74.709314 74.72301 74.713722
|
||||
55500 1525.2554 -890.36734 1294.5154 2.2938491 1481.5565 85.222591 -4.1321435 -7.2322453 -7.5028572 -7.5979369 -58.470473 -56.91003 -54.983461 -0.67325171 -0.68237059 -0.82452296 136.68218 136.64126 136.71384 99.888262 99.903988 99.885655 74.709774 74.736014 74.716975
|
||||
57000 1480.851 -891.41709 -148.33291 2.2938491 1481.401 80.316901 -4.1321436 -7.262647 -7.5256821 -7.6034232 -58.185727 -56.55166 -54.966948 -0.69905198 -0.64380996 -0.84814546 136.677 136.64844 136.7165 99.891933 99.904202 99.884534 74.70914 74.736681 74.716403
|
||||
58500 1546.9102 -892.66057 1089.3405 2.2938491 1481.4299 78.801721 -4.1321113 -7.276498 -7.5191946 -7.617463 -58.32857 -56.257777 -54.959089 -0.67949464 -0.65491266 -0.85310199 136.67479 136.64503 136.70605 99.885427 99.899987 99.884663 74.714168 74.737379 74.714314
|
||||
60000 1485.6648 -893.08278 -428.03608 2.2938491 1481.7631 79.689946 -4.1321441 -7.2552452 -7.5131486 -7.57811 -58.354213 -56.020669 -55.063017 -0.69757949 -0.6589713 -0.84658488 136.67189 136.63503 136.69828 99.877882 99.900844 99.87896 74.707924 74.735972 74.703597
|
||||
61500 1495.0662 -890.78023 1028.7889 2.2938491 1481.9678 75.884372 -4.1320422 -7.2080989 -7.5371914 -7.5381901 -58.053737 -56.190462 -55.148238 -0.69885347 -0.63670212 -0.87555185 136.65839 136.62158 136.68603 99.869396 99.894708 99.868716 74.704861 74.735992 74.700569
|
||||
63000 1409.6818 -887.95961 -1304.652 2.2938491 1482.3126 76.410022 -4.1319825 -7.2523905 -7.5152373 -7.5536513 -58.73159 -56.137578 -54.799791 -0.73461753 -0.67809249 -0.88492027 136.65593 136.62329 136.67831 99.868652 99.888176 99.869266 74.703693 74.730048 74.701284
|
||||
64500 1582.31 -895.49087 1119.2594 2.2938491 1482.1186 66.626242 -4.1320087 -7.2521942 -7.5234826 -7.5594736 -58.305867 -56.601233 -54.537783 -0.7563263 -0.68942681 -0.89444015 136.64507 136.61842 136.66703 99.860683 99.882098 99.86589 74.702368 74.723763 74.693042
|
||||
66000 1468.6429 -891.90582 -773.99786 2.2938491 1482.414 56.160228 -4.1318961 -7.2436172 -7.5080588 -7.5819411 -57.982694 -56.370777 -54.739699 -0.75092608 -0.69652428 -0.90242579 136.62154 136.60352 136.65359 99.85017 99.872559 99.849715 74.698926 74.716783 74.691294
|
||||
67500 1592.9841 -894.17166 -373.28608 2.2938491 1482.4608 66.22665 -4.1319088 -7.2020048 -7.5343208 -7.6502267 -57.737091 -56.058804 -54.410576 -0.74973866 -0.71379313 -0.92874192 136.61811 136.60579 136.64811 99.851858 99.868577 99.85379 74.695471 74.703568 74.688361
|
||||
69000 1451.6708 -892.24332 -42.454938 2.2938491 1482.3952 64.462379 -4.1318409 -7.2084429 -7.5095889 -7.6621307 -58.007656 -55.977537 -54.39909 -0.74311576 -0.67139652 -0.91195038 136.63393 136.60861 136.63564 99.845601 99.865271 99.865085 74.704656 74.707684 74.682318
|
||||
70500 1541.8751 -890.84273 603.87446 2.2938491 1482.1352 69.651346 -4.1319184 -7.1867148 -7.4795063 -7.6774435 -57.597661 -55.972955 -54.365809 -0.72507444 -0.63500349 -0.909513 136.63512 136.60177 136.63362 99.845987 99.867527 99.865623 74.698143 74.701585 74.674848
|
||||
72000 1469.8975 -890.17779 -712.95338 2.2938491 1482.2905 73.091503 -4.1319489 -7.1766057 -7.4591194 -7.660856 -57.657616 -55.981892 -54.095734 -0.71782602 -0.61875736 -0.91469335 136.63573 136.60382 136.63383 99.845901 99.869082 99.866108 74.699376 74.701787 74.672946
|
||||
73500 1571.7762 -894.46891 1835.3759 2.2938491 1482.42 84.062922 -4.1319557 -7.2310516 -7.4816168 -7.6691216 -57.820079 -55.90879 -54.134789 -0.73871067 -0.64971193 -0.93750027 136.63865 136.60893 136.64184 99.848872 99.876734 99.869374 74.696526 74.703769 74.671271
|
||||
75000 1668.0665 -889.10379 319.58734 2.2938491 1482.5795 91.590228 -4.1319353 -7.2136142 -7.4546526 -7.6863632 -57.99287 -55.973671 -54.462176 -0.7272861 -0.64541622 -0.9505418 136.64301 136.61457 136.65062 99.855439 99.877747 99.869599 74.701819 74.706548 74.682155
|
||||
76500 1660.1105 -891.61038 2128.1078 2.2938491 1482.4578 91.208675 -4.1318581 -7.2797412 -7.5002006 -7.6971338 -58.256724 -55.882133 -54.72244 -0.74105804 -0.65844257 -0.98078027 136.64403 136.6142 136.65487 99.855009 99.878188 99.868938 74.703354 74.70937 74.68632
|
||||
78000 1551.7441 -890.77214 -121.70935 2.2938491 1482.3519 85.597023 -4.1317377 -7.2689985 -7.4957494 -7.7185745 -58.313372 -56.092493 -54.841116 -0.75183521 -0.65377647 -0.97014055 136.62932 136.61045 136.63974 99.849688 99.867005 99.861641 74.698504 74.705574 74.688265
|
||||
79500 1451.11 -892.82037 -632.95505 2.2938491 1482.3476 87.575027 -4.1317651 -7.2403953 -7.4775336 -7.6689122 -58.32666 -56.035227 -54.817357 -0.72487208 -0.63508667 -0.96802939 136.62952 136.60836 136.63433 99.846727 99.865255 99.865022 74.698105 74.698515 74.685562
|
||||
81000 1497.4722 -891.00907 -173.43837 2.2938491 1482.3832 86.788447 -4.1317009 -7.270206 -7.4485143 -7.6702474 -58.081079 -55.896158 -54.762508 -0.72740498 -0.65433219 -0.95969011 136.62378 136.60331 136.63421 99.844906 99.86253 99.858317 74.695022 74.698559 74.689157
|
||||
82500 1555.7129 -892.58366 1904.2361 2.2938491 1482.3558 93.090261 -4.1317057 -7.2690799 -7.4631718 -7.7113864 -58.043005 -56.089191 -54.702244 -0.74777178 -0.68581389 -1.0039008 136.62292 136.59848 136.6349 99.844402 99.867354 99.856268 74.688752 74.699686 74.686532
|
||||
84000 1567.5762 -893.4426 1395.2965 2.2938491 1482.5162 94.678844 -4.1316985 -7.2414617 -7.4514971 -7.7059415 -57.823672 -56.159106 -54.697355 -0.73591992 -0.67263169 -0.99293636 136.62485 136.60365 136.63538 99.84546 99.868588 99.859502 74.694287 74.699557 74.688432
|
||||
85500 1432.2278 -889.0106 -1377.5411 2.2938491 1482.3155 93.438709 -4.1317406 -7.2231164 -7.4908049 -7.7049396 -57.502557 -56.145262 -54.63067 -0.75954036 -0.65582508 -1.0183515 136.6309 136.61047 136.64107 99.849588 99.871028 99.864254 74.699439 74.70335 74.691002
|
||||
87000 1460.2447 -891.89246 -0.80016568 2.2938491 1482.3382 88.386804 -4.1316936 -7.2264011 -7.5056543 -7.709398 -57.406671 -55.971898 -54.886302 -0.74942793 -0.65651161 -1.0146109 136.6237 136.59887 136.63315 99.842443 99.867697 99.856739 74.697165 74.70443 74.683402
|
||||
88500 1440.2891 -893.33008 524.68194 2.2938491 1482.3143 88.757788 -4.1317107 -7.2539574 -7.5019633 -7.6970553 -57.100672 -56.001078 -54.967854 -0.72231568 -0.67329128 -1.0062405 136.62754 136.60076 136.63746 99.841603 99.871714 99.857299 74.700219 74.708928 74.688224
|
||||
90000 1516.1386 -896.83736 514.25183 2.2938491 1482.4324 93.624187 -4.1316721 -7.2661783 -7.4872817 -7.6621711 -57.153939 -55.675044 -55.038702 -0.71162973 -0.65640585 -0.9901763 136.62634 136.5973 136.63636 99.840724 99.872434 99.853565 74.696616 74.71085 74.68682
|
||||
91500 1607.5754 -891.45362 -335.12175 2.2938491 1482.3634 96.295552 -4.1317168 -7.2512482 -7.4855921 -7.6563828 -57.333312 -55.871451 -54.885579 -0.71855253 -0.66451595 -0.9784755 136.62406 136.60485 136.63801 99.845387 99.869057 99.856498 74.69518 74.707799 74.689867
|
||||
93000 1460.9577 -891.0447 1910.5719 2.2938491 1482.5495 95.612581 -4.1316835 -7.2345819 -7.4872574 -7.6900538 -57.577838 -55.778305 -55.190243 -0.72452799 -0.67622846 -0.95134216 136.6155 136.58928 136.6336 99.838615 99.867719 99.849452 74.687208 74.706541 74.685971
|
||||
94500 1470.6227 -892.26051 270.39634 2.2938491 1482.5672 94.112066 -4.1317045 -7.2341279 -7.4928727 -7.6545536 -57.426957 -56.064962 -55.047123 -0.70451968 -0.67591615 -0.92282964 136.61646 136.59089 136.64185 99.840845 99.870383 99.849979 74.688749 74.709584 74.686957
|
||||
96000 1761.7597 -889.19794 2653.3494 2.2938491 1482.3672 85.211301 -4.1316762 -7.2539691 -7.4631657 -7.6913375 -57.327731 -55.963801 -55.013515 -0.71090453 -0.69574107 -0.92155635 136.60972 136.58428 136.62883 99.832904 99.864366 99.847749 74.688857 74.708236 74.682281
|
||||
97500 1481.5876 -894.20788 -389.53494 2.2938491 1482.2533 89.07951 -4.1317073 -7.25095 -7.4753287 -7.6606804 -57.47475 -56.096252 -55.158143 -0.71560129 -0.68873446 -0.93406162 136.61564 136.58736 136.63462 99.838049 99.868876 99.848771 74.686838 74.711562 74.683471
|
||||
99000 1495.5155 -891.01063 1680.8863 2.2938491 1482.2267 97.208165 -4.1317016 -7.277595 -7.5192558 -7.6344538 -57.476542 -56.383856 -54.882305 -0.74400485 -0.68726404 -0.94799728 136.61907 136.59346 136.63796 99.842727 99.870409 99.853088 74.685523 74.708843 74.684813
|
||||
100500 1467.1581 -889.95317 242.60103 2.2938491 1481.9829 97.224982 -4.1317571 -7.252584 -7.5076801 -7.6611416 -57.552637 -56.14004 -55.018801 -0.75385025 -0.69209438 -0.94398412 136.6207 136.60141 136.63777 99.846229 99.86929 99.857689 74.69078 74.705759 74.687925
|
||||
102000 1613.876 -891.23745 1375.2231 2.2938491 1481.8918 94.379877 -4.1317123 -7.2522696 -7.490171 -7.6514314 -57.635642 -55.888914 -54.994388 -0.75241502 -0.68960669 -0.91645246 136.62344 136.60488 136.63347 99.847338 99.865247 99.856123 74.695679 74.707583 74.693448
|
||||
103500 1366.8885 -892.68641 -434.73129 2.2938491 1481.866 97.233875 -4.1317222 -7.2341862 -7.4693846 -7.6427203 -57.848484 -55.98048 -55.261348 -0.74622204 -0.68309934 -0.92443719 136.62181 136.61267 136.63941 99.856541 99.863371 99.859527 74.696212 74.702525 74.694062
|
||||
105000 1566.8173 -889.64302 52.134848 2.2938491 1481.9555 94.617908 -4.131708 -7.2078092 -7.490984 -7.6511905 -57.877166 -55.970863 -55.392031 -0.74617361 -0.69517832 -0.94219586 136.62317 136.61282 136.63557 99.853702 99.862156 99.858588 74.697837 74.703415 74.693222
|
||||
106500 1510.7795 -891.83105 912.04973 2.2938491 1481.9273 94.050693 -4.1317245 -7.2274362 -7.4958029 -7.6473799 -57.9481 -55.855934 -55.405593 -0.7612426 -0.70193323 -0.94170435 136.61865 136.60991 136.63015 99.851136 99.858763 99.857942 74.697833 74.700173 74.690954
|
||||
108000 1455.2205 -886.40658 557.80643 2.2938491 1481.8672 90.932719 -4.131639 -7.2156616 -7.5140992 -7.6592343 -57.875096 -56.121921 -55.441901 -0.77520355 -0.7082224 -0.95332709 136.61521 136.60854 136.62307 99.844819 99.853589 99.857619 74.706032 74.702008 74.690719
|
||||
109500 1591.694 -890.12115 2111.7582 2.2938491 1481.9081 90.818335 -4.1316826 -7.2099875 -7.5036851 -7.6146732 -57.901962 -56.080481 -55.335907 -0.77541222 -0.70215363 -0.94640585 136.62449 136.62284 136.63316 99.852345 99.858242 99.864241 74.712062 74.706711 74.695773
|
||||
111000 1401.5464 -889.70209 -1162.998 2.2938491 1481.8995 90.785361 -4.1317103 -7.2232569 -7.4975842 -7.6122167 -57.814589 -56.145176 -55.237091 -0.77101386 -0.71297505 -0.93787376 136.62319 136.62624 136.63278 99.855678 99.855147 99.865946 74.710261 74.703628 74.698218
|
||||
112500 1661.4542 -893.40947 3577.1279 2.2938491 1482.0712 91.936529 -4.1316922 -7.2363752 -7.490673 -7.6041227 -57.793279 -56.031961 -55.425678 -0.76646862 -0.71410904 -0.9310629 136.61332 136.62225 136.62704 99.856804 99.84979 99.862862 74.707371 74.696176 74.697236
|
||||
114000 1547.0639 -887.44417 1477.9344 2.2938491 1482.0257 92.747503 -4.131727 -7.2300662 -7.4797162 -7.5970492 -57.853023 -55.961882 -55.370161 -0.75229192 -0.6895434 -0.93030859 136.61656 136.62515 136.62686 99.855862 99.853722 99.86337 74.71008 74.698813 74.695278
|
||||
115500 1439.5189 -890.25524 1449.2504 2.2938491 1482.1027 93.092922 -4.1317311 -7.2248464 -7.4844791 -7.577668 -57.724672 -55.908203 -55.477058 -0.75703148 -0.69213445 -0.93063769 136.61287 136.62652 136.63064 99.861066 99.855191 99.860674 74.707263 74.699878 74.698782
|
||||
117000 1484.5557 -888.52105 62.875599 2.2938491 1481.939 88.920925 -4.1316902 -7.2401277 -7.4688263 -7.5738313 -57.623793 -55.827804 -55.470646 -0.7670686 -0.70720567 -0.94065827 136.61043 136.62028 136.62637 99.856362 99.852679 99.856577 74.7054 74.702523 74.700062
|
||||
118500 1544.5557 -897.27305 290.28551 2.2938491 1482.0321 82.378509 -4.1316258 -7.2550568 -7.4962409 -7.6069951 -57.791253 -55.82989 -55.246167 -0.7749151 -0.72530054 -0.96204389 136.60394 136.61474 136.6218 99.851596 99.848741 99.849294 74.707077 74.705425 74.700726
|
||||
120000 1478.3947 -892.7268 -577.38167 2.2938491 1481.8729 84.389547 -4.1316655 -7.2406756 -7.4760807 -7.571379 -57.99213 -55.95264 -55.45397 -0.77057679 -0.71238268 -0.94097166 136.60946 136.62355 136.62508 99.855739 99.849821 99.856483 74.708864 74.703347 74.704105
|
||||
121500 1529.2571 -890.35258 214.27253 2.2938491 1481.8862 79.172239 -4.131618 -7.2321448 -7.4640098 -7.5859318 -57.999026 -55.743602 -55.374383 -0.76556556 -0.72763717 -0.94266473 136.60096 136.62176 136.61876 99.853547 99.843769 99.850416 74.711419 74.702896 74.703593
|
||||
123000 1592.6338 -895.89179 1618.5405 2.2938491 1481.8996 82.460382 -4.1316142 -7.2304535 -7.4384951 -7.5700086 -57.853634 -55.668494 -55.236154 -0.75305506 -0.73385059 -0.93874018 136.59877 136.61927 136.61316 99.852817 99.840785 99.851696 74.710721 74.698867 74.700648
|
||||
124500 1481.1564 -896.96342 324.3934 2.2938491 1481.8895 85.319881 -4.1316244 -7.2264693 -7.4227219 -7.5551714 -57.777484 -55.785962 -55.26024 -0.75234123 -0.73009637 -0.93269204 136.59932 136.61758 136.61173 99.852222 99.841031 99.851213 74.709885 74.698336 74.698938
|
||||
126000 1366.1089 -891.93997 -658.32428 2.2938491 1481.7226 78.355779 -4.1316207 -7.2488328 -7.4329154 -7.5647275 -57.916784 -55.857672 -55.218103 -0.76146388 -0.73488986 -0.92639796 136.5948 136.61742 136.60582 99.851304 99.835211 99.848225 74.709524 74.694785 74.702522
|
||||
127500 1505.7295 -893.82427 1963.9643 2.2938491 1481.8782 87.640052 -4.1316687 -7.277167 -7.4400402 -7.5639761 -57.931692 -55.857053 -55.327085 -0.77752365 -0.7559997 -0.93064472 136.60295 136.6295 136.61443 99.859242 99.841072 99.856065 74.711211 74.693396 74.703574
|
||||
129000 1544.571 -892.03159 -527.07176 2.2938491 1482.0193 87.794364 -4.1316821 -7.2698344 -7.4346091 -7.5684319 -57.869829 -55.877329 -55.269055 -0.77585053 -0.73210247 -0.92680166 136.60317 136.63098 136.61634 99.86071 99.839607 99.856208 74.712198 74.695158 74.705047
|
||||
130500 1563.3858 -889.50411 -87.198132 2.2938491 1482.0526 81.485975 -4.1316493 -7.2663101 -7.4269998 -7.5691984 -57.836151 -55.897446 -55.110745 -0.7681867 -0.72744291 -0.91874044 136.59693 136.63004 136.61117 99.858337 99.836672 99.849979 74.711563 74.695134 74.708137
|
||||
132000 1553.6055 -896.15176 740.11093 2.2938491 1481.9674 80.783301 -4.1316735 -7.2824836 -7.4350446 -7.5489937 -57.950565 -55.829897 -55.147418 -0.79446196 -0.73309725 -0.92126843 136.59425 136.62943 136.61481 99.860995 99.838059 99.848436 74.708412 74.695423 74.708926
|
||||
133500 1385.0177 -892.27993 -907.20247 2.2938491 1481.8295 79.187393 -4.1316431 -7.2781202 -7.4600968 -7.5283409 -58.068566 -55.837667 -54.995174 -0.79075959 -0.72422066 -0.92463565 136.58806 136.62239 136.6053 99.858416 99.830029 99.847215 74.70793 74.690917 74.708181
|
||||
135000 1483.9097 -893.96772 -2166.9672 2.2938491 1481.8458 79.724142 -4.1316572 -7.2532514 -7.4529684 -7.5151627 -58.117754 -55.762813 -55.044672 -0.78734824 -0.71937479 -0.9191986 136.5908 136.62612 136.60205 99.856567 99.829771 99.850178 74.711435 74.688994 74.708456
|
||||
136500 1600.2522 -890.70516 609.13895 2.2938491 1481.92 83.006512 -4.1316674 -7.258606 -7.4315875 -7.5020899 -58.1938 -55.794999 -54.94864 -0.77941653 -0.72340994 -0.90867059 136.5924 136.62407 136.6027 99.858372 99.830876 99.850851 74.70873 74.687502 74.705977
|
||||
138000 1502.6753 -890.61112 391.94407 2.2938491 1482.0167 76.016016 -4.1316051 -7.2681189 -7.4332901 -7.5246594 -58.549025 -55.68375 -55.083251 -0.7721303 -0.73534454 -0.91398112 136.5902 136.61295 136.59058 99.848968 99.826477 99.845811 74.7088 74.685769 74.700689
|
||||
139500 1356.6079 -892.88412 443.66566 2.2938491 1482.1012 75.175931 -4.1315823 -7.272648 -7.4202164 -7.5435138 -58.430256 -55.645142 -55.177498 -0.77281637 -0.74277362 -0.90655462 136.58594 136.60941 136.58868 99.8471 99.825215 99.844524 74.704379 74.684246 74.698048
|
||||
141000 1536.8299 -891.3964 1488.9232 2.2938491 1482.1777 70.161617 -4.1315549 -7.2870883 -7.4331937 -7.5306099 -58.52421 -55.722214 -55.042544 -0.74933771 -0.74261337 -0.87760623 136.58324 136.61276 136.58989 99.849169 99.823054 99.843296 74.706773 74.681129 74.703048
|
||||
142500 1436.4404 -893.92271 574.36968 2.2938491 1482.0701 72.237377 -4.1316031 -7.2838066 -7.4093453 -7.5146661 -58.526669 -55.658527 -54.961371 -0.75069722 -0.74058553 -0.87613316 136.58937 136.61441 136.59146 99.848728 99.827923 99.846928 74.706061 74.681733 74.697755
|
||||
144000 1489.9179 -891.89057 874.84954 2.2938491 1482.1193 76.069588 -4.1316094 -7.2964678 -7.3973197 -7.5029947 -58.56494 -55.90659 -54.948484 -0.74022244 -0.75134582 -0.87359031 136.59283 136.61825 136.59298 99.85297 99.828592 99.848855 74.708201 74.681372 74.698936
|
||||
145500 1498.8873 -892.88995 -375.19001 2.2938491 1482.1293 78.637484 -4.1316333 -7.28757 -7.3758785 -7.5097553 -58.819672 -55.915661 -54.947745 -0.73771147 -0.76005783 -0.87268243 136.59805 136.62289 136.59468 99.853239 99.831254 99.853326 74.712898 74.684719 74.697923
|
||||
147000 1522.292 -888.44727 1193.3345 2.2938491 1482.274 82.096416 -4.1316355 -7.2628288 -7.3837513 -7.5079984 -58.864236 -55.949971 -55.052575 -0.72231418 -0.74804745 -0.87292368 136.60062 136.62844 136.59425 99.855419 99.831528 99.855082 74.715145 74.682637 74.701191
|
||||
148500 1570.9693 -893.72505 672.43585 2.2938491 1482.3953 88.359724 -4.1316418 -7.2884009 -7.3644359 -7.5112899 -58.807712 -55.988036 -55.099847 -0.72835513 -0.74530355 -0.87637008 136.60096 136.6326 136.59779 99.857791 99.834031 99.857841 74.715094 74.683359 74.70131
|
||||
150000 1449.0081 -891.81638 -714.54867 2.2938491 1482.3667 90.591195 -4.1316589 -7.3037214 -7.3497793 -7.5219215 -58.757005 -56.00609 -55.081797 -0.72611841 -0.75187625 -0.87207291 136.60564 136.63782 136.59487 99.857615 99.835445 99.86176 74.718484 74.683132 74.699142
|
||||
Loop time of 18.3423 on 4 procs for 150000 steps with 216 atoms
|
||||
|
||||
Performance: 541.227 ns/day, 0.044 hours/ns, 8177.811 timesteps/s
|
||||
99.9% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 12.192 | 12.302 | 12.366 | 2.0 | 67.07
|
||||
Neigh | 0.16441 | 0.16492 | 0.16576 | 0.1 | 0.90
|
||||
Comm | 2.4159 | 2.4795 | 2.5866 | 4.3 | 13.52
|
||||
Output | 0.0030494 | 0.0033533 | 0.0042086 | 0.9 | 0.02
|
||||
Modify | 3.1243 | 3.1322 | 3.1398 | 0.3 | 17.08
|
||||
Other | | 0.2608 | | | 1.42
|
||||
|
||||
Nlocal: 54 ave 54 max 54 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 334.75 ave 338 max 331 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 1426.5 ave 1439 max 1408 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 1 1
|
||||
|
||||
Total # of neighbors = 5706
|
||||
Ave neighs/atom = 26.416667
|
||||
Neighbor list builds = 2567
|
||||
Dangerous builds = 0
|
||||
|
||||
# Output final values
|
||||
|
||||
include final_output.in
|
||||
# Average moduli for cubic crystals
|
||||
|
||||
variable C11cubic equal (${C11}+${C22}+${C33})/3.0
|
||||
variable C11cubic equal (133.317541070292+${C22}+${C33})/3.0
|
||||
variable C11cubic equal (133.317541070292+133.303658933287+${C33})/3.0
|
||||
variable C11cubic equal (133.317541070292+133.303658933287+133.088561493082)/3.0
|
||||
variable C12cubic equal (${C12}+${C13}+${C23})/3.0
|
||||
variable C12cubic equal (73.9923654361203+${C13}+${C23})/3.0
|
||||
variable C12cubic equal (73.9923654361203+73.9312552589804+${C23})/3.0
|
||||
variable C12cubic equal (73.9923654361203+73.9312552589804+73.8270687089798)/3.0
|
||||
variable C44cubic equal (${C44}+${C55}+${C66})/3.0
|
||||
variable C44cubic equal (43.1084188147025+${C55}+${C66})/3.0
|
||||
variable C44cubic equal (43.1084188147025+45.8371646999798+${C66})/3.0
|
||||
variable C44cubic equal (43.1084188147025+45.8371646999798+46.7877718062386)/3.0
|
||||
|
||||
variable bulkmodulus equal (${C11cubic}+2*${C12cubic})/3.0
|
||||
variable bulkmodulus equal (133.236587165554+2*${C12cubic})/3.0
|
||||
variable bulkmodulus equal (133.236587165554+2*73.9168964680268)/3.0
|
||||
variable shearmodulus1 equal ${C44cubic}
|
||||
variable shearmodulus1 equal 45.2444517736403
|
||||
variable shearmodulus2 equal (${C11cubic}-${C12cubic})/2.0
|
||||
variable shearmodulus2 equal (133.236587165554-${C12cubic})/2.0
|
||||
variable shearmodulus2 equal (133.236587165554-73.9168964680268)/2.0
|
||||
variable poissonratio equal 1.0/(1.0+${C11cubic}/${C12cubic})
|
||||
variable poissonratio equal 1.0/(1.0+133.236587165554/${C12cubic})
|
||||
variable poissonratio equal 1.0/(1.0+133.236587165554/73.9168964680268)
|
||||
|
||||
# For Stillinger-Weber silicon, the analytical results
|
||||
# are known to be (E. R. Cowley, 1988):
|
||||
# C11 = 151.4 GPa
|
||||
# C12 = 76.4 GPa
|
||||
# C44 = 56.4 GPa
|
||||
|
||||
#print "========================================="
|
||||
#print "Components of the Elastic Constant Tensor"
|
||||
#print "========================================="
|
||||
|
||||
print "Elastic Constant C11 = ${C11} ${cunits}"
|
||||
Elastic Constant C11 = 133.317541070292 GPa
|
||||
print "Elastic Constant C22 = ${C22} ${cunits}"
|
||||
Elastic Constant C22 = 133.303658933287 GPa
|
||||
print "Elastic Constant C33 = ${C33} ${cunits}"
|
||||
Elastic Constant C33 = 133.088561493082 GPa
|
||||
|
||||
print "Elastic Constant C12 = ${C12} ${cunits}"
|
||||
Elastic Constant C12 = 73.9923654361203 GPa
|
||||
print "Elastic Constant C13 = ${C13} ${cunits}"
|
||||
Elastic Constant C13 = 73.9312552589804 GPa
|
||||
print "Elastic Constant C23 = ${C23} ${cunits}"
|
||||
Elastic Constant C23 = 73.8270687089798 GPa
|
||||
|
||||
print "Elastic Constant C44 = ${C44} ${cunits}"
|
||||
Elastic Constant C44 = 43.1084188147025 GPa
|
||||
print "Elastic Constant C55 = ${C55} ${cunits}"
|
||||
Elastic Constant C55 = 45.8371646999798 GPa
|
||||
print "Elastic Constant C66 = ${C66} ${cunits}"
|
||||
Elastic Constant C66 = 46.7877718062386 GPa
|
||||
|
||||
print "Elastic Constant C14 = ${C14} ${cunits}"
|
||||
Elastic Constant C14 = 0.0767019895461112 GPa
|
||||
print "Elastic Constant C15 = ${C15} ${cunits}"
|
||||
Elastic Constant C15 = 0.160081312432549 GPa
|
||||
print "Elastic Constant C16 = ${C16} ${cunits}"
|
||||
Elastic Constant C16 = -0.0672322473606912 GPa
|
||||
|
||||
print "Elastic Constant C24 = ${C24} ${cunits}"
|
||||
Elastic Constant C24 = -0.0980703737031021 GPa
|
||||
print "Elastic Constant C25 = ${C25} ${cunits}"
|
||||
Elastic Constant C25 = 0.425094496914652 GPa
|
||||
print "Elastic Constant C26 = ${C26} ${cunits}"
|
||||
Elastic Constant C26 = -0.061665192022258 GPa
|
||||
|
||||
print "Elastic Constant C34 = ${C34} ${cunits}"
|
||||
Elastic Constant C34 = -0.0939770954478323 GPa
|
||||
print "Elastic Constant C35 = ${C35} ${cunits}"
|
||||
Elastic Constant C35 = 0.10019558502976 GPa
|
||||
print "Elastic Constant C36 = ${C36} ${cunits}"
|
||||
Elastic Constant C36 = 0.246165012383149 GPa
|
||||
|
||||
print "Elastic Constant C45 = ${C45} ${cunits}"
|
||||
Elastic Constant C45 = 0.451034755300606 GPa
|
||||
print "Elastic Constant C46 = ${C46} ${cunits}"
|
||||
Elastic Constant C46 = 0.53971304682664 GPa
|
||||
print "Elastic Constant C56 = ${C56} ${cunits}"
|
||||
Elastic Constant C56 = -0.243078648160722 GPa
|
||||
|
||||
print "========================================="
|
||||
=========================================
|
||||
print "Average properties for a cubic crystal"
|
||||
Average properties for a cubic crystal
|
||||
print "========================================="
|
||||
=========================================
|
||||
|
||||
print "Bulk Modulus = ${bulkmodulus} ${cunits}"
|
||||
Bulk Modulus = 93.6901267005359 GPa
|
||||
print "Shear Modulus 1 = ${shearmodulus1} ${cunits}"
|
||||
Shear Modulus 1 = 45.2444517736403 GPa
|
||||
print "Shear Modulus 2 = ${shearmodulus2} ${cunits}"
|
||||
Shear Modulus 2 = 29.6598453487636 GPa
|
||||
print "Poisson Ratio = ${poissonratio}"
|
||||
Poisson Ratio = 0.356821884775895
|
||||
|
||||
# summarize sampling protocol
|
||||
|
||||
variable tmp equal atoms
|
||||
print "Number of atoms = ${tmp}"
|
||||
Number of atoms = 216
|
||||
print "Stress sampling interval = ${nevery}"
|
||||
Stress sampling interval = 10
|
||||
variable tmp equal ${nrun}/${nevery}
|
||||
variable tmp equal 150000/${nevery}
|
||||
variable tmp equal 150000/10
|
||||
print "Stress sample count = ${tmp}"
|
||||
Stress sample count = 15000
|
||||
print "Born sampling interval = ${neveryborn}"
|
||||
Born sampling interval = 100
|
||||
variable tmp equal ${nrun}/${neveryborn}
|
||||
variable tmp equal 150000/${neveryborn}
|
||||
variable tmp equal 150000/100
|
||||
print "Born sample count = ${tmp}"
|
||||
Born sample count = 1500
|
||||
Total wall time: 0:00:19
|
||||
662
examples/ELASTIC_T/BORN_MATRIX/Silicon/log.16May22.tri.g++.4
Normal file
662
examples/ELASTIC_T/BORN_MATRIX/Silicon/log.16May22.tri.g++.4
Normal file
@ -0,0 +1,662 @@
|
||||
|
||||
# select temperature and pressure (lattice constant)
|
||||
|
||||
variable temp index 1477.0 # temperature of initial sample
|
||||
variable a index 5.457 # lattice constant
|
||||
|
||||
# select sampling parameters, important for speed/convergence
|
||||
|
||||
variable nthermo index 1500 # interval for thermo output
|
||||
variable nevery index 10 # stress sampling interval
|
||||
variable neveryborn index 100 # Born sampling interval
|
||||
variable timestep index 0.000766 # timestep
|
||||
variable nlat index 3 # number of lattice unit cells
|
||||
|
||||
# other settings
|
||||
|
||||
variable mass1 index 28.06 # mass
|
||||
variable tdamp index 0.01 # time constant for thermostat
|
||||
variable seed index 123457 # seed for thermostat
|
||||
variable thermostat index 1 # 0 if NVE, 1 if NVT
|
||||
variable delta index 1.0e-6 # Born numdiff strain magnitude
|
||||
|
||||
# hard-coded rules-of-thumb for run length, etc.
|
||||
|
||||
variable nfreq equal ${nthermo} # interval for averaging output
|
||||
variable nfreq equal 1500
|
||||
variable nrepeat equal floor(${nfreq}/${nevery}) # number of samples
|
||||
variable nrepeat equal floor(1500/${nevery})
|
||||
variable nrepeat equal floor(1500/10)
|
||||
variable nrepeatborn equal floor(${nfreq}/${neveryborn}) # number of samples
|
||||
variable nrepeatborn equal floor(1500/${neveryborn})
|
||||
variable nrepeatborn equal floor(1500/100)
|
||||
variable nequil equal 10*${nthermo} # length of equilibration run
|
||||
variable nequil equal 10*1500
|
||||
variable nrun equal 100*${nthermo} # length of equilibrated run
|
||||
variable nrun equal 100*1500
|
||||
|
||||
# this generates a general triclinic cell
|
||||
# conforming to LAMMPS cell (upper triangular)
|
||||
|
||||
units metal
|
||||
box tilt large
|
||||
|
||||
# unit lattice vectors are
|
||||
# a1 = (a1x 0 0)
|
||||
# a2 = (a2x a2y 0)
|
||||
# a3 = (a3x a3y a3z)
|
||||
|
||||
variable a1x index 1
|
||||
variable a2x index 0
|
||||
variable a2y index 1
|
||||
variable a3x index 0
|
||||
variable a3y index 0
|
||||
variable a3z index 1
|
||||
variable atmp equal $a
|
||||
variable atmp equal 5.457
|
||||
variable l index $a
|
||||
variable l index 5.457
|
||||
variable basis index "basis 0 0 0 basis 0.25 0.25 0.25 basis 0 0.5 0.5 basis 0.25 0.75 0.75 basis 0.5 0 0.5 basis 0.75 0.25 0.75 basis 0.5 0.5 0 basis 0.75 0.75 0.25"
|
||||
lattice custom ${l} a1 ${a1x} 0 0 a2 ${a2x} ${a2y} 0 a3 ${a3x} ${a3y} ${a3z} ${basis} spacing 1 1 1
|
||||
lattice custom 3.8586817049349893 a1 ${a1x} 0 0 a2 ${a2x} ${a2y} 0 a3 ${a3x} ${a3y} ${a3z} ${basis} spacing 1 1 1
|
||||
lattice custom 3.8586817049349893 a1 1.0 0 0 a2 ${a2x} ${a2y} 0 a3 ${a3x} ${a3y} ${a3z} ${basis} spacing 1 1 1
|
||||
lattice custom 3.8586817049349893 a1 1.0 0 0 a2 0.4999999999999999 ${a2y} 0 a3 ${a3x} ${a3y} ${a3z} ${basis} spacing 1 1 1
|
||||
lattice custom 3.8586817049349893 a1 1.0 0 0 a2 0.4999999999999999 0.8660254037844385 0 a3 ${a3x} ${a3y} ${a3z} ${basis} spacing 1 1 1
|
||||
lattice custom 3.8586817049349893 a1 1.0 0 0 a2 0.4999999999999999 0.8660254037844385 0 a3 0.5 ${a3y} ${a3z} ${basis} spacing 1 1 1
|
||||
lattice custom 3.8586817049349893 a1 1.0 0 0 a2 0.4999999999999999 0.8660254037844385 0 a3 0.5 0.2886751345948129 ${a3z} ${basis} spacing 1 1 1
|
||||
lattice custom 3.8586817049349893 a1 1.0 0 0 a2 0.4999999999999999 0.8660254037844385 0 a3 0.5 0.2886751345948129 0.8164965809277259 ${basis} spacing 1 1 1
|
||||
lattice custom 3.8586817049349893 a1 1.0 0 0 a2 0.4999999999999999 0.8660254037844385 0 a3 0.5 0.2886751345948129 0.8164965809277259 basis 0 0 0 basis 0.25 0.25 0.25 spacing 1 1 1
|
||||
Lattice spacing in x,y,z = 3.8586817 3.8586817 3.8586817
|
||||
|
||||
region box prism 0 ${a1x} 0 ${a2y} 0 ${a3z} ${a2x} ${a3x} ${a3y}
|
||||
region box prism 0 1.0 0 ${a2y} 0 ${a3z} ${a2x} ${a3x} ${a3y}
|
||||
region box prism 0 1.0 0 0.8660254037844385 0 ${a3z} ${a2x} ${a3x} ${a3y}
|
||||
region box prism 0 1.0 0 0.8660254037844385 0 0.8164965809277259 ${a2x} ${a3x} ${a3y}
|
||||
region box prism 0 1.0 0 0.8660254037844385 0 0.8164965809277259 0.4999999999999999 ${a3x} ${a3y}
|
||||
region box prism 0 1.0 0 0.8660254037844385 0 0.8164965809277259 0.4999999999999999 0.5 ${a3y}
|
||||
region box prism 0 1.0 0 0.8660254037844385 0 0.8164965809277259 0.4999999999999999 0.5 0.2886751345948129
|
||||
|
||||
create_box 1 box
|
||||
Created triclinic box = (0 0 0) to (3.8586817 3.3417164 3.1506004) with tilt (1.9293409 1.9293409 1.1139055)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 2 atoms
|
||||
using lattice units in triclinic box = (0 0 0) to (3.8586817 3.3417164 3.1506004) with tilt (1.9293409 1.9293409 1.1139055)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
mass 1 ${mass1}
|
||||
mass 1 28.06
|
||||
replicate ${nlat} ${nlat} ${nlat}
|
||||
replicate 5 ${nlat} ${nlat}
|
||||
replicate 5 5 ${nlat}
|
||||
replicate 5 5 5
|
||||
Replicating atoms ...
|
||||
triclinic box = (0 0 0) to (19.293409 16.708582 15.753002) with tilt (9.6467043 9.6467043 5.5695273)
|
||||
2 by 1 by 2 MPI processor grid
|
||||
250 atoms
|
||||
replicate CPU = 0.000 seconds
|
||||
velocity all create ${temp} 87287
|
||||
velocity all create 1477.0 87287
|
||||
|
||||
|
||||
|
||||
# Compute initial state
|
||||
|
||||
include potential.in
|
||||
# NOTE: This script can be modified for different pair styles
|
||||
# See in.elastic for more info.
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
# Choose potential
|
||||
pair_style sw
|
||||
pair_coeff * * Si.sw Si
|
||||
Reading sw potential file Si.sw with DATE: 2007-06-11
|
||||
|
||||
# Setup neighbor style
|
||||
neighbor 1.0 nsq
|
||||
neigh_modify once no every 1 delay 0 check yes
|
||||
|
||||
# Setup MD
|
||||
|
||||
timestep ${timestep}
|
||||
timestep 0.000766
|
||||
fix 4 all nve
|
||||
if "${thermostat} == 1" then "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
|
||||
fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}
|
||||
fix 5 all langevin 1477.0 ${temp} ${tdamp} ${seed}
|
||||
fix 5 all langevin 1477.0 1477.0 ${tdamp} ${seed}
|
||||
fix 5 all langevin 1477.0 1477.0 0.01 ${seed}
|
||||
fix 5 all langevin 1477.0 1477.0 0.01 123457
|
||||
|
||||
|
||||
thermo_style custom step temp pe press density
|
||||
run ${nequil}
|
||||
run 15000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 4.77118
|
||||
ghost atom cutoff = 4.77118
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair sw, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/nsq
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.058 | 3.058 | 3.059 Mbytes
|
||||
Step Temp PotEng Press Density
|
||||
0 1477 -1083.8249 -4258.3947 2.2938491
|
||||
15000 1496.4515 -1030.8279 1702.5821 2.2938491
|
||||
Loop time of 1.93162 on 4 procs for 15000 steps with 250 atoms
|
||||
|
||||
Performance: 513.941 ns/day, 0.047 hours/ns, 7765.521 timesteps/s
|
||||
99.9% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.233 | 1.4215 | 1.6958 | 14.2 | 73.59
|
||||
Neigh | 0.020173 | 0.022348 | 0.025604 | 1.3 | 1.16
|
||||
Comm | 0.15771 | 0.43281 | 0.62056 | 25.8 | 22.41
|
||||
Output | 1.2841e-05 | 1.4604e-05 | 1.9543e-05 | 0.0 | 0.00
|
||||
Modify | 0.021536 | 0.025134 | 0.030087 | 2.0 | 1.30
|
||||
Other | | 0.02978 | | | 1.54
|
||||
|
||||
Nlocal: 62.5 ave 74 max 58 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 429.5 ave 465 max 391 min
|
||||
Histogram: 1 0 0 1 0 0 0 1 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 1649.5 ave 1943 max 1526 min
|
||||
Histogram: 2 1 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 6598
|
||||
Ave neighs/atom = 26.392
|
||||
Neighbor list builds = 261
|
||||
Dangerous builds = 0
|
||||
|
||||
# Run dynamics
|
||||
|
||||
include potential.in
|
||||
# NOTE: This script can be modified for different pair styles
|
||||
# See in.elastic for more info.
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
# Choose potential
|
||||
pair_style sw
|
||||
pair_coeff * * Si.sw Si
|
||||
Reading sw potential file Si.sw with DATE: 2007-06-11
|
||||
|
||||
# Setup neighbor style
|
||||
neighbor 1.0 nsq
|
||||
neigh_modify once no every 1 delay 0 check yes
|
||||
|
||||
# Setup MD
|
||||
|
||||
timestep ${timestep}
|
||||
timestep 0.000766
|
||||
fix 4 all nve
|
||||
if "${thermostat} == 1" then "fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
|
||||
fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}
|
||||
fix 5 all langevin 1477.0 ${temp} ${tdamp} ${seed}
|
||||
fix 5 all langevin 1477.0 1477.0 ${tdamp} ${seed}
|
||||
fix 5 all langevin 1477.0 1477.0 0.01 ${seed}
|
||||
fix 5 all langevin 1477.0 1477.0 0.01 123457
|
||||
|
||||
|
||||
include output.in
|
||||
# Setup output
|
||||
|
||||
# Stress fluctuation term F
|
||||
|
||||
compute stress all pressure thermo_temp
|
||||
variable s1 equal c_stress[1]
|
||||
variable s2 equal c_stress[2]
|
||||
variable s3 equal c_stress[3]
|
||||
variable s4 equal c_stress[6]
|
||||
variable s5 equal c_stress[5]
|
||||
variable s6 equal c_stress[4]
|
||||
|
||||
variable s11 equal v_s1*v_s1
|
||||
variable s22 equal v_s2*v_s2
|
||||
variable s33 equal v_s3*v_s3
|
||||
variable s44 equal v_s4*v_s4
|
||||
variable s55 equal v_s5*v_s5
|
||||
variable s66 equal v_s6*v_s6
|
||||
variable s33 equal v_s3*v_s3
|
||||
variable s12 equal v_s1*v_s2
|
||||
variable s13 equal v_s1*v_s3
|
||||
variable s14 equal v_s1*v_s4
|
||||
variable s15 equal v_s1*v_s5
|
||||
variable s16 equal v_s1*v_s6
|
||||
variable s23 equal v_s2*v_s3
|
||||
variable s24 equal v_s2*v_s4
|
||||
variable s25 equal v_s2*v_s5
|
||||
variable s26 equal v_s2*v_s6
|
||||
variable s34 equal v_s3*v_s4
|
||||
variable s35 equal v_s3*v_s5
|
||||
variable s36 equal v_s3*v_s6
|
||||
variable s45 equal v_s4*v_s5
|
||||
variable s46 equal v_s4*v_s6
|
||||
variable s56 equal v_s5*v_s6
|
||||
|
||||
variable mytemp equal temp
|
||||
variable mypress equal press
|
||||
variable mype equal pe/atoms
|
||||
fix avt all ave/time ${nevery} ${nrepeat} ${nfreq} v_mytemp ave running
|
||||
fix avt all ave/time 10 ${nrepeat} ${nfreq} v_mytemp ave running
|
||||
fix avt all ave/time 10 150 ${nfreq} v_mytemp ave running
|
||||
fix avt all ave/time 10 150 1500 v_mytemp ave running
|
||||
fix avp all ave/time ${nevery} ${nrepeat} ${nfreq} v_mypress ave running
|
||||
fix avp all ave/time 10 ${nrepeat} ${nfreq} v_mypress ave running
|
||||
fix avp all ave/time 10 150 ${nfreq} v_mypress ave running
|
||||
fix avp all ave/time 10 150 1500 v_mypress ave running
|
||||
fix avpe all ave/time ${nevery} ${nrepeat} ${nfreq} v_mype ave running
|
||||
fix avpe all ave/time 10 ${nrepeat} ${nfreq} v_mype ave running
|
||||
fix avpe all ave/time 10 150 ${nfreq} v_mype ave running
|
||||
fix avpe all ave/time 10 150 1500 v_mype ave running
|
||||
fix avs all ave/time ${nevery} ${nrepeat} ${nfreq} v_s1 v_s2 v_s3 v_s4 v_s5 v_s6 ave running
|
||||
fix avs all ave/time 10 ${nrepeat} ${nfreq} v_s1 v_s2 v_s3 v_s4 v_s5 v_s6 ave running
|
||||
fix avs all ave/time 10 150 ${nfreq} v_s1 v_s2 v_s3 v_s4 v_s5 v_s6 ave running
|
||||
fix avs all ave/time 10 150 1500 v_s1 v_s2 v_s3 v_s4 v_s5 v_s6 ave running
|
||||
fix avssq all ave/time ${nevery} ${nrepeat} ${nfreq} v_s11 v_s22 v_s33 v_s44 v_s55 v_s66 v_s12 v_s13 v_s14 v_s15 v_s16 v_s23 v_s24 v_s25 v_s26 v_s34 v_s35 v_s36 v_s45 v_s46 v_s56 ave running
|
||||
fix avssq all ave/time 10 ${nrepeat} ${nfreq} v_s11 v_s22 v_s33 v_s44 v_s55 v_s66 v_s12 v_s13 v_s14 v_s15 v_s16 v_s23 v_s24 v_s25 v_s26 v_s34 v_s35 v_s36 v_s45 v_s46 v_s56 ave running
|
||||
fix avssq all ave/time 10 150 ${nfreq} v_s11 v_s22 v_s33 v_s44 v_s55 v_s66 v_s12 v_s13 v_s14 v_s15 v_s16 v_s23 v_s24 v_s25 v_s26 v_s34 v_s35 v_s36 v_s45 v_s46 v_s56 ave running
|
||||
fix avssq all ave/time 10 150 1500 v_s11 v_s22 v_s33 v_s44 v_s55 v_s66 v_s12 v_s13 v_s14 v_s15 v_s16 v_s23 v_s24 v_s25 v_s26 v_s34 v_s35 v_s36 v_s45 v_s46 v_s56 ave running
|
||||
|
||||
# bar to GPa
|
||||
variable pconv equal 1.0e5/1.0e9
|
||||
variable cunits index GPa
|
||||
# metal unit constants from LAMMPS
|
||||
# force->nktv2p = 1.6021765e6;
|
||||
# force->boltz = 8.617343e-5;
|
||||
variable boltz equal 8.617343e-5
|
||||
variable nktv2p equal 1.6021765e6
|
||||
variable vkt equal vol/(${boltz}*${temp})/${nktv2p}
|
||||
variable vkt equal vol/(8.617343e-05*${temp})/${nktv2p}
|
||||
variable vkt equal vol/(8.617343e-05*1477.0)/${nktv2p}
|
||||
variable vkt equal vol/(8.617343e-05*1477.0)/1602176.5
|
||||
variable ffac equal ${pconv}*${vkt}
|
||||
variable ffac equal 0.0001*${vkt}
|
||||
variable ffac equal 0.0001*0.0249027696047235
|
||||
|
||||
variable F11 equal -(f_avssq[1]-f_avs[1]*f_avs[1])*${ffac}
|
||||
variable F11 equal -(f_avssq[1]-f_avs[1]*f_avs[1])*2.49027696047235e-06
|
||||
variable F22 equal -(f_avssq[2]-f_avs[2]*f_avs[2])*${ffac}
|
||||
variable F22 equal -(f_avssq[2]-f_avs[2]*f_avs[2])*2.49027696047235e-06
|
||||
variable F33 equal -(f_avssq[3]-f_avs[3]*f_avs[3])*${ffac}
|
||||
variable F33 equal -(f_avssq[3]-f_avs[3]*f_avs[3])*2.49027696047235e-06
|
||||
variable F44 equal -(f_avssq[4]-f_avs[4]*f_avs[4])*${ffac}
|
||||
variable F44 equal -(f_avssq[4]-f_avs[4]*f_avs[4])*2.49027696047235e-06
|
||||
variable F55 equal -(f_avssq[5]-f_avs[5]*f_avs[5])*${ffac}
|
||||
variable F55 equal -(f_avssq[5]-f_avs[5]*f_avs[5])*2.49027696047235e-06
|
||||
variable F66 equal -(f_avssq[6]-f_avs[6]*f_avs[6])*${ffac}
|
||||
variable F66 equal -(f_avssq[6]-f_avs[6]*f_avs[6])*2.49027696047235e-06
|
||||
|
||||
variable F12 equal -(f_avssq[7]-f_avs[1]*f_avs[2])*${ffac}
|
||||
variable F12 equal -(f_avssq[7]-f_avs[1]*f_avs[2])*2.49027696047235e-06
|
||||
variable F13 equal -(f_avssq[8]-f_avs[1]*f_avs[3])*${ffac}
|
||||
variable F13 equal -(f_avssq[8]-f_avs[1]*f_avs[3])*2.49027696047235e-06
|
||||
variable F14 equal -(f_avssq[9]-f_avs[1]*f_avs[4])*${ffac}
|
||||
variable F14 equal -(f_avssq[9]-f_avs[1]*f_avs[4])*2.49027696047235e-06
|
||||
variable F15 equal -(f_avssq[10]-f_avs[1]*f_avs[5])*${ffac}
|
||||
variable F15 equal -(f_avssq[10]-f_avs[1]*f_avs[5])*2.49027696047235e-06
|
||||
variable F16 equal -(f_avssq[11]-f_avs[1]*f_avs[6])*${ffac}
|
||||
variable F16 equal -(f_avssq[11]-f_avs[1]*f_avs[6])*2.49027696047235e-06
|
||||
|
||||
variable F23 equal -(f_avssq[12]-f_avs[2]*f_avs[3])*${ffac}
|
||||
variable F23 equal -(f_avssq[12]-f_avs[2]*f_avs[3])*2.49027696047235e-06
|
||||
variable F24 equal -(f_avssq[13]-f_avs[2]*f_avs[4])*${ffac}
|
||||
variable F24 equal -(f_avssq[13]-f_avs[2]*f_avs[4])*2.49027696047235e-06
|
||||
variable F25 equal -(f_avssq[14]-f_avs[2]*f_avs[5])*${ffac}
|
||||
variable F25 equal -(f_avssq[14]-f_avs[2]*f_avs[5])*2.49027696047235e-06
|
||||
variable F26 equal -(f_avssq[15]-f_avs[2]*f_avs[6])*${ffac}
|
||||
variable F26 equal -(f_avssq[15]-f_avs[2]*f_avs[6])*2.49027696047235e-06
|
||||
|
||||
variable F34 equal -(f_avssq[16]-f_avs[3]*f_avs[4])*${ffac}
|
||||
variable F34 equal -(f_avssq[16]-f_avs[3]*f_avs[4])*2.49027696047235e-06
|
||||
variable F35 equal -(f_avssq[17]-f_avs[3]*f_avs[5])*${ffac}
|
||||
variable F35 equal -(f_avssq[17]-f_avs[3]*f_avs[5])*2.49027696047235e-06
|
||||
variable F36 equal -(f_avssq[18]-f_avs[3]*f_avs[6])*${ffac}
|
||||
variable F36 equal -(f_avssq[18]-f_avs[3]*f_avs[6])*2.49027696047235e-06
|
||||
|
||||
variable F45 equal -(f_avssq[19]-f_avs[4]*f_avs[5])*${ffac}
|
||||
variable F45 equal -(f_avssq[19]-f_avs[4]*f_avs[5])*2.49027696047235e-06
|
||||
variable F46 equal -(f_avssq[20]-f_avs[4]*f_avs[6])*${ffac}
|
||||
variable F46 equal -(f_avssq[20]-f_avs[4]*f_avs[6])*2.49027696047235e-06
|
||||
|
||||
variable F56 equal -(f_avssq[21]-f_avs[5]*f_avs[6])*${ffac}
|
||||
variable F56 equal -(f_avssq[21]-f_avs[5]*f_avs[6])*2.49027696047235e-06
|
||||
|
||||
# Born term
|
||||
|
||||
compute virial all pressure NULL virial
|
||||
compute born all born/matrix numdiff ${delta} virial
|
||||
compute born all born/matrix numdiff 1.0e-6 virial
|
||||
fix avborn all ave/time ${neveryborn} ${nrepeatborn} ${nfreq} c_born[*] ave running
|
||||
fix avborn all ave/time 100 ${nrepeatborn} ${nfreq} c_born[*] ave running
|
||||
fix avborn all ave/time 100 15 ${nfreq} c_born[*] ave running
|
||||
fix avborn all ave/time 100 15 1500 c_born[*] ave running
|
||||
|
||||
variable bfac equal ${pconv}*${nktv2p}/vol
|
||||
variable bfac equal 0.0001*${nktv2p}/vol
|
||||
variable bfac equal 0.0001*1602176.5/vol
|
||||
variable B vector f_avborn*${bfac}
|
||||
variable B vector f_avborn*0.0315499354029305
|
||||
|
||||
# Kinetic term
|
||||
|
||||
variable kfac equal ${pconv}*${nktv2p}*atoms*${boltz}*${temp}/vol
|
||||
variable kfac equal 0.0001*${nktv2p}*atoms*${boltz}*${temp}/vol
|
||||
variable kfac equal 0.0001*1602176.5*atoms*${boltz}*${temp}/vol
|
||||
variable kfac equal 0.0001*1602176.5*atoms*8.617343e-05*${temp}/vol
|
||||
variable kfac equal 0.0001*1602176.5*atoms*8.617343e-05*1477.0/vol
|
||||
variable K11 equal 4.0*${kfac}
|
||||
variable K11 equal 4.0*1.00390440086865
|
||||
variable K22 equal 4.0*${kfac}
|
||||
variable K22 equal 4.0*1.00390440086865
|
||||
variable K33 equal 4.0*${kfac}
|
||||
variable K33 equal 4.0*1.00390440086865
|
||||
variable K44 equal 2.0*${kfac}
|
||||
variable K44 equal 2.0*1.00390440086865
|
||||
variable K55 equal 2.0*${kfac}
|
||||
variable K55 equal 2.0*1.00390440086865
|
||||
variable K66 equal 2.0*${kfac}
|
||||
variable K66 equal 2.0*1.00390440086865
|
||||
|
||||
# Add F, K, and B together
|
||||
|
||||
variable C11 equal v_F11+v_B[1]+v_K11
|
||||
variable C22 equal v_F22+v_B[2]+v_K22
|
||||
variable C33 equal v_F33+v_B[3]+v_K33
|
||||
variable C44 equal v_F44+v_B[4]+v_K44
|
||||
variable C55 equal v_F55+v_B[5]+v_K55
|
||||
variable C66 equal v_F66+v_B[6]+v_K66
|
||||
|
||||
variable C12 equal v_F12+v_B[7]
|
||||
variable C13 equal v_F13+v_B[8]
|
||||
variable C14 equal v_F14+v_B[9]
|
||||
variable C15 equal v_F15+v_B[10]
|
||||
variable C16 equal v_F16+v_B[11]
|
||||
|
||||
variable C23 equal v_F23+v_B[12]
|
||||
variable C24 equal v_F24+v_B[13]
|
||||
variable C25 equal v_F25+v_B[14]
|
||||
variable C26 equal v_F26+v_B[15]
|
||||
|
||||
variable C34 equal v_F34+v_B[16]
|
||||
variable C35 equal v_F35+v_B[17]
|
||||
variable C36 equal v_F36+v_B[18]
|
||||
|
||||
variable C45 equal v_F45+v_B[19]
|
||||
variable C46 equal v_F46+v_B[20]
|
||||
|
||||
variable C56 equal v_F56+v_B[21]
|
||||
|
||||
thermo ${nthermo}
|
||||
thermo 1500
|
||||
thermo_style custom step temp pe press density f_avt f_avp f_avpe v_F11 v_F22 v_F33 v_F44 v_F55 v_F66 v_F12 v_F13 v_F23 v_B[*8] v_B[12]
|
||||
|
||||
thermo_modify norm no
|
||||
|
||||
run ${nrun}
|
||||
run 150000
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.808 | 3.808 | 3.809 Mbytes
|
||||
Step Temp PotEng Press Density f_avt f_avp f_avpe v_F11 v_F22 v_F33 v_F44 v_F55 v_F66 v_F12 v_F13 v_F23 v_B[1] v_B[2] v_B[3] v_B[4] v_B[5] v_B[6] v_B[7] v_B[8] v_B[12]
|
||||
0 1496.4515 -1030.8279 1702.5821 2.2938491 0 0 0 -0 -0 -0 -0 -0 -0 -0 -0 -0 0 0 0 0 0 0 0 0 0
|
||||
1500 1488.0457 -1029.7336 235.49231 2.2938491 1491.6476 -209.95869 -4.1259067 -63.72574 -52.347237 -72.863469 -20.2529 -21.202225 -36.80768 15.820914 36.256996 27.837899 205.06161 205.28482 228.74061 53.516205 53.666764 76.479575 51.898427 28.841484 28.947835
|
||||
3000 1375.6945 -1032.3272 -1432.388 2.2938491 1483.7188 -14.944433 -4.1309886 -67.857182 -50.461537 -79.041956 -20.359329 -18.394118 -30.634049 16.973116 39.991949 29.200709 205.96072 205.57169 228.76797 53.760188 53.974806 76.829718 51.809223 28.715153 28.726595
|
||||
4500 1526.5784 -1034.4597 1558.1337 2.2938491 1482.7867 -70.886348 -4.1310256 -67.022382 -54.684704 -77.069485 -22.576461 -17.672784 -32.228898 21.458044 38.393569 27.72595 204.72251 205.88009 229.07903 53.899658 53.829006 76.717342 51.727843 28.636004 28.863718
|
||||
6000 1491.1951 -1030.0995 562.54917 2.2938491 1482.4806 -60.021349 -4.1307545 -66.909586 -58.886858 -80.148099 -22.601629 -19.09635 -33.473899 22.377747 38.855891 30.853996 204.70732 205.70649 229.01661 53.84119 53.800462 76.711553 51.690081 28.694904 28.797116
|
||||
7500 1330.8214 -1035.6828 -1407.4142 2.2938491 1480.7544 -63.898974 -4.1310393 -62.886575 -58.471219 -80.882593 -20.651266 -18.941729 -34.494541 18.287621 38.644547 32.466665 204.67832 205.92138 228.89129 53.887237 53.779706 76.803588 51.754653 28.661714 28.868533
|
||||
9000 1377.3139 -1030.6102 -814.50808 2.2938491 1480.0394 -57.969892 -4.1308955 -62.399927 -57.505746 -80.761377 -20.199819 -21.000829 -36.738929 17.319159 39.700869 31.315234 204.64296 206.17515 228.48224 53.911268 53.704831 76.8708 51.796155 28.641886 28.861077
|
||||
10500 1419.4538 -1032.4784 -554.39941 2.2938491 1481.1811 -7.9992199 -4.1309985 -59.045791 -61.164487 -82.861664 -19.890936 -21.168588 -35.873778 16.458244 37.100379 35.570692 204.9188 205.93531 228.57289 53.947197 53.739418 76.918077 51.784088 28.653206 28.87283
|
||||
12000 1442.3335 -1030.2902 -131.99922 2.2938491 1482.4991 25.724832 -4.1307257 -58.119089 -60.519191 -82.155615 -20.069823 -21.727839 -36.795312 16.944019 35.542297 35.788632 205.06536 205.89715 228.49105 53.949154 53.764738 76.945863 51.812548 28.698335 28.903557
|
||||
13500 1618.255 -1034.0691 448.39746 2.2938491 1482.9429 33.42958 -4.1306128 -59.840288 -61.599932 -82.215965 -20.598551 -21.492035 -36.443374 17.607876 36.241716 35.998172 205.07866 205.84943 228.61637 53.944979 53.774191 76.903895 51.792701 28.74114 28.89238
|
||||
15000 1364.3796 -1029.6878 -966.13025 2.2938491 1483.2726 65.784103 -4.1306007 -58.826126 -60.177687 -80.570212 -20.026628 -22.061421 -37.332987 16.618347 35.824117 34.991167 205.15731 205.79483 228.63407 53.929721 53.813353 76.896163 51.776923 28.752029 28.878669
|
||||
16500 1669.1757 -1031.0699 43.341777 2.2938491 1483.2491 18.99268 -4.1304591 -59.962016 -59.15211 -80.102432 -20.399129 -22.025441 -37.82746 17.082159 36.290705 33.775651 205.14266 205.7193 228.63038 53.925355 53.785453 76.855119 51.737872 28.759369 28.898142
|
||||
18000 1550.5382 -1027.3945 -1246.0289 2.2938491 1483.6491 5.7408759 -4.1303353 -59.35016 -58.728701 -78.818663 -20.150701 -21.942883 -37.891844 17.203814 35.337637 33.285126 205.13384 205.6063 228.57531 53.891378 53.769275 76.832714 51.74568 28.791121 28.877624
|
||||
19500 1629.5036 -1036.9849 -451.26178 2.2938491 1484.1226 27.288331 -4.1304459 -58.665989 -60.109261 -78.714857 -20.404554 -21.983442 -37.992827 17.117122 34.608111 34.643094 205.23998 205.53366 228.59186 53.890849 53.787956 76.856299 51.736162 28.786354 28.85888
|
||||
21000 1472.5544 -1032.859 -20.186692 2.2938491 1483.3486 19.365496 -4.130639 -59.030496 -61.687931 -79.499878 -21.045487 -21.978669 -37.750071 17.282482 34.752705 35.830146 205.166 205.4977 228.68839 53.897034 53.798516 76.833481 51.716388 28.777538 28.853221
|
||||
22500 1538.3331 -1029.4222 -1516.1779 2.2938491 1483.9369 9.3663668 -4.1304658 -59.601342 -61.528294 -79.886775 -21.058116 -21.744815 -37.415441 17.458006 35.03524 35.490302 205.15957 205.3737 228.66857 53.875938 53.82329 76.813455 51.710539 28.807394 28.846491
|
||||
24000 1640.6306 -1032.8747 1820.5076 2.2938491 1484.3582 -2.9605818 -4.1303985 -60.752912 -62.308755 -80.507722 -21.295171 -21.728498 -37.85529 17.636088 35.38702 36.141494 205.19032 205.28915 228.69633 53.859405 53.858117 76.802512 51.728172 28.822365 28.83436
|
||||
25500 1432.5405 -1036.4177 165.16737 2.2938491 1483.2229 8.3729002 -4.1307362 -60.653401 -61.891943 -80.020623 -21.215377 -21.694568 -37.770769 17.468376 35.128883 36.013452 205.2687 205.29914 228.65445 53.868129 53.866433 76.831986 51.734064 28.809762 28.823143
|
||||
27000 1459.7165 -1032.2704 555.49626 2.2938491 1483.5999 29.734336 -4.1307773 -60.348436 -62.451484 -79.397912 -21.536942 -21.312644 -37.473352 18.07619 34.322981 36.063688 205.28479 205.36871 228.6014 53.882785 53.860318 76.843783 51.736186 28.791218 28.824958
|
||||
28500 1398.7866 -1032.325 -228.86327 2.2938491 1482.9241 10.135953 -4.1308163 -60.923204 -62.1935 -80.289996 -21.326799 -21.465421 -37.781979 17.525986 35.112803 36.122375 205.33196 205.38849 228.51467 53.877397 53.85885 76.855869 51.748421 28.791318 28.810646
|
||||
30000 1609.4626 -1026.1198 2151.4352 2.2938491 1482.737 -6.9747499 -4.130764 -62.14162 -62.578377 -79.864982 -21.683154 -21.501264 -37.647952 18.064145 35.592848 35.670682 205.30816 205.42759 228.45924 53.874997 53.845931 76.855299 51.757648 28.798886 28.822951
|
||||
31500 1535.1988 -1030.7627 1962.4562 2.2938491 1482.9354 -2.7241836 -4.1306143 -61.870375 -62.851578 -80.524128 -21.560593 -21.908782 -38.604429 18.110966 35.564598 36.054336 205.32395 205.40536 228.48839 53.874999 53.854825 76.856925 51.764937 28.810228 28.831593
|
||||
33000 1570.1208 -1026.2494 351.76291 2.2938491 1482.996 -7.4807931 -4.130577 -62.238722 -63.288756 -80.80606 -21.615247 -21.67204 -38.37626 18.053097 35.862534 36.372658 205.33168 205.41606 228.43691 53.871561 53.849411 76.854679 51.770903 28.813329 28.832923
|
||||
34500 1432.3272 -1031.7548 419.21972 2.2938491 1482.7892 -28.425324 -4.1304667 -61.926882 -63.333125 -80.201249 -21.557493 -21.477997 -38.188053 17.990156 35.484765 36.40502 205.32852 205.36594 228.42193 53.858032 53.85339 76.845155 51.776258 28.810311 28.83193
|
||||
36000 1461.1221 -1031.0936 -732.09091 2.2938491 1482.7576 -17.70291 -4.1306165 -62.179266 -62.986391 -81.351014 -21.399698 -21.423609 -38.39933 17.389924 36.483096 36.528136 205.36025 205.37113 228.45226 53.869219 53.85851 76.853637 51.780873 28.812037 28.835983
|
||||
37500 1504.8525 -1035.0799 1917.6077 2.2938491 1482.2878 -23.877209 -4.1306315 -62.332808 -63.43488 -81.773513 -21.40584 -21.375369 -38.287661 17.372388 36.472678 37.074729 205.36817 205.37669 228.40654 53.854172 53.855291 76.849674 51.775051 28.80071 28.818624
|
||||
39000 1467.8385 -1033.4844 685.3059 2.2938491 1481.8721 -31.824125 -4.1307881 -63.029639 -63.482571 -82.632663 -21.710699 -21.140028 -38.056647 17.507416 37.185033 37.136598 205.33141 205.38158 228.41356 53.864319 53.853944 76.842991 51.764685 28.788943 28.816327
|
||||
40500 1471.3714 -1035.0313 -661.11589 2.2938491 1482.1911 -28.660441 -4.1307331 -63.073554 -63.301254 -81.939449 -21.849646 -21.333366 -38.459438 17.701055 36.929221 36.777905 205.3174 205.38828 228.42064 53.864766 53.857226 76.830391 51.764266 28.789323 28.813992
|
||||
42000 1524.1294 -1035.634 2140.1687 2.2938491 1481.9241 -26.308067 -4.1307414 -63.243189 -62.730676 -81.627378 -21.801779 -21.351359 -38.561895 17.541375 37.122985 36.480135 205.34025 205.40651 228.42086 53.866239 53.864292 76.836071 51.765489 28.788169 28.810743
|
||||
43500 1432.3705 -1034.551 526.49996 2.2938491 1482.1016 -20.246935 -4.1307637 -62.7724 -62.037498 -80.906378 -21.565193 -21.248644 -38.30893 17.35505 36.763529 35.974546 205.35875 205.40419 228.41899 53.869164 53.863535 76.833317 51.761902 28.785203 28.815597
|
||||
45000 1490.388 -1032.0658 956.44619 2.2938491 1482.0953 -16.260449 -4.1307284 -62.718709 -61.819139 -80.292247 -21.55464 -21.249523 -38.355562 17.650135 36.482629 35.521216 205.36793 205.41743 228.39993 53.868999 53.866369 76.841723 51.766771 28.793869 28.808214
|
||||
46500 1356.2575 -1032.0811 -502.03492 2.2938491 1482.1181 -12.636107 -4.13075 -62.68624 -61.442684 -80.301091 -21.478828 -21.171205 -38.25252 17.41833 36.696398 35.405695 205.36772 205.38631 228.3701 53.859688 53.869887 76.850495 51.770439 28.794225 28.795947
|
||||
48000 1462.4861 -1032.4019 657.08276 2.2938491 1482.05 -21.340898 -4.1306466 -62.635163 -61.415766 -79.917249 -21.386814 -21.256478 -38.35836 17.260015 36.61439 35.397473 205.30205 205.37133 228.40523 53.861273 53.865346 76.83163 51.771796 28.797153 28.801011
|
||||
49500 1403.792 -1033.3865 -106.37364 2.2938491 1481.9419 -13.709551 -4.1307951 -62.875109 -61.637029 -79.597373 -21.505971 -21.141812 -38.230756 17.55599 36.546467 35.220436 205.29491 205.41266 228.39157 53.866215 53.872264 76.830304 51.758539 28.787714 28.79857
|
||||
51000 1438.1787 -1032.0109 -1059.9064 2.2938491 1481.6449 -15.09976 -4.1309897 -62.670557 -61.561705 -79.379648 -21.567968 -21.055659 -38.015182 17.671904 36.332941 35.014233 205.32924 205.40088 228.39835 53.868539 53.885315 76.822335 51.745659 28.789851 28.792545
|
||||
52500 1382.2099 -1033.058 -1259.1214 2.2938491 1481.5946 -20.300497 -4.13093 -63.232758 -62.310412 -79.804684 -21.802267 -21.260561 -38.419579 18.056561 36.720771 34.972269 205.34284 205.35156 228.41342 53.864857 53.891003 76.81602 51.732483 28.791137 28.791887
|
||||
54000 1533.7764 -1028.7613 1714.1927 2.2938491 1481.7208 -28.620488 -4.1308301 -63.113526 -61.903055 -79.382866 -21.730147 -21.21458 -38.316562 18.001225 36.474036 34.681959 205.34377 205.31381 228.39872 53.84474 53.889496 76.812664 51.743856 28.802121 28.781409
|
||||
55500 1523.4727 -1033.3641 -612.71038 2.2938491 1481.8812 -36.263593 -4.1307128 -63.926005 -61.676301 -79.572696 -21.935651 -21.124984 -38.120805 18.30654 36.789152 34.374772 205.31795 205.35529 228.36668 53.847443 53.882195 76.806901 51.74734 28.814592 28.796537
|
||||
57000 1491.3678 -1026.9983 -1119.4609 2.2938491 1481.9455 -36.326068 -4.1306892 -63.595683 -61.564985 -79.974258 -21.822985 -21.136666 -38.16275 18.083171 36.766293 34.707154 205.29618 205.33458 228.38626 53.852279 53.878924 76.797511 51.735536 28.815462 28.802463
|
||||
58500 1438.7756 -1027.9678 -1657.13 2.2938491 1481.9051 -46.49998 -4.1306702 -63.970101 -61.372119 -79.511332 -21.995264 -21.032781 -38.038112 18.401226 36.639522 34.227378 205.29966 205.32376 228.38361 53.852024 53.875838 76.788068 51.734772 28.81576 28.803892
|
||||
60000 1325.4993 -1034.1913 -2362.9866 2.2938491 1481.5012 -44.903145 -4.1307851 -63.963407 -61.431254 -79.683191 -22.024759 -21.138562 -38.223052 18.153279 36.826694 34.405325 205.27702 205.36875 228.40644 53.856994 53.875391 76.799152 51.731492 28.811173 28.797945
|
||||
61500 1505.9305 -1036.2556 132.06247 2.2938491 1481.6293 -37.731588 -4.1308223 -64.381464 -61.674639 -80.188334 -22.158723 -21.108889 -38.248855 18.390358 37.059536 34.455424 205.23517 205.35912 228.41484 53.864166 53.876015 76.794352 51.722323 28.804043 28.801179
|
||||
63000 1534.39 -1039.4484 1046.653 2.2938491 1481.7949 -33.380601 -4.1308464 -64.068931 -61.368649 -79.704263 -22.130922 -21.067286 -38.215994 18.495768 36.761782 34.189797 205.22412 205.35391 228.43945 53.869115 53.87449 76.793337 51.712686 28.794684 28.800456
|
||||
64500 1361.7518 -1030.5694 790.72852 2.2938491 1481.8251 -28.691877 -4.1308571 -64.06363 -61.273278 -79.676705 -22.16565 -21.02496 -38.172259 18.638855 36.719131 34.006715 205.20559 205.35747 228.42261 53.874341 53.871631 76.797534 51.715519 28.789202 28.800286
|
||||
66000 1493.9592 -1034.8315 -83.381519 2.2938491 1481.8804 -28.444673 -4.130839 -63.871998 -60.922315 -79.543208 -22.084939 -21.051796 -38.178075 18.469097 36.653501 33.983218 205.17353 205.37012 228.4333 53.873209 53.87128 76.793735 51.715772 28.787185 28.799271
|
||||
67500 1421.276 -1033.8109 -435.15037 2.2938491 1482.0268 -15.717566 -4.1308595 -63.961701 -61.265171 -79.32614 -22.181352 -20.923325 -37.927752 18.58702 36.575619 34.041641 205.20462 205.4057 228.41483 53.873248 53.867409 76.806453 51.725025 28.781635 28.790933
|
||||
69000 1462.71 -1031.786 2044.924 2.2938491 1482.0808 -12.41913 -4.1308487 -63.537939 -61.572781 -79.813735 -22.037844 -20.940539 -37.978104 18.246032 36.52598 34.631512 205.21991 205.43641 228.3772 53.872474 53.864337 76.817521 51.736948 28.777643 28.790877
|
||||
70500 1460.7684 -1032.5687 -950.70337 2.2938491 1482.2232 -6.1090924 -4.1308194 -62.959394 -61.457796 -79.687401 -21.885475 -20.919469 -37.921646 18.034683 36.313758 34.737829 205.22464 205.41986 228.36249 53.872577 53.869324 76.818318 51.735068 28.780852 28.790481
|
||||
72000 1421.4484 -1031.353 1648.2423 2.2938491 1482.362 -8.171728 -4.1308339 -62.919483 -61.526828 -79.571975 -21.913281 -20.822948 -37.684888 18.014821 36.170823 34.809531 205.23354 205.40265 228.37137 53.876829 53.868192 76.821146 51.735902 28.781575 28.799457
|
||||
73500 1752.498 -1034.2169 1469.9503 2.2938491 1482.5906 -3.8737403 -4.130845 -62.630533 -61.309844 -79.729568 -21.758626 -20.825548 -37.860657 17.748076 36.259904 34.845837 205.22997 205.41547 228.3844 53.883713 53.868296 76.824464 51.735899 28.783023 28.803298
|
||||
75000 1520.6212 -1036.5004 837.2324 2.2938491 1482.4238 -0.1913038 -4.1308831 -62.821147 -61.828489 -79.567323 -21.889326 -20.789721 -37.714104 17.879632 36.22222 34.919953 205.2442 205.41386 228.37542 53.88291 53.867274 76.830786 51.73158 28.778935 28.794923
|
||||
76500 1439.6706 -1034.3536 3.867216 2.2938491 1482.3799 2.9201733 -4.1309078 -63.110409 -61.628579 -79.646303 -21.943803 -20.784043 -37.709136 18.090962 36.339502 34.640705 205.22882 205.4377 228.37991 53.889722 53.867867 76.832127 51.730291 28.776106 28.800613
|
||||
78000 1472.2878 -1032.0488 606.92009 2.2938491 1482.4315 4.0162921 -4.1308864 -63.18742 -61.476216 -79.518345 -21.915006 -20.795344 -37.685095 18.160875 36.317768 34.562962 205.21304 205.4681 228.35132 53.888419 53.860959 76.832795 51.726368 28.769804 28.803835
|
||||
79500 1512.5998 -1031.4782 -608.33112 2.2938491 1482.4683 -4.9946179 -4.1308672 -63.136709 -61.38976 -79.342774 -21.877029 -20.790716 -37.765995 18.082202 36.307384 34.529887 205.20173 205.45621 228.33612 53.884127 53.85096 76.827797 51.725854 28.764443 28.800151
|
||||
81000 1517.4109 -1028.3826 -2043.4874 2.2938491 1482.2404 -19.291403 -4.130792 -62.826972 -61.57491 -78.919307 -21.815485 -20.773717 -37.72361 18.034102 35.870919 34.590596 205.18765 205.42705 228.3524 53.878666 53.848387 76.814541 51.723458 28.771787 28.801959
|
||||
82500 1495.0416 -1034.9971 -919.28281 2.2938491 1482.5918 -7.0685741 -4.1308239 -62.741622 -61.394991 -78.779816 -21.795693 -20.713253 -37.628978 18.028438 35.854382 34.286915 205.18358 205.42059 228.39152 53.88507 53.855289 76.812978 51.718793 28.771939 28.803997
|
||||
84000 1491.0232 -1032.0478 1693.2093 2.2938491 1482.6179 -13.503477 -4.1306843 -62.623399 -61.545116 -78.875891 -21.831602 -20.760705 -37.783204 18.049826 35.698982 34.461373 205.18823 205.41432 228.37952 53.880292 53.848427 76.812319 51.723745 28.776002 28.809842
|
||||
85500 1432.7633 -1032.698 -881.37505 2.2938491 1482.5743 -10.555756 -4.1306695 -62.232152 -61.412377 -78.830213 -21.727847 -20.801103 -37.812275 17.923531 35.499394 34.546639 205.19889 205.41789 228.36824 53.880011 53.849407 76.819282 51.727384 28.780783 28.812392
|
||||
87000 1485.3288 -1032.6691 158.89155 2.2938491 1482.5535 -6.3950299 -4.1307187 -62.169286 -61.063223 -78.970108 -21.61197 -20.763121 -37.82023 17.757088 35.636063 34.438868 205.1894 205.43526 228.38369 53.883498 53.850233 76.819949 51.726626 28.776566 28.814967
|
||||
88500 1504.1685 -1034.896 -576.81489 2.2938491 1482.5577 -4.2302198 -4.1307273 -62.060242 -60.91541 -79.120582 -21.5292 -20.789763 -37.890171 17.627385 35.769308 34.444455 205.17713 205.41733 228.41274 53.884038 53.851418 76.815226 51.720575 28.778578 28.81437
|
||||
90000 1449.8972 -1033.1249 16.828339 2.2938491 1482.5956 -3.7681039 -4.1306958 -62.088756 -60.725318 -79.170616 -21.492856 -20.734831 -37.741223 17.584396 35.868249 34.318289 205.18548 205.4084 228.40148 53.880047 53.853611 76.816207 51.723692 28.779781 28.809322
|
||||
91500 1416.2681 -1033.1616 -16.270943 2.2938491 1482.4743 -10.282897 -4.1306355 -62.133545 -60.706158 -79.069992 -21.526357 -20.751961 -37.744268 17.678691 35.77502 34.270056 205.20409 205.40965 228.38688 53.875395 53.853283 76.818389 51.731399 28.784679 28.812085
|
||||
93000 1641.0262 -1032.9652 1541.4778 2.2938491 1482.7239 -0.21530915 -4.1306987 -62.103472 -60.524542 -78.94244 -21.416169 -20.762777 -37.724968 17.503079 35.79639 34.254575 205.21819 205.4208 228.38518 53.874775 53.859201 76.82538 51.73286 28.787014 28.806284
|
||||
94500 1446.894 -1033.0546 -1172.8149 2.2938491 1482.6464 3.4467336 -4.1307822 -62.347354 -60.242764 -79.472893 -21.34953 -20.717759 -37.687715 17.289476 36.186844 34.277361 205.23165 205.43019 228.39821 53.884069 53.865596 76.827934 51.732077 28.786882 28.805655
|
||||
96000 1542.079 -1029.6926 322.45446 2.2938491 1482.5441 4.6485293 -4.1308136 -62.206988 -59.973518 -79.080994 -21.288972 -20.760823 -37.729071 17.259751 36.128248 33.998066 205.24388 205.42381 228.41608 53.886007 53.867776 76.82741 51.731615 28.791259 28.805397
|
||||
97500 1487.9454 -1034.7172 820.51649 2.2938491 1482.5632 8.5386652 -4.1308234 -62.143296 -60.101635 -78.931963 -21.290736 -20.716267 -37.692871 17.462016 36.002029 33.918161 205.26305 205.43429 228.40827 53.888433 53.870451 76.826913 51.728767 28.791481 28.804241
|
||||
99000 1368.2594 -1031.2037 593.35668 2.2938491 1482.6064 5.0925632 -4.1307682 -61.963501 -60.016279 -78.857674 -21.245113 -20.75973 -37.759628 17.293147 36.020666 33.897023 205.26324 205.41903 228.40538 53.882522 53.868615 76.826529 51.734223 28.797165 28.804278
|
||||
100500 1442.5153 -1033.8773 -538.06378 2.2938491 1482.5806 8.0051295 -4.1307853 -61.807415 -59.816464 -78.885211 -21.182274 -20.821701 -37.887086 17.136467 36.03321 33.886956 205.29244 205.41979 228.40702 53.882321 53.875874 76.834725 51.739661 28.801012 28.804575
|
||||
102000 1523.8256 -1030.5549 1412.4566 2.2938491 1482.5866 4.0411856 -4.1307569 -61.444398 -59.781654 -78.484191 -21.18101 -20.822776 -37.865635 17.152952 35.720218 33.798513 205.2959 205.39482 228.41979 53.878609 53.877207 76.830098 51.741804 28.807055 28.805499
|
||||
103500 1577.9333 -1030.2793 16.968578 2.2938491 1482.4554 1.2961629 -4.1307672 -61.397825 -59.829587 -78.4479 -21.161504 -20.867524 -37.888147 17.149447 35.662363 33.851317 205.28757 205.3981 228.43413 53.882435 53.873014 76.827589 51.735462 28.805202 28.810239
|
||||
105000 1337.0075 -1031.8541 -2721.9544 2.2938491 1482.4268 -4.353932 -4.1307412 -61.705223 -59.747259 -78.609622 -21.165441 -20.851207 -37.876114 17.14923 35.951734 33.665587 205.27089 205.39074 228.43789 53.879034 53.870275 76.822978 51.73248 28.802281 28.81082
|
||||
106500 1422.8946 -1030.8343 -800.38058 2.2938491 1482.5115 -4.0049886 -4.1307542 -61.643384 -59.644844 -78.475169 -21.104781 -20.828498 -37.805234 16.983794 35.924403 33.682427 205.27511 205.39208 228.44888 53.881421 53.873402 76.821913 51.730452 28.801513 28.816076
|
||||
108000 1576.0145 -1032.7976 973.46949 2.2938491 1482.6158 3.0627527 -4.1307693 -61.632096 -59.704639 -78.39173 -21.106554 -20.866293 -37.84322 16.999887 35.7367 33.736853 205.27847 205.39567 228.46373 53.883841 53.8794 76.823598 51.724192 28.797812 28.814282
|
||||
109500 1469.798 -1035.4088 -1513.3569 2.2938491 1482.5815 -2.3554776 -4.1307587 -61.409226 -59.368417 -78.056976 -20.987396 -20.922787 -37.905832 16.80989 35.603164 33.571735 205.29739 205.39186 228.45528 53.881647 53.883201 76.826509 51.727265 28.803221 28.816387
|
||||
111000 1450.1364 -1034.8692 535.01425 2.2938491 1482.5086 -4.9493018 -4.1307925 -61.853187 -59.298301 -78.058449 -21.0476 -20.870886 -37.809302 16.931849 35.815648 33.395258 205.30581 205.38706 228.47139 53.885853 53.883453 76.822939 51.72578 28.798242 28.817665
|
||||
112500 1449.2612 -1032.1626 -707.9713 2.2938491 1482.6231 -5.6051571 -4.1307318 -61.617376 -59.400658 -77.86748 -21.058008 -20.900491 -37.885275 16.941367 35.595081 33.457412 205.31006 205.37483 228.46421 53.884923 53.884787 76.818386 51.725453 28.799728 28.818511
|
||||
114000 1472.8275 -1037.0664 -442.38894 2.2938491 1482.8034 -1.1760851 -4.13075 -61.604652 -59.42193 -77.729625 -21.108945 -20.839988 -37.816934 17.027186 35.528809 33.333712 205.2996 205.40083 228.47441 53.889449 53.885434 76.822691 51.72532 28.799205 28.817456
|
||||
115500 1412.2073 -1033.3813 -859.54093 2.2938491 1482.7115 -6.3971107 -4.1307164 -61.582698 -59.540524 -77.958489 -21.065292 -20.841779 -37.81416 17.014851 35.663213 33.266402 205.30868 205.39757 228.44955 53.887583 53.882631 76.821441 51.730925 28.798319 28.820824
|
||||
117000 1460.2307 -1028.9074 -1164.6613 2.2938491 1482.657 -7.8697826 -4.1307244 -61.82235 -59.692597 -77.850871 -21.124418 -20.764516 -37.690786 17.155656 35.649724 33.269516 205.30451 205.41455 228.45187 53.893125 53.885988 76.81911 51.730761 28.798798 28.824658
|
||||
118500 1493.0731 -1028.7066 -260.29362 2.2938491 1482.7469 -1.8511441 -4.1307413 -61.826554 -59.86035 -77.828964 -21.126638 -20.753378 -37.660607 17.198524 35.664955 33.285591 205.31841 205.42978 228.43324 53.895373 53.888281 76.82351 51.731769 28.799645 28.824431
|
||||
120000 1345.6123 -1029.9346 -1895.5256 2.2938491 1482.7843 -4.5972195 -4.1307269 -61.669058 -59.838425 -77.745234 -21.161305 -20.848334 -37.830906 17.174454 35.604439 33.297851 205.32668 205.43762 228.42017 53.889381 53.883438 76.823854 51.733939 28.794303 28.822327
|
||||
121500 1407.0748 -1031.8136 426.75808 2.2938491 1482.8284 -1.6468876 -4.1307603 -61.64701 -59.903233 -77.693914 -21.163628 -20.835781 -37.828167 17.171387 35.563809 33.348664 205.34563 205.44066 228.4023 53.88813 53.886137 76.827345 51.735371 28.794168 28.819736
|
||||
123000 1526.2861 -1032.537 852.79109 2.2938491 1482.9332 5.0560365 -4.1307796 -61.724187 -59.904131 -77.473899 -21.179869 -20.815648 -37.857571 17.267887 35.516275 33.238968 205.36759 205.43856 228.38631 53.885394 53.886842 76.832314 51.732243 28.791888 28.813868
|
||||
124500 1529.8037 -1031.1582 -92.453284 2.2938491 1483.0597 8.0257434 -4.130767 -61.73912 -59.872674 -77.532647 -21.149928 -20.801849 -37.741413 17.188 35.59366 33.235229 205.37362 205.43069 228.39692 53.88626 53.886586 76.834567 51.73587 28.793201 28.81626
|
||||
126000 1496.3891 -1033.1452 -367.03965 2.2938491 1483.0771 4.6045133 -4.1307269 -61.729431 -59.954414 -77.338248 -21.179207 -20.784619 -37.762061 17.353033 35.439541 33.189469 205.36796 205.44072 228.37772 53.885265 53.881811 76.830859 51.738138 28.792247 28.818739
|
||||
127500 1466.1306 -1030.612 -926.29759 2.2938491 1483.133 11.366773 -4.1307722 -61.602447 -59.920526 -77.282372 -21.159672 -20.75159 -37.719968 17.307656 35.296921 33.236486 205.37779 205.44691 228.38745 53.887086 53.885763 76.836326 51.737488 28.792599 28.815257
|
||||
129000 1569.3651 -1032.9186 -442.35004 2.2938491 1483.1369 10.328658 -4.1307387 -61.543466 -59.942662 -77.483904 -21.119911 -20.722378 -37.671723 17.281249 35.232627 33.459675 205.36599 205.43931 228.40108 53.884216 53.882413 76.831442 51.737409 28.790919 28.811477
|
||||
130500 1421.911 -1031.8139 -758.70123 2.2938491 1483.0449 11.4085 -4.1307613 -61.333773 -59.934246 -77.426746 -21.113826 -20.713965 -37.674443 17.157344 35.141168 33.569733 205.36146 205.44547 228.4022 53.886232 53.879268 76.832738 51.73627 28.786769 28.811493
|
||||
132000 1524.2191 -1037.407 -480.85722 2.2938491 1482.8528 8.9287162 -4.1308006 -61.561432 -60.092757 -77.742507 -21.167795 -20.674863 -37.639706 17.29371 35.275171 33.678108 205.36428 205.45116 228.4058 53.889052 53.879475 76.834536 51.73562 28.786514 28.811264
|
||||
133500 1494.6866 -1034.7465 416.3259 2.2938491 1482.8997 8.7918538 -4.1307995 -61.539391 -60.210309 -78.095947 -21.12506 -20.675829 -37.641619 17.068859 35.348266 34.049804 205.37443 205.45053 228.39031 53.888328 53.87864 76.837876 51.741192 28.786138 28.811558
|
||||
135000 1569.7047 -1036.5833 1648.5811 2.2938491 1482.8373 16.413757 -4.1308862 -61.379715 -60.19875 -77.885213 -21.077149 -20.659689 -37.571815 17.039133 35.160383 34.027006 205.38045 205.47385 228.40044 53.89379 53.883916 76.84446 51.74077 28.782168 28.811503
|
||||
136500 1434.076 -1032.3999 1440.6873 2.2938491 1482.8065 20.877471 -4.130942 -61.250129 -60.36518 -77.797762 -21.173422 -20.644652 -37.555746 17.168354 34.98673 34.050232 205.39567 205.46987 228.41208 53.893145 53.888561 76.850201 51.742217 28.782951 28.809364
|
||||
138000 1435.6229 -1027.2932 -1994.0334 2.2938491 1482.9676 28.338068 -4.1309771 -61.286555 -60.502324 -77.929763 -21.144817 -20.627874 -37.5188 16.99209 35.098588 34.233379 205.38967 205.48076 228.41949 53.897481 53.889052 76.852273 51.743864 28.782553 28.811336
|
||||
139500 1351.2102 -1032.4433 -239.90235 2.2938491 1482.9605 27.292315 -4.1309341 -61.209087 -60.465858 -77.765563 -21.106356 -20.671478 -37.691344 16.943971 35.047976 34.174565 205.38424 205.48042 228.42161 53.896767 53.885832 76.847548 51.746591 28.779555 28.812114
|
||||
141000 1467.5087 -1031.9354 -532.99883 2.2938491 1482.8932 24.307649 -4.1309051 -61.070518 -60.441795 -77.624715 -21.086802 -20.640868 -37.683803 17.017529 34.883575 34.096205 205.37075 205.48554 228.42021 53.896931 53.882672 76.844472 51.745488 28.777347 28.815227
|
||||
142500 1426.8036 -1029.0269 475.29365 2.2938491 1482.9486 28.873848 -4.1309222 -61.253743 -60.394307 -77.623948 -21.117683 -20.666512 -37.724806 17.009433 34.985626 34.037536 205.38057 205.50055 228.40554 53.898614 53.880885 76.846518 51.744358 28.772507 28.8159
|
||||
144000 1442.207 -1031.8281 666.41114 2.2938491 1482.9324 27.849865 -4.1309475 -61.168217 -60.212673 -77.584118 -21.079119 -20.692903 -37.826824 16.878262 35.048543 34.002324 205.37899 205.51754 228.39212 53.90079 53.88167 76.847699 51.746645 28.771418 28.817434
|
||||
145500 1513.7861 -1032.8894 103.68291 2.2938491 1483.1433 26.889484 -4.1309369 -61.076852 -60.104649 -77.709917 -21.033322 -20.670939 -37.779427 16.717574 35.122343 34.057639 205.3625 205.52972 228.37916 53.90269 53.879604 76.847902 51.74393 28.76916 28.820449
|
||||
147000 1403.8295 -1038.4747 125.48856 2.2938491 1483.0944 25.436764 -4.1309291 -61.058221 -60.015165 -77.827606 -21.025708 -20.75728 -37.905513 16.756237 35.091941 34.043829 205.36839 205.52553 228.38543 53.902592 53.879578 76.848283 51.744624 28.771608 28.822339
|
||||
148500 1570.4334 -1030.4725 1176.9001 2.2938491 1482.9036 26.018243 -4.1309919 -60.988967 -59.970975 -77.596029 -21.062881 -20.789165 -38.050798 16.784906 34.917316 34.005084 205.36511 205.5204 228.39472 53.905268 53.883557 76.849572 51.742284 28.771597 28.820426
|
||||
150000 1637.0679 -1032.2165 1094.5581 2.2938491 1482.9569 27.608241 -4.1310012 -61.014673 -59.868323 -77.559954 -21.028486 -20.762668 -37.995752 16.75055 34.948738 33.9703 205.36993 205.53181 228.3843 53.905331 53.882296 76.852069 51.742975 28.773161 28.820754
|
||||
Loop time of 23.1063 on 4 procs for 150000 steps with 250 atoms
|
||||
|
||||
Performance: 429.638 ns/day, 0.056 hours/ns, 6491.724 timesteps/s
|
||||
99.9% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 13.514 | 15.049 | 16.345 | 27.6 | 65.13
|
||||
Neigh | 0.22265 | 0.23987 | 0.26064 | 2.8 | 1.04
|
||||
Comm | 2.4163 | 3.7264 | 5.2764 | 56.0 | 16.13
|
||||
Output | 0.0032872 | 0.0035512 | 0.0043178 | 0.7 | 0.02
|
||||
Modify | 3.7671 | 3.7877 | 3.8007 | 0.7 | 16.39
|
||||
Other | | 0.2998 | | | 1.30
|
||||
|
||||
Nlocal: 62.5 ave 88 max 40 min
|
||||
Histogram: 1 0 0 0 2 0 0 0 0 1
|
||||
Nghost: 432.75 ave 543 max 326 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 1650.5 ave 2334 max 1048 min
|
||||
Histogram: 1 0 0 0 2 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 6602
|
||||
Ave neighs/atom = 26.408
|
||||
Neighbor list builds = 2667
|
||||
Dangerous builds = 0
|
||||
|
||||
# Output final values
|
||||
|
||||
include final_output.in
|
||||
# Average moduli for cubic crystals
|
||||
|
||||
variable C11cubic equal (${C11}+${C22}+${C33})/3.0
|
||||
variable C11cubic equal (148.370873646034+${C22}+${C33})/3.0
|
||||
variable C11cubic equal (148.370873646034+149.679104177467+${C33})/3.0
|
||||
variable C11cubic equal (148.370873646034+149.679104177467+154.839963498785)/3.0
|
||||
variable C12cubic equal (${C12}+${C13}+${C23})/3.0
|
||||
variable C12cubic equal (68.4935246016777+${C13}+${C23})/3.0
|
||||
variable C12cubic equal (68.4935246016777+63.7218992685599+${C23})/3.0
|
||||
variable C12cubic equal (68.4935246016777+63.7218992685599+62.7910539636263)/3.0
|
||||
variable C44cubic equal (${C44}+${C55}+${C66})/3.0
|
||||
variable C44cubic equal (34.8846541689484+${C55}+${C66})/3.0
|
||||
variable C44cubic equal (34.8846541689484+35.1274361331555+${C66})/3.0
|
||||
variable C44cubic equal (34.8846541689484+35.1274361331555+40.8641262264389)/3.0
|
||||
|
||||
variable bulkmodulus equal (${C11cubic}+2*${C12cubic})/3.0
|
||||
variable bulkmodulus equal (150.963313774095+2*${C12cubic})/3.0
|
||||
variable bulkmodulus equal (150.963313774095+2*65.0021592779546)/3.0
|
||||
variable shearmodulus1 equal ${C44cubic}
|
||||
variable shearmodulus1 equal 36.9587388428476
|
||||
variable shearmodulus2 equal (${C11cubic}-${C12cubic})/2.0
|
||||
variable shearmodulus2 equal (150.963313774095-${C12cubic})/2.0
|
||||
variable shearmodulus2 equal (150.963313774095-65.0021592779546)/2.0
|
||||
variable poissonratio equal 1.0/(1.0+${C11cubic}/${C12cubic})
|
||||
variable poissonratio equal 1.0/(1.0+150.963313774095/${C12cubic})
|
||||
variable poissonratio equal 1.0/(1.0+150.963313774095/65.0021592779546)
|
||||
|
||||
# For Stillinger-Weber silicon, the analytical results
|
||||
# are known to be (E. R. Cowley, 1988):
|
||||
# C11 = 151.4 GPa
|
||||
# C12 = 76.4 GPa
|
||||
# C44 = 56.4 GPa
|
||||
|
||||
#print "========================================="
|
||||
#print "Components of the Elastic Constant Tensor"
|
||||
#print "========================================="
|
||||
|
||||
print "Elastic Constant C11 = ${C11} ${cunits}"
|
||||
Elastic Constant C11 = 148.370873646034 GPa
|
||||
print "Elastic Constant C22 = ${C22} ${cunits}"
|
||||
Elastic Constant C22 = 149.679104177467 GPa
|
||||
print "Elastic Constant C33 = ${C33} ${cunits}"
|
||||
Elastic Constant C33 = 154.839963498785 GPa
|
||||
|
||||
print "Elastic Constant C12 = ${C12} ${cunits}"
|
||||
Elastic Constant C12 = 68.4935246016777 GPa
|
||||
print "Elastic Constant C13 = ${C13} ${cunits}"
|
||||
Elastic Constant C13 = 63.7218992685599 GPa
|
||||
print "Elastic Constant C23 = ${C23} ${cunits}"
|
||||
Elastic Constant C23 = 62.7910539636263 GPa
|
||||
|
||||
print "Elastic Constant C44 = ${C44} ${cunits}"
|
||||
Elastic Constant C44 = 34.8846541689484 GPa
|
||||
print "Elastic Constant C55 = ${C55} ${cunits}"
|
||||
Elastic Constant C55 = 35.1274361331555 GPa
|
||||
print "Elastic Constant C66 = ${C66} ${cunits}"
|
||||
Elastic Constant C66 = 40.8641262264389 GPa
|
||||
|
||||
print "Elastic Constant C14 = ${C14} ${cunits}"
|
||||
Elastic Constant C14 = 6.92404731313863 GPa
|
||||
print "Elastic Constant C15 = ${C15} ${cunits}"
|
||||
Elastic Constant C15 = -0.241854528091832 GPa
|
||||
print "Elastic Constant C16 = ${C16} ${cunits}"
|
||||
Elastic Constant C16 = -0.348583506816062 GPa
|
||||
|
||||
print "Elastic Constant C24 = ${C24} ${cunits}"
|
||||
Elastic Constant C24 = -8.12880441353851 GPa
|
||||
print "Elastic Constant C25 = ${C25} ${cunits}"
|
||||
Elastic Constant C25 = 0.489292435379784 GPa
|
||||
print "Elastic Constant C26 = ${C26} ${cunits}"
|
||||
Elastic Constant C26 = 0.823159952503936 GPa
|
||||
|
||||
print "Elastic Constant C34 = ${C34} ${cunits}"
|
||||
Elastic Constant C34 = 0.696244884461012 GPa
|
||||
print "Elastic Constant C35 = ${C35} ${cunits}"
|
||||
Elastic Constant C35 = 0.0721961245198595 GPa
|
||||
print "Elastic Constant C36 = ${C36} ${cunits}"
|
||||
Elastic Constant C36 = -0.201416093587799 GPa
|
||||
|
||||
print "Elastic Constant C45 = ${C45} ${cunits}"
|
||||
Elastic Constant C45 = -0.310665193707046 GPa
|
||||
print "Elastic Constant C46 = ${C46} ${cunits}"
|
||||
Elastic Constant C46 = -0.491041219509184 GPa
|
||||
print "Elastic Constant C56 = ${C56} ${cunits}"
|
||||
Elastic Constant C56 = 7.93280717781775 GPa
|
||||
|
||||
print "========================================="
|
||||
=========================================
|
||||
print "Average properties for a cubic crystal"
|
||||
Average properties for a cubic crystal
|
||||
print "========================================="
|
||||
=========================================
|
||||
|
||||
print "Bulk Modulus = ${bulkmodulus} ${cunits}"
|
||||
Bulk Modulus = 93.6558774433347 GPa
|
||||
print "Shear Modulus 1 = ${shearmodulus1} ${cunits}"
|
||||
Shear Modulus 1 = 36.9587388428476 GPa
|
||||
print "Shear Modulus 2 = ${shearmodulus2} ${cunits}"
|
||||
Shear Modulus 2 = 42.9805772480702 GPa
|
||||
print "Poisson Ratio = ${poissonratio}"
|
||||
Poisson Ratio = 0.300984033972359
|
||||
|
||||
# summarize sampling protocol
|
||||
|
||||
variable tmp equal atoms
|
||||
print "Number of atoms = ${tmp}"
|
||||
Number of atoms = 250
|
||||
print "Stress sampling interval = ${nevery}"
|
||||
Stress sampling interval = 10
|
||||
variable tmp equal ${nrun}/${nevery}
|
||||
variable tmp equal 150000/${nevery}
|
||||
variable tmp equal 150000/10
|
||||
print "Stress sample count = ${tmp}"
|
||||
Stress sample count = 15000
|
||||
print "Born sampling interval = ${neveryborn}"
|
||||
Born sampling interval = 100
|
||||
variable tmp equal ${nrun}/${neveryborn}
|
||||
variable tmp equal 150000/${neveryborn}
|
||||
variable tmp equal 150000/100
|
||||
print "Born sample count = ${tmp}"
|
||||
Born sample count = 1500
|
||||
Total wall time: 0:00:25
|
||||
141
examples/ELASTIC_T/BORN_MATRIX/Silicon/output.in
Normal file
141
examples/ELASTIC_T/BORN_MATRIX/Silicon/output.in
Normal file
@ -0,0 +1,141 @@
|
||||
# Setup output
|
||||
|
||||
# Stress fluctuation term F
|
||||
|
||||
compute stress all pressure thermo_temp
|
||||
variable s1 equal c_stress[1]
|
||||
variable s2 equal c_stress[2]
|
||||
variable s3 equal c_stress[3]
|
||||
variable s4 equal c_stress[6]
|
||||
variable s5 equal c_stress[5]
|
||||
variable s6 equal c_stress[4]
|
||||
|
||||
variable s11 equal v_s1*v_s1
|
||||
variable s22 equal v_s2*v_s2
|
||||
variable s33 equal v_s3*v_s3
|
||||
variable s44 equal v_s4*v_s4
|
||||
variable s55 equal v_s5*v_s5
|
||||
variable s66 equal v_s6*v_s6
|
||||
variable s33 equal v_s3*v_s3
|
||||
variable s12 equal v_s1*v_s2
|
||||
variable s13 equal v_s1*v_s3
|
||||
variable s14 equal v_s1*v_s4
|
||||
variable s15 equal v_s1*v_s5
|
||||
variable s16 equal v_s1*v_s6
|
||||
variable s23 equal v_s2*v_s3
|
||||
variable s24 equal v_s2*v_s4
|
||||
variable s25 equal v_s2*v_s5
|
||||
variable s26 equal v_s2*v_s6
|
||||
variable s34 equal v_s3*v_s4
|
||||
variable s35 equal v_s3*v_s5
|
||||
variable s36 equal v_s3*v_s6
|
||||
variable s45 equal v_s4*v_s5
|
||||
variable s46 equal v_s4*v_s6
|
||||
variable s56 equal v_s5*v_s6
|
||||
|
||||
variable mytemp equal temp
|
||||
variable mypress equal press
|
||||
variable mype equal pe/atoms
|
||||
fix avt all ave/time ${nevery} ${nrepeat} ${nfreq} v_mytemp ave running
|
||||
fix avp all ave/time ${nevery} ${nrepeat} ${nfreq} v_mypress ave running
|
||||
fix avpe all ave/time ${nevery} ${nrepeat} ${nfreq} v_mype ave running
|
||||
fix avs all ave/time ${nevery} ${nrepeat} ${nfreq} v_s1 v_s2 v_s3 v_s4 v_s5 v_s6 ave running
|
||||
fix avssq all ave/time ${nevery} ${nrepeat} ${nfreq} &
|
||||
v_s11 v_s22 v_s33 v_s44 v_s55 v_s66 &
|
||||
v_s12 v_s13 v_s14 v_s15 v_s16 &
|
||||
v_s23 v_s24 v_s25 v_s26 &
|
||||
v_s34 v_s35 v_s36 &
|
||||
v_s45 v_s46 &
|
||||
v_s56 &
|
||||
ave running
|
||||
|
||||
# bar to GPa
|
||||
variable pconv equal 1.0e5/1.0e9
|
||||
variable cunits index GPa
|
||||
# metal unit constants from LAMMPS
|
||||
# force->nktv2p = 1.6021765e6;
|
||||
# force->boltz = 8.617343e-5;
|
||||
variable boltz equal 8.617343e-5
|
||||
variable nktv2p equal 1.6021765e6
|
||||
variable vkt equal vol/(${boltz}*${temp})/${nktv2p}
|
||||
variable ffac equal ${pconv}*${vkt}
|
||||
|
||||
variable F11 equal -(f_avssq[1]-f_avs[1]*f_avs[1])*${ffac}
|
||||
variable F22 equal -(f_avssq[2]-f_avs[2]*f_avs[2])*${ffac}
|
||||
variable F33 equal -(f_avssq[3]-f_avs[3]*f_avs[3])*${ffac}
|
||||
variable F44 equal -(f_avssq[4]-f_avs[4]*f_avs[4])*${ffac}
|
||||
variable F55 equal -(f_avssq[5]-f_avs[5]*f_avs[5])*${ffac}
|
||||
variable F66 equal -(f_avssq[6]-f_avs[6]*f_avs[6])*${ffac}
|
||||
|
||||
variable F12 equal -(f_avssq[7]-f_avs[1]*f_avs[2])*${ffac}
|
||||
variable F13 equal -(f_avssq[8]-f_avs[1]*f_avs[3])*${ffac}
|
||||
variable F14 equal -(f_avssq[9]-f_avs[1]*f_avs[4])*${ffac}
|
||||
variable F15 equal -(f_avssq[10]-f_avs[1]*f_avs[5])*${ffac}
|
||||
variable F16 equal -(f_avssq[11]-f_avs[1]*f_avs[6])*${ffac}
|
||||
|
||||
variable F23 equal -(f_avssq[12]-f_avs[2]*f_avs[3])*${ffac}
|
||||
variable F24 equal -(f_avssq[13]-f_avs[2]*f_avs[4])*${ffac}
|
||||
variable F25 equal -(f_avssq[14]-f_avs[2]*f_avs[5])*${ffac}
|
||||
variable F26 equal -(f_avssq[15]-f_avs[2]*f_avs[6])*${ffac}
|
||||
|
||||
variable F34 equal -(f_avssq[16]-f_avs[3]*f_avs[4])*${ffac}
|
||||
variable F35 equal -(f_avssq[17]-f_avs[3]*f_avs[5])*${ffac}
|
||||
variable F36 equal -(f_avssq[18]-f_avs[3]*f_avs[6])*${ffac}
|
||||
|
||||
variable F45 equal -(f_avssq[19]-f_avs[4]*f_avs[5])*${ffac}
|
||||
variable F46 equal -(f_avssq[20]-f_avs[4]*f_avs[6])*${ffac}
|
||||
|
||||
variable F56 equal -(f_avssq[21]-f_avs[5]*f_avs[6])*${ffac}
|
||||
|
||||
# Born term
|
||||
|
||||
compute virial all pressure NULL virial
|
||||
compute born all born/matrix numdiff ${delta} virial
|
||||
fix avborn all ave/time ${neveryborn} ${nrepeatborn} ${nfreq} c_born[*] ave running
|
||||
|
||||
variable bfac equal ${pconv}*${nktv2p}/vol
|
||||
variable B vector f_avborn*${bfac}
|
||||
|
||||
# Kinetic term
|
||||
|
||||
variable kfac equal ${pconv}*${nktv2p}*atoms*${boltz}*${temp}/vol
|
||||
variable K11 equal 4.0*${kfac}
|
||||
variable K22 equal 4.0*${kfac}
|
||||
variable K33 equal 4.0*${kfac}
|
||||
variable K44 equal 2.0*${kfac}
|
||||
variable K55 equal 2.0*${kfac}
|
||||
variable K66 equal 2.0*${kfac}
|
||||
|
||||
# Add F, K, and B together
|
||||
|
||||
variable C11 equal v_F11+v_B[1]+v_K11
|
||||
variable C22 equal v_F22+v_B[2]+v_K22
|
||||
variable C33 equal v_F33+v_B[3]+v_K33
|
||||
variable C44 equal v_F44+v_B[4]+v_K44
|
||||
variable C55 equal v_F55+v_B[5]+v_K55
|
||||
variable C66 equal v_F66+v_B[6]+v_K66
|
||||
|
||||
variable C12 equal v_F12+v_B[7]
|
||||
variable C13 equal v_F13+v_B[8]
|
||||
variable C14 equal v_F14+v_B[9]
|
||||
variable C15 equal v_F15+v_B[10]
|
||||
variable C16 equal v_F16+v_B[11]
|
||||
|
||||
variable C23 equal v_F23+v_B[12]
|
||||
variable C24 equal v_F24+v_B[13]
|
||||
variable C25 equal v_F25+v_B[14]
|
||||
variable C26 equal v_F26+v_B[15]
|
||||
|
||||
variable C34 equal v_F34+v_B[16]
|
||||
variable C35 equal v_F35+v_B[17]
|
||||
variable C36 equal v_F36+v_B[18]
|
||||
|
||||
variable C45 equal v_F45+v_B[19]
|
||||
variable C46 equal v_F46+v_B[20]
|
||||
|
||||
variable C56 equal v_F56+v_B[21]
|
||||
|
||||
thermo ${nthermo}
|
||||
thermo_style custom step temp pe press density f_avt f_avp f_avpe v_F11 v_F22 v_F33 v_F44 v_F55 v_F66 v_F12 v_F13 v_F23 v_B[*8] v_B[12]
|
||||
|
||||
thermo_modify norm no
|
||||
21
examples/ELASTIC_T/BORN_MATRIX/Silicon/potential.in
Normal file
21
examples/ELASTIC_T/BORN_MATRIX/Silicon/potential.in
Normal file
@ -0,0 +1,21 @@
|
||||
# NOTE: This script can be modified for different pair styles
|
||||
# See in.elastic for more info.
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
# Choose potential
|
||||
pair_style sw
|
||||
pair_coeff * * Si.sw Si
|
||||
|
||||
# Setup neighbor style
|
||||
neighbor 1.0 nsq
|
||||
neigh_modify once no every 1 delay 0 check yes
|
||||
|
||||
# Setup MD
|
||||
|
||||
timestep ${timestep}
|
||||
fix 4 all nve
|
||||
if "${thermostat} == 1" then &
|
||||
"fix 5 all langevin ${temp} ${temp} ${tdamp} ${seed}"
|
||||
|
||||
|
||||
1
examples/ELASTIC_T/DEFORMATION/Silicon/Si.sw
Symbolic link
1
examples/ELASTIC_T/DEFORMATION/Silicon/Si.sw
Symbolic link
@ -0,0 +1 @@
|
||||
../../../../potentials/Si.sw
|
||||
@ -2,7 +2,7 @@
|
||||
# See in.elastic for more info.
|
||||
|
||||
# we must undefine any fix ave/* fix before using reset_timestep
|
||||
if "$(is_defined(fix,avp)" then "unfix avp"
|
||||
if "$(is_defined(fix,avp))" then "unfix avp"
|
||||
reset_timestep 0
|
||||
|
||||
# Choose potential
|
||||
@ -1,18 +0,0 @@
|
||||
# DATE: 2007-06-11 CONTRIBUTOR: Aidan Thompson, athomps@sandia.gov CITATION: Stillinger and Weber, Phys Rev B, 31, 5262, (1985)
|
||||
# Stillinger-Weber parameters for various elements and mixtures
|
||||
# multiple entries can be added to this file, LAMMPS reads the ones it needs
|
||||
# these entries are in LAMMPS "metal" units:
|
||||
# epsilon = eV; sigma = Angstroms
|
||||
# other quantities are unitless
|
||||
|
||||
# format of a single entry (one or more lines):
|
||||
# element 1, element 2, element 3,
|
||||
# epsilon, sigma, a, lambda, gamma, costheta0, A, B, p, q, tol
|
||||
|
||||
# Here are the original parameters in metal units, for Silicon from:
|
||||
#
|
||||
# Stillinger and Weber, Phys. Rev. B, v. 31, p. 5262, (1985)
|
||||
#
|
||||
|
||||
Si Si Si 2.1683 2.0951 1.80 21.0 1.20 -0.333333333333
|
||||
7.049556277 0.6022245584 4.0 0.0 0.0
|
||||
@ -46,17 +46,17 @@ energy flux, and dTemp/dZ = temperature gradient.
|
||||
|
||||
(1) in.langevin
|
||||
|
||||
dQ = 8000 * 0.5*(0.905+0.947) / 100 / 18.82^2 / 2
|
||||
dQ = 8000 * 0.5*(0.890+0.883) / 100 / 18.82^2 / 2
|
||||
8000 atoms
|
||||
0.5*(0.905+0.947) = from log file =
|
||||
0.5*(0.890+0.883) = from log file =
|
||||
ave of total in/out energy for 2 regions normalized by # of atoms
|
||||
100 = 20,000 steps at 0.005 tau timestep = run time in tau
|
||||
xy box area = 18.82^2
|
||||
divide by 2 since energy flux goes in 2 directions due to periodic z
|
||||
dTemp = 0.578 from log file for average Temp difference between 2 regions
|
||||
dTemp = 0.574 from log file for average Temp difference between 2 regions
|
||||
dZ = 18.82
|
||||
|
||||
Kappa = 3.41
|
||||
Kappa = 3.29
|
||||
|
||||
(2) in.heat
|
||||
|
||||
@ -82,17 +82,17 @@ dZ = 18.82
|
||||
|
||||
Kappa = 3.45
|
||||
|
||||
(4) in.mp
|
||||
(4) in.mp
|
||||
|
||||
dQ = 15087 / 100 / 18.82^2 / 2
|
||||
15087 = cumulative delta energy, tallied by fix thermal/conductivity
|
||||
dQ = 15068 / 100 / 18.82^2 / 2
|
||||
15068 = cumulative delta energy, tallied by fix thermal/conductivity
|
||||
100 = 20,000 steps at 0.005 tau timestep = run time in tau
|
||||
xy box area = 18.82^2
|
||||
divide by 2 since energy flux goes in 2 directions due to periodic z
|
||||
dTemp = 1.16 from log file for average Temp difference between 2 regions
|
||||
dTemp = 1.175 from log file for average Temp difference between 2 regions
|
||||
dZ = 18.82
|
||||
|
||||
Kappa = 3.45
|
||||
Kappa = 3.41
|
||||
|
||||
(5) in.heatflux
|
||||
|
||||
@ -101,4 +101,4 @@ integration of the formulas discussed on the compute heat/flux doc
|
||||
page - the resulting value prints at the end of the run and is in the
|
||||
log file
|
||||
|
||||
Kappa = 3.78
|
||||
Kappa = 3.88
|
||||
|
||||
@ -3,36 +3,36 @@
|
||||
|
||||
# settings
|
||||
|
||||
variable x equal 10
|
||||
variable y equal 10
|
||||
variable z equal 20
|
||||
variable x equal 10
|
||||
variable y equal 10
|
||||
variable z equal 20
|
||||
|
||||
variable rho equal 0.6
|
||||
variable rho equal 0.6
|
||||
variable t equal 1.35
|
||||
variable rc equal 2.5
|
||||
variable rc equal 2.5
|
||||
|
||||
#variable rho equal 0.85
|
||||
#variable rho equal 0.85
|
||||
#variable t equal 0.7
|
||||
#variable rc equal 3.0
|
||||
#variable rc equal 3.0
|
||||
|
||||
# setup problem
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc ${rho}
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass 1 1.0
|
||||
lattice fcc ${rho}
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create $t 87287
|
||||
velocity all create $t 87287
|
||||
|
||||
pair_style lj/cut ${rc}
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_style lj/cut ${rc}
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1
|
||||
|
||||
# heat layers
|
||||
|
||||
@ -44,33 +44,40 @@ compute Tcold all temp/region cold
|
||||
# 1st equilibration run
|
||||
|
||||
fix 1 all nvt temp $t $t 0.5
|
||||
thermo 100
|
||||
thermo 100
|
||||
run 1000
|
||||
|
||||
velocity all scale $t
|
||||
velocity all scale $t
|
||||
|
||||
unfix 1
|
||||
unfix 1
|
||||
|
||||
# 2nd equilibration run
|
||||
|
||||
fix 1 all nve
|
||||
fix 1 all nve
|
||||
fix hot all ehex 1 100.0 region hot
|
||||
fix cold all ehex 1 -100.0 region cold
|
||||
|
||||
thermo_style custom step temp c_Thot c_Tcold
|
||||
thermo 1000
|
||||
run 10000
|
||||
thermo_modify colname c_Thot Temp_hot colname c_Tcold Temp_cold
|
||||
thermo 1000
|
||||
run 10000
|
||||
|
||||
# thermal conductivity calculation
|
||||
|
||||
compute ke all ke/atom
|
||||
variable temp atom c_ke/1.5
|
||||
compute ke all ke/atom
|
||||
variable temp atom c_ke/1.5
|
||||
|
||||
compute layers all chunk/atom bin/1d z lower 0.05 units reduced
|
||||
fix 2 all ave/chunk 10 100 1000 layers v_temp file profile.ehex
|
||||
fix 2 all ave/chunk 10 100 1000 layers v_temp file profile.ehex
|
||||
|
||||
variable tdiff equal f_2[11][3]-f_2[1][3]
|
||||
variable tdiff equal f_2[1][3]-f_2[11][3]
|
||||
fix ave all ave/time 1 1 1000 v_tdiff ave running start 13000
|
||||
|
||||
variable kappa equal (100/(lx*ly)/2.0)*(lz/2.0)/f_ave
|
||||
|
||||
thermo_style custom step temp c_Thot c_Tcold v_tdiff f_ave
|
||||
thermo_modify colname c_Thot Temp_hot colname c_Tcold Temp_cold &
|
||||
colname v_tdiff dTemp_step colname f_ave dTemp
|
||||
|
||||
run 20000
|
||||
print "Running average thermal conductivity: $(v_kappa:%.2f)"
|
||||
|
||||
@ -3,36 +3,36 @@
|
||||
|
||||
# settings
|
||||
|
||||
variable x equal 10
|
||||
variable y equal 10
|
||||
variable z equal 20
|
||||
variable x equal 10
|
||||
variable y equal 10
|
||||
variable z equal 20
|
||||
|
||||
variable rho equal 0.6
|
||||
variable rho equal 0.6
|
||||
variable t equal 1.35
|
||||
variable rc equal 2.5
|
||||
variable rc equal 2.5
|
||||
|
||||
#variable rho equal 0.85
|
||||
#variable rho equal 0.85
|
||||
#variable t equal 0.7
|
||||
#variable rc equal 3.0
|
||||
#variable rc equal 3.0
|
||||
|
||||
# setup problem
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc ${rho}
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass 1 1.0
|
||||
lattice fcc ${rho}
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create $t 87287
|
||||
velocity all create $t 87287
|
||||
|
||||
pair_style lj/cut ${rc}
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_style lj/cut ${rc}
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1
|
||||
|
||||
# heat layers
|
||||
|
||||
@ -44,33 +44,39 @@ compute Tcold all temp/region cold
|
||||
# 1st equilibration run
|
||||
|
||||
fix 1 all nvt temp $t $t 0.5
|
||||
thermo 100
|
||||
thermo 100
|
||||
run 1000
|
||||
|
||||
velocity all scale $t
|
||||
velocity all scale $t
|
||||
|
||||
unfix 1
|
||||
unfix 1
|
||||
|
||||
# 2nd equilibration run
|
||||
|
||||
fix 1 all nve
|
||||
fix 1 all nve
|
||||
fix hot all heat 1 100.0 region hot
|
||||
fix cold all heat 1 -100.0 region cold
|
||||
|
||||
thermo_style custom step temp c_Thot c_Tcold
|
||||
thermo 1000
|
||||
thermo_modify colname c_Thot Temp_hot colname c_Tcold Temp_cold
|
||||
thermo 1000
|
||||
run 10000
|
||||
|
||||
# thermal conductivity calculation
|
||||
|
||||
compute ke all ke/atom
|
||||
variable temp atom c_ke/1.5
|
||||
compute ke all ke/atom
|
||||
variable temp atom c_ke/1.5
|
||||
|
||||
compute layers all chunk/atom bin/1d z lower 0.05 units reduced
|
||||
fix 2 all ave/chunk 10 100 1000 layers v_temp file profile.heat
|
||||
fix 2 all ave/chunk 10 100 1000 layers v_temp file profile.heat
|
||||
|
||||
variable tdiff equal f_2[11][3]-f_2[1][3]
|
||||
variable tdiff equal f_2[1][3]-f_2[11][3]
|
||||
fix ave all ave/time 1 1 1000 v_tdiff ave running start 13000
|
||||
|
||||
variable kappa equal (100/(lx*ly)/2.0)*(lz/2.0)/f_ave
|
||||
thermo_style custom step temp c_Thot c_Tcold v_tdiff f_ave
|
||||
thermo_modify colname c_Thot Temp_hot colname c_Tcold Temp_cold &
|
||||
colname v_tdiff dTemp_step colname f_ave dTemp
|
||||
|
||||
run 20000
|
||||
print "Running average thermal conductivity: $(v_kappa:%.2f)"
|
||||
|
||||
@ -3,17 +3,17 @@
|
||||
|
||||
# settings
|
||||
|
||||
variable x equal 10
|
||||
variable y equal 10
|
||||
variable z equal 10
|
||||
variable x equal 10
|
||||
variable y equal 10
|
||||
variable z equal 10
|
||||
|
||||
variable rho equal 0.6
|
||||
variable rho equal 0.6
|
||||
variable t equal 1.35
|
||||
variable rc equal 2.5
|
||||
variable rc equal 2.5
|
||||
|
||||
#variable rho equal 0.85
|
||||
#variable rho equal 0.85
|
||||
#variable t equal 0.7
|
||||
#variable rc equal 3.0
|
||||
#variable rc equal 3.0
|
||||
|
||||
variable p equal 200 # correlation length
|
||||
variable s equal 10 # sample interval
|
||||
@ -21,32 +21,32 @@ variable d equal $p*$s # dump interval
|
||||
|
||||
# setup problem
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc ${rho}
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass 1 1.0
|
||||
lattice fcc ${rho}
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create $t 87287
|
||||
velocity all create $t 87287
|
||||
|
||||
pair_style lj/cut ${rc}
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_style lj/cut ${rc}
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1
|
||||
|
||||
# 1st equilibration run
|
||||
|
||||
fix 1 all nvt temp $t $t 0.5
|
||||
thermo 100
|
||||
run 1000
|
||||
fix 1 all nvt temp $t $t 0.5
|
||||
thermo 100
|
||||
run 1000
|
||||
|
||||
velocity all scale $t
|
||||
velocity all scale $t
|
||||
|
||||
unfix 1
|
||||
unfix 1
|
||||
|
||||
# thermal conductivity calculation
|
||||
|
||||
@ -60,20 +60,23 @@ variable Jx equal c_flux[1]/vol
|
||||
variable Jy equal c_flux[2]/vol
|
||||
variable Jz equal c_flux[3]/vol
|
||||
|
||||
fix 1 all nve
|
||||
fix 1 all nve
|
||||
fix JJ all ave/correlate $s $p $d &
|
||||
c_flux[1] c_flux[2] c_flux[3] type auto &
|
||||
file profile.heatflux ave running
|
||||
file profile.heatflux ave running
|
||||
|
||||
variable scale equal $s*dt/$t/$t/vol
|
||||
variable k11 equal trap(f_JJ[3])*${scale}
|
||||
variable k22 equal trap(f_JJ[4])*${scale}
|
||||
variable k33 equal trap(f_JJ[5])*${scale}
|
||||
variable kappa equal (v_k11+v_k22+v_k33)/3.0
|
||||
|
||||
thermo $d
|
||||
thermo_style custom step temp v_Jx v_Jy v_Jz v_k11 v_k22 v_k33
|
||||
thermo $d
|
||||
thermo_style custom step temp v_Jx v_Jy v_Jz v_k11 v_k22 v_k33 v_kappa
|
||||
thermo_modify colname v_Jx Jx colname v_Jy Jy colname v_Jz Jz &
|
||||
colname v_k11 kappa_11 colname v_k22 kappa_22 &
|
||||
colname v_k33 kappa_33 colname v_kappa kappa
|
||||
|
||||
run 100000
|
||||
|
||||
variable kappa equal (v_k11+v_k22+v_k33)/3.0
|
||||
print "running average conductivity: ${kappa}"
|
||||
print "Running average thermal conductivity: $(v_kappa:%.2f)"
|
||||
|
||||
@ -3,40 +3,40 @@
|
||||
|
||||
# settings
|
||||
|
||||
variable x equal 10
|
||||
variable y equal 10
|
||||
variable z equal 20
|
||||
variable x equal 10
|
||||
variable y equal 10
|
||||
variable z equal 20
|
||||
|
||||
variable rho equal 0.6
|
||||
variable rho equal 0.6
|
||||
variable t equal 1.35
|
||||
variable rc equal 2.5
|
||||
variable rc equal 2.5
|
||||
variable tlo equal 1.0
|
||||
variable thi equal 1.70
|
||||
|
||||
#variable rho equal 0.85
|
||||
#variable rho equal 0.85
|
||||
#variable t equal 0.7
|
||||
#variable rc equal 3.0
|
||||
#variable rc equal 3.0
|
||||
#variable tlo equal 0.3
|
||||
#variable thi equal 1.0
|
||||
|
||||
# setup problem
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc ${rho}
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass 1 1.0
|
||||
lattice fcc ${rho}
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create $t 87287
|
||||
velocity all create $t 87287
|
||||
|
||||
pair_style lj/cut ${rc}
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_style lj/cut ${rc}
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1
|
||||
|
||||
# heat layers
|
||||
|
||||
@ -48,16 +48,16 @@ compute Tcold all temp/region cold
|
||||
# 1st equilibration run
|
||||
|
||||
fix 1 all nvt temp $t $t 0.5
|
||||
thermo 100
|
||||
thermo 100
|
||||
run 1000
|
||||
|
||||
velocity all scale $t
|
||||
velocity all scale $t
|
||||
|
||||
unfix 1
|
||||
unfix 1
|
||||
|
||||
# 2nd equilibration run
|
||||
|
||||
fix 1 all nve
|
||||
fix 1 all nve
|
||||
fix hot all langevin ${thi} ${thi} 1.0 59804 tally yes
|
||||
fix cold all langevin ${tlo} ${tlo} 1.0 287859 tally yes
|
||||
fix_modify hot temp Thot
|
||||
@ -65,14 +65,17 @@ fix_modify cold temp Tcold
|
||||
|
||||
variable tdiff equal c_Thot-c_Tcold
|
||||
thermo_style custom step temp c_Thot c_Tcold f_hot f_cold v_tdiff
|
||||
thermo 1000
|
||||
run 10000
|
||||
thermo_modify colname c_Thot Temp_hot colname c_Tcold Temp_cold &
|
||||
colname f_hot E_hot colname f_cold E_cold &
|
||||
colname v_tdiff dTemp_step
|
||||
thermo 1000
|
||||
run 10000
|
||||
|
||||
# thermal conductivity calculation
|
||||
# reset langevin thermostats to zero energy accumulation
|
||||
|
||||
compute ke all ke/atom
|
||||
variable temp atom c_ke/1.5
|
||||
compute ke all ke/atom
|
||||
variable temp atom c_ke/1.5
|
||||
|
||||
fix hot all langevin ${thi} ${thi} 1.0 59804 tally yes
|
||||
fix cold all langevin ${tlo} ${tlo} 1.0 287859 tally yes
|
||||
@ -81,8 +84,15 @@ fix_modify cold temp Tcold
|
||||
|
||||
fix ave all ave/time 10 100 1000 v_tdiff ave running
|
||||
thermo_style custom step temp c_Thot c_Tcold f_hot f_cold v_tdiff f_ave
|
||||
thermo_modify colname c_Thot Temp_hot colname c_Tcold Temp_cold &
|
||||
colname f_hot E_hot colname f_cold E_cold &
|
||||
colname v_tdiff dTemp_step colname f_ave dTemp
|
||||
|
||||
compute layers all chunk/atom bin/1d z lower 0.05 units reduced
|
||||
fix 2 all ave/chunk 10 100 1000 layers v_temp file profile.langevin
|
||||
fix 2 all ave/chunk 10 100 1000 layers v_temp file profile.langevin
|
||||
|
||||
variable start_time equal time
|
||||
variable kappa equal (0.5*(abs(f_hot)+abs(f_cold))/(time-${start_time})/(lx*ly)/2.0)*(lz/2.0)/f_ave
|
||||
|
||||
run 20000
|
||||
print "Running average thermal conductivity: $(v_kappa:%.2f)"
|
||||
|
||||
@ -1,73 +1,77 @@
|
||||
# sample LAMMPS input script for thermal conductivity of liquid LJ
|
||||
# Muller-Plathe method via fix thermal_conductivity
|
||||
# Muller-Plathe method via fix thermal_conductivity
|
||||
|
||||
# settings
|
||||
|
||||
variable x equal 10
|
||||
variable y equal 10
|
||||
variable z equal 20
|
||||
variable x equal 10
|
||||
variable y equal 10
|
||||
variable z equal 20
|
||||
|
||||
variable rho equal 0.6
|
||||
variable rho equal 0.6
|
||||
variable t equal 1.35
|
||||
variable rc equal 2.5
|
||||
variable rc equal 2.5
|
||||
|
||||
#variable rho equal 0.85
|
||||
#variable rho equal 0.85
|
||||
#variable t equal 0.7
|
||||
#variable rc equal 3.0
|
||||
#variable rc equal 3.0
|
||||
|
||||
# setup problem
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc ${rho}
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass 1 1.0
|
||||
lattice fcc ${rho}
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create $t 87287
|
||||
velocity all create $t 87287
|
||||
|
||||
pair_style lj/cut ${rc}
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
pair_style lj/cut ${rc}
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1
|
||||
|
||||
# 1st equilibration run
|
||||
|
||||
fix 1 all nvt temp $t $t 0.5
|
||||
thermo 100
|
||||
run 1000
|
||||
fix 1 all nvt temp $t $t 0.5
|
||||
thermo 100
|
||||
run 1000
|
||||
|
||||
velocity all scale $t
|
||||
velocity all scale $t
|
||||
|
||||
unfix 1
|
||||
unfix 1
|
||||
|
||||
# 2nd equilibration run
|
||||
|
||||
compute ke all ke/atom
|
||||
variable temp atom c_ke/1.5
|
||||
compute ke all ke/atom
|
||||
variable temp atom c_ke/1.5
|
||||
|
||||
fix 1 all nve
|
||||
fix 1 all nve
|
||||
|
||||
compute layers all chunk/atom bin/1d z lower 0.05 units reduced
|
||||
fix 2 all ave/chunk 10 100 1000 layers v_temp file profile.mp
|
||||
|
||||
fix 3 all thermal/conductivity 10 z 20
|
||||
fix 2 all ave/chunk 10 100 1000 layers v_temp file profile.mp
|
||||
fix 3 all thermal/conductivity 10 z 20
|
||||
|
||||
variable tdiff equal f_2[11][3]-f_2[1][3]
|
||||
thermo_style custom step temp epair etotal f_3 v_tdiff
|
||||
thermo_style custom step temp epair etotal f_3 v_tdiff
|
||||
thermo_modify colname f_3 E_delta colname v_tdiff dTemp_step
|
||||
|
||||
thermo 1000
|
||||
run 20000
|
||||
thermo 1000
|
||||
run 20000
|
||||
|
||||
# thermal conductivity calculation
|
||||
# reset fix thermal/conductivity to zero energy accumulation
|
||||
fix 3 all thermal/conductivity 10 z 20
|
||||
|
||||
fix 3 all thermal/conductivity 10 z 20
|
||||
variable start_time equal time
|
||||
variable kappa equal (f_3/(time-${start_time})/(lx*ly)/2.0)*(lz/2.0)/f_ave
|
||||
|
||||
fix ave all ave/time 1 1 1000 v_tdiff ave running
|
||||
thermo_style custom step temp epair etotal f_3 v_tdiff f_ave
|
||||
thermo_style custom step temp epair etotal f_3 v_tdiff f_ave
|
||||
thermo_modify colname f_3 E_delta colname v_tdiff dTemp_step colname f_ave dTemp
|
||||
|
||||
run 20000
|
||||
run 20000
|
||||
print "Running average thermal conductivity: $(v_kappa:%.2f)"
|
||||
|
||||
@ -1,225 +0,0 @@
|
||||
LAMMPS (13 Oct 2016)
|
||||
# sample LAMMPS input script for thermal conductivity of liquid LJ
|
||||
# use fix ehex to add/subtract energy from 2 regions
|
||||
|
||||
# settings
|
||||
|
||||
variable x equal 10
|
||||
variable y equal 10
|
||||
variable z equal 20
|
||||
|
||||
variable rho equal 0.6
|
||||
variable t equal 1.35
|
||||
variable rc equal 2.5
|
||||
|
||||
#variable rho equal 0.85
|
||||
#variable t equal 0.7
|
||||
#variable rc equal 3.0
|
||||
|
||||
# setup problem
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc ${rho}
|
||||
lattice fcc 0.6
|
||||
Lattice spacing in x,y,z = 1.88207 1.88207 1.88207
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 10 0 $y 0 $z
|
||||
region box block 0 10 0 10 0 $z
|
||||
region box block 0 10 0 10 0 20
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (18.8207 18.8207 37.6414)
|
||||
2 by 1 by 4 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 8000 atoms
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create $t 87287
|
||||
velocity all create 1.35 87287
|
||||
|
||||
pair_style lj/cut ${rc}
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1
|
||||
|
||||
# heat layers
|
||||
|
||||
region hot block INF INF INF INF 0 1
|
||||
region cold block INF INF INF INF 10 11
|
||||
compute Thot all temp/region hot
|
||||
compute Tcold all temp/region cold
|
||||
|
||||
# 1st equilibration run
|
||||
|
||||
fix 1 all nvt temp $t $t 0.5
|
||||
fix 1 all nvt temp 1.35 $t 0.5
|
||||
fix 1 all nvt temp 1.35 1.35 0.5
|
||||
thermo 100
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4 -> bins = 14 14 27
|
||||
Memory usage per processor = 2.55761 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.35 -4.1241917 0 -2.0994448 -3.1961612
|
||||
100 1.1819832 -3.7640881 0 -1.991335 0.53985757
|
||||
200 1.2578365 -3.7395333 0 -1.8530144 0.69591862
|
||||
300 1.3282971 -3.7215427 0 -1.7293461 0.79036065
|
||||
400 1.3714367 -3.7043826 0 -1.6474847 0.85873226
|
||||
500 1.3590952 -3.6707735 0 -1.6323855 0.99602024
|
||||
600 1.3575117 -3.7118244 0 -1.6758114 0.81454305
|
||||
700 1.3284444 -3.7075488 0 -1.7151313 0.81136596
|
||||
800 1.3419995 -3.7155648 0 -1.7028172 0.82925676
|
||||
900 1.3562214 -3.6965609 0 -1.6624831 0.88908117
|
||||
1000 1.3732017 -3.7100044 0 -1.6504594 0.83982701
|
||||
Loop time of 0.889114 on 8 procs for 1000 steps with 8000 atoms
|
||||
|
||||
Performance: 485876.777 tau/day, 1124.715 timesteps/s
|
||||
99.3% CPU use with 8 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.48042 | 0.50311 | 0.52772 | 1.9 | 56.59
|
||||
Neigh | 0.22997 | 0.23203 | 0.23466 | 0.3 | 26.10
|
||||
Comm | 0.081187 | 0.10484 | 0.1285 | 4.2 | 11.79
|
||||
Output | 0.00027299 | 0.00028226 | 0.000314 | 0.1 | 0.03
|
||||
Modify | 0.028298 | 0.032276 | 0.037612 | 2.0 | 3.63
|
||||
Other | | 0.01658 | | | 1.86
|
||||
|
||||
Nlocal: 1000 ave 1020 max 982 min
|
||||
Histogram: 1 0 2 1 0 1 1 1 0 1
|
||||
Nghost: 2299.5 ave 2331 max 2268 min
|
||||
Histogram: 1 1 1 1 0 0 0 3 0 1
|
||||
Neighs: 27122 ave 28382 max 26337 min
|
||||
Histogram: 2 0 2 1 1 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 216976
|
||||
Ave neighs/atom = 27.122
|
||||
Neighbor list builds = 162
|
||||
Dangerous builds = 0
|
||||
|
||||
velocity all scale $t
|
||||
velocity all scale 1.35
|
||||
|
||||
unfix 1
|
||||
|
||||
# 2nd equilibration run
|
||||
|
||||
fix 1 all nve
|
||||
fix hot all ehex 1 100.0 region hot
|
||||
fix cold all ehex 1 -100.0 region cold
|
||||
|
||||
thermo_style custom step temp c_Thot c_Tcold
|
||||
thermo 1000
|
||||
run 10000
|
||||
Memory usage per processor = 2.80761 Mbytes
|
||||
Step Temp c_Thot c_Tcold
|
||||
1000 1.35 1.431295 1.2955644
|
||||
2000 1.3537291 1.6418772 1.1875127
|
||||
3000 1.3615152 1.6451299 1.1769094
|
||||
4000 1.3612129 1.5281727 1.2022419
|
||||
5000 1.3552182 1.6672955 1.2212864
|
||||
6000 1.3643442 1.6072213 1.2390567
|
||||
7000 1.3665773 1.6909819 1.1466611
|
||||
8000 1.375741 1.6144274 1.1691231
|
||||
9000 1.3701136 1.8238424 1.136342
|
||||
10000 1.3563004 1.8059065 1.1547129
|
||||
11000 1.3794051 1.692299 1.0515688
|
||||
Loop time of 10.5555 on 8 procs for 10000 steps with 8000 atoms
|
||||
|
||||
Performance: 409265.976 tau/day, 947.375 timesteps/s
|
||||
99.4% CPU use with 8 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 4.1863 | 5.0134 | 5.8326 | 28.0 | 47.50
|
||||
Neigh | 2.1559 | 2.4232 | 2.6516 | 14.2 | 22.96
|
||||
Comm | 0.80561 | 1.8126 | 2.8852 | 58.4 | 17.17
|
||||
Output | 0.00044537 | 0.00064856 | 0.00077057 | 0.5 | 0.01
|
||||
Modify | 0.81915 | 0.94285 | 1.0571 | 9.5 | 8.93
|
||||
Other | | 0.3628 | | | 3.44
|
||||
|
||||
Nlocal: 1000 ave 1105 max 883 min
|
||||
Histogram: 1 1 2 0 0 0 0 0 2 2
|
||||
Nghost: 2319.38 ave 2502 max 2114 min
|
||||
Histogram: 1 3 0 0 0 0 0 0 0 4
|
||||
Neighs: 27387.9 ave 32453 max 21803 min
|
||||
Histogram: 2 2 0 0 0 0 0 0 0 4
|
||||
|
||||
Total # of neighbors = 219103
|
||||
Ave neighs/atom = 27.3879
|
||||
Neighbor list builds = 1696
|
||||
Dangerous builds = 0
|
||||
|
||||
# thermal conductivity calculation
|
||||
|
||||
compute ke all ke/atom
|
||||
variable temp atom c_ke/1.5
|
||||
|
||||
compute layers all chunk/atom bin/1d z lower 0.05 units reduced
|
||||
fix 2 all ave/chunk 10 100 1000 layers v_temp file profile.ehex
|
||||
|
||||
variable tdiff equal f_2[11][3]-f_2[1][3]
|
||||
fix ave all ave/time 1 1 1000 v_tdiff ave running start 13000
|
||||
thermo_style custom step temp c_Thot c_Tcold v_tdiff f_ave
|
||||
|
||||
run 20000
|
||||
Memory usage per processor = 3.0578 Mbytes
|
||||
Step Temp c_Thot c_Tcold v_tdiff f_ave
|
||||
11000 1.3794051 1.6903393 1.0515688 0 0
|
||||
12000 1.3799777 1.8004888 1.1032219 -0.63860014 0
|
||||
13000 1.3733605 1.7823094 1.0553582 -0.65827891 -0.65827891
|
||||
14000 1.3749743 1.7852256 1.1674016 -0.68463005 -0.67145448
|
||||
15000 1.3863795 1.8538127 1.0056247 -0.73524813 -0.69271903
|
||||
16000 1.3731955 1.7518546 1.0741458 -0.74810775 -0.70656621
|
||||
17000 1.3771856 1.9016869 1.0090502 -0.73999567 -0.7132521
|
||||
18000 1.3766032 1.7616195 1.1142155 -0.73769104 -0.71732526
|
||||
19000 1.3815934 1.7791247 1.1406987 -0.73617832 -0.72001855
|
||||
20000 1.3725543 1.8637436 1.0799364 -0.73435569 -0.7218107
|
||||
21000 1.3817369 1.8808771 1.0642524 -0.76702329 -0.72683432
|
||||
22000 1.3968704 1.840287 1.072304 -0.82496419 -0.7366473
|
||||
23000 1.3895558 1.9427293 1.0766665 -0.75363908 -0.73819201
|
||||
24000 1.3900493 1.9883976 1.1081017 -0.86394774 -0.74867166
|
||||
25000 1.3838912 1.8853041 1.0795751 -0.83043902 -0.75496145
|
||||
26000 1.3912105 1.9330259 1.1070335 -0.79880182 -0.75809291
|
||||
27000 1.3891151 1.8548451 1.0676153 -0.81856523 -0.7621244
|
||||
28000 1.3942624 1.9796706 1.1251407 -0.81762456 -0.76559316
|
||||
29000 1.3819302 1.8619138 1.0495292 -0.78627491 -0.76680973
|
||||
30000 1.3968366 1.883107 1.1004588 -0.83902548 -0.77082172
|
||||
31000 1.3822489 1.8220413 1.0322271 -0.7550338 -0.76999077
|
||||
Loop time of 22.7579 on 8 procs for 20000 steps with 8000 atoms
|
||||
|
||||
Performance: 379649.018 tau/day, 878.817 timesteps/s
|
||||
99.3% CPU use with 8 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 7.4811 | 10.102 | 12.63 | 68.7 | 44.39
|
||||
Neigh | 4.0495 | 4.9884 | 5.8366 | 37.8 | 21.92
|
||||
Comm | 1.6695 | 4.9483 | 8.493 | 130.7 | 21.74
|
||||
Output | 0.0010517 | 0.0017769 | 0.0019059 | 0.7 | 0.01
|
||||
Modify | 1.6903 | 1.9371 | 2.2355 | 14.8 | 8.51
|
||||
Other | | 0.7799 | | | 3.43
|
||||
|
||||
Nlocal: 1000 ave 1121 max 857 min
|
||||
Histogram: 2 0 1 1 0 0 0 0 1 3
|
||||
Nghost: 2299.75 ave 2541 max 2067 min
|
||||
Histogram: 3 1 0 0 0 0 0 0 2 2
|
||||
Neighs: 27487.2 ave 33361 max 20651 min
|
||||
Histogram: 2 1 1 0 0 0 0 0 0 4
|
||||
|
||||
Total # of neighbors = 219898
|
||||
Ave neighs/atom = 27.4872
|
||||
Neighbor list builds = 3474
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:34
|
||||
@ -1,225 +0,0 @@
|
||||
LAMMPS (13 Oct 2016)
|
||||
# sample LAMMPS input script for thermal conductivity of liquid LJ
|
||||
# use fix heat to add/subtract energy from 2 regions
|
||||
|
||||
# settings
|
||||
|
||||
variable x equal 10
|
||||
variable y equal 10
|
||||
variable z equal 20
|
||||
|
||||
variable rho equal 0.6
|
||||
variable t equal 1.35
|
||||
variable rc equal 2.5
|
||||
|
||||
#variable rho equal 0.85
|
||||
#variable t equal 0.7
|
||||
#variable rc equal 3.0
|
||||
|
||||
# setup problem
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc ${rho}
|
||||
lattice fcc 0.6
|
||||
Lattice spacing in x,y,z = 1.88207 1.88207 1.88207
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 10 0 $y 0 $z
|
||||
region box block 0 10 0 10 0 $z
|
||||
region box block 0 10 0 10 0 20
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (18.8207 18.8207 37.6414)
|
||||
2 by 1 by 4 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 8000 atoms
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create $t 87287
|
||||
velocity all create 1.35 87287
|
||||
|
||||
pair_style lj/cut ${rc}
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1
|
||||
|
||||
# heat layers
|
||||
|
||||
region hot block INF INF INF INF 0 1
|
||||
region cold block INF INF INF INF 10 11
|
||||
compute Thot all temp/region hot
|
||||
compute Tcold all temp/region cold
|
||||
|
||||
# 1st equilibration run
|
||||
|
||||
fix 1 all nvt temp $t $t 0.5
|
||||
fix 1 all nvt temp 1.35 $t 0.5
|
||||
fix 1 all nvt temp 1.35 1.35 0.5
|
||||
thermo 100
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4 -> bins = 14 14 27
|
||||
Memory usage per processor = 2.55761 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.35 -4.1241917 0 -2.0994448 -3.1961612
|
||||
100 1.1819832 -3.7640881 0 -1.991335 0.53985757
|
||||
200 1.2578365 -3.7395333 0 -1.8530144 0.69591862
|
||||
300 1.3282971 -3.7215427 0 -1.7293461 0.79036065
|
||||
400 1.3714367 -3.7043826 0 -1.6474847 0.85873226
|
||||
500 1.3590952 -3.6707735 0 -1.6323855 0.99602024
|
||||
600 1.3575117 -3.7118244 0 -1.6758114 0.81454305
|
||||
700 1.3284444 -3.7075488 0 -1.7151313 0.81136596
|
||||
800 1.3419995 -3.7155648 0 -1.7028172 0.82925676
|
||||
900 1.3562214 -3.6965609 0 -1.6624831 0.88908117
|
||||
1000 1.3732017 -3.7100044 0 -1.6504594 0.83982701
|
||||
Loop time of 0.872163 on 8 procs for 1000 steps with 8000 atoms
|
||||
|
||||
Performance: 495320.223 tau/day, 1146.575 timesteps/s
|
||||
99.5% CPU use with 8 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.48598 | 0.49768 | 0.50892 | 1.1 | 57.06
|
||||
Neigh | 0.22855 | 0.23236 | 0.23463 | 0.5 | 26.64
|
||||
Comm | 0.082584 | 0.093727 | 0.10748 | 2.9 | 10.75
|
||||
Output | 0.0002718 | 0.00028038 | 0.00031757 | 0.1 | 0.03
|
||||
Modify | 0.028934 | 0.031425 | 0.03322 | 0.8 | 3.60
|
||||
Other | | 0.01668 | | | 1.91
|
||||
|
||||
Nlocal: 1000 ave 1020 max 982 min
|
||||
Histogram: 1 0 2 1 0 1 1 1 0 1
|
||||
Nghost: 2299.5 ave 2331 max 2268 min
|
||||
Histogram: 1 1 1 1 0 0 0 3 0 1
|
||||
Neighs: 27122 ave 28382 max 26337 min
|
||||
Histogram: 2 0 2 1 1 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 216976
|
||||
Ave neighs/atom = 27.122
|
||||
Neighbor list builds = 162
|
||||
Dangerous builds = 0
|
||||
|
||||
velocity all scale $t
|
||||
velocity all scale 1.35
|
||||
|
||||
unfix 1
|
||||
|
||||
# 2nd equilibration run
|
||||
|
||||
fix 1 all nve
|
||||
fix hot all heat 1 100.0 region hot
|
||||
fix cold all heat 1 -100.0 region cold
|
||||
|
||||
thermo_style custom step temp c_Thot c_Tcold
|
||||
thermo 1000
|
||||
run 10000
|
||||
Memory usage per processor = 2.55761 Mbytes
|
||||
Step Temp c_Thot c_Tcold
|
||||
1000 1.35 1.431295 1.2955644
|
||||
2000 1.3518468 1.5562602 1.154905
|
||||
3000 1.3477229 1.5890075 1.2395414
|
||||
4000 1.3487175 1.5491615 1.2019696
|
||||
5000 1.3594394 1.5780597 1.1824492
|
||||
6000 1.3583923 1.541735 1.1675586
|
||||
7000 1.3700321 1.6735877 1.1279114
|
||||
8000 1.3631993 1.6367675 1.0697225
|
||||
9000 1.3739201 1.6846211 1.1138829
|
||||
10000 1.3751455 1.8039471 1.1500399
|
||||
11000 1.3716416 1.833336 1.1267278
|
||||
Loop time of 10.3395 on 8 procs for 10000 steps with 8000 atoms
|
||||
|
||||
Performance: 417815.278 tau/day, 967.165 timesteps/s
|
||||
99.5% CPU use with 8 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 4.2189 | 4.9657 | 5.6225 | 25.3 | 48.03
|
||||
Neigh | 2.1359 | 2.4223 | 2.6741 | 14.8 | 23.43
|
||||
Comm | 0.83801 | 1.6773 | 2.6984 | 57.1 | 16.22
|
||||
Output | 0.00042701 | 0.00046191 | 0.00052905 | 0.1 | 0.00
|
||||
Modify | 1.0143 | 1.0895 | 1.1846 | 5.7 | 10.54
|
||||
Other | | 0.1844 | | | 1.78
|
||||
|
||||
Nlocal: 1000 ave 1131 max 878 min
|
||||
Histogram: 3 1 0 0 0 0 0 1 1 2
|
||||
Nghost: 2312.88 ave 2525 max 2114 min
|
||||
Histogram: 2 2 0 0 0 0 0 1 1 2
|
||||
Neighs: 27457 ave 33797 max 21031 min
|
||||
Histogram: 3 1 0 0 0 0 0 0 1 3
|
||||
|
||||
Total # of neighbors = 219656
|
||||
Ave neighs/atom = 27.457
|
||||
Neighbor list builds = 1691
|
||||
Dangerous builds = 0
|
||||
|
||||
# thermal conductivity calculation
|
||||
|
||||
compute ke all ke/atom
|
||||
variable temp atom c_ke/1.5
|
||||
|
||||
compute layers all chunk/atom bin/1d z lower 0.05 units reduced
|
||||
fix 2 all ave/chunk 10 100 1000 layers v_temp file profile.heat
|
||||
|
||||
variable tdiff equal f_2[11][3]-f_2[1][3]
|
||||
fix ave all ave/time 1 1 1000 v_tdiff ave running start 13000
|
||||
thermo_style custom step temp c_Thot c_Tcold v_tdiff f_ave
|
||||
|
||||
run 20000
|
||||
Memory usage per processor = 2.8078 Mbytes
|
||||
Step Temp c_Thot c_Tcold v_tdiff f_ave
|
||||
11000 1.3716416 1.833336 1.1267278 0 0
|
||||
12000 1.3703433 1.7829467 1.1194444 -0.66044316 0
|
||||
13000 1.3686734 1.8334366 1.1193477 -0.71431978 -0.71431978
|
||||
14000 1.3856987 1.8048077 1.1052708 -0.73112558 -0.72272268
|
||||
15000 1.3820117 1.7460559 1.110725 -0.72927647 -0.72490728
|
||||
16000 1.3911309 1.923603 1.1161499 -0.77407515 -0.73719925
|
||||
17000 1.3841301 1.7276486 1.0283807 -0.77278638 -0.74431667
|
||||
18000 1.3888918 1.7944951 1.0532944 -0.75665895 -0.74637372
|
||||
19000 1.3876032 1.838174 1.059715 -0.71342263 -0.74166642
|
||||
20000 1.3724644 1.8297128 1.1439176 -0.77352223 -0.7456484
|
||||
21000 1.3798921 1.7968403 1.0288381 -0.70077132 -0.74066206
|
||||
22000 1.3763952 1.8202225 1.0658157 -0.75629111 -0.74222496
|
||||
23000 1.3911378 1.8691478 1.018589 -0.76094865 -0.74392711
|
||||
24000 1.3867754 1.7826523 1.09347 -0.80367344 -0.74890597
|
||||
25000 1.385877 1.9029313 1.0815131 -0.73559505 -0.74788206
|
||||
26000 1.3791773 1.8904022 1.0151678 -0.7729123 -0.74966993
|
||||
27000 1.3800063 1.729283 1.127594 -0.71473941 -0.74734123
|
||||
28000 1.3757197 1.7823772 1.084523 -0.73849831 -0.74678855
|
||||
29000 1.3777555 1.8287284 1.0715132 -0.70375514 -0.74425717
|
||||
30000 1.3821118 1.7382856 1.1078333 -0.79892499 -0.74729427
|
||||
31000 1.3870476 1.8410063 1.1235958 -0.76218423 -0.74807795
|
||||
Loop time of 22.4057 on 8 procs for 20000 steps with 8000 atoms
|
||||
|
||||
Performance: 385616.132 tau/day, 892.630 timesteps/s
|
||||
99.3% CPU use with 8 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 7.6116 | 10.003 | 12.262 | 64.3 | 44.65
|
||||
Neigh | 4.038 | 4.9528 | 5.8822 | 37.6 | 22.10
|
||||
Comm | 1.6649 | 4.7143 | 7.6339 | 124.9 | 21.04
|
||||
Output | 0.00098443 | 0.0017504 | 0.0018921 | 0.7 | 0.01
|
||||
Modify | 2.1819 | 2.3289 | 2.6598 | 12.6 | 10.39
|
||||
Other | | 0.4047 | | | 1.81
|
||||
|
||||
Nlocal: 1000 ave 1134 max 850 min
|
||||
Histogram: 2 1 0 1 0 0 0 1 0 3
|
||||
Nghost: 2307.75 ave 2561 max 2083 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 2 2
|
||||
Neighs: 27561.1 ave 34071 max 19891 min
|
||||
Histogram: 2 1 1 0 0 0 0 0 1 3
|
||||
|
||||
Total # of neighbors = 220489
|
||||
Ave neighs/atom = 27.5611
|
||||
Neighbor list builds = 3442
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:33
|
||||
@ -1,230 +0,0 @@
|
||||
LAMMPS (13 Oct 2016)
|
||||
# sample LAMMPS input script for thermal conductivity of liquid LJ
|
||||
# Green-Kubo method via compute heat/flux and fix ave/correlate
|
||||
|
||||
# settings
|
||||
|
||||
variable x equal 10
|
||||
variable y equal 10
|
||||
variable z equal 10
|
||||
|
||||
variable rho equal 0.6
|
||||
variable t equal 1.35
|
||||
variable rc equal 2.5
|
||||
|
||||
#variable rho equal 0.85
|
||||
#variable t equal 0.7
|
||||
#variable rc equal 3.0
|
||||
|
||||
variable p equal 200 # correlation length
|
||||
variable s equal 10 # sample interval
|
||||
variable d equal $p*$s # dump interval
|
||||
variable d equal 200*$s
|
||||
variable d equal 200*10
|
||||
|
||||
# setup problem
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc ${rho}
|
||||
lattice fcc 0.6
|
||||
Lattice spacing in x,y,z = 1.88207 1.88207 1.88207
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 10 0 $y 0 $z
|
||||
region box block 0 10 0 10 0 $z
|
||||
region box block 0 10 0 10 0 10
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (18.8207 18.8207 18.8207)
|
||||
2 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 4000 atoms
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create $t 87287
|
||||
velocity all create 1.35 87287
|
||||
|
||||
pair_style lj/cut ${rc}
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1
|
||||
|
||||
# 1st equilibration run
|
||||
|
||||
fix 1 all nvt temp $t $t 0.5
|
||||
fix 1 all nvt temp 1.35 $t 0.5
|
||||
fix 1 all nvt temp 1.35 1.35 0.5
|
||||
thermo 100
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4 -> bins = 14 14 14
|
||||
Memory usage per processor = 2.52285 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.35 -4.1241917 0 -2.0996979 -3.1962625
|
||||
100 1.1997886 -3.7796264 0 -1.9803934 0.4889458
|
||||
200 1.271238 -3.7354981 0 -1.8291178 0.6873844
|
||||
300 1.3346808 -3.6942841 0 -1.6927634 0.84332881
|
||||
400 1.4020848 -3.7118654 0 -1.6092641 0.87670585
|
||||
500 1.3723622 -3.6917931 0 -1.6337644 0.92172921
|
||||
600 1.3451676 -3.7281573 0 -1.7109103 0.76029091
|
||||
700 1.3021567 -3.6876155 0 -1.7348687 0.82721085
|
||||
800 1.3489121 -3.7082852 0 -1.6854229 0.86438061
|
||||
900 1.3708803 -3.6966168 0 -1.6408103 0.921415
|
||||
1000 1.3640742 -3.7075319 0 -1.6619322 0.86651332
|
||||
Loop time of 0.457959 on 8 procs for 1000 steps with 4000 atoms
|
||||
|
||||
Performance: 943316.262 tau/day, 2183.602 timesteps/s
|
||||
98.9% CPU use with 8 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.23307 | 0.24263 | 0.2466 | 1.0 | 52.98
|
||||
Neigh | 0.10661 | 0.11011 | 0.11166 | 0.5 | 24.04
|
||||
Comm | 0.069595 | 0.075354 | 0.087444 | 2.2 | 16.45
|
||||
Output | 0.00028014 | 0.00028831 | 0.00031686 | 0.1 | 0.06
|
||||
Modify | 0.01694 | 0.01904 | 0.021602 | 1.2 | 4.16
|
||||
Other | | 0.01053 | | | 2.30
|
||||
|
||||
Nlocal: 500 ave 510 max 479 min
|
||||
Histogram: 1 0 0 0 0 2 1 1 0 3
|
||||
Nghost: 1519 ave 1539 max 1509 min
|
||||
Histogram: 2 0 4 0 0 0 0 1 0 1
|
||||
Neighs: 13553.8 ave 14051 max 12567 min
|
||||
Histogram: 1 0 0 0 1 0 2 1 1 2
|
||||
|
||||
Total # of neighbors = 108430
|
||||
Ave neighs/atom = 27.1075
|
||||
Neighbor list builds = 155
|
||||
Dangerous builds = 0
|
||||
|
||||
velocity all scale $t
|
||||
velocity all scale 1.35
|
||||
|
||||
unfix 1
|
||||
|
||||
# thermal conductivity calculation
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
compute myKE all ke/atom
|
||||
compute myPE all pe/atom
|
||||
compute myStress all stress/atom NULL virial
|
||||
compute flux all heat/flux myKE myPE myStress
|
||||
variable Jx equal c_flux[1]/vol
|
||||
variable Jy equal c_flux[2]/vol
|
||||
variable Jz equal c_flux[3]/vol
|
||||
|
||||
fix 1 all nve
|
||||
fix JJ all ave/correlate $s $p $d c_flux[1] c_flux[2] c_flux[3] type auto file profile.heatflux ave running
|
||||
fix JJ all ave/correlate 10 $p $d c_flux[1] c_flux[2] c_flux[3] type auto file profile.heatflux ave running
|
||||
fix JJ all ave/correlate 10 200 $d c_flux[1] c_flux[2] c_flux[3] type auto file profile.heatflux ave running
|
||||
fix JJ all ave/correlate 10 200 2000 c_flux[1] c_flux[2] c_flux[3] type auto file profile.heatflux ave running
|
||||
|
||||
variable scale equal $s*dt/$t/$t/vol
|
||||
variable scale equal 10*dt/$t/$t/vol
|
||||
variable scale equal 10*dt/1.35/$t/vol
|
||||
variable scale equal 10*dt/1.35/1.35/vol
|
||||
variable k11 equal trap(f_JJ[3])*${scale}
|
||||
variable k11 equal trap(f_JJ[3])*4.11522633744856e-06
|
||||
variable k22 equal trap(f_JJ[4])*${scale}
|
||||
variable k22 equal trap(f_JJ[4])*4.11522633744856e-06
|
||||
variable k33 equal trap(f_JJ[5])*${scale}
|
||||
variable k33 equal trap(f_JJ[5])*4.11522633744856e-06
|
||||
|
||||
thermo $d
|
||||
thermo 2000
|
||||
thermo_style custom step temp v_Jx v_Jy v_Jz v_k11 v_k22 v_k33
|
||||
|
||||
run 100000
|
||||
Memory usage per processor = 4.39785 Mbytes
|
||||
Step Temp v_Jx v_Jy v_Jz v_k11 v_k22 v_k33
|
||||
0 1.35 0.012561273 -0.087295611 -0.037041124 0.014429409 0.69689289 0.12547278
|
||||
2000 1.3455113 -0.034571206 -0.17570902 -0.057218308 -1.6110148 7.9287556 8.5035767
|
||||
4000 1.3477761 -0.029528723 0.018790489 0.056107464 7.698411 1.9459053 9.9605272
|
||||
6000 1.3411436 -0.20281149 0.2184806 0.036024028 4.6533075 1.6223216 3.7246529
|
||||
8000 1.3561682 0.12038719 0.034930957 0.12173601 4.6450263 1.9032849 2.7566363
|
||||
10000 1.3397694 -0.14241489 -0.10956496 0.053088086 6.4191535 3.1582257 2.2786677
|
||||
12000 1.3410756 0.0033462395 0.14337321 0.16381733 5.9663779 1.6774436 1.7442075
|
||||
14000 1.3484928 0.0080419803 -0.080232102 0.039035519 4.9483626 1.6210893 1.6103343
|
||||
16000 1.3414836 -0.11063045 -0.031557643 0.032060333 6.1381241 1.438198 1.5831541
|
||||
18000 1.3488617 0.15908507 -0.021418806 -0.13992507 5.9198613 1.1016464 1.2905478
|
||||
20000 1.3535727 0.13217689 0.071933521 -0.028452943 6.3746606 1.003194 1.7007101
|
||||
22000 1.3408534 -0.078953557 -0.0022323663 -0.22979033 5.0105241 1.1489328 1.720847
|
||||
24000 1.34722 0.074784199 -0.071218632 0.15238165 4.4835452 0.94086945 3.1603615
|
||||
26000 1.3539218 0.052534363 0.10419096 0.1866213 4.2233104 1.3973253 3.2802881
|
||||
28000 1.3510105 0.0080425673 -0.03723976 0.20758595 5.261917 1.1931088 3.498831
|
||||
30000 1.3410807 -0.043957884 0.065683978 0.015386362 4.3815277 1.5000017 3.2237565
|
||||
32000 1.34766 -0.060481287 0.17142383 0.034367135 4.0974942 1.1637027 3.3771953
|
||||
34000 1.3417583 -0.10055844 0.050237668 0.06974988 4.1478021 1.0235517 2.9440249
|
||||
36000 1.3468728 0.09375756 -0.17875264 -0.063513807 4.4412987 0.71084371 3.4316313
|
||||
38000 1.3496868 -0.038635804 0.117965 0.018050271 4.962332 0.41701129 3.4690212
|
||||
40000 1.3403452 -0.092158116 0.14432655 -0.062258229 4.9980486 0.3762815 3.1688552
|
||||
42000 1.3498661 0.085807945 0.010256385 -0.002956898 4.8200626 0.29278287 3.094633
|
||||
44000 1.3564084 -0.07415163 -0.051327929 -0.18457986 4.7070907 0.3358167 3.0741797
|
||||
46000 1.3435866 -0.013911463 0.081813372 0.022628846 4.6043718 0.3682401 2.9956189
|
||||
48000 1.350611 0.036512747 0.080481423 -0.22973181 4.5648715 0.32728516 3.8573343
|
||||
50000 1.3421783 0.057665789 0.075597141 0.17377918 4.4278473 0.5383886 3.5866168
|
||||
52000 1.3473497 -0.11159587 -0.09688769 0.19876168 4.3876613 0.43408155 3.4786305
|
||||
54000 1.3459495 -0.15341705 0.063996148 -0.0038254597 4.8434026 0.62047297 3.445187
|
||||
56000 1.3545654 -0.082406034 0.089232864 -0.024355614 4.546051 0.7367607 3.3694561
|
||||
58000 1.3577504 0.082844384 0.019500036 0.073721698 4.4061886 1.4575694 3.2754066
|
||||
60000 1.348614 -0.16190321 -0.048576343 0.093820555 4.2946463 1.3416919 3.1159234
|
||||
62000 1.3551143 0.097443296 -0.04420265 -0.25713945 4.1260882 1.2550603 3.063215
|
||||
64000 1.346239 0.019198575 -0.095746619 0.18383922 4.5691519 1.2615165 2.9935539
|
||||
66000 1.3535383 -0.0035547901 -0.1753318 0.014025292 4.5371394 1.0740671 2.9362916
|
||||
68000 1.3421249 -0.18217113 0.077901408 0.04314081 5.1644747 1.0218342 2.9789097
|
||||
70000 1.3446114 0.029565781 -0.13771336 0.050328878 5.4811405 1.0430806 2.9748623
|
||||
72000 1.3692655 0.005711741 0.13966773 -0.062638787 5.3033385 1.1040582 2.7599218
|
||||
74000 1.3405365 -0.054281977 0.038019086 -0.024980877 5.1246258 2.0782965 2.725331
|
||||
76000 1.3644178 0.040847675 -0.051968108 -0.12259032 5.1218657 1.8504273 2.6804003
|
||||
78000 1.353792 -0.093663092 0.018784967 -0.073871437 5.025196 1.7789709 2.5339006
|
||||
80000 1.3520982 -0.09407101 0.010328039 0.0028841073 5.1410049 1.855057 2.6935895
|
||||
82000 1.3447597 -0.11935066 -0.2184608 0.073543056 5.2645334 1.7883077 4.2012292
|
||||
84000 1.3712151 -0.064367612 0.021246872 -0.033571866 5.0479674 1.8947341 4.3856536
|
||||
86000 1.3453867 -0.029842112 -0.042297039 0.05422886 5.0667777 2.0365983 4.4542311
|
||||
88000 1.3439543 -0.21625828 -0.028119372 -0.010320332 4.9946428 2.3095763 4.3429587
|
||||
90000 1.3472579 0.058391002 0.037139373 0.03424008 5.0599004 2.8132794 4.4503426
|
||||
92000 1.361788 0.028891114 0.072799744 -0.12035229 4.8759851 2.5130025 4.2747068
|
||||
94000 1.3440566 0.043421348 0.049653856 -0.060444094 4.8884081 2.5072981 4.3105221
|
||||
96000 1.3537566 0.088733517 -0.11449828 -0.049852036 4.8115085 2.4780963 4.2213579
|
||||
98000 1.3373399 0.25457663 -0.041723778 0.00084565184 4.7163394 2.4100822 4.485536
|
||||
100000 1.3487502 0.046333889 0.1247351 0.063467467 4.6563279 2.4049358 4.5742925
|
||||
Loop time of 49.532 on 8 procs for 100000 steps with 4000 atoms
|
||||
|
||||
Performance: 872163.631 tau/day, 2018.897 timesteps/s
|
||||
99.6% CPU use with 8 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 27.027 | 27.478 | 28.167 | 6.9 | 55.48
|
||||
Neigh | 11.257 | 11.369 | 11.491 | 2.3 | 22.95
|
||||
Comm | 6.6783 | 7.6942 | 8.2758 | 19.3 | 15.53
|
||||
Output | 0.0075166 | 0.024356 | 0.026799 | 4.1 | 0.05
|
||||
Modify | 1.7374 | 1.7617 | 1.7845 | 1.0 | 3.56
|
||||
Other | | 1.205 | | | 2.43
|
||||
|
||||
Nlocal: 500 ave 505 max 491 min
|
||||
Histogram: 1 0 0 1 0 1 0 2 2 1
|
||||
Nghost: 1529.88 ave 1548 max 1508 min
|
||||
Histogram: 1 1 0 0 1 1 2 0 0 2
|
||||
Neighs: 13569.8 ave 13906 max 13235 min
|
||||
Histogram: 1 1 0 1 1 1 1 1 0 1
|
||||
|
||||
Total # of neighbors = 108558
|
||||
Ave neighs/atom = 27.1395
|
||||
Neighbor list builds = 16041
|
||||
Dangerous builds = 0
|
||||
|
||||
variable kappa equal (v_k11+v_k22+v_k33)/3.0
|
||||
print "running average conductivity: ${kappa}"
|
||||
running average conductivity: 3.8785187495769
|
||||
Total wall time: 0:00:50
|
||||
@ -1,245 +0,0 @@
|
||||
LAMMPS (13 Oct 2016)
|
||||
# sample LAMMPS input script for thermal conductivity of liquid LJ
|
||||
# thermostatting 2 regions via fix langevin
|
||||
|
||||
# settings
|
||||
|
||||
variable x equal 10
|
||||
variable y equal 10
|
||||
variable z equal 20
|
||||
|
||||
variable rho equal 0.6
|
||||
variable t equal 1.35
|
||||
variable rc equal 2.5
|
||||
variable tlo equal 1.0
|
||||
variable thi equal 1.70
|
||||
|
||||
#variable rho equal 0.85
|
||||
#variable t equal 0.7
|
||||
#variable rc equal 3.0
|
||||
#variable tlo equal 0.3
|
||||
#variable thi equal 1.0
|
||||
|
||||
# setup problem
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc ${rho}
|
||||
lattice fcc 0.6
|
||||
Lattice spacing in x,y,z = 1.88207 1.88207 1.88207
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 10 0 $y 0 $z
|
||||
region box block 0 10 0 10 0 $z
|
||||
region box block 0 10 0 10 0 20
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (18.8207 18.8207 37.6414)
|
||||
2 by 1 by 4 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 8000 atoms
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create $t 87287
|
||||
velocity all create 1.35 87287
|
||||
|
||||
pair_style lj/cut ${rc}
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1
|
||||
|
||||
# heat layers
|
||||
|
||||
region hot block INF INF INF INF 0 1
|
||||
region cold block INF INF INF INF 10 11
|
||||
compute Thot all temp/region hot
|
||||
compute Tcold all temp/region cold
|
||||
|
||||
# 1st equilibration run
|
||||
|
||||
fix 1 all nvt temp $t $t 0.5
|
||||
fix 1 all nvt temp 1.35 $t 0.5
|
||||
fix 1 all nvt temp 1.35 1.35 0.5
|
||||
thermo 100
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4 -> bins = 14 14 27
|
||||
Memory usage per processor = 2.55761 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.35 -4.1241917 0 -2.0994448 -3.1961612
|
||||
100 1.1819832 -3.7640881 0 -1.991335 0.53985757
|
||||
200 1.2578365 -3.7395333 0 -1.8530144 0.69591862
|
||||
300 1.3282971 -3.7215427 0 -1.7293461 0.79036065
|
||||
400 1.3714367 -3.7043826 0 -1.6474847 0.85873226
|
||||
500 1.3590952 -3.6707735 0 -1.6323855 0.99602024
|
||||
600 1.3575117 -3.7118244 0 -1.6758114 0.81454305
|
||||
700 1.3284444 -3.7075488 0 -1.7151313 0.81136596
|
||||
800 1.3419995 -3.7155648 0 -1.7028172 0.82925676
|
||||
900 1.3562214 -3.6965609 0 -1.6624831 0.88908117
|
||||
1000 1.3732017 -3.7100044 0 -1.6504594 0.83982701
|
||||
Loop time of 0.876399 on 8 procs for 1000 steps with 8000 atoms
|
||||
|
||||
Performance: 492926.111 tau/day, 1141.033 timesteps/s
|
||||
99.4% CPU use with 8 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.47963 | 0.4975 | 0.51846 | 1.6 | 56.77
|
||||
Neigh | 0.22878 | 0.23186 | 0.23458 | 0.4 | 26.46
|
||||
Comm | 0.081789 | 0.096763 | 0.11865 | 3.6 | 11.04
|
||||
Output | 0.000247 | 0.00025409 | 0.00028944 | 0.1 | 0.03
|
||||
Modify | 0.02689 | 0.033982 | 0.042612 | 2.9 | 3.88
|
||||
Other | | 0.01604 | | | 1.83
|
||||
|
||||
Nlocal: 1000 ave 1020 max 982 min
|
||||
Histogram: 1 0 2 1 0 1 1 1 0 1
|
||||
Nghost: 2299.5 ave 2331 max 2268 min
|
||||
Histogram: 1 1 1 1 0 0 0 3 0 1
|
||||
Neighs: 27122 ave 28382 max 26337 min
|
||||
Histogram: 2 0 2 1 1 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 216976
|
||||
Ave neighs/atom = 27.122
|
||||
Neighbor list builds = 162
|
||||
Dangerous builds = 0
|
||||
|
||||
velocity all scale $t
|
||||
velocity all scale 1.35
|
||||
|
||||
unfix 1
|
||||
|
||||
# 2nd equilibration run
|
||||
|
||||
fix 1 all nve
|
||||
fix hot all langevin ${thi} ${thi} 1.0 59804 tally yes
|
||||
fix hot all langevin 1.7 ${thi} 1.0 59804 tally yes
|
||||
fix hot all langevin 1.7 1.7 1.0 59804 tally yes
|
||||
fix cold all langevin ${tlo} ${tlo} 1.0 287859 tally yes
|
||||
fix cold all langevin 1 ${tlo} 1.0 287859 tally yes
|
||||
fix cold all langevin 1 1 1.0 287859 tally yes
|
||||
fix_modify hot temp Thot
|
||||
fix_modify cold temp Tcold
|
||||
|
||||
variable tdiff equal c_Thot-c_Tcold
|
||||
thermo_style custom step temp c_Thot c_Tcold f_hot f_cold v_tdiff
|
||||
thermo 1000
|
||||
run 10000
|
||||
Memory usage per processor = 3.30761 Mbytes
|
||||
Step Temp c_Thot c_Tcold f_hot f_cold v_tdiff
|
||||
1000 1.35 1.431295 1.2955644 -0 -0 0.13573065
|
||||
2000 1.3593243 1.6602094 1.0898701 -0.13903162 0.14234352 0.57033928
|
||||
3000 1.3412163 1.6308839 1.0677742 -0.2214765 0.25871329 0.56310968
|
||||
4000 1.3275359 1.5248034 1.0792345 -0.26908328 0.34211202 0.44556887
|
||||
5000 1.3230922 1.6266046 1.0523802 -0.33175886 0.43533756 0.5742244
|
||||
6000 1.3037036 1.6021737 1.0408166 -0.3639815 0.49869333 0.56135712
|
||||
7000 1.2903225 1.5701119 1.0603548 -0.40000421 0.55547714 0.50975712
|
||||
8000 1.3050677 1.6420218 1.0221774 -0.46368839 0.60293974 0.61984444
|
||||
9000 1.2950977 1.7153984 1.0583242 -0.51871512 0.66389344 0.65707419
|
||||
10000 1.3100216 1.6680668 1.0871293 -0.57485359 0.7161839 0.58093752
|
||||
11000 1.297052 1.6486494 1.088903 -0.60276081 0.75900024 0.55974633
|
||||
Loop time of 11.5988 on 8 procs for 10000 steps with 8000 atoms
|
||||
|
||||
Performance: 372451.299 tau/day, 862.156 timesteps/s
|
||||
99.4% CPU use with 8 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 4.0544 | 4.9719 | 5.8426 | 34.5 | 42.87
|
||||
Neigh | 2.0735 | 2.3933 | 2.7208 | 18.8 | 20.63
|
||||
Comm | 0.91559 | 1.9788 | 3.1216 | 70.5 | 17.06
|
||||
Output | 0.0005753 | 0.00068495 | 0.00080419 | 0.3 | 0.01
|
||||
Modify | 1.9354 | 1.9837 | 2.0321 | 2.6 | 17.10
|
||||
Other | | 0.2705 | | | 2.33
|
||||
|
||||
Nlocal: 1000 ave 1112 max 841 min
|
||||
Histogram: 1 1 0 2 0 0 0 0 1 3
|
||||
Nghost: 2294.38 ave 2506 max 2077 min
|
||||
Histogram: 2 1 1 0 0 0 0 1 1 2
|
||||
Neighs: 27441.9 ave 32651 max 19438 min
|
||||
Histogram: 1 1 0 2 0 0 0 0 0 4
|
||||
|
||||
Total # of neighbors = 219535
|
||||
Ave neighs/atom = 27.4419
|
||||
Neighbor list builds = 1674
|
||||
Dangerous builds = 0
|
||||
|
||||
# thermal conductivity calculation
|
||||
# reset langevin thermostats to zero energy accumulation
|
||||
|
||||
compute ke all ke/atom
|
||||
variable temp atom c_ke/1.5
|
||||
|
||||
fix hot all langevin ${thi} ${thi} 1.0 59804 tally yes
|
||||
fix hot all langevin 1.7 ${thi} 1.0 59804 tally yes
|
||||
fix hot all langevin 1.7 1.7 1.0 59804 tally yes
|
||||
fix cold all langevin ${tlo} ${tlo} 1.0 287859 tally yes
|
||||
fix cold all langevin 1 ${tlo} 1.0 287859 tally yes
|
||||
fix cold all langevin 1 1 1.0 287859 tally yes
|
||||
fix_modify hot temp Thot
|
||||
fix_modify cold temp Tcold
|
||||
|
||||
fix ave all ave/time 10 100 1000 v_tdiff ave running
|
||||
thermo_style custom step temp c_Thot c_Tcold f_hot f_cold v_tdiff f_ave
|
||||
|
||||
compute layers all chunk/atom bin/1d z lower 0.05 units reduced
|
||||
fix 2 all ave/chunk 10 100 1000 layers v_temp file profile.langevin
|
||||
|
||||
run 20000
|
||||
Memory usage per processor = 3.5578 Mbytes
|
||||
Step Temp c_Thot c_Tcold f_hot f_cold v_tdiff f_ave
|
||||
11000 1.297052 1.6473904 1.088903 -0 -0 0.55848738 0
|
||||
12000 1.2792808 1.6043738 1.0658375 -0.012256975 0.04611547 0.53853632 0.54492428
|
||||
13000 1.2787101 1.7035572 1.1159037 -0.073806664 0.099529002 0.58765348 0.5581748
|
||||
14000 1.289918 1.4642237 1.1073937 -0.11428779 0.13931657 0.35683005 0.56816328
|
||||
15000 1.2932964 1.5032665 1.0523148 -0.17247717 0.19001309 0.45095174 0.57436291
|
||||
16000 1.3025037 1.5424316 1.1185175 -0.22598282 0.22640921 0.42391405 0.56973168
|
||||
17000 1.3009667 1.5582105 1.0745661 -0.27544101 0.26143452 0.48364439 0.5700118
|
||||
18000 1.2970255 1.5019842 1.0228322 -0.31195285 0.31203237 0.479152 0.56544644
|
||||
19000 1.2880631 1.5290587 1.0976483 -0.34645573 0.34243366 0.43141047 0.56338309
|
||||
20000 1.3119675 1.6284144 1.1102294 -0.40922326 0.39217092 0.51818503 0.56614474
|
||||
21000 1.2838063 1.6670934 0.97721382 -0.43809329 0.46021572 0.68987962 0.5686161
|
||||
22000 1.2925041 1.7050682 1.0984963 -0.4871305 0.50520177 0.6065719 0.57226368
|
||||
23000 1.2746463 1.6388503 1.0286701 -0.51212873 0.56478515 0.6101802 0.57290996
|
||||
24000 1.2745381 1.7085713 1.1362975 -0.54529463 0.58540408 0.57227375 0.57296767
|
||||
25000 1.2776401 1.5259253 1.0415158 -0.58389862 0.62623289 0.48440948 0.57386374
|
||||
26000 1.2661888 1.4760829 0.99145001 -0.62638032 0.68155754 0.48463289 0.57021631
|
||||
27000 1.2923677 1.6070495 1.0300276 -0.70014343 0.70236265 0.5770219 0.57001637
|
||||
28000 1.2961449 1.7052335 1.0805793 -0.74856241 0.75775659 0.62465427 0.56927907
|
||||
29000 1.2969474 1.5520176 1.1249649 -0.78900962 0.79539202 0.42705264 0.56986986
|
||||
30000 1.2900596 1.6556864 1.0302676 -0.84180996 0.87187683 0.6254189 0.57245841
|
||||
31000 1.2923209 1.6752068 1.0156911 -0.89036148 0.88285227 0.65951571 0.57358134
|
||||
Loop time of 24.1059 on 8 procs for 20000 steps with 8000 atoms
|
||||
|
||||
Performance: 358418.039 tau/day, 829.671 timesteps/s
|
||||
99.4% CPU use with 8 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 7.5967 | 9.9644 | 12.189 | 62.9 | 41.34
|
||||
Neigh | 3.9305 | 4.7817 | 5.594 | 34.5 | 19.84
|
||||
Comm | 1.7656 | 4.5624 | 7.6382 | 122.3 | 18.93
|
||||
Output | 0.0011697 | 0.0018933 | 0.0020008 | 0.6 | 0.01
|
||||
Modify | 4.1386 | 4.2107 | 4.3622 | 3.8 | 17.47
|
||||
Other | | 0.5848 | | | 2.43
|
||||
|
||||
Nlocal: 1000 ave 1118 max 875 min
|
||||
Histogram: 2 1 1 0 0 0 0 0 2 2
|
||||
Nghost: 2298.62 ave 2535 max 2063 min
|
||||
Histogram: 3 1 0 0 0 0 0 0 1 3
|
||||
Neighs: 27462.4 ave 32904 max 21333 min
|
||||
Histogram: 2 2 0 0 0 0 0 0 0 4
|
||||
|
||||
Total # of neighbors = 219699
|
||||
Ave neighs/atom = 27.4624
|
||||
Neighbor list builds = 3340
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:36
|
||||
@ -1,232 +0,0 @@
|
||||
LAMMPS (13 Oct 2016)
|
||||
# sample LAMMPS input script for thermal conductivity of liquid LJ
|
||||
# Muller-Plathe method via fix thermal_conductivity
|
||||
|
||||
# settings
|
||||
|
||||
variable x equal 10
|
||||
variable y equal 10
|
||||
variable z equal 20
|
||||
|
||||
variable rho equal 0.6
|
||||
variable t equal 1.35
|
||||
variable rc equal 2.5
|
||||
|
||||
#variable rho equal 0.85
|
||||
#variable t equal 0.7
|
||||
#variable rc equal 3.0
|
||||
|
||||
# setup problem
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc ${rho}
|
||||
lattice fcc 0.6
|
||||
Lattice spacing in x,y,z = 1.88207 1.88207 1.88207
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 10 0 $y 0 $z
|
||||
region box block 0 10 0 10 0 $z
|
||||
region box block 0 10 0 10 0 20
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (18.8207 18.8207 37.6414)
|
||||
2 by 1 by 4 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 8000 atoms
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create $t 87287
|
||||
velocity all create 1.35 87287
|
||||
|
||||
pair_style lj/cut ${rc}
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1
|
||||
|
||||
# 1st equilibration run
|
||||
|
||||
fix 1 all nvt temp $t $t 0.5
|
||||
fix 1 all nvt temp 1.35 $t 0.5
|
||||
fix 1 all nvt temp 1.35 1.35 0.5
|
||||
thermo 100
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4 -> bins = 14 14 27
|
||||
Memory usage per processor = 2.55761 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.35 -4.1241917 0 -2.0994448 -3.1961612
|
||||
100 1.1819832 -3.7640881 0 -1.991335 0.53985757
|
||||
200 1.2578365 -3.7395333 0 -1.8530144 0.69591862
|
||||
300 1.3282971 -3.7215427 0 -1.7293461 0.79036065
|
||||
400 1.3714367 -3.7043826 0 -1.6474847 0.85873226
|
||||
500 1.3590952 -3.6707735 0 -1.6323855 0.99602024
|
||||
600 1.3575117 -3.7118244 0 -1.6758114 0.81454305
|
||||
700 1.3284444 -3.7075488 0 -1.7151313 0.81136596
|
||||
800 1.3419995 -3.7155648 0 -1.7028172 0.82925676
|
||||
900 1.3562214 -3.6965609 0 -1.6624831 0.88908117
|
||||
1000 1.3732017 -3.7100044 0 -1.6504594 0.83982701
|
||||
Loop time of 0.875524 on 8 procs for 1000 steps with 8000 atoms
|
||||
|
||||
Performance: 493418.774 tau/day, 1142.173 timesteps/s
|
||||
99.5% CPU use with 8 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.48279 | 0.49681 | 0.51174 | 1.2 | 56.74
|
||||
Neigh | 0.22868 | 0.23169 | 0.23454 | 0.4 | 26.46
|
||||
Comm | 0.084792 | 0.098391 | 0.11603 | 3.4 | 11.24
|
||||
Output | 0.00027204 | 0.00027871 | 0.00031137 | 0.1 | 0.03
|
||||
Modify | 0.027863 | 0.032316 | 0.039397 | 2.3 | 3.69
|
||||
Other | | 0.01605 | | | 1.83
|
||||
|
||||
Nlocal: 1000 ave 1020 max 982 min
|
||||
Histogram: 1 0 2 1 0 1 1 1 0 1
|
||||
Nghost: 2299.5 ave 2331 max 2268 min
|
||||
Histogram: 1 1 1 1 0 0 0 3 0 1
|
||||
Neighs: 27122 ave 28382 max 26337 min
|
||||
Histogram: 2 0 2 1 1 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 216976
|
||||
Ave neighs/atom = 27.122
|
||||
Neighbor list builds = 162
|
||||
Dangerous builds = 0
|
||||
|
||||
velocity all scale $t
|
||||
velocity all scale 1.35
|
||||
|
||||
unfix 1
|
||||
|
||||
# 2nd equilibration run
|
||||
|
||||
compute ke all ke/atom
|
||||
variable temp atom c_ke/1.5
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
compute layers all chunk/atom bin/1d z lower 0.05 units reduced
|
||||
fix 2 all ave/chunk 10 100 1000 layers v_temp file profile.mp
|
||||
|
||||
fix 3 all thermal/conductivity 10 z 20
|
||||
|
||||
variable tdiff equal f_2[11][3]-f_2[1][3]
|
||||
thermo_style custom step temp epair etotal f_3 v_tdiff
|
||||
|
||||
thermo 1000
|
||||
run 20000
|
||||
Memory usage per processor = 2.8078 Mbytes
|
||||
Step Temp E_pair TotEng f_3 v_tdiff
|
||||
1000 1.35 -3.7100044 -1.6852575 0 0
|
||||
2000 1.3572899 -3.7210084 -1.6853282 873.12373 0.26058005
|
||||
3000 1.359979 -3.7268343 -1.6871208 1750.6998 0.40845169
|
||||
4000 1.3677509 -3.7394553 -1.6880853 2565.8064 0.63828485
|
||||
5000 1.3742987 -3.750287 -1.6890966 3373.2897 0.70173279
|
||||
6000 1.3950535 -3.7827674 -1.6904487 4162.6672 0.83210131
|
||||
7000 1.3843852 -3.7679238 -1.6916056 4947.5882 0.92719731
|
||||
8000 1.396125 -3.7861373 -1.6922116 5703.4508 0.92426948
|
||||
9000 1.4135104 -3.812624 -1.6926234 6465.5676 1.0412501
|
||||
10000 1.4092351 -3.8065359 -1.6929474 7242.2986 1.0772505
|
||||
11000 1.3966916 -3.7874302 -1.6926547 8007.3229 1.056805
|
||||
12000 1.4111272 -3.8089829 -1.6925567 8750.8648 1.097621
|
||||
13000 1.4091888 -3.8074873 -1.6939684 9514.7196 1.0734167
|
||||
14000 1.4132159 -3.8134636 -1.6939046 10284.269 1.1643391
|
||||
15000 1.3991348 -3.7928819 -1.694442 11051.851 1.0716016
|
||||
16000 1.4055537 -3.8013252 -1.6932583 11836.812 1.1506479
|
||||
17000 1.4127928 -3.8141054 -1.6951811 12626.124 1.1301728
|
||||
18000 1.4118868 -3.8119733 -1.6944077 13391.631 1.1521394
|
||||
19000 1.4209268 -3.826811 -1.6956872 14180.009 1.0929393
|
||||
20000 1.4093812 -3.8083875 -1.6945801 14969.574 1.2113183
|
||||
21000 1.4202317 -3.8255696 -1.6954884 15735.893 1.161082
|
||||
Loop time of 21.0741 on 8 procs for 20000 steps with 8000 atoms
|
||||
|
||||
Performance: 409982.223 tau/day, 949.033 timesteps/s
|
||||
99.3% CPU use with 8 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 7.4932 | 10.005 | 12.426 | 70.1 | 47.48
|
||||
Neigh | 4.0592 | 5.0894 | 6.0544 | 41.7 | 24.15
|
||||
Comm | 1.7793 | 5.0312 | 8.5027 | 134.6 | 23.87
|
||||
Output | 0.00058484 | 0.00060964 | 0.0007031 | 0.1 | 0.00
|
||||
Modify | 0.39735 | 0.4211 | 0.43467 | 2.3 | 2.00
|
||||
Other | | 0.5269 | | | 2.50
|
||||
|
||||
Nlocal: 1000 ave 1188 max 806 min
|
||||
Histogram: 2 1 1 0 0 0 0 0 2 2
|
||||
Nghost: 2300.5 ave 2645 max 1963 min
|
||||
Histogram: 3 1 0 0 0 0 0 0 1 3
|
||||
Neighs: 27897 ave 37064 max 18367 min
|
||||
Histogram: 2 2 0 0 0 0 0 0 0 4
|
||||
|
||||
Total # of neighbors = 223176
|
||||
Ave neighs/atom = 27.897
|
||||
Neighbor list builds = 3537
|
||||
Dangerous builds = 0
|
||||
|
||||
# thermal conductivity calculation
|
||||
# reset fix thermal/conductivity to zero energy accumulation
|
||||
|
||||
fix 3 all thermal/conductivity 10 z 20
|
||||
|
||||
fix ave all ave/time 1 1 1000 v_tdiff ave running
|
||||
thermo_style custom step temp epair etotal f_3 v_tdiff f_ave
|
||||
|
||||
run 20000
|
||||
Memory usage per processor = 3.05853 Mbytes
|
||||
Step Temp E_pair TotEng f_3 v_tdiff f_ave
|
||||
21000 1.4202317 -3.8255696 -1.6954884 0 1.161082 1.161082
|
||||
22000 1.4090517 -3.808543 -1.6952296 745.83128 1.1780376 1.1695598
|
||||
23000 1.4261394 -3.8350237 -1.696082 1516.9526 1.1393504 1.15949
|
||||
24000 1.4103907 -3.8098769 -1.6945553 2290.0213 1.1962529 1.1686807
|
||||
25000 1.4205929 -3.8266444 -1.6960213 3028.2748 1.1355183 1.1620482
|
||||
26000 1.4148587 -3.8168728 -1.69485 3788.0858 1.1902606 1.1667503
|
||||
27000 1.4226648 -3.8297832 -1.6960528 4580.4932 1.2378446 1.1769066
|
||||
28000 1.4167854 -3.8205958 -1.6956834 5328.2357 1.2038835 1.1802787
|
||||
29000 1.4208636 -3.8267081 -1.6956791 6077.036 1.1970863 1.1821462
|
||||
30000 1.420575 -3.8256917 -1.6950955 6840.5407 1.1884497 1.1827766
|
||||
31000 1.4233235 -3.8318045 -1.6970861 7576.9859 1.2088723 1.1851489
|
||||
32000 1.418912 -3.8229407 -1.6948388 8319.9854 1.1604002 1.1830865
|
||||
33000 1.4161289 -3.8211375 -1.6972096 9097.8598 1.1381183 1.1796274
|
||||
34000 1.3982574 -3.7915345 -1.6944106 9819.5817 1.1809721 1.1797235
|
||||
35000 1.4211314 -3.8267235 -1.6952929 10604.381 1.157812 1.1782627
|
||||
36000 1.4181668 -3.8217718 -1.6947876 11332.942 1.1843186 1.1786412
|
||||
37000 1.4092823 -3.8094817 -1.6958226 12068.55 1.1043391 1.1742705
|
||||
38000 1.4220481 -3.8278441 -1.6950386 12815.406 1.1996255 1.1756791
|
||||
39000 1.4146432 -3.8175526 -1.6958531 13565.714 1.149226 1.1742868
|
||||
40000 1.4088356 -3.8079173 -1.694928 14309.801 1.1710565 1.1741253
|
||||
41000 1.4058693 -3.8043119 -1.6957716 15067.894 1.1839862 1.1745949
|
||||
Loop time of 22.0429 on 8 procs for 20000 steps with 8000 atoms
|
||||
|
||||
Performance: 391962.361 tau/day, 907.320 timesteps/s
|
||||
99.3% CPU use with 8 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 6.8314 | 10.063 | 12.978 | 88.0 | 45.65
|
||||
Neigh | 3.8802 | 5.2398 | 6.5269 | 52.7 | 23.77
|
||||
Comm | 1.828 | 5.8112 | 10.14 | 160.2 | 26.36
|
||||
Output | 0.00050211 | 0.00052819 | 0.00060391 | 0.1 | 0.00
|
||||
Modify | 0.39313 | 0.41984 | 0.4453 | 3.3 | 1.90
|
||||
Other | | 0.5084 | | | 2.31
|
||||
|
||||
Nlocal: 1000 ave 1188 max 810 min
|
||||
Histogram: 2 1 1 0 0 0 0 1 1 2
|
||||
Nghost: 2304.5 ave 2648 max 1970 min
|
||||
Histogram: 3 1 0 0 0 0 0 0 1 3
|
||||
Neighs: 27885.2 ave 36431 max 18556 min
|
||||
Histogram: 2 2 0 0 0 0 0 0 1 3
|
||||
|
||||
Total # of neighbors = 223082
|
||||
Ave neighs/atom = 27.8852
|
||||
Neighbor list builds = 3626
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:44
|
||||
244
examples/KAPPA/log.15May22.ehex.g++.8
Normal file
244
examples/KAPPA/log.15May22.ehex.g++.8
Normal file
@ -0,0 +1,244 @@
|
||||
LAMMPS (4 May 2022)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# sample LAMMPS input script for thermal conductivity of liquid LJ
|
||||
# use fix ehex to add/subtract energy from 2 regions
|
||||
|
||||
# settings
|
||||
|
||||
variable x equal 10
|
||||
variable y equal 10
|
||||
variable z equal 20
|
||||
|
||||
variable rho equal 0.6
|
||||
variable t equal 1.35
|
||||
variable rc equal 2.5
|
||||
|
||||
#variable rho equal 0.85
|
||||
#variable t equal 0.7
|
||||
#variable rc equal 3.0
|
||||
|
||||
# setup problem
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc ${rho}
|
||||
lattice fcc 0.6
|
||||
Lattice spacing in x,y,z = 1.8820721 1.8820721 1.8820721
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 10 0 $y 0 $z
|
||||
region box block 0 10 0 10 0 $z
|
||||
region box block 0 10 0 10 0 20
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (18.820721 18.820721 37.641441)
|
||||
2 by 1 by 4 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 8000 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (18.820721 18.820721 37.641441)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create $t 87287
|
||||
velocity all create 1.35 87287
|
||||
|
||||
pair_style lj/cut ${rc}
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1
|
||||
|
||||
# heat layers
|
||||
|
||||
region hot block INF INF INF INF 0 1
|
||||
region cold block INF INF INF INF 10 11
|
||||
compute Thot all temp/region hot
|
||||
compute Tcold all temp/region cold
|
||||
|
||||
# 1st equilibration run
|
||||
|
||||
fix 1 all nvt temp $t $t 0.5
|
||||
fix 1 all nvt temp 1.35 $t 0.5
|
||||
fix 1 all nvt temp 1.35 1.35 0.5
|
||||
thermo 100
|
||||
run 1000
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 14 14 27
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.152 | 3.152 | 3.152 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.35 -4.1241917 0 -2.0994448 -3.1961612
|
||||
100 1.1819832 -3.7640881 0 -1.991335 0.53985757
|
||||
200 1.2578365 -3.7395333 0 -1.8530144 0.69591862
|
||||
300 1.3282971 -3.7215427 0 -1.7293461 0.79036065
|
||||
400 1.3714367 -3.7043826 0 -1.6474847 0.85873226
|
||||
500 1.3590952 -3.6707735 0 -1.6323855 0.99602024
|
||||
600 1.3575117 -3.7118244 0 -1.6758114 0.81454305
|
||||
700 1.3284444 -3.7075488 0 -1.7151313 0.81136596
|
||||
800 1.3419995 -3.7155648 0 -1.7028172 0.82925676
|
||||
900 1.3562214 -3.6965609 0 -1.6624831 0.88908117
|
||||
1000 1.3732017 -3.7100044 0 -1.6504594 0.83982701
|
||||
Loop time of 0.925673 on 8 procs for 1000 steps with 8000 atoms
|
||||
|
||||
Performance: 466687.339 tau/day, 1080.295 timesteps/s
|
||||
98.5% CPU use with 8 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.5071 | 0.52493 | 0.5485 | 1.7 | 56.71
|
||||
Neigh | 0.23405 | 0.23912 | 0.24396 | 0.7 | 25.83
|
||||
Comm | 0.084007 | 0.10338 | 0.12987 | 4.9 | 11.17
|
||||
Output | 0.00030358 | 0.00048259 | 0.0017229 | 0.0 | 0.05
|
||||
Modify | 0.035045 | 0.043306 | 0.051758 | 3.2 | 4.68
|
||||
Other | | 0.01446 | | | 1.56
|
||||
|
||||
Nlocal: 1000 ave 1020 max 982 min
|
||||
Histogram: 1 0 2 1 0 1 1 1 0 1
|
||||
Nghost: 2299.5 ave 2331 max 2268 min
|
||||
Histogram: 1 1 1 1 0 0 0 3 0 1
|
||||
Neighs: 27122 ave 28382 max 26337 min
|
||||
Histogram: 2 0 2 1 1 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 216976
|
||||
Ave neighs/atom = 27.122
|
||||
Neighbor list builds = 162
|
||||
Dangerous builds = 0
|
||||
|
||||
velocity all scale $t
|
||||
velocity all scale 1.35
|
||||
|
||||
unfix 1
|
||||
|
||||
# 2nd equilibration run
|
||||
|
||||
fix 1 all nve
|
||||
fix hot all ehex 1 100.0 region hot
|
||||
fix cold all ehex 1 -100.0 region cold
|
||||
|
||||
thermo_style custom step temp c_Thot c_Tcold
|
||||
thermo_modify colname c_Thot Temp_hot colname c_Tcold Temp_cold
|
||||
thermo 1000
|
||||
run 10000
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.406 | 3.406 | 3.406 Mbytes
|
||||
Step Temp Temp_hot Temp_cold
|
||||
1000 1.35 1.431295 1.2955644
|
||||
2000 1.3537291 1.6418772 1.1875127
|
||||
3000 1.3615152 1.6451299 1.1769094
|
||||
4000 1.3612129 1.5281727 1.2022419
|
||||
5000 1.3552182 1.6672955 1.2212864
|
||||
6000 1.3643442 1.6072213 1.2390567
|
||||
7000 1.3665773 1.6909819 1.1466611
|
||||
8000 1.375741 1.6144274 1.1691231
|
||||
9000 1.3701136 1.8238424 1.136342
|
||||
10000 1.3563004 1.8059065 1.1547129
|
||||
11000 1.3794051 1.692299 1.0515688
|
||||
Loop time of 10.4087 on 8 procs for 10000 steps with 8000 atoms
|
||||
|
||||
Performance: 415036.696 tau/day, 960.733 timesteps/s
|
||||
98.8% CPU use with 8 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 4.2937 | 5.0957 | 5.741 | 23.2 | 48.96
|
||||
Neigh | 2.1995 | 2.4735 | 2.7099 | 13.0 | 23.76
|
||||
Comm | 0.81056 | 1.5944 | 2.6024 | 51.8 | 15.32
|
||||
Output | 0.00049738 | 0.00074599 | 0.0021147 | 0.0 | 0.01
|
||||
Modify | 0.92166 | 1.0638 | 1.1348 | 7.9 | 10.22
|
||||
Other | | 0.1804 | | | 1.73
|
||||
|
||||
Nlocal: 1000 ave 1105 max 883 min
|
||||
Histogram: 1 1 2 0 0 0 0 0 2 2
|
||||
Nghost: 2319.38 ave 2502 max 2114 min
|
||||
Histogram: 1 3 0 0 0 0 0 0 0 4
|
||||
Neighs: 27387.9 ave 32453 max 21803 min
|
||||
Histogram: 2 2 0 0 0 0 0 0 0 4
|
||||
|
||||
Total # of neighbors = 219103
|
||||
Ave neighs/atom = 27.387875
|
||||
Neighbor list builds = 1696
|
||||
Dangerous builds = 0
|
||||
|
||||
# thermal conductivity calculation
|
||||
|
||||
compute ke all ke/atom
|
||||
variable temp atom c_ke/1.5
|
||||
|
||||
compute layers all chunk/atom bin/1d z lower 0.05 units reduced
|
||||
fix 2 all ave/chunk 10 100 1000 layers v_temp file profile.ehex
|
||||
|
||||
variable tdiff equal f_2[1][3]-f_2[11][3]
|
||||
fix ave all ave/time 1 1 1000 v_tdiff ave running start 13000
|
||||
|
||||
variable kappa equal (100/(lx*ly)/2.0)*(lz/2.0)/f_ave
|
||||
|
||||
thermo_style custom step temp c_Thot c_Tcold v_tdiff f_ave
|
||||
WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:903)
|
||||
thermo_modify colname c_Thot Temp_hot colname c_Tcold Temp_cold colname v_tdiff dTemp_step colname f_ave dTemp
|
||||
|
||||
run 20000
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.656 | 3.657 | 3.658 Mbytes
|
||||
Step Temp Temp_hot Temp_cold dTemp_step dTemp
|
||||
11000 1.3794051 1.6903393 1.0515688 0 0
|
||||
12000 1.3799777 1.8004888 1.1032219 0.63860014 0
|
||||
13000 1.3733605 1.7823094 1.0553582 0.65827891 0.65827891
|
||||
14000 1.3749743 1.7852256 1.1674016 0.68463005 0.67145448
|
||||
15000 1.3863795 1.8538127 1.0056247 0.73524813 0.69271903
|
||||
16000 1.3731955 1.7518546 1.0741458 0.74810775 0.70656621
|
||||
17000 1.3771856 1.9016869 1.0090502 0.73999567 0.7132521
|
||||
18000 1.3766032 1.7616195 1.1142155 0.73769104 0.71732526
|
||||
19000 1.3815934 1.7791247 1.1406987 0.73617832 0.72001855
|
||||
20000 1.3725543 1.8637436 1.0799364 0.73435569 0.7218107
|
||||
21000 1.3817369 1.8808771 1.0642524 0.76702329 0.72683432
|
||||
22000 1.3968704 1.840287 1.072304 0.82496419 0.7366473
|
||||
23000 1.3895558 1.9427293 1.0766665 0.75363908 0.73819201
|
||||
24000 1.3900493 1.9883976 1.1081017 0.86394774 0.74867166
|
||||
25000 1.3838912 1.8853041 1.0795751 0.83043902 0.75496145
|
||||
26000 1.3912105 1.9330259 1.1070335 0.79880182 0.75809291
|
||||
27000 1.3891151 1.8548451 1.0676153 0.81856523 0.7621244
|
||||
28000 1.3942624 1.9796706 1.1251407 0.81762456 0.76559316
|
||||
29000 1.3819302 1.8619138 1.0495292 0.78627491 0.76680973
|
||||
30000 1.3968366 1.883107 1.1004588 0.83902548 0.77082172
|
||||
31000 1.3822489 1.8220413 1.0322271 0.7550338 0.76999077
|
||||
Loop time of 23.253 on 8 procs for 20000 steps with 8000 atoms
|
||||
|
||||
Performance: 371564.581 tau/day, 860.103 timesteps/s
|
||||
98.9% CPU use with 8 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 8.0778 | 10.624 | 13.006 | 62.2 | 45.69
|
||||
Neigh | 4.358 | 5.32 | 6.1917 | 35.5 | 22.88
|
||||
Comm | 1.5574 | 4.6136 | 8.0947 | 127.6 | 19.84
|
||||
Output | 0.0025729 | 0.0027796 | 0.0041615 | 1.0 | 0.01
|
||||
Modify | 2.0737 | 2.2922 | 2.4432 | 9.2 | 9.86
|
||||
Other | | 0.4005 | | | 1.72
|
||||
|
||||
Nlocal: 1000 ave 1121 max 857 min
|
||||
Histogram: 2 0 1 1 0 0 0 0 1 3
|
||||
Nghost: 2299.75 ave 2541 max 2067 min
|
||||
Histogram: 3 1 0 0 0 0 0 0 2 2
|
||||
Neighs: 27487.2 ave 33361 max 20651 min
|
||||
Histogram: 2 1 1 0 0 0 0 0 0 4
|
||||
|
||||
Total # of neighbors = 219898
|
||||
Ave neighs/atom = 27.48725
|
||||
Neighbor list builds = 3474
|
||||
Dangerous builds = 0
|
||||
print "Running average thermal conductivity: $(v_kappa:%.2f)"
|
||||
Running average thermal conductivity: 3.45
|
||||
Total wall time: 0:00:34
|
||||
243
examples/KAPPA/log.15May22.heat.g++.8
Normal file
243
examples/KAPPA/log.15May22.heat.g++.8
Normal file
@ -0,0 +1,243 @@
|
||||
LAMMPS (4 May 2022)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# sample LAMMPS input script for thermal conductivity of liquid LJ
|
||||
# use fix heat to add/subtract energy from 2 regions
|
||||
|
||||
# settings
|
||||
|
||||
variable x equal 10
|
||||
variable y equal 10
|
||||
variable z equal 20
|
||||
|
||||
variable rho equal 0.6
|
||||
variable t equal 1.35
|
||||
variable rc equal 2.5
|
||||
|
||||
#variable rho equal 0.85
|
||||
#variable t equal 0.7
|
||||
#variable rc equal 3.0
|
||||
|
||||
# setup problem
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc ${rho}
|
||||
lattice fcc 0.6
|
||||
Lattice spacing in x,y,z = 1.8820721 1.8820721 1.8820721
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 10 0 $y 0 $z
|
||||
region box block 0 10 0 10 0 $z
|
||||
region box block 0 10 0 10 0 20
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (18.820721 18.820721 37.641441)
|
||||
2 by 1 by 4 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 8000 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (18.820721 18.820721 37.641441)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create $t 87287
|
||||
velocity all create 1.35 87287
|
||||
|
||||
pair_style lj/cut ${rc}
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1
|
||||
|
||||
# heat layers
|
||||
|
||||
region hot block INF INF INF INF 0 1
|
||||
region cold block INF INF INF INF 10 11
|
||||
compute Thot all temp/region hot
|
||||
compute Tcold all temp/region cold
|
||||
|
||||
# 1st equilibration run
|
||||
|
||||
fix 1 all nvt temp $t $t 0.5
|
||||
fix 1 all nvt temp 1.35 $t 0.5
|
||||
fix 1 all nvt temp 1.35 1.35 0.5
|
||||
thermo 100
|
||||
run 1000
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 14 14 27
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.152 | 3.152 | 3.152 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.35 -4.1241917 0 -2.0994448 -3.1961612
|
||||
100 1.1819832 -3.7640881 0 -1.991335 0.53985757
|
||||
200 1.2578365 -3.7395333 0 -1.8530144 0.69591862
|
||||
300 1.3282971 -3.7215427 0 -1.7293461 0.79036065
|
||||
400 1.3714367 -3.7043826 0 -1.6474847 0.85873226
|
||||
500 1.3590952 -3.6707735 0 -1.6323855 0.99602024
|
||||
600 1.3575117 -3.7118244 0 -1.6758114 0.81454305
|
||||
700 1.3284444 -3.7075488 0 -1.7151313 0.81136596
|
||||
800 1.3419995 -3.7155648 0 -1.7028172 0.82925676
|
||||
900 1.3562214 -3.6965609 0 -1.6624831 0.88908117
|
||||
1000 1.3732017 -3.7100044 0 -1.6504594 0.83982701
|
||||
Loop time of 0.944921 on 8 procs for 1000 steps with 8000 atoms
|
||||
|
||||
Performance: 457180.899 tau/day, 1058.289 timesteps/s
|
||||
98.4% CPU use with 8 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.53036 | 0.5381 | 0.55265 | 1.0 | 56.95
|
||||
Neigh | 0.24246 | 0.24602 | 0.25063 | 0.5 | 26.04
|
||||
Comm | 0.092773 | 0.10258 | 0.11364 | 2.3 | 10.86
|
||||
Output | 0.0003103 | 0.0004958 | 0.0017848 | 0.0 | 0.05
|
||||
Modify | 0.033332 | 0.043019 | 0.054672 | 3.7 | 4.55
|
||||
Other | | 0.0147 | | | 1.56
|
||||
|
||||
Nlocal: 1000 ave 1020 max 982 min
|
||||
Histogram: 1 0 2 1 0 1 1 1 0 1
|
||||
Nghost: 2299.5 ave 2331 max 2268 min
|
||||
Histogram: 1 1 1 1 0 0 0 3 0 1
|
||||
Neighs: 27122 ave 28382 max 26337 min
|
||||
Histogram: 2 0 2 1 1 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 216976
|
||||
Ave neighs/atom = 27.122
|
||||
Neighbor list builds = 162
|
||||
Dangerous builds = 0
|
||||
|
||||
velocity all scale $t
|
||||
velocity all scale 1.35
|
||||
|
||||
unfix 1
|
||||
|
||||
# 2nd equilibration run
|
||||
|
||||
fix 1 all nve
|
||||
fix hot all heat 1 100.0 region hot
|
||||
fix cold all heat 1 -100.0 region cold
|
||||
|
||||
thermo_style custom step temp c_Thot c_Tcold
|
||||
thermo_modify colname c_Thot Temp_hot colname c_Tcold Temp_cold
|
||||
thermo 1000
|
||||
run 10000
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.156 | 3.156 | 3.156 Mbytes
|
||||
Step Temp Temp_hot Temp_cold
|
||||
1000 1.35 1.431295 1.2955644
|
||||
2000 1.3518468 1.5562602 1.154905
|
||||
3000 1.3477229 1.5890075 1.2395414
|
||||
4000 1.3487175 1.5491615 1.2019696
|
||||
5000 1.3594394 1.5780597 1.1824492
|
||||
6000 1.3583923 1.541735 1.1675586
|
||||
7000 1.3700321 1.6735877 1.1279114
|
||||
8000 1.3631993 1.6367675 1.0697225
|
||||
9000 1.3739201 1.6846211 1.1138829
|
||||
10000 1.3751455 1.8039471 1.1500399
|
||||
11000 1.3716416 1.833336 1.1267278
|
||||
Loop time of 11.4492 on 8 procs for 10000 steps with 8000 atoms
|
||||
|
||||
Performance: 377320.435 tau/day, 873.427 timesteps/s
|
||||
98.7% CPU use with 8 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 4.6062 | 5.3944 | 6.169 | 26.0 | 47.12
|
||||
Neigh | 2.3148 | 2.6122 | 2.8769 | 14.9 | 22.82
|
||||
Comm | 0.82337 | 1.7921 | 2.9417 | 59.6 | 15.65
|
||||
Output | 0.00052195 | 0.00073566 | 0.0020974 | 0.0 | 0.01
|
||||
Modify | 1.4086 | 1.4856 | 1.6791 | 9.2 | 12.98
|
||||
Other | | 0.1641 | | | 1.43
|
||||
|
||||
Nlocal: 1000 ave 1131 max 878 min
|
||||
Histogram: 3 1 0 0 0 0 0 1 1 2
|
||||
Nghost: 2312.88 ave 2525 max 2114 min
|
||||
Histogram: 2 2 0 0 0 0 0 1 1 2
|
||||
Neighs: 27457 ave 33797 max 21031 min
|
||||
Histogram: 3 1 0 0 0 0 0 0 1 3
|
||||
|
||||
Total # of neighbors = 219656
|
||||
Ave neighs/atom = 27.457
|
||||
Neighbor list builds = 1691
|
||||
Dangerous builds = 0
|
||||
|
||||
# thermal conductivity calculation
|
||||
|
||||
compute ke all ke/atom
|
||||
variable temp atom c_ke/1.5
|
||||
|
||||
compute layers all chunk/atom bin/1d z lower 0.05 units reduced
|
||||
fix 2 all ave/chunk 10 100 1000 layers v_temp file profile.heat
|
||||
|
||||
variable tdiff equal f_2[1][3]-f_2[11][3]
|
||||
fix ave all ave/time 1 1 1000 v_tdiff ave running start 13000
|
||||
|
||||
variable kappa equal (100/(lx*ly)/2.0)*(lz/2.0)/f_ave
|
||||
thermo_style custom step temp c_Thot c_Tcold v_tdiff f_ave
|
||||
WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:903)
|
||||
thermo_modify colname c_Thot Temp_hot colname c_Tcold Temp_cold colname v_tdiff dTemp_step colname f_ave dTemp
|
||||
|
||||
run 20000
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.406 | 3.407 | 3.408 Mbytes
|
||||
Step Temp Temp_hot Temp_cold dTemp_step dTemp
|
||||
11000 1.3716416 1.833336 1.1267278 0 0
|
||||
12000 1.3703433 1.7829467 1.1194444 0.66044316 0
|
||||
13000 1.3686734 1.8334366 1.1193477 0.71431978 0.71431978
|
||||
14000 1.3856987 1.8048077 1.1052708 0.73112558 0.72272268
|
||||
15000 1.3820117 1.7460559 1.110725 0.72927647 0.72490728
|
||||
16000 1.3911309 1.923603 1.1161499 0.77407515 0.73719925
|
||||
17000 1.3841301 1.7276486 1.0283807 0.77278638 0.74431667
|
||||
18000 1.3888918 1.7944951 1.0532944 0.75665895 0.74637372
|
||||
19000 1.3876032 1.838174 1.059715 0.71342263 0.74166642
|
||||
20000 1.3724644 1.8297128 1.1439176 0.77352223 0.7456484
|
||||
21000 1.3798921 1.7968403 1.0288381 0.70077132 0.74066206
|
||||
22000 1.3763952 1.8202225 1.0658157 0.75629111 0.74222496
|
||||
23000 1.3911378 1.8691478 1.018589 0.76094865 0.74392711
|
||||
24000 1.3867754 1.7826523 1.09347 0.80367344 0.74890597
|
||||
25000 1.385877 1.9029313 1.0815131 0.73559505 0.74788206
|
||||
26000 1.3791773 1.8904022 1.0151678 0.7729123 0.74966993
|
||||
27000 1.3800063 1.729283 1.127594 0.71473941 0.74734123
|
||||
28000 1.3757197 1.7823772 1.084523 0.73849831 0.74678855
|
||||
29000 1.3777555 1.8287284 1.0715132 0.70375514 0.74425717
|
||||
30000 1.3821118 1.7382856 1.1078333 0.79892499 0.74729427
|
||||
31000 1.3870476 1.8410063 1.1235958 0.76218423 0.74807795
|
||||
Loop time of 26.9314 on 8 procs for 20000 steps with 8000 atoms
|
||||
|
||||
Performance: 320814.865 tau/day, 742.627 timesteps/s
|
||||
97.4% CPU use with 8 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 8.5017 | 11.183 | 13.664 | 67.1 | 41.52
|
||||
Neigh | 4.5072 | 5.5343 | 6.4781 | 37.9 | 20.55
|
||||
Comm | 2.6028 | 5.7342 | 9.01 | 118.2 | 21.29
|
||||
Output | 0.0041722 | 0.0082705 | 0.0088616 | 1.7 | 0.03
|
||||
Modify | 3.7207 | 4.0439 | 4.4497 | 13.7 | 15.02
|
||||
Other | | 0.4277 | | | 1.59
|
||||
|
||||
Nlocal: 1000 ave 1134 max 850 min
|
||||
Histogram: 2 1 0 1 0 0 0 1 0 3
|
||||
Nghost: 2307.75 ave 2561 max 2083 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 2 2
|
||||
Neighs: 27561.1 ave 34071 max 19891 min
|
||||
Histogram: 2 1 1 0 0 0 0 0 1 3
|
||||
|
||||
Total # of neighbors = 220489
|
||||
Ave neighs/atom = 27.561125
|
||||
Neighbor list builds = 3442
|
||||
Dangerous builds = 0
|
||||
print "Running average thermal conductivity: $(v_kappa:%.2f)"
|
||||
Running average thermal conductivity: 3.55
|
||||
Total wall time: 0:00:39
|
||||
241
examples/KAPPA/log.15May22.heatflux.g++.8
Normal file
241
examples/KAPPA/log.15May22.heatflux.g++.8
Normal file
@ -0,0 +1,241 @@
|
||||
LAMMPS (4 May 2022)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# sample LAMMPS input script for thermal conductivity of liquid LJ
|
||||
# Green-Kubo method via compute heat/flux and fix ave/correlate
|
||||
|
||||
# settings
|
||||
|
||||
variable x equal 10
|
||||
variable y equal 10
|
||||
variable z equal 10
|
||||
|
||||
variable rho equal 0.6
|
||||
variable t equal 1.35
|
||||
variable rc equal 2.5
|
||||
|
||||
#variable rho equal 0.85
|
||||
#variable t equal 0.7
|
||||
#variable rc equal 3.0
|
||||
|
||||
variable p equal 200 # correlation length
|
||||
variable s equal 10 # sample interval
|
||||
variable d equal $p*$s # dump interval
|
||||
variable d equal 200*$s
|
||||
variable d equal 200*10
|
||||
|
||||
# setup problem
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc ${rho}
|
||||
lattice fcc 0.6
|
||||
Lattice spacing in x,y,z = 1.8820721 1.8820721 1.8820721
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 10 0 $y 0 $z
|
||||
region box block 0 10 0 10 0 $z
|
||||
region box block 0 10 0 10 0 10
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (18.820721 18.820721 18.820721)
|
||||
2 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 4000 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (18.820721 18.820721 18.820721)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create $t 87287
|
||||
velocity all create 1.35 87287
|
||||
|
||||
pair_style lj/cut ${rc}
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1
|
||||
|
||||
# 1st equilibration run
|
||||
|
||||
fix 1 all nvt temp $t $t 0.5
|
||||
fix 1 all nvt temp 1.35 $t 0.5
|
||||
fix 1 all nvt temp 1.35 1.35 0.5
|
||||
thermo 100
|
||||
run 1000
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 14 14 14
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.108 | 3.108 | 3.108 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.35 -4.1241917 0 -2.0996979 -3.1962625
|
||||
100 1.1997886 -3.7796264 0 -1.9803934 0.4889458
|
||||
200 1.271238 -3.7354981 0 -1.8291178 0.6873844
|
||||
300 1.3346808 -3.6942841 0 -1.6927634 0.84332881
|
||||
400 1.4020848 -3.7118654 0 -1.6092641 0.87670585
|
||||
500 1.3723622 -3.6917931 0 -1.6337644 0.92172921
|
||||
600 1.3451676 -3.7281573 0 -1.7109103 0.76029091
|
||||
700 1.3021567 -3.6876155 0 -1.7348687 0.82721085
|
||||
800 1.3489121 -3.7082852 0 -1.6854229 0.86438061
|
||||
900 1.3708803 -3.6966168 0 -1.6408103 0.921415
|
||||
1000 1.3640742 -3.7075319 0 -1.6619322 0.86651332
|
||||
Loop time of 0.508902 on 8 procs for 1000 steps with 4000 atoms
|
||||
|
||||
Performance: 848886.657 tau/day, 1965.015 timesteps/s
|
||||
98.2% CPU use with 8 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.25474 | 0.26957 | 0.27746 | 1.4 | 52.97
|
||||
Neigh | 0.11684 | 0.12283 | 0.13178 | 1.3 | 24.14
|
||||
Comm | 0.07187 | 0.089583 | 0.10975 | 3.5 | 17.60
|
||||
Output | 0.00026594 | 0.00041865 | 0.0014818 | 0.0 | 0.08
|
||||
Modify | 0.016091 | 0.017624 | 0.018502 | 0.7 | 3.46
|
||||
Other | | 0.008882 | | | 1.75
|
||||
|
||||
Nlocal: 500 ave 510 max 479 min
|
||||
Histogram: 1 0 0 0 0 2 1 1 0 3
|
||||
Nghost: 1519 ave 1539 max 1509 min
|
||||
Histogram: 2 0 4 0 0 0 0 1 0 1
|
||||
Neighs: 13553.8 ave 14051 max 12567 min
|
||||
Histogram: 1 0 0 0 1 0 2 1 1 2
|
||||
|
||||
Total # of neighbors = 108430
|
||||
Ave neighs/atom = 27.1075
|
||||
Neighbor list builds = 155
|
||||
Dangerous builds = 0
|
||||
|
||||
velocity all scale $t
|
||||
velocity all scale 1.35
|
||||
|
||||
unfix 1
|
||||
|
||||
# thermal conductivity calculation
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
compute myKE all ke/atom
|
||||
compute myPE all pe/atom
|
||||
compute myStress all stress/atom NULL virial
|
||||
compute flux all heat/flux myKE myPE myStress
|
||||
variable Jx equal c_flux[1]/vol
|
||||
variable Jy equal c_flux[2]/vol
|
||||
variable Jz equal c_flux[3]/vol
|
||||
|
||||
fix 1 all nve
|
||||
fix JJ all ave/correlate $s $p $d c_flux[1] c_flux[2] c_flux[3] type auto file profile.heatflux ave running
|
||||
fix JJ all ave/correlate 10 $p $d c_flux[1] c_flux[2] c_flux[3] type auto file profile.heatflux ave running
|
||||
fix JJ all ave/correlate 10 200 $d c_flux[1] c_flux[2] c_flux[3] type auto file profile.heatflux ave running
|
||||
fix JJ all ave/correlate 10 200 2000 c_flux[1] c_flux[2] c_flux[3] type auto file profile.heatflux ave running
|
||||
|
||||
variable scale equal $s*dt/$t/$t/vol
|
||||
variable scale equal 10*dt/$t/$t/vol
|
||||
variable scale equal 10*dt/1.35/$t/vol
|
||||
variable scale equal 10*dt/1.35/1.35/vol
|
||||
variable k11 equal trap(f_JJ[3])*${scale}
|
||||
variable k11 equal trap(f_JJ[3])*4.11522633744856e-06
|
||||
variable k22 equal trap(f_JJ[4])*${scale}
|
||||
variable k22 equal trap(f_JJ[4])*4.11522633744856e-06
|
||||
variable k33 equal trap(f_JJ[5])*${scale}
|
||||
variable k33 equal trap(f_JJ[5])*4.11522633744856e-06
|
||||
variable kappa equal (v_k11+v_k22+v_k33)/3.0
|
||||
|
||||
thermo $d
|
||||
thermo 2000
|
||||
thermo_style custom step temp v_Jx v_Jy v_Jz v_k11 v_k22 v_k33 v_kappa
|
||||
thermo_modify colname v_Jx Jx colname v_Jy Jy colname v_Jz Jz colname v_k11 kappa_11 colname v_k22 kappa_22 colname v_k33 kappa_33 colname v_kappa kappa
|
||||
|
||||
run 100000
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.986 | 4.986 | 4.986 Mbytes
|
||||
Step Temp Jx Jy Jz kappa_11 kappa_22 kappa_33 kappa
|
||||
0 1.35 0.012561273 -0.087295611 -0.037041124 0.014429409 0.69689289 0.12547278 0.27893169
|
||||
2000 1.3455113 -0.034571206 -0.17570902 -0.057218308 -1.6110148 7.9287556 8.5035767 4.9404392
|
||||
4000 1.3477761 -0.029528723 0.018790489 0.056107464 7.698411 1.9459053 9.9605272 6.5349478
|
||||
6000 1.3411436 -0.20281149 0.2184806 0.036024028 4.6533075 1.6223216 3.7246529 3.3334273
|
||||
8000 1.3561682 0.12038719 0.034930957 0.12173601 4.6450263 1.9032849 2.7566363 3.1016492
|
||||
10000 1.3397694 -0.14241489 -0.10956496 0.053088086 6.4191535 3.1582257 2.2786677 3.9520156
|
||||
12000 1.3410756 0.0033462395 0.14337321 0.16381733 5.9663779 1.6774436 1.7442075 3.129343
|
||||
14000 1.3484928 0.0080419803 -0.080232102 0.039035519 4.9483626 1.6210893 1.6103343 2.7265954
|
||||
16000 1.3414836 -0.11063045 -0.031557643 0.032060333 6.1381241 1.438198 1.5831541 3.0531587
|
||||
18000 1.3488617 0.15908507 -0.021418806 -0.13992507 5.9198613 1.1016464 1.2905478 2.7706852
|
||||
20000 1.3535727 0.13217689 0.071933521 -0.028452943 6.3746606 1.003194 1.7007101 3.0261882
|
||||
22000 1.3408534 -0.078953557 -0.0022323663 -0.22979033 5.0105241 1.1489328 1.720847 2.626768
|
||||
24000 1.34722 0.074784199 -0.071218632 0.15238165 4.4835452 0.94086945 3.1603615 2.8615921
|
||||
26000 1.3539218 0.052534363 0.10419096 0.1866213 4.2233104 1.3973253 3.2802881 2.9669746
|
||||
28000 1.3510105 0.0080425673 -0.03723976 0.20758595 5.261917 1.1931088 3.498831 3.3179523
|
||||
30000 1.3410807 -0.043957884 0.065683978 0.015386362 4.3815277 1.5000017 3.2237565 3.0350953
|
||||
32000 1.34766 -0.060481287 0.17142383 0.034367135 4.0974942 1.1637027 3.3771953 2.8794641
|
||||
34000 1.3417583 -0.10055844 0.050237668 0.06974988 4.1478021 1.0235517 2.9440249 2.7051263
|
||||
36000 1.3468728 0.09375756 -0.17875264 -0.063513807 4.4412987 0.71084371 3.4316313 2.8612579
|
||||
38000 1.3496868 -0.038635804 0.117965 0.018050271 4.962332 0.41701129 3.4690212 2.9494548
|
||||
40000 1.3403452 -0.092158116 0.14432655 -0.062258229 4.9980486 0.3762815 3.1688552 2.8477284
|
||||
42000 1.3498661 0.085807945 0.010256385 -0.002956898 4.8200626 0.29278287 3.094633 2.7358261
|
||||
44000 1.3564084 -0.07415163 -0.051327929 -0.18457986 4.7070907 0.3358167 3.0741797 2.7056957
|
||||
46000 1.3435866 -0.013911463 0.081813372 0.022628846 4.6043718 0.3682401 2.9956189 2.6560769
|
||||
48000 1.350611 0.036512747 0.080481423 -0.22973181 4.5648715 0.32728516 3.8573343 2.916497
|
||||
50000 1.3421783 0.057665789 0.075597141 0.17377918 4.4278473 0.5383886 3.5866168 2.8509509
|
||||
52000 1.3473497 -0.11159587 -0.09688769 0.19876168 4.3876613 0.43408155 3.4786305 2.7667911
|
||||
54000 1.3459495 -0.15341705 0.063996148 -0.0038254597 4.8434026 0.62047297 3.445187 2.9696875
|
||||
56000 1.3545654 -0.082406034 0.089232864 -0.024355614 4.546051 0.7367607 3.3694561 2.8840893
|
||||
58000 1.3577504 0.082844384 0.019500036 0.073721698 4.4061886 1.4575694 3.2754066 3.0463882
|
||||
60000 1.348614 -0.16190321 -0.048576343 0.093820555 4.2946463 1.3416919 3.1159234 2.9174205
|
||||
62000 1.3551143 0.097443296 -0.04420265 -0.25713945 4.1260882 1.2550603 3.063215 2.8147879
|
||||
64000 1.346239 0.019198575 -0.095746619 0.18383922 4.5691519 1.2615165 2.9935539 2.9414074
|
||||
66000 1.3535383 -0.0035547901 -0.1753318 0.014025292 4.5371394 1.0740671 2.9362916 2.8491661
|
||||
68000 1.3421249 -0.18217113 0.077901408 0.04314081 5.1644747 1.0218342 2.9789097 3.0550729
|
||||
70000 1.3446114 0.029565781 -0.13771336 0.050328878 5.4811405 1.0430806 2.9748623 3.1663612
|
||||
72000 1.3692655 0.005711741 0.13966773 -0.062638787 5.3033385 1.1040582 2.7599218 3.0557729
|
||||
74000 1.3405365 -0.054281977 0.038019086 -0.024980877 5.1246258 2.0782965 2.725331 3.3094177
|
||||
76000 1.3644178 0.040847675 -0.051968108 -0.12259032 5.1218657 1.8504273 2.6804003 3.2175644
|
||||
78000 1.353792 -0.093663092 0.018784967 -0.073871437 5.025196 1.7789709 2.5339006 3.1126891
|
||||
80000 1.3520982 -0.09407101 0.010328039 0.0028841073 5.1410049 1.855057 2.6935895 3.2298838
|
||||
82000 1.3447597 -0.11935066 -0.2184608 0.073543056 5.2645334 1.7883077 4.2012292 3.7513568
|
||||
84000 1.3712151 -0.064367612 0.021246872 -0.033571866 5.0479674 1.8947341 4.3856536 3.7761184
|
||||
86000 1.3453867 -0.029842112 -0.042297039 0.05422886 5.0667777 2.0365983 4.4542311 3.8525357
|
||||
88000 1.3439543 -0.21625828 -0.028119372 -0.010320332 4.9946428 2.3095763 4.3429587 3.8823926
|
||||
90000 1.3472579 0.058391002 0.037139373 0.03424008 5.0599004 2.8132794 4.4503426 4.1078408
|
||||
92000 1.361788 0.028891114 0.072799744 -0.12035229 4.8759851 2.5130025 4.2747068 3.8878981
|
||||
94000 1.3440566 0.043421348 0.049653856 -0.060444094 4.8884081 2.5072981 4.3105221 3.9020761
|
||||
96000 1.3537566 0.088733517 -0.11449828 -0.049852036 4.8115085 2.4780963 4.2213579 3.8369876
|
||||
98000 1.3373399 0.25457663 -0.041723778 0.00084565184 4.7163394 2.4100822 4.485536 3.8706525
|
||||
100000 1.3487502 0.046333889 0.1247351 0.063467467 4.6563279 2.4049358 4.5742925 3.8785187
|
||||
Loop time of 53.5266 on 8 procs for 100000 steps with 4000 atoms
|
||||
|
||||
Performance: 807074.833 tau/day, 1868.229 timesteps/s
|
||||
98.9% CPU use with 8 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 29.794 | 30.392 | 31.376 | 8.7 | 56.78
|
||||
Neigh | 12.248 | 12.475 | 12.79 | 4.5 | 23.31
|
||||
Comm | 6.5584 | 7.5712 | 8.3818 | 19.5 | 14.14
|
||||
Output | 0.016848 | 0.067296 | 0.074694 | 7.4 | 0.13
|
||||
Modify | 2.0311 | 2.0593 | 2.1324 | 2.1 | 3.85
|
||||
Other | | 0.9616 | | | 1.80
|
||||
|
||||
Nlocal: 500 ave 505 max 491 min
|
||||
Histogram: 1 0 0 1 0 1 0 2 2 1
|
||||
Nghost: 1529.88 ave 1548 max 1508 min
|
||||
Histogram: 1 1 0 0 1 1 2 0 0 2
|
||||
Neighs: 13569.8 ave 13906 max 13235 min
|
||||
Histogram: 1 1 0 1 1 1 1 1 0 1
|
||||
|
||||
Total # of neighbors = 108558
|
||||
Ave neighs/atom = 27.1395
|
||||
Neighbor list builds = 16041
|
||||
Dangerous builds = 0
|
||||
|
||||
print "Running average thermal conductivity: $(v_kappa:%.2f)"
|
||||
Running average thermal conductivity: 3.88
|
||||
Total wall time: 0:00:54
|
||||
265
examples/KAPPA/log.15May22.langevin.g++.8
Normal file
265
examples/KAPPA/log.15May22.langevin.g++.8
Normal file
@ -0,0 +1,265 @@
|
||||
LAMMPS (4 May 2022)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# sample LAMMPS input script for thermal conductivity of liquid LJ
|
||||
# thermostatting 2 regions via fix langevin
|
||||
|
||||
# settings
|
||||
|
||||
variable x equal 10
|
||||
variable y equal 10
|
||||
variable z equal 20
|
||||
|
||||
variable rho equal 0.6
|
||||
variable t equal 1.35
|
||||
variable rc equal 2.5
|
||||
variable tlo equal 1.0
|
||||
variable thi equal 1.70
|
||||
|
||||
#variable rho equal 0.85
|
||||
#variable t equal 0.7
|
||||
#variable rc equal 3.0
|
||||
#variable tlo equal 0.3
|
||||
#variable thi equal 1.0
|
||||
|
||||
# setup problem
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc ${rho}
|
||||
lattice fcc 0.6
|
||||
Lattice spacing in x,y,z = 1.8820721 1.8820721 1.8820721
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 10 0 $y 0 $z
|
||||
region box block 0 10 0 10 0 $z
|
||||
region box block 0 10 0 10 0 20
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (18.820721 18.820721 37.641441)
|
||||
2 by 1 by 4 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 8000 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (18.820721 18.820721 37.641441)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create $t 87287
|
||||
velocity all create 1.35 87287
|
||||
|
||||
pair_style lj/cut ${rc}
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1
|
||||
|
||||
# heat layers
|
||||
|
||||
region hot block INF INF INF INF 0 1
|
||||
region cold block INF INF INF INF 10 11
|
||||
compute Thot all temp/region hot
|
||||
compute Tcold all temp/region cold
|
||||
|
||||
# 1st equilibration run
|
||||
|
||||
fix 1 all nvt temp $t $t 0.5
|
||||
fix 1 all nvt temp 1.35 $t 0.5
|
||||
fix 1 all nvt temp 1.35 1.35 0.5
|
||||
thermo 100
|
||||
run 1000
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 14 14 27
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.152 | 3.152 | 3.152 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.35 -4.1241917 0 -2.0994448 -3.1961612
|
||||
100 1.1819832 -3.7640881 0 -1.991335 0.53985757
|
||||
200 1.2578365 -3.7395333 0 -1.8530144 0.69591862
|
||||
300 1.3282971 -3.7215427 0 -1.7293461 0.79036065
|
||||
400 1.3714367 -3.7043826 0 -1.6474847 0.85873226
|
||||
500 1.3590952 -3.6707735 0 -1.6323855 0.99602024
|
||||
600 1.3575117 -3.7118244 0 -1.6758114 0.81454305
|
||||
700 1.3284444 -3.7075488 0 -1.7151313 0.81136596
|
||||
800 1.3419995 -3.7155648 0 -1.7028172 0.82925676
|
||||
900 1.3562214 -3.6965609 0 -1.6624831 0.88908117
|
||||
1000 1.3732017 -3.7100044 0 -1.6504594 0.83982701
|
||||
Loop time of 0.988841 on 8 procs for 1000 steps with 8000 atoms
|
||||
|
||||
Performance: 436874.916 tau/day, 1011.285 timesteps/s
|
||||
98.4% CPU use with 8 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.54855 | 0.56275 | 0.57326 | 1.1 | 56.91
|
||||
Neigh | 0.25337 | 0.2589 | 0.26473 | 0.7 | 26.18
|
||||
Comm | 0.096617 | 0.10927 | 0.11899 | 2.2 | 11.05
|
||||
Output | 0.00032266 | 0.00051276 | 0.0018134 | 0.0 | 0.05
|
||||
Modify | 0.034998 | 0.042756 | 0.055888 | 4.0 | 4.32
|
||||
Other | | 0.01466 | | | 1.48
|
||||
|
||||
Nlocal: 1000 ave 1020 max 982 min
|
||||
Histogram: 1 0 2 1 0 1 1 1 0 1
|
||||
Nghost: 2299.5 ave 2331 max 2268 min
|
||||
Histogram: 1 1 1 1 0 0 0 3 0 1
|
||||
Neighs: 27122 ave 28382 max 26337 min
|
||||
Histogram: 2 0 2 1 1 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 216976
|
||||
Ave neighs/atom = 27.122
|
||||
Neighbor list builds = 162
|
||||
Dangerous builds = 0
|
||||
|
||||
velocity all scale $t
|
||||
velocity all scale 1.35
|
||||
|
||||
unfix 1
|
||||
|
||||
# 2nd equilibration run
|
||||
|
||||
fix 1 all nve
|
||||
fix hot all langevin ${thi} ${thi} 1.0 59804 tally yes
|
||||
fix hot all langevin 1.7 ${thi} 1.0 59804 tally yes
|
||||
fix hot all langevin 1.7 1.7 1.0 59804 tally yes
|
||||
fix cold all langevin ${tlo} ${tlo} 1.0 287859 tally yes
|
||||
fix cold all langevin 1 ${tlo} 1.0 287859 tally yes
|
||||
fix cold all langevin 1 1 1.0 287859 tally yes
|
||||
fix_modify hot temp Thot
|
||||
fix_modify cold temp Tcold
|
||||
|
||||
variable tdiff equal c_Thot-c_Tcold
|
||||
thermo_style custom step temp c_Thot c_Tcold f_hot f_cold v_tdiff
|
||||
thermo_modify colname c_Thot Temp_hot colname c_Tcold Temp_cold colname f_hot E_hot colname f_cold E_cold colname v_tdiff dTemp_step
|
||||
thermo 1000
|
||||
run 10000
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.906 | 3.906 | 3.906 Mbytes
|
||||
Step Temp Temp_hot Temp_cold E_hot E_cold dTemp_step
|
||||
1000 1.35 1.431295 1.2955644 -0 -0 0.13573065
|
||||
2000 1.3593243 1.6602094 1.0898701 -0.13903162 0.14234352 0.57033928
|
||||
3000 1.3412163 1.6308839 1.0677742 -0.2214765 0.25871329 0.56310968
|
||||
4000 1.3275359 1.5248034 1.0792345 -0.26908328 0.34211202 0.44556887
|
||||
5000 1.3230922 1.6266046 1.0523802 -0.33175886 0.43533756 0.5742244
|
||||
6000 1.3037036 1.6021737 1.0408166 -0.3639815 0.49869333 0.56135712
|
||||
7000 1.2903225 1.5701119 1.0603548 -0.40000421 0.55547714 0.50975712
|
||||
8000 1.3050677 1.6420218 1.0221774 -0.46368839 0.60293974 0.61984444
|
||||
9000 1.2950977 1.7153984 1.0583242 -0.51871512 0.66389344 0.65707419
|
||||
10000 1.3100216 1.6680668 1.0871293 -0.57485359 0.7161839 0.58093752
|
||||
11000 1.297052 1.6486494 1.088903 -0.60276081 0.75900024 0.55974633
|
||||
Loop time of 12.8698 on 8 procs for 10000 steps with 8000 atoms
|
||||
|
||||
Performance: 335670.145 tau/day, 777.014 timesteps/s
|
||||
99.0% CPU use with 8 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 4.6624 | 5.5614 | 6.4055 | 30.4 | 43.21
|
||||
Neigh | 2.3761 | 2.7104 | 3.0796 | 19.6 | 21.06
|
||||
Comm | 0.8473 | 1.9587 | 3.0217 | 68.6 | 15.22
|
||||
Output | 0.00068778 | 0.00099949 | 0.0025433 | 0.0 | 0.01
|
||||
Modify | 2.2811 | 2.3753 | 2.4584 | 3.8 | 18.46
|
||||
Other | | 0.2629 | | | 2.04
|
||||
|
||||
Nlocal: 1000 ave 1112 max 841 min
|
||||
Histogram: 1 1 0 2 0 0 0 0 1 3
|
||||
Nghost: 2294.38 ave 2506 max 2077 min
|
||||
Histogram: 2 1 1 0 0 0 0 1 1 2
|
||||
Neighs: 27441.9 ave 32651 max 19438 min
|
||||
Histogram: 1 1 0 2 0 0 0 0 0 4
|
||||
|
||||
Total # of neighbors = 219535
|
||||
Ave neighs/atom = 27.441875
|
||||
Neighbor list builds = 1674
|
||||
Dangerous builds = 0
|
||||
|
||||
# thermal conductivity calculation
|
||||
# reset langevin thermostats to zero energy accumulation
|
||||
|
||||
compute ke all ke/atom
|
||||
variable temp atom c_ke/1.5
|
||||
|
||||
fix hot all langevin ${thi} ${thi} 1.0 59804 tally yes
|
||||
fix hot all langevin 1.7 ${thi} 1.0 59804 tally yes
|
||||
fix hot all langevin 1.7 1.7 1.0 59804 tally yes
|
||||
fix cold all langevin ${tlo} ${tlo} 1.0 287859 tally yes
|
||||
fix cold all langevin 1 ${tlo} 1.0 287859 tally yes
|
||||
fix cold all langevin 1 1 1.0 287859 tally yes
|
||||
fix_modify hot temp Thot
|
||||
fix_modify cold temp Tcold
|
||||
|
||||
fix ave all ave/time 10 100 1000 v_tdiff ave running
|
||||
thermo_style custom step temp c_Thot c_Tcold f_hot f_cold v_tdiff f_ave
|
||||
WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:903)
|
||||
thermo_modify colname c_Thot Temp_hot colname c_Tcold Temp_cold colname f_hot E_hot colname f_cold E_cold colname v_tdiff dTemp_step colname f_ave dTemp
|
||||
|
||||
compute layers all chunk/atom bin/1d z lower 0.05 units reduced
|
||||
fix 2 all ave/chunk 10 100 1000 layers v_temp file profile.langevin
|
||||
|
||||
variable start_time equal time
|
||||
variable kappa equal (0.5*(abs(f_hot)+abs(f_cold))/(time-${start_time})/(lx*ly)/2.0)*(lz/2.0)/f_ave
|
||||
variable kappa equal (0.5*(abs(f_hot)+abs(f_cold))/(time-55)/(lx*ly)/2.0)*(lz/2.0)/f_ave
|
||||
|
||||
run 20000
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.156 | 4.157 | 4.159 Mbytes
|
||||
Step Temp Temp_hot Temp_cold E_hot E_cold dTemp_step dTemp
|
||||
11000 1.297052 1.6473904 1.088903 -0 -0 0.55848738 0
|
||||
12000 1.2792808 1.6043738 1.0658375 -0.012256975 0.04611547 0.53853632 0.54492428
|
||||
13000 1.2787101 1.7035572 1.1159037 -0.073806664 0.099529002 0.58765348 0.5581748
|
||||
14000 1.289918 1.4642237 1.1073937 -0.11428779 0.13931657 0.35683005 0.56816328
|
||||
15000 1.2932964 1.5032665 1.0523148 -0.17247717 0.19001309 0.45095174 0.57436291
|
||||
16000 1.3025037 1.5424316 1.1185175 -0.22598282 0.22640921 0.42391405 0.56973168
|
||||
17000 1.3009667 1.5582105 1.0745661 -0.27544101 0.26143452 0.48364439 0.5700118
|
||||
18000 1.2970255 1.5019842 1.0228322 -0.31195285 0.31203237 0.479152 0.56544644
|
||||
19000 1.2880631 1.5290587 1.0976483 -0.34645573 0.34243366 0.43141047 0.56338309
|
||||
20000 1.3119675 1.6284144 1.1102294 -0.40922326 0.39217092 0.51818503 0.56614474
|
||||
21000 1.2838063 1.6670934 0.97721382 -0.43809329 0.46021572 0.68987962 0.5686161
|
||||
22000 1.2925041 1.7050682 1.0984963 -0.4871305 0.50520177 0.6065719 0.57226368
|
||||
23000 1.2746463 1.6388503 1.0286701 -0.51212873 0.56478515 0.6101802 0.57290996
|
||||
24000 1.2745381 1.7085713 1.1362975 -0.54529463 0.58540408 0.57227375 0.57296767
|
||||
25000 1.2776401 1.5259253 1.0415158 -0.58389862 0.62623289 0.48440948 0.57386374
|
||||
26000 1.2661888 1.4760829 0.99145001 -0.62638032 0.68155754 0.48463289 0.57021631
|
||||
27000 1.2923677 1.6070495 1.0300276 -0.70014343 0.70236265 0.5770219 0.57001637
|
||||
28000 1.2961449 1.7052335 1.0805793 -0.74856241 0.75775659 0.62465427 0.56927907
|
||||
29000 1.2969474 1.5520176 1.1249649 -0.78900962 0.79539202 0.42705264 0.56986986
|
||||
30000 1.2900596 1.6556864 1.0302676 -0.84180996 0.87187683 0.6254189 0.57245841
|
||||
31000 1.2923209 1.6752068 1.0156911 -0.89036148 0.88285227 0.65951571 0.57358134
|
||||
Loop time of 26.7885 on 8 procs for 20000 steps with 8000 atoms
|
||||
|
||||
Performance: 322526.365 tau/day, 746.589 timesteps/s
|
||||
98.8% CPU use with 8 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 8.7499 | 11.122 | 13.336 | 57.7 | 41.52
|
||||
Neigh | 4.4966 | 5.3849 | 6.2482 | 33.9 | 20.10
|
||||
Comm | 1.6944 | 4.5797 | 7.4844 | 118.6 | 17.10
|
||||
Output | 0.0026407 | 0.0029145 | 0.0048103 | 1.3 | 0.01
|
||||
Modify | 4.9295 | 5.0982 | 5.1704 | 3.6 | 19.03
|
||||
Other | | 0.6013 | | | 2.24
|
||||
|
||||
Nlocal: 1000 ave 1118 max 875 min
|
||||
Histogram: 2 1 1 0 0 0 0 0 2 2
|
||||
Nghost: 2298.62 ave 2535 max 2063 min
|
||||
Histogram: 3 1 0 0 0 0 0 0 1 3
|
||||
Neighs: 27462.4 ave 32904 max 21333 min
|
||||
Histogram: 2 2 0 0 0 0 0 0 0 4
|
||||
|
||||
Total # of neighbors = 219699
|
||||
Ave neighs/atom = 27.462375
|
||||
Neighbor list builds = 3340
|
||||
Dangerous builds = 0
|
||||
print "Running average thermal conductivity: $(v_kappa:%.2f)"
|
||||
Running average thermal conductivity: 3.29
|
||||
Total wall time: 0:00:40
|
||||
250
examples/KAPPA/log.15May22.mp.g++.8
Normal file
250
examples/KAPPA/log.15May22.mp.g++.8
Normal file
@ -0,0 +1,250 @@
|
||||
LAMMPS (4 May 2022)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# sample LAMMPS input script for thermal conductivity of liquid LJ
|
||||
# Muller-Plathe method via fix thermal_conductivity
|
||||
|
||||
# settings
|
||||
|
||||
variable x equal 10
|
||||
variable y equal 10
|
||||
variable z equal 20
|
||||
|
||||
variable rho equal 0.6
|
||||
variable t equal 1.35
|
||||
variable rc equal 2.5
|
||||
|
||||
#variable rho equal 0.85
|
||||
#variable t equal 0.7
|
||||
#variable rc equal 3.0
|
||||
|
||||
# setup problem
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc ${rho}
|
||||
lattice fcc 0.6
|
||||
Lattice spacing in x,y,z = 1.8820721 1.8820721 1.8820721
|
||||
region box block 0 $x 0 $y 0 $z
|
||||
region box block 0 10 0 $y 0 $z
|
||||
region box block 0 10 0 10 0 $z
|
||||
region box block 0 10 0 10 0 20
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (18.820721 18.820721 37.641441)
|
||||
2 by 1 by 4 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 8000 atoms
|
||||
using lattice units in orthogonal box = (0 0 0) to (18.820721 18.820721 37.641441)
|
||||
create_atoms CPU = 0.000 seconds
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create $t 87287
|
||||
velocity all create 1.35 87287
|
||||
|
||||
pair_style lj/cut ${rc}
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1
|
||||
|
||||
# 1st equilibration run
|
||||
|
||||
fix 1 all nvt temp $t $t 0.5
|
||||
fix 1 all nvt temp 1.35 $t 0.5
|
||||
fix 1 all nvt temp 1.35 1.35 0.5
|
||||
thermo 100
|
||||
run 1000
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 14 14 27
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.152 | 3.152 | 3.152 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.35 -4.1241917 0 -2.0994448 -3.1961612
|
||||
100 1.1819832 -3.7640881 0 -1.991335 0.53985757
|
||||
200 1.2578365 -3.7395333 0 -1.8530144 0.69591862
|
||||
300 1.3282971 -3.7215427 0 -1.7293461 0.79036065
|
||||
400 1.3714367 -3.7043826 0 -1.6474847 0.85873226
|
||||
500 1.3590952 -3.6707735 0 -1.6323855 0.99602024
|
||||
600 1.3575117 -3.7118244 0 -1.6758114 0.81454305
|
||||
700 1.3284444 -3.7075488 0 -1.7151313 0.81136596
|
||||
800 1.3419995 -3.7155648 0 -1.7028172 0.82925676
|
||||
900 1.3562214 -3.6965609 0 -1.6624831 0.88908117
|
||||
1000 1.3732017 -3.7100044 0 -1.6504594 0.83982701
|
||||
Loop time of 1.03873 on 8 procs for 1000 steps with 8000 atoms
|
||||
|
||||
Performance: 415892.564 tau/day, 962.714 timesteps/s
|
||||
97.8% CPU use with 8 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.54665 | 0.56747 | 0.59729 | 2.1 | 54.63
|
||||
Neigh | 0.2534 | 0.26165 | 0.2706 | 1.1 | 25.19
|
||||
Comm | 0.098389 | 0.13291 | 0.15562 | 5.0 | 12.80
|
||||
Output | 0.00031975 | 0.00050654 | 0.0018105 | 0.0 | 0.05
|
||||
Modify | 0.03478 | 0.054868 | 0.082358 | 7.5 | 5.28
|
||||
Other | | 0.02134 | | | 2.05
|
||||
|
||||
Nlocal: 1000 ave 1020 max 982 min
|
||||
Histogram: 1 0 2 1 0 1 1 1 0 1
|
||||
Nghost: 2299.5 ave 2331 max 2268 min
|
||||
Histogram: 1 1 1 1 0 0 0 3 0 1
|
||||
Neighs: 27122 ave 28382 max 26337 min
|
||||
Histogram: 2 0 2 1 1 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 216976
|
||||
Ave neighs/atom = 27.122
|
||||
Neighbor list builds = 162
|
||||
Dangerous builds = 0
|
||||
|
||||
velocity all scale $t
|
||||
velocity all scale 1.35
|
||||
|
||||
unfix 1
|
||||
|
||||
# 2nd equilibration run
|
||||
|
||||
compute ke all ke/atom
|
||||
variable temp atom c_ke/1.5
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
compute layers all chunk/atom bin/1d z lower 0.05 units reduced
|
||||
fix 2 all ave/chunk 10 100 1000 layers v_temp file profile.mp
|
||||
fix 3 all thermal/conductivity 10 z 20
|
||||
|
||||
variable tdiff equal f_2[11][3]-f_2[1][3]
|
||||
thermo_style custom step temp epair etotal f_3 v_tdiff
|
||||
thermo_modify colname f_3 E_delta colname v_tdiff dTemp_step
|
||||
|
||||
thermo 1000
|
||||
run 20000
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.406 | 3.406 | 3.406 Mbytes
|
||||
Step Temp E_pair TotEng E_delta dTemp_step
|
||||
1000 1.35 -3.7100044 -1.6852575 0 0
|
||||
2000 1.3572899 -3.7210084 -1.6853282 873.12373 0.26058005
|
||||
3000 1.359979 -3.7268343 -1.6871208 1750.6998 0.40845169
|
||||
4000 1.3677509 -3.7394553 -1.6880853 2565.8064 0.63828485
|
||||
5000 1.3742987 -3.750287 -1.6890966 3373.2897 0.70173279
|
||||
6000 1.3950535 -3.7827674 -1.6904487 4162.6672 0.83210131
|
||||
7000 1.3843852 -3.7679238 -1.6916056 4947.5882 0.92719731
|
||||
8000 1.396125 -3.7861373 -1.6922116 5703.4508 0.92426948
|
||||
9000 1.4135104 -3.812624 -1.6926234 6465.5676 1.0412501
|
||||
10000 1.4092351 -3.8065359 -1.6929474 7242.2986 1.0772505
|
||||
11000 1.3966916 -3.7874302 -1.6926547 8007.3229 1.056805
|
||||
12000 1.4111272 -3.8089829 -1.6925567 8750.8648 1.097621
|
||||
13000 1.4091888 -3.8074873 -1.6939684 9514.7196 1.0734167
|
||||
14000 1.4132159 -3.8134636 -1.6939046 10284.269 1.1643391
|
||||
15000 1.3991348 -3.7928819 -1.694442 11051.851 1.0716016
|
||||
16000 1.4055537 -3.8013252 -1.6932583 11836.812 1.1506479
|
||||
17000 1.4127928 -3.8141054 -1.6951811 12626.124 1.1301728
|
||||
18000 1.4118868 -3.8119733 -1.6944077 13391.631 1.1521394
|
||||
19000 1.4209268 -3.826811 -1.6956872 14180.009 1.0929393
|
||||
20000 1.4093812 -3.8083875 -1.6945801 14969.574 1.2113183
|
||||
21000 1.4202317 -3.8255696 -1.6954884 15735.893 1.161082
|
||||
Loop time of 22.6178 on 8 procs for 20000 steps with 8000 atoms
|
||||
|
||||
Performance: 381999.512 tau/day, 884.258 timesteps/s
|
||||
98.8% CPU use with 8 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 8.3142 | 10.998 | 13.345 | 66.5 | 48.63
|
||||
Neigh | 4.6124 | 5.6787 | 6.7232 | 39.5 | 25.11
|
||||
Comm | 1.7439 | 4.8855 | 8.2779 | 135.0 | 21.60
|
||||
Output | 0.00062485 | 0.0010388 | 0.0039271 | 3.4 | 0.00
|
||||
Modify | 0.47103 | 0.48945 | 0.50317 | 1.6 | 2.16
|
||||
Other | | 0.5651 | | | 2.50
|
||||
|
||||
Nlocal: 1000 ave 1188 max 806 min
|
||||
Histogram: 2 1 1 0 0 0 0 0 2 2
|
||||
Nghost: 2300.5 ave 2645 max 1963 min
|
||||
Histogram: 3 1 0 0 0 0 0 0 1 3
|
||||
Neighs: 27897 ave 37064 max 18367 min
|
||||
Histogram: 2 2 0 0 0 0 0 0 0 4
|
||||
|
||||
Total # of neighbors = 223176
|
||||
Ave neighs/atom = 27.897
|
||||
Neighbor list builds = 3537
|
||||
Dangerous builds = 0
|
||||
|
||||
# thermal conductivity calculation
|
||||
# reset fix thermal/conductivity to zero energy accumulation
|
||||
fix 3 all thermal/conductivity 10 z 20
|
||||
|
||||
variable start_time equal time
|
||||
variable kappa equal (f_3/(time-${start_time})/(lx*ly)/2.0)*(lz/2.0)/f_ave
|
||||
variable kappa equal (f_3/(time-105)/(lx*ly)/2.0)*(lz/2.0)/f_ave
|
||||
|
||||
fix ave all ave/time 1 1 1000 v_tdiff ave running
|
||||
thermo_style custom step temp epair etotal f_3 v_tdiff f_ave
|
||||
WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:903)
|
||||
thermo_modify colname f_3 E_delta colname v_tdiff dTemp_step colname f_ave dTemp
|
||||
|
||||
run 20000
|
||||
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.657 | 3.658 | 3.66 Mbytes
|
||||
Step Temp E_pair TotEng E_delta dTemp_step dTemp
|
||||
21000 1.4202317 -3.8255696 -1.6954884 0 1.161082 1.161082
|
||||
22000 1.4090517 -3.808543 -1.6952296 745.83128 1.1780376 1.1695598
|
||||
23000 1.4261394 -3.8350237 -1.696082 1516.9526 1.1393504 1.15949
|
||||
24000 1.4103907 -3.8098769 -1.6945553 2290.0213 1.1962529 1.1686807
|
||||
25000 1.4205929 -3.8266444 -1.6960213 3028.2748 1.1355183 1.1620482
|
||||
26000 1.4148587 -3.8168728 -1.69485 3788.0858 1.1902606 1.1667503
|
||||
27000 1.4226648 -3.8297832 -1.6960528 4580.4932 1.2378446 1.1769066
|
||||
28000 1.4167854 -3.8205958 -1.6956834 5328.2357 1.2038835 1.1802787
|
||||
29000 1.4208636 -3.8267081 -1.6956791 6077.036 1.1970863 1.1821462
|
||||
30000 1.420575 -3.8256917 -1.6950955 6840.5407 1.1884497 1.1827766
|
||||
31000 1.4233235 -3.8318045 -1.6970861 7576.9859 1.2088723 1.1851489
|
||||
32000 1.418912 -3.8229407 -1.6948388 8319.9854 1.1604002 1.1830865
|
||||
33000 1.4161289 -3.8211375 -1.6972096 9097.8598 1.1381183 1.1796274
|
||||
34000 1.3982574 -3.7915345 -1.6944106 9819.5817 1.1809721 1.1797235
|
||||
35000 1.4211314 -3.8267235 -1.6952929 10604.381 1.157812 1.1782627
|
||||
36000 1.4181668 -3.8217718 -1.6947876 11332.942 1.1843186 1.1786412
|
||||
37000 1.4092823 -3.8094817 -1.6958226 12068.55 1.1043391 1.1742705
|
||||
38000 1.4220481 -3.8278441 -1.6950386 12815.406 1.1996255 1.1756791
|
||||
39000 1.4146432 -3.8175526 -1.6958531 13565.714 1.149226 1.1742868
|
||||
40000 1.4088356 -3.8079173 -1.694928 14309.801 1.1710565 1.1741253
|
||||
41000 1.4058693 -3.8043119 -1.6957716 15067.894 1.1839862 1.1745949
|
||||
Loop time of 25.6385 on 8 procs for 20000 steps with 8000 atoms
|
||||
|
||||
Performance: 336993.233 tau/day, 780.077 timesteps/s
|
||||
97.3% CPU use with 8 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 7.7138 | 11.167 | 14.153 | 84.0 | 43.55
|
||||
Neigh | 4.5428 | 5.9625 | 7.3617 | 51.3 | 23.26
|
||||
Comm | 2.6229 | 6.7861 | 10.884 | 145.3 | 26.47
|
||||
Output | 0.00056897 | 0.0026943 | 0.012204 | 6.9 | 0.01
|
||||
Modify | 0.51819 | 0.5869 | 0.63774 | 5.3 | 2.29
|
||||
Other | | 1.134 | | | 4.42
|
||||
|
||||
Nlocal: 1000 ave 1188 max 810 min
|
||||
Histogram: 2 1 1 0 0 0 0 1 1 2
|
||||
Nghost: 2304.5 ave 2648 max 1970 min
|
||||
Histogram: 3 1 0 0 0 0 0 0 1 3
|
||||
Neighs: 27885.2 ave 36431 max 18556 min
|
||||
Histogram: 2 2 0 0 0 0 0 0 1 3
|
||||
|
||||
Total # of neighbors = 223082
|
||||
Ave neighs/atom = 27.88525
|
||||
Neighbor list builds = 3626
|
||||
Dangerous builds = 0
|
||||
print "Running average thermal conductivity: $(v_kappa:%.2f)"
|
||||
Running average thermal conductivity: 3.41
|
||||
Total wall time: 0:00:49
|
||||
@ -1,7 +1,7 @@
|
||||
# Chunk-averaged data for fix 2 and group all
|
||||
# Timestep Number-of-chunks Total-count
|
||||
# Chunk Coord1 Ncount v_temp
|
||||
12000 20 8000
|
||||
12000 20 7999.999999999999
|
||||
1 0.025 322.07 1.73032
|
||||
2 0.075 335.51 1.65791
|
||||
3 0.125 357.07 1.53477
|
||||
@ -106,7 +106,7 @@
|
||||
18 0.875 370.35 1.51929
|
||||
19 0.925 343.49 1.65411
|
||||
20 0.975 321.75 1.75211
|
||||
17000 20 8000
|
||||
17000 20 7999.999999999999
|
||||
1 0.025 318.58 1.8062
|
||||
2 0.075 337.39 1.69943
|
||||
3 0.125 358.44 1.55342
|
||||
@ -127,7 +127,7 @@
|
||||
18 0.875 369.91 1.52963
|
||||
19 0.925 341.44 1.67071
|
||||
20 0.975 323.96 1.73861
|
||||
18000 20 8000
|
||||
18000 20 7999.999999999999
|
||||
1 0.025 317.87 1.80462
|
||||
2 0.075 332.85 1.71643
|
||||
3 0.125 362.41 1.57728
|
||||
@ -232,7 +232,7 @@
|
||||
18 0.875 365.42 1.56694
|
||||
19 0.925 344.8 1.66482
|
||||
20 0.975 324.45 1.72464
|
||||
23000 20 8000
|
||||
23000 20 7999.999999999999
|
||||
1 0.025 315.27 1.82283
|
||||
2 0.075 322.63 1.75617
|
||||
3 0.125 347.3 1.63336
|
||||
@ -253,7 +253,7 @@
|
||||
18 0.875 368.53 1.56939
|
||||
19 0.925 336.56 1.71021
|
||||
20 0.975 322.19 1.82027
|
||||
24000 20 8000
|
||||
24000 20 7999.999999999999
|
||||
1 0.025 306.22 1.91199
|
||||
2 0.075 325.76 1.76881
|
||||
3 0.125 343.41 1.68121
|
||||
@ -274,7 +274,7 @@
|
||||
18 0.875 363.38 1.56251
|
||||
19 0.925 345.4 1.62224
|
||||
20 0.975 319.21 1.72973
|
||||
25000 20 8000
|
||||
25000 20 8000.000000000001
|
||||
1 0.025 303.93 1.87595
|
||||
2 0.075 322.5 1.78136
|
||||
3 0.125 343.89 1.65601
|
||||
@ -295,7 +295,7 @@
|
||||
18 0.875 376.49 1.55894
|
||||
19 0.925 341.1 1.66486
|
||||
20 0.975 314.78 1.80037
|
||||
26000 20 8000
|
||||
26000 20 8000.000000000001
|
||||
1 0.025 309.14 1.86335
|
||||
2 0.075 330.35 1.77588
|
||||
3 0.125 340.93 1.71637
|
||||
@ -358,7 +358,7 @@
|
||||
18 0.875 373.37 1.52955
|
||||
19 0.925 347.43 1.71897
|
||||
20 0.975 322.56 1.77263
|
||||
29000 20 8000
|
||||
29000 20 8000.000000000002
|
||||
1 0.025 306.32 1.84427
|
||||
2 0.075 315.37 1.72189
|
||||
3 0.125 336.28 1.63534
|
||||
@ -379,7 +379,7 @@
|
||||
18 0.875 366.76 1.54522
|
||||
19 0.925 344.85 1.66404
|
||||
20 0.975 329.22 1.71205
|
||||
30000 20 8000
|
||||
30000 20 8000.000000000001
|
||||
1 0.025 308.09 1.89207
|
||||
2 0.075 319.03 1.81272
|
||||
3 0.125 338.19 1.69232
|
||||
@ -22,7 +22,7 @@
|
||||
18 0.875 362.38 1.58774
|
||||
19 0.925 356.68 1.58572
|
||||
20 0.975 346.2 1.63678
|
||||
13000 20 8000
|
||||
13000 20 8000.000000000001
|
||||
1 0.025 318.55 1.78446
|
||||
2 0.075 339.57 1.6873
|
||||
3 0.125 352.13 1.60227
|
||||
@ -85,7 +85,7 @@
|
||||
18 0.875 361.55 1.55703
|
||||
19 0.925 346.41 1.62695
|
||||
20 0.975 330.15 1.72757
|
||||
16000 20 8000
|
||||
16000 20 8000.000000000001
|
||||
1 0.025 306.33 1.8508
|
||||
2 0.075 334.86 1.68695
|
||||
3 0.125 356.87 1.59134
|
||||
@ -106,7 +106,7 @@
|
||||
18 0.875 365.76 1.54801
|
||||
19 0.925 343.74 1.64342
|
||||
20 0.975 322.59 1.75857
|
||||
17000 20 8000
|
||||
17000 20 7999.999999999999
|
||||
1 0.025 310.93 1.82241
|
||||
2 0.075 329.92 1.75204
|
||||
3 0.125 350.13 1.60837
|
||||
@ -148,7 +148,7 @@
|
||||
18 0.875 369.25 1.54246
|
||||
19 0.925 345.61 1.63271
|
||||
20 0.975 327.09 1.75129
|
||||
19000 20 8000
|
||||
19000 20 8000.000000000001
|
||||
1 0.025 315.61 1.79908
|
||||
2 0.075 329.82 1.70308
|
||||
3 0.125 343.96 1.63278
|
||||
@ -169,7 +169,7 @@
|
||||
18 0.875 360.65 1.57203
|
||||
19 0.925 346.34 1.63047
|
||||
20 0.975 326.01 1.71263
|
||||
20000 20 8000
|
||||
20000 20 8000.000000000002
|
||||
1 0.025 317.33 1.87602
|
||||
2 0.075 333.96 1.71854
|
||||
3 0.125 345.85 1.68538
|
||||
@ -232,7 +232,7 @@
|
||||
18 0.875 362.32 1.54729
|
||||
19 0.925 346.31 1.64909
|
||||
20 0.975 333.09 1.71265
|
||||
23000 20 8000
|
||||
23000 20 7999.999999999999
|
||||
1 0.025 305.23 1.85561
|
||||
2 0.075 316.24 1.7503
|
||||
3 0.125 342.29 1.63776
|
||||
@ -274,7 +274,7 @@
|
||||
18 0.875 368.15 1.57185
|
||||
19 0.925 354.02 1.62554
|
||||
20 0.975 333.59 1.75438
|
||||
25000 20 8000
|
||||
25000 20 8000.000000000001
|
||||
1 0.025 313.64 1.80634
|
||||
2 0.075 324.05 1.71933
|
||||
3 0.125 343.33 1.61348
|
||||
@ -316,7 +316,7 @@
|
||||
18 0.875 366.7 1.55646
|
||||
19 0.925 348.6 1.65512
|
||||
20 0.975 319.29 1.77302
|
||||
27000 20 8000
|
||||
27000 20 7999.999999999999
|
||||
1 0.025 316.89 1.80217
|
||||
2 0.075 321.88 1.73459
|
||||
3 0.125 345.89 1.63671
|
||||
@ -379,7 +379,7 @@
|
||||
18 0.875 367.09 1.55544
|
||||
19 0.925 346.8 1.60587
|
||||
20 0.975 326.99 1.68799
|
||||
30000 20 8000
|
||||
30000 20 8000.000000000001
|
||||
1 0.025 321.81 1.8543
|
||||
2 0.075 331.9 1.76078
|
||||
3 0.125 347.94 1.66013
|
||||
@ -400,7 +400,7 @@
|
||||
18 0.875 364.12 1.5531
|
||||
19 0.925 345.41 1.63361
|
||||
20 0.975 338.35 1.75235
|
||||
31000 20 8000
|
||||
31000 20 7999.999999999999
|
||||
1 0.025 310.01 1.8588
|
||||
2 0.075 325.87 1.67311
|
||||
3 0.125 346.92 1.60961
|
||||
10254
examples/KAPPA/profile.15May22.heatflux.g++.8
Normal file
10254
examples/KAPPA/profile.15May22.heatflux.g++.8
Normal file
File diff suppressed because it is too large
Load Diff
423
examples/KAPPA/profile.15May22.langevin.g++.8
Normal file
423
examples/KAPPA/profile.15May22.langevin.g++.8
Normal file
@ -0,0 +1,423 @@
|
||||
# Chunk-averaged data for fix 2 and group all
|
||||
# Timestep Number-of-chunks Total-count
|
||||
# Chunk Coord1 Ncount v_temp
|
||||
12000 20 7999.999999999999
|
||||
1 0.025 324.43 1.60834
|
||||
2 0.075 341.61 1.53785
|
||||
3 0.125 350.2 1.4877
|
||||
4 0.175 365.04 1.40516
|
||||
5 0.225 384.69 1.37298
|
||||
6 0.275 400.18 1.2663
|
||||
7 0.325 422.73 1.21391
|
||||
8 0.375 425.88 1.19949
|
||||
9 0.425 441.44 1.16103
|
||||
10 0.475 458.76 1.10454
|
||||
11 0.525 462.96 1.06491
|
||||
12 0.575 453.69 1.11021
|
||||
13 0.625 445.18 1.13249
|
||||
14 0.675 429.54 1.1833
|
||||
15 0.725 424.53 1.19473
|
||||
16 0.775 406.08 1.28831
|
||||
17 0.825 392.23 1.31652
|
||||
18 0.875 375.15 1.39838
|
||||
19 0.925 352.49 1.43048
|
||||
20 0.975 343.19 1.5113
|
||||
13000 20 7999.999999999999
|
||||
1 0.025 320.93 1.60531
|
||||
2 0.075 329.08 1.51669
|
||||
3 0.125 351.01 1.44205
|
||||
4 0.175 365.64 1.43138
|
||||
5 0.225 389.07 1.38133
|
||||
6 0.275 404 1.28582
|
||||
7 0.325 419.56 1.25282
|
||||
8 0.375 431.92 1.19591
|
||||
9 0.425 438.64 1.15536
|
||||
10 0.475 455.91 1.09308
|
||||
11 0.525 464 1.03551
|
||||
12 0.575 457.67 1.06902
|
||||
13 0.625 449.45 1.11096
|
||||
14 0.675 430.75 1.18392
|
||||
15 0.725 423.28 1.18573
|
||||
16 0.775 404.94 1.28146
|
||||
17 0.825 383.93 1.34686
|
||||
18 0.875 375.52 1.35266
|
||||
19 0.925 355.34 1.43395
|
||||
20 0.975 349.36 1.53054
|
||||
14000 20 8000
|
||||
1 0.025 313.38 1.6469
|
||||
2 0.075 331.44 1.54306
|
||||
3 0.125 352.25 1.51324
|
||||
4 0.175 365.46 1.45977
|
||||
5 0.225 387.26 1.36427
|
||||
6 0.275 399.65 1.29783
|
||||
7 0.325 424.16 1.22245
|
||||
8 0.375 431.2 1.19612
|
||||
9 0.425 439.18 1.15236
|
||||
10 0.475 454.35 1.11403
|
||||
11 0.525 462.79 1.0599
|
||||
12 0.575 465.42 1.06573
|
||||
13 0.625 456.66 1.11626
|
||||
14 0.675 441.23 1.16256
|
||||
15 0.725 431.9 1.21099
|
||||
16 0.775 405.4 1.29476
|
||||
17 0.825 384.39 1.36375
|
||||
18 0.875 362.37 1.40844
|
||||
19 0.925 359.21 1.44356
|
||||
20 0.975 332.3 1.55831
|
||||
15000 20 8000
|
||||
1 0.025 317 1.63147
|
||||
2 0.075 327.18 1.55353
|
||||
3 0.125 352.32 1.50536
|
||||
4 0.175 361.61 1.44141
|
||||
5 0.225 390.66 1.32555
|
||||
6 0.275 408.59 1.2666
|
||||
7 0.325 409.22 1.27698
|
||||
8 0.375 426.21 1.20889
|
||||
9 0.425 439.13 1.14093
|
||||
10 0.475 456.79 1.10607
|
||||
11 0.525 469.6 1.03968
|
||||
12 0.575 470.28 1.04713
|
||||
13 0.625 454.2 1.10267
|
||||
14 0.675 433.89 1.18593
|
||||
15 0.725 424.87 1.22485
|
||||
16 0.775 406.98 1.27526
|
||||
17 0.825 392.62 1.3427
|
||||
18 0.875 361.38 1.46987
|
||||
19 0.925 360.57 1.47829
|
||||
20 0.975 336.9 1.56324
|
||||
16000 20 8000
|
||||
1 0.025 319.31 1.59474
|
||||
2 0.075 330.99 1.56731
|
||||
3 0.125 352.96 1.49519
|
||||
4 0.175 361.25 1.45436
|
||||
5 0.225 387.65 1.35571
|
||||
6 0.275 403.15 1.3022
|
||||
7 0.325 416.18 1.24996
|
||||
8 0.375 430.75 1.19106
|
||||
9 0.425 440.21 1.15903
|
||||
10 0.475 457.38 1.1148
|
||||
11 0.525 467.86 1.04407
|
||||
12 0.575 468.13 1.06024
|
||||
13 0.625 451.32 1.14854
|
||||
14 0.675 444.39 1.18686
|
||||
15 0.725 416.55 1.24119
|
||||
16 0.775 401.95 1.29217
|
||||
17 0.825 390.06 1.32567
|
||||
18 0.875 366.74 1.40477
|
||||
19 0.925 351.55 1.5
|
||||
20 0.975 341.62 1.56779
|
||||
17000 20 8000
|
||||
1 0.025 327.13 1.63827
|
||||
2 0.075 327.24 1.60613
|
||||
3 0.125 347.89 1.48608
|
||||
4 0.175 366.31 1.43192
|
||||
5 0.225 386.23 1.36766
|
||||
6 0.275 400.19 1.30784
|
||||
7 0.325 419.68 1.23504
|
||||
8 0.375 430.47 1.2079
|
||||
9 0.425 446.6 1.1614
|
||||
10 0.475 455.77 1.11162
|
||||
11 0.525 470.4 1.06723
|
||||
12 0.575 463.91 1.09678
|
||||
13 0.625 452.59 1.14022
|
||||
14 0.675 437.09 1.19035
|
||||
15 0.725 419.45 1.24363
|
||||
16 0.775 402.68 1.32395
|
||||
17 0.825 390.72 1.3516
|
||||
18 0.875 377.43 1.39837
|
||||
19 0.925 348.47 1.45723
|
||||
20 0.975 329.75 1.54812
|
||||
18000 20 7999.999999999999
|
||||
1 0.025 326.78 1.58515
|
||||
2 0.075 331.84 1.55152
|
||||
3 0.125 350.47 1.52315
|
||||
4 0.175 376.83 1.42354
|
||||
5 0.225 378.24 1.35515
|
||||
6 0.275 393.93 1.3185
|
||||
7 0.325 417.15 1.27872
|
||||
8 0.375 427.9 1.19008
|
||||
9 0.425 444.87 1.14026
|
||||
10 0.475 453.82 1.08571
|
||||
11 0.525 473.39 1.04867
|
||||
12 0.575 467.16 1.08732
|
||||
13 0.625 447.08 1.13176
|
||||
14 0.675 433.94 1.18893
|
||||
15 0.725 419.93 1.23404
|
||||
16 0.775 405.57 1.28696
|
||||
17 0.825 384.45 1.35102
|
||||
18 0.875 367.82 1.43603
|
||||
19 0.925 364.03 1.47601
|
||||
20 0.975 334.8 1.5772
|
||||
19000 20 7999.999999999997
|
||||
1 0.025 323.97 1.59796
|
||||
2 0.075 336.58 1.53743
|
||||
3 0.125 352.05 1.45973
|
||||
4 0.175 371.69 1.40717
|
||||
5 0.225 372.72 1.40247
|
||||
6 0.275 402.96 1.30387
|
||||
7 0.325 420.51 1.23992
|
||||
8 0.375 428.49 1.21072
|
||||
9 0.425 445.18 1.17064
|
||||
10 0.475 460.02 1.10207
|
||||
11 0.525 468.51 1.05067
|
||||
12 0.575 458.36 1.09387
|
||||
13 0.625 447.9 1.14489
|
||||
14 0.675 440.86 1.16244
|
||||
15 0.725 424.91 1.23075
|
||||
16 0.775 396.52 1.33119
|
||||
17 0.825 380.16 1.37678
|
||||
18 0.875 365.47 1.465
|
||||
19 0.925 359.74 1.47827
|
||||
20 0.975 343.4 1.58725
|
||||
20000 20 8000.000000000001
|
||||
1 0.025 323.95 1.65649
|
||||
2 0.075 339.96 1.55391
|
||||
3 0.125 356.26 1.45521
|
||||
4 0.175 369.64 1.41802
|
||||
5 0.225 376.49 1.40659
|
||||
6 0.275 400.24 1.3042
|
||||
7 0.325 423 1.23659
|
||||
8 0.375 428.73 1.1654
|
||||
9 0.425 443.16 1.13211
|
||||
10 0.475 461.94 1.08865
|
||||
11 0.525 468.5 1.07004
|
||||
12 0.575 454.26 1.10352
|
||||
13 0.625 445.98 1.14782
|
||||
14 0.675 442.13 1.17822
|
||||
15 0.725 424.51 1.219
|
||||
16 0.775 402.86 1.32306
|
||||
17 0.825 374.2 1.37628
|
||||
18 0.875 370.01 1.45695
|
||||
19 0.925 360.09 1.52285
|
||||
20 0.975 334.09 1.58501
|
||||
21000 20 8000.000000000002
|
||||
1 0.025 318.7 1.63137
|
||||
2 0.075 328.87 1.55928
|
||||
3 0.125 354.61 1.47208
|
||||
4 0.175 356.23 1.46995
|
||||
5 0.225 382.73 1.3906
|
||||
6 0.275 401.41 1.31083
|
||||
7 0.325 427.86 1.25352
|
||||
8 0.375 436.72 1.22226
|
||||
9 0.425 447.32 1.15639
|
||||
10 0.475 468.67 1.06828
|
||||
11 0.525 476.2 1.04168
|
||||
12 0.575 463.51 1.09368
|
||||
13 0.625 449.06 1.1474
|
||||
14 0.675 439.67 1.16907
|
||||
15 0.725 422.56 1.2318
|
||||
16 0.775 403.12 1.28624
|
||||
17 0.825 373.64 1.39466
|
||||
18 0.875 372.85 1.43131
|
||||
19 0.925 347.12 1.4907
|
||||
20 0.975 329.15 1.58361
|
||||
22000 20 8000
|
||||
1 0.025 323.04 1.65324
|
||||
2 0.075 327.43 1.59461
|
||||
3 0.125 341.42 1.51506
|
||||
4 0.175 363.04 1.46508
|
||||
5 0.225 380.92 1.35762
|
||||
6 0.275 405.36 1.26996
|
||||
7 0.325 421.99 1.21208
|
||||
8 0.375 438.21 1.15484
|
||||
9 0.425 450.59 1.13146
|
||||
10 0.475 466.59 1.07633
|
||||
11 0.525 472.73 1.04547
|
||||
12 0.575 460.35 1.0978
|
||||
13 0.625 450.49 1.10972
|
||||
14 0.675 438.69 1.17936
|
||||
15 0.725 425.26 1.23081
|
||||
16 0.775 409.48 1.28984
|
||||
17 0.825 391.1 1.34589
|
||||
18 0.875 349.83 1.47302
|
||||
19 0.925 346.53 1.51295
|
||||
20 0.975 336.95 1.54093
|
||||
23000 20 7999.999999999999
|
||||
1 0.025 320.63 1.6202
|
||||
2 0.075 329.18 1.5672
|
||||
3 0.125 346.15 1.51599
|
||||
4 0.175 365.66 1.45131
|
||||
5 0.225 390.33 1.32981
|
||||
6 0.275 412.23 1.27024
|
||||
7 0.325 424.94 1.23151
|
||||
8 0.375 435.15 1.17617
|
||||
9 0.425 450.77 1.10713
|
||||
10 0.475 467.2 1.07882
|
||||
11 0.525 468.45 1.04111
|
||||
12 0.575 459.21 1.09284
|
||||
13 0.625 447.57 1.14279
|
||||
14 0.675 435.43 1.16402
|
||||
15 0.725 428.73 1.19954
|
||||
16 0.775 410.05 1.29416
|
||||
17 0.825 390.83 1.34801
|
||||
18 0.875 359.74 1.42129
|
||||
19 0.925 335.33 1.53287
|
||||
20 0.975 322.42 1.58982
|
||||
24000 20 7999.999999999999
|
||||
1 0.025 322.77 1.62757
|
||||
2 0.075 333.67 1.54744
|
||||
3 0.125 340.7 1.49219
|
||||
4 0.175 371.07 1.37482
|
||||
5 0.225 396.34 1.29492
|
||||
6 0.275 406.63 1.26711
|
||||
7 0.325 420.98 1.22028
|
||||
8 0.375 431.7 1.17677
|
||||
9 0.425 440.14 1.1432
|
||||
10 0.475 462.31 1.06847
|
||||
11 0.525 470.25 1.05525
|
||||
12 0.575 455.44 1.08106
|
||||
13 0.625 440.86 1.13575
|
||||
14 0.675 436.63 1.17026
|
||||
15 0.725 429.05 1.17415
|
||||
16 0.775 410.9 1.24948
|
||||
17 0.825 390.25 1.31711
|
||||
18 0.875 368.49 1.40466
|
||||
19 0.925 350.81 1.52444
|
||||
20 0.975 321.01 1.57808
|
||||
25000 20 7999.999999999999
|
||||
1 0.025 312.02 1.63505
|
||||
2 0.075 333.94 1.54845
|
||||
3 0.125 361.11 1.46317
|
||||
4 0.175 371.97 1.42115
|
||||
5 0.225 389.69 1.3367
|
||||
6 0.275 402.08 1.2905
|
||||
7 0.325 416.43 1.26101
|
||||
8 0.375 429.57 1.18853
|
||||
9 0.425 447.99 1.14676
|
||||
10 0.475 464.52 1.0761
|
||||
11 0.525 459.96 1.05077
|
||||
12 0.575 449.99 1.09404
|
||||
13 0.625 452 1.11846
|
||||
14 0.675 438.85 1.18532
|
||||
15 0.725 416.43 1.21052
|
||||
16 0.775 412.52 1.24262
|
||||
17 0.825 395.41 1.30407
|
||||
18 0.875 374.13 1.37692
|
||||
19 0.925 350.86 1.45984
|
||||
20 0.975 320.53 1.56642
|
||||
26000 20 8000
|
||||
1 0.025 324.31 1.57356
|
||||
2 0.075 331.81 1.52556
|
||||
3 0.125 351.72 1.46615
|
||||
4 0.175 365.82 1.41152
|
||||
5 0.225 382.98 1.36225
|
||||
6 0.275 402.12 1.28798
|
||||
7 0.325 406.32 1.25829
|
||||
8 0.375 435.27 1.18647
|
||||
9 0.425 453.49 1.12037
|
||||
10 0.475 462.89 1.09729
|
||||
11 0.525 465.45 1.05474
|
||||
12 0.575 459.03 1.08394
|
||||
13 0.625 448.32 1.16267
|
||||
14 0.675 434.71 1.1915
|
||||
15 0.725 425.43 1.21359
|
||||
16 0.775 413.68 1.23755
|
||||
17 0.825 391.44 1.31345
|
||||
18 0.875 372.59 1.3671
|
||||
19 0.925 340.17 1.46078
|
||||
20 0.975 332.45 1.48651
|
||||
27000 20 8000
|
||||
1 0.025 325.04 1.60375
|
||||
2 0.075 340.02 1.53577
|
||||
3 0.125 352.49 1.49596
|
||||
4 0.175 374.65 1.41462
|
||||
5 0.225 385.42 1.36199
|
||||
6 0.275 403.05 1.30961
|
||||
7 0.325 417 1.21797
|
||||
8 0.375 424.93 1.19576
|
||||
9 0.425 452.06 1.13328
|
||||
10 0.475 455.29 1.08635
|
||||
11 0.525 458.96 1.03785
|
||||
12 0.575 458.09 1.08787
|
||||
13 0.625 451.41 1.10371
|
||||
14 0.675 435.56 1.13536
|
||||
15 0.725 422.9 1.20972
|
||||
16 0.775 400.12 1.285
|
||||
17 0.825 383.69 1.33289
|
||||
18 0.875 367.99 1.39547
|
||||
19 0.925 361.31 1.41919
|
||||
20 0.975 330.02 1.55009
|
||||
28000 20 7999.999999999999
|
||||
1 0.025 318.46 1.62382
|
||||
2 0.075 330.06 1.57404
|
||||
3 0.125 338.21 1.488
|
||||
4 0.175 371.39 1.40315
|
||||
5 0.225 385.8 1.33727
|
||||
6 0.275 394.56 1.29576
|
||||
7 0.325 420.5 1.26925
|
||||
8 0.375 432.46 1.21155
|
||||
9 0.425 447.74 1.15185
|
||||
10 0.475 466.84 1.08894
|
||||
11 0.525 469.04 1.06609
|
||||
12 0.575 458.69 1.09989
|
||||
13 0.625 454.28 1.10128
|
||||
14 0.675 436.53 1.18166
|
||||
15 0.725 426.9 1.23579
|
||||
16 0.775 407 1.28821
|
||||
17 0.825 390.7 1.35529
|
||||
18 0.875 365.86 1.41439
|
||||
19 0.925 353.34 1.50022
|
||||
20 0.975 331.64 1.55571
|
||||
29000 20 7999.999999999999
|
||||
1 0.025 320.19 1.63312
|
||||
2 0.075 330.09 1.55618
|
||||
3 0.125 345.39 1.52058
|
||||
4 0.175 370.48 1.45503
|
||||
5 0.225 386.9 1.37045
|
||||
6 0.275 401.31 1.2871
|
||||
7 0.325 414.98 1.24079
|
||||
8 0.375 434.79 1.18965
|
||||
9 0.425 444.5 1.1383
|
||||
10 0.475 460.4 1.08551
|
||||
11 0.525 467.26 1.05446
|
||||
12 0.575 455.03 1.08066
|
||||
13 0.625 443.27 1.14657
|
||||
14 0.675 436.29 1.17181
|
||||
15 0.725 425.15 1.22791
|
||||
16 0.775 406.92 1.27781
|
||||
17 0.825 393.46 1.31495
|
||||
18 0.875 364.46 1.42001
|
||||
19 0.925 362.69 1.46134
|
||||
20 0.975 336.44 1.57142
|
||||
30000 20 8000.000000000002
|
||||
1 0.025 321.57 1.64563
|
||||
2 0.075 326.85 1.50756
|
||||
3 0.125 352.98 1.46667
|
||||
4 0.175 361.94 1.45273
|
||||
5 0.225 384.16 1.3508
|
||||
6 0.275 404.3 1.30642
|
||||
7 0.325 415.56 1.25403
|
||||
8 0.375 430.6 1.15564
|
||||
9 0.425 452.93 1.13491
|
||||
10 0.475 458.02 1.10193
|
||||
11 0.525 475.16 1.0281
|
||||
12 0.575 467.05 1.07923
|
||||
13 0.625 446.84 1.11758
|
||||
14 0.675 427.85 1.18775
|
||||
15 0.725 412.68 1.28358
|
||||
16 0.775 410.05 1.27221
|
||||
17 0.825 384.47 1.3378
|
||||
18 0.875 372.1 1.4467
|
||||
19 0.925 354.14 1.44309
|
||||
20 0.975 340.75 1.53467
|
||||
31000 20 8000
|
||||
1 0.025 317.97 1.65122
|
||||
2 0.075 334.2 1.5323
|
||||
3 0.125 349.7 1.44318
|
||||
4 0.175 370.34 1.40175
|
||||
5 0.225 379.65 1.36819
|
||||
6 0.275 393.79 1.30774
|
||||
7 0.325 419.2 1.23684
|
||||
8 0.375 439 1.1804
|
||||
9 0.425 453.77 1.15198
|
||||
10 0.475 457.34 1.12122
|
||||
11 0.525 471.86 1.05773
|
||||
12 0.575 464.13 1.0945
|
||||
13 0.625 452.97 1.13525
|
||||
14 0.675 431.7 1.19934
|
||||
15 0.725 415.95 1.27097
|
||||
16 0.775 399.2 1.31547
|
||||
17 0.825 390.04 1.36643
|
||||
18 0.875 370.85 1.41883
|
||||
19 0.925 356.88 1.45535
|
||||
20 0.975 331.46 1.55832
|
||||
843
examples/KAPPA/profile.15May22.mp.g++.8
Normal file
843
examples/KAPPA/profile.15May22.mp.g++.8
Normal file
@ -0,0 +1,843 @@
|
||||
# Chunk-averaged data for fix 2 and group all
|
||||
# Timestep Number-of-chunks Total-count
|
||||
# Chunk Coord1 Ncount v_temp
|
||||
2000 20 8000
|
||||
1 0.025 415.5 1.23034
|
||||
2 0.075 407.29 1.27112
|
||||
3 0.125 401.07 1.31449
|
||||
4 0.175 403.87 1.33329
|
||||
5 0.225 397.86 1.34078
|
||||
6 0.275 408.33 1.29533
|
||||
7 0.325 402.93 1.36409
|
||||
8 0.375 397.74 1.39609
|
||||
9 0.425 398.17 1.40146
|
||||
10 0.475 397.59 1.3936
|
||||
11 0.525 383.76 1.49092
|
||||
12 0.575 386.73 1.4368
|
||||
13 0.625 397.06 1.4032
|
||||
14 0.675 399.3 1.38434
|
||||
15 0.725 403.13 1.31729
|
||||
16 0.775 403.94 1.33694
|
||||
17 0.825 393.99 1.36073
|
||||
18 0.875 400.45 1.32511
|
||||
19 0.925 397 1.33562
|
||||
20 0.975 404.29 1.30232
|
||||
3000 20 8000
|
||||
1 0.025 453.29 1.16593
|
||||
2 0.075 430.98 1.24608
|
||||
3 0.125 420.46 1.29064
|
||||
4 0.175 410.05 1.34905
|
||||
5 0.225 406.49 1.35403
|
||||
6 0.275 404.57 1.32764
|
||||
7 0.325 403.17 1.37253
|
||||
8 0.375 389.98 1.37702
|
||||
9 0.425 382.06 1.41632
|
||||
10 0.475 362.76 1.50583
|
||||
11 0.525 343.2 1.57438
|
||||
12 0.575 365.36 1.49547
|
||||
13 0.625 382.12 1.43187
|
||||
14 0.675 390.94 1.39664
|
||||
15 0.725 397.43 1.35572
|
||||
16 0.775 401.56 1.34566
|
||||
17 0.825 404.03 1.36849
|
||||
18 0.875 401.92 1.35928
|
||||
19 0.925 420.45 1.30529
|
||||
20 0.975 429.18 1.2345
|
||||
4000 20 8000
|
||||
1 0.025 461.68 1.09513
|
||||
2 0.075 445.9 1.1703
|
||||
3 0.125 417.25 1.25346
|
||||
4 0.175 413.5 1.29839
|
||||
5 0.225 412.16 1.31817
|
||||
6 0.275 410.01 1.33067
|
||||
7 0.325 393.96 1.41075
|
||||
8 0.375 388.36 1.43959
|
||||
9 0.425 376.79 1.47735
|
||||
10 0.475 343.24 1.62046
|
||||
11 0.525 336.49 1.73341
|
||||
12 0.575 355.25 1.59289
|
||||
13 0.625 368.83 1.52958
|
||||
14 0.675 384.29 1.44883
|
||||
15 0.725 384.95 1.44867
|
||||
16 0.775 399.09 1.37753
|
||||
17 0.825 407.15 1.35782
|
||||
18 0.875 417.77 1.27865
|
||||
19 0.925 435.5 1.22981
|
||||
20 0.975 447.83 1.145
|
||||
5000 20 8000
|
||||
1 0.025 481.54 1.06332
|
||||
2 0.075 459.14 1.15776
|
||||
3 0.125 436.8 1.2544
|
||||
4 0.175 427.68 1.28406
|
||||
5 0.225 418.49 1.31404
|
||||
6 0.275 404.7 1.34013
|
||||
7 0.325 386.23 1.4184
|
||||
8 0.375 366.51 1.51168
|
||||
9 0.425 359.76 1.55376
|
||||
10 0.475 344.12 1.63837
|
||||
11 0.525 317.95 1.76505
|
||||
12 0.575 344.56 1.62566
|
||||
13 0.625 358.49 1.58144
|
||||
14 0.675 371.68 1.52153
|
||||
15 0.725 390.66 1.40598
|
||||
16 0.775 394.03 1.41308
|
||||
17 0.825 410.92 1.35719
|
||||
18 0.875 428.12 1.29761
|
||||
19 0.925 439.58 1.23596
|
||||
20 0.975 459.04 1.13188
|
||||
6000 20 8000
|
||||
1 0.025 484.05 1.02101
|
||||
2 0.075 464.77 1.14032
|
||||
3 0.125 441.56 1.21524
|
||||
4 0.175 430.64 1.27264
|
||||
5 0.225 414.33 1.34252
|
||||
6 0.275 402.88 1.39052
|
||||
7 0.325 390.62 1.45296
|
||||
8 0.375 371.05 1.54253
|
||||
9 0.425 351.27 1.58741
|
||||
10 0.475 331.08 1.75438
|
||||
11 0.525 314.04 1.85311
|
||||
12 0.575 332.86 1.66407
|
||||
13 0.625 350.4 1.6121
|
||||
14 0.675 372.28 1.52051
|
||||
15 0.725 386.14 1.4603
|
||||
16 0.775 404.37 1.3925
|
||||
17 0.825 414.42 1.33616
|
||||
18 0.875 422.3 1.28014
|
||||
19 0.925 447.55 1.18358
|
||||
20 0.975 473.39 1.09396
|
||||
7000 20 8000.000000000001
|
||||
1 0.025 489.77 1.01792
|
||||
2 0.075 471.91 1.11387
|
||||
3 0.125 446.04 1.21504
|
||||
4 0.175 430.11 1.28371
|
||||
5 0.225 425.52 1.34288
|
||||
6 0.275 398.21 1.42032
|
||||
7 0.325 389.63 1.48032
|
||||
8 0.375 368.99 1.54959
|
||||
9 0.425 346.79 1.63726
|
||||
10 0.475 320.96 1.76265
|
||||
11 0.525 301.06 1.94512
|
||||
12 0.575 323.85 1.7268
|
||||
13 0.625 349.63 1.59565
|
||||
14 0.675 368.23 1.5252
|
||||
15 0.725 381.4 1.47823
|
||||
16 0.775 402.1 1.39655
|
||||
17 0.825 417.24 1.35212
|
||||
18 0.875 436.02 1.24569
|
||||
19 0.925 457.7 1.18478
|
||||
20 0.975 474.84 1.08226
|
||||
8000 20 7999.999999999999
|
||||
1 0.025 492.27 1.00238
|
||||
2 0.075 472.22 1.08445
|
||||
3 0.125 456.24 1.17253
|
||||
4 0.175 433.01 1.25584
|
||||
5 0.225 421.07 1.34958
|
||||
6 0.275 403.99 1.39611
|
||||
7 0.325 394.24 1.46711
|
||||
8 0.375 361.11 1.60367
|
||||
9 0.425 345.19 1.67064
|
||||
10 0.475 304.53 1.91686
|
||||
11 0.525 300.46 1.92665
|
||||
12 0.575 324.95 1.78176
|
||||
13 0.625 347.5 1.64653
|
||||
14 0.675 375.87 1.55407
|
||||
15 0.725 382.66 1.45232
|
||||
16 0.775 405.6 1.39472
|
||||
17 0.825 415.82 1.32315
|
||||
18 0.875 434.11 1.26514
|
||||
19 0.925 450.78 1.18232
|
||||
20 0.975 478.38 1.08409
|
||||
9000 20 8000
|
||||
1 0.025 498.52 0.987753
|
||||
2 0.075 483.39 1.07811
|
||||
3 0.125 458.42 1.17891
|
||||
4 0.175 437.26 1.25608
|
||||
5 0.225 425.47 1.33684
|
||||
6 0.275 400.94 1.40144
|
||||
7 0.325 379.9 1.46405
|
||||
8 0.375 362.9 1.58147
|
||||
9 0.425 334.61 1.70056
|
||||
10 0.475 304.32 1.92655
|
||||
11 0.525 290.36 2.029
|
||||
12 0.575 324 1.81241
|
||||
13 0.625 349.25 1.67868
|
||||
14 0.675 366.02 1.58848
|
||||
15 0.725 387.27 1.49739
|
||||
16 0.775 401.65 1.42398
|
||||
17 0.825 421.53 1.35991
|
||||
18 0.875 438.32 1.27023
|
||||
19 0.925 453.99 1.19099
|
||||
20 0.975 481.88 1.07411
|
||||
10000 20 8000
|
||||
1 0.025 495.91 1.02396
|
||||
2 0.075 479.75 1.09749
|
||||
3 0.125 464.37 1.16865
|
||||
4 0.175 448.55 1.2321
|
||||
5 0.225 427.82 1.31599
|
||||
6 0.275 405.2 1.40859
|
||||
7 0.325 386.61 1.50757
|
||||
8 0.375 361.78 1.62331
|
||||
9 0.425 335.89 1.71317
|
||||
10 0.475 306.28 1.92814
|
||||
11 0.525 286.59 2.10121
|
||||
12 0.575 312.84 1.87522
|
||||
13 0.625 327.02 1.75002
|
||||
14 0.675 355.42 1.59423
|
||||
15 0.725 388.74 1.46947
|
||||
16 0.775 404.28 1.37944
|
||||
17 0.825 425.92 1.30689
|
||||
18 0.875 438.45 1.25073
|
||||
19 0.925 464.97 1.16505
|
||||
20 0.975 483.61 1.07809
|
||||
11000 20 8000
|
||||
1 0.025 495.2 1.01386
|
||||
2 0.075 484.21 1.07067
|
||||
3 0.125 460.47 1.1714
|
||||
4 0.175 441.39 1.24352
|
||||
5 0.225 421.62 1.35118
|
||||
6 0.275 413.63 1.39485
|
||||
7 0.325 377.63 1.53879
|
||||
8 0.375 358.62 1.63489
|
||||
9 0.425 335.82 1.71199
|
||||
10 0.475 296.08 1.87748
|
||||
11 0.525 275.31 2.07066
|
||||
12 0.575 303.37 1.92447
|
||||
13 0.625 336.08 1.7294
|
||||
14 0.675 369.17 1.61632
|
||||
15 0.725 392.94 1.47845
|
||||
16 0.775 411.21 1.40711
|
||||
17 0.825 423.06 1.34782
|
||||
18 0.875 449.38 1.23997
|
||||
19 0.925 469.49 1.17047
|
||||
20 0.975 485.32 1.08514
|
||||
12000 20 8000.000000000001
|
||||
1 0.025 499.94 0.976175
|
||||
2 0.075 484.73 1.04765
|
||||
3 0.125 452.84 1.14754
|
||||
4 0.175 439.2 1.25483
|
||||
5 0.225 418.27 1.32751
|
||||
6 0.275 399.76 1.43016
|
||||
7 0.325 375.81 1.54015
|
||||
8 0.375 358.06 1.61819
|
||||
9 0.425 334.51 1.74269
|
||||
10 0.475 318.33 1.88764
|
||||
11 0.525 290.59 2.0738
|
||||
12 0.575 315.71 1.87709
|
||||
13 0.625 346.35 1.75256
|
||||
14 0.675 364.88 1.58804
|
||||
15 0.725 390.81 1.48594
|
||||
16 0.775 406.81 1.36652
|
||||
17 0.825 424.7 1.32707
|
||||
18 0.875 437.76 1.26768
|
||||
19 0.925 458.54 1.14744
|
||||
20 0.975 482.4 1.0652
|
||||
13000 20 8000.000000000001
|
||||
1 0.025 498.95 1.00629
|
||||
2 0.075 481.8 1.08497
|
||||
3 0.125 465.5 1.15572
|
||||
4 0.175 439.6 1.27346
|
||||
5 0.225 420.07 1.32751
|
||||
6 0.275 398.74 1.4143
|
||||
7 0.325 373.87 1.54317
|
||||
8 0.375 357.6 1.60275
|
||||
9 0.425 333.01 1.71416
|
||||
10 0.475 304.94 1.89779
|
||||
11 0.525 282.9 2.07971
|
||||
12 0.575 306.18 1.92825
|
||||
13 0.625 332.83 1.77058
|
||||
14 0.675 366.83 1.61928
|
||||
15 0.725 394.59 1.50562
|
||||
16 0.775 409.8 1.36867
|
||||
17 0.825 429.6 1.30989
|
||||
18 0.875 447.23 1.25447
|
||||
19 0.925 467.1 1.15291
|
||||
20 0.975 488.86 1.07235
|
||||
14000 20 7999.999999999999
|
||||
1 0.025 496.1 0.997899
|
||||
2 0.075 481.33 1.08357
|
||||
3 0.125 460.33 1.17037
|
||||
4 0.175 442.89 1.22771
|
||||
5 0.225 432.46 1.29769
|
||||
6 0.275 408.55 1.41384
|
||||
7 0.325 382.76 1.52974
|
||||
8 0.375 354.76 1.69221
|
||||
9 0.425 333.4 1.77158
|
||||
10 0.475 303.77 1.95666
|
||||
11 0.525 282.62 2.16224
|
||||
12 0.575 301.72 1.96
|
||||
13 0.625 331.53 1.7852
|
||||
14 0.675 360.45 1.61926
|
||||
15 0.725 391.12 1.47428
|
||||
16 0.775 402.17 1.40985
|
||||
17 0.825 426.87 1.31585
|
||||
18 0.875 451.08 1.20686
|
||||
19 0.925 468.23 1.12015
|
||||
20 0.975 487.86 1.04
|
||||
15000 20 8000
|
||||
1 0.025 494.96 1.00997
|
||||
2 0.075 484.85 1.07119
|
||||
3 0.125 465.32 1.15501
|
||||
4 0.175 451.13 1.28189
|
||||
5 0.225 432.63 1.3514
|
||||
6 0.275 409.64 1.41611
|
||||
7 0.325 387.99 1.50709
|
||||
8 0.375 359.1 1.67587
|
||||
9 0.425 319.61 1.80869
|
||||
10 0.475 297.13 1.94798
|
||||
11 0.525 279.39 2.08157
|
||||
12 0.575 293.36 1.97315
|
||||
13 0.625 328.88 1.73315
|
||||
14 0.675 359.33 1.59731
|
||||
15 0.725 380.92 1.53292
|
||||
16 0.775 412.79 1.38478
|
||||
17 0.825 428.6 1.3283
|
||||
18 0.875 451.13 1.24183
|
||||
19 0.925 471.2 1.15387
|
||||
20 0.975 492.04 1.05427
|
||||
16000 20 8000
|
||||
1 0.025 498.76 1.00751
|
||||
2 0.075 486.07 1.06924
|
||||
3 0.125 463.16 1.14356
|
||||
4 0.175 440.19 1.22518
|
||||
5 0.225 424.57 1.32559
|
||||
6 0.275 405.23 1.40373
|
||||
7 0.325 379.23 1.5187
|
||||
8 0.375 351.52 1.6514
|
||||
9 0.425 328.47 1.79752
|
||||
10 0.475 308.34 1.93207
|
||||
11 0.525 284.45 2.15816
|
||||
12 0.575 303.88 1.91137
|
||||
13 0.625 328.34 1.77897
|
||||
14 0.675 364.04 1.62015
|
||||
15 0.725 383.29 1.52178
|
||||
16 0.775 406.23 1.41383
|
||||
17 0.825 428.16 1.31354
|
||||
18 0.875 448.55 1.21095
|
||||
19 0.925 476.65 1.12303
|
||||
20 0.975 490.87 1.06309
|
||||
17000 20 7999.999999999999
|
||||
1 0.025 501.98 1.01754
|
||||
2 0.075 486.12 1.05803
|
||||
3 0.125 465.09 1.15248
|
||||
4 0.175 441.99 1.25562
|
||||
5 0.225 425.54 1.33308
|
||||
6 0.275 410.2 1.42708
|
||||
7 0.325 378.31 1.53566
|
||||
8 0.375 360.5 1.66967
|
||||
9 0.425 322.62 1.79432
|
||||
10 0.475 298.06 1.91418
|
||||
11 0.525 271.38 2.14772
|
||||
12 0.575 297.14 2.00242
|
||||
13 0.625 338.4 1.77976
|
||||
14 0.675 366.13 1.60422
|
||||
15 0.725 385.58 1.50921
|
||||
16 0.775 405.78 1.41669
|
||||
17 0.825 425.57 1.29765
|
||||
18 0.875 455.72 1.22147
|
||||
19 0.925 477.11 1.13711
|
||||
20 0.975 486.78 1.07397
|
||||
18000 20 8000
|
||||
1 0.025 498.53 1.00361
|
||||
2 0.075 484.14 1.07365
|
||||
3 0.125 466.81 1.14334
|
||||
4 0.175 446.28 1.25392
|
||||
5 0.225 429.82 1.31988
|
||||
6 0.275 409.11 1.40489
|
||||
7 0.325 375.93 1.54725
|
||||
8 0.375 361.94 1.65295
|
||||
9 0.425 319.61 1.87399
|
||||
10 0.475 303.84 1.96221
|
||||
11 0.525 279.97 2.15575
|
||||
12 0.575 299.25 1.96922
|
||||
13 0.625 332.28 1.75356
|
||||
14 0.675 359.25 1.6522
|
||||
15 0.725 380.35 1.51572
|
||||
16 0.775 406.49 1.41932
|
||||
17 0.825 432.58 1.31968
|
||||
18 0.875 454.68 1.18799
|
||||
19 0.925 475.07 1.09877
|
||||
20 0.975 484.07 1.05265
|
||||
19000 20 8000.000000000002
|
||||
1 0.025 496.66 1.0156
|
||||
2 0.075 485.35 1.06088
|
||||
3 0.125 474.92 1.14949
|
||||
4 0.175 449 1.25605
|
||||
5 0.225 425.41 1.30965
|
||||
6 0.275 413 1.41073
|
||||
7 0.325 374.61 1.52877
|
||||
8 0.375 356.02 1.68783
|
||||
9 0.425 329.04 1.76522
|
||||
10 0.475 296.34 1.97294
|
||||
11 0.525 286.89 2.10854
|
||||
12 0.575 295.44 1.99154
|
||||
13 0.625 323.05 1.81865
|
||||
14 0.675 347.29 1.73547
|
||||
15 0.725 385.59 1.50272
|
||||
16 0.775 411.84 1.39649
|
||||
17 0.825 429.6 1.31633
|
||||
18 0.875 454.83 1.1834
|
||||
19 0.925 474.56 1.11023
|
||||
20 0.975 490.56 1.06466
|
||||
20000 20 8000.000000000001
|
||||
1 0.025 497.85 0.99282
|
||||
2 0.075 487.37 1.04837
|
||||
3 0.125 471.74 1.09553
|
||||
4 0.175 446.52 1.22126
|
||||
5 0.225 424.82 1.30532
|
||||
6 0.275 410.74 1.42656
|
||||
7 0.325 380.93 1.53516
|
||||
8 0.375 355.4 1.65857
|
||||
9 0.425 322.61 1.81947
|
||||
10 0.475 297.3 1.91324
|
||||
11 0.525 273.06 2.20414
|
||||
12 0.575 289.42 2.06116
|
||||
13 0.625 331.09 1.81766
|
||||
14 0.675 355.92 1.70999
|
||||
15 0.725 383.07 1.53642
|
||||
16 0.775 415.95 1.4193
|
||||
17 0.825 436.21 1.31576
|
||||
18 0.875 456.31 1.23326
|
||||
19 0.925 475.98 1.13736
|
||||
20 0.975 487.71 1.06652
|
||||
21000 20 7999.999999999999
|
||||
1 0.025 503.21 0.995771
|
||||
2 0.075 495.59 1.04263
|
||||
3 0.125 474.11 1.13994
|
||||
4 0.175 448.06 1.25062
|
||||
5 0.225 434.05 1.32938
|
||||
6 0.275 404.47 1.42051
|
||||
7 0.325 381.25 1.55729
|
||||
8 0.375 351.08 1.69745
|
||||
9 0.425 322.7 1.79452
|
||||
10 0.475 299.28 2.00033
|
||||
11 0.525 285.68 2.15685
|
||||
12 0.575 297.47 1.96695
|
||||
13 0.625 319.43 1.85021
|
||||
14 0.675 352.79 1.64302
|
||||
15 0.725 367.53 1.57944
|
||||
16 0.775 406.65 1.39256
|
||||
17 0.825 435.09 1.28822
|
||||
18 0.875 449.28 1.23652
|
||||
19 0.925 475.48 1.1495
|
||||
20 0.975 496.8 1.03688
|
||||
22000 20 7999.999999999999
|
||||
1 0.025 497.19 0.996225
|
||||
2 0.075 493.87 1.05005
|
||||
3 0.125 475.98 1.12092
|
||||
4 0.175 453.37 1.20514
|
||||
5 0.225 428.25 1.30239
|
||||
6 0.275 399.42 1.42903
|
||||
7 0.325 377.16 1.54299
|
||||
8 0.375 360.79 1.64886
|
||||
9 0.425 322.45 1.8429
|
||||
10 0.475 295.32 2.0194
|
||||
11 0.525 287.08 2.17426
|
||||
12 0.575 295.19 2.02787
|
||||
13 0.625 319.9 1.83753
|
||||
14 0.675 358.93 1.69102
|
||||
15 0.725 385.56 1.55536
|
||||
16 0.775 400.38 1.45737
|
||||
17 0.825 431.64 1.29292
|
||||
18 0.875 449.86 1.20792
|
||||
19 0.925 476.09 1.09488
|
||||
20 0.975 491.57 1.03881
|
||||
23000 20 7999.999999999998
|
||||
1 0.025 507.31 1.00367
|
||||
2 0.075 486.4 1.07184
|
||||
3 0.125 473.37 1.13177
|
||||
4 0.175 456.71 1.19923
|
||||
5 0.225 432.3 1.30093
|
||||
6 0.275 397.8 1.44177
|
||||
7 0.325 387.52 1.54053
|
||||
8 0.375 354.6 1.67654
|
||||
9 0.425 327.4 1.8169
|
||||
10 0.475 294.88 1.99021
|
||||
11 0.525 278.73 2.14303
|
||||
12 0.575 293.86 2.04347
|
||||
13 0.625 324.94 1.83323
|
||||
14 0.675 347.61 1.6904
|
||||
15 0.725 381.27 1.52896
|
||||
16 0.775 402.63 1.44314
|
||||
17 0.825 427.36 1.31052
|
||||
18 0.875 455.94 1.20602
|
||||
19 0.925 475.71 1.13512
|
||||
20 0.975 493.66 1.05051
|
||||
24000 20 8000.000000000001
|
||||
1 0.025 504.64 0.985652
|
||||
2 0.075 490.29 1.05237
|
||||
3 0.125 469.12 1.12814
|
||||
4 0.175 451.87 1.21062
|
||||
5 0.225 427.82 1.3163
|
||||
6 0.275 402.9 1.43723
|
||||
7 0.325 379.97 1.53308
|
||||
8 0.375 347.42 1.68004
|
||||
9 0.425 323.13 1.81549
|
||||
10 0.475 308.38 1.97757
|
||||
11 0.525 279.53 2.1819
|
||||
12 0.575 299.62 2.00055
|
||||
13 0.625 324.26 1.87237
|
||||
14 0.675 352.32 1.68098
|
||||
15 0.725 377.34 1.54702
|
||||
16 0.775 409.89 1.43395
|
||||
17 0.825 427.12 1.34268
|
||||
18 0.875 451.75 1.21299
|
||||
19 0.925 474.3 1.11654
|
||||
20 0.975 498.33 1.00615
|
||||
25000 20 8000
|
||||
1 0.025 500.55 0.995351
|
||||
2 0.075 500.94 1.03443
|
||||
3 0.125 472.74 1.11252
|
||||
4 0.175 448.56 1.23702
|
||||
5 0.225 430.06 1.33992
|
||||
6 0.275 404.72 1.4289
|
||||
7 0.325 376.39 1.54933
|
||||
8 0.375 346.24 1.72513
|
||||
9 0.425 325.14 1.8621
|
||||
10 0.475 307.41 1.91707
|
||||
11 0.525 283.66 2.13087
|
||||
12 0.575 295.66 2.01836
|
||||
13 0.625 327.45 1.81425
|
||||
14 0.675 348.78 1.67148
|
||||
15 0.725 373.31 1.54729
|
||||
16 0.775 407.19 1.38813
|
||||
17 0.825 431.85 1.30049
|
||||
18 0.875 451.96 1.22141
|
||||
19 0.925 474.12 1.14478
|
||||
20 0.975 493.27 1.05984
|
||||
26000 20 7999.999999999999
|
||||
1 0.025 505.63 0.98446
|
||||
2 0.075 490.07 1.05745
|
||||
3 0.125 473.96 1.10503
|
||||
4 0.175 451.76 1.23689
|
||||
5 0.225 426.64 1.33683
|
||||
6 0.275 399.3 1.41422
|
||||
7 0.325 377.71 1.55415
|
||||
8 0.375 360.4 1.67301
|
||||
9 0.425 329.27 1.79403
|
||||
10 0.475 298.59 1.96731
|
||||
11 0.525 283.25 2.17472
|
||||
12 0.575 290.71 2.01438
|
||||
13 0.625 324.19 1.81009
|
||||
14 0.675 356.7 1.66344
|
||||
15 0.725 374.74 1.57603
|
||||
16 0.775 409.1 1.41369
|
||||
17 0.825 436.88 1.29343
|
||||
18 0.875 453.95 1.221
|
||||
19 0.925 466.02 1.13892
|
||||
20 0.975 491.13 1.05412
|
||||
27000 20 8000
|
||||
1 0.025 502.1 0.999709
|
||||
2 0.075 493.37 1.05445
|
||||
3 0.125 472.7 1.1232
|
||||
4 0.175 448.57 1.21628
|
||||
5 0.225 426.7 1.2944
|
||||
6 0.275 402.3 1.45418
|
||||
7 0.325 367.76 1.58564
|
||||
8 0.375 357.82 1.63849
|
||||
9 0.425 336.47 1.76532
|
||||
10 0.475 299.71 1.96108
|
||||
11 0.525 269.16 2.23755
|
||||
12 0.575 302.74 1.99101
|
||||
13 0.625 329.06 1.80009
|
||||
14 0.675 356.43 1.67893
|
||||
15 0.725 374.04 1.55009
|
||||
16 0.775 407.47 1.44769
|
||||
17 0.825 432.53 1.32373
|
||||
18 0.875 457.41 1.21077
|
||||
19 0.925 468.51 1.11895
|
||||
20 0.975 495.15 1.04297
|
||||
28000 20 8000
|
||||
1 0.025 504.84 0.98293
|
||||
2 0.075 485.88 1.05845
|
||||
3 0.125 481.77 1.11007
|
||||
4 0.175 456.42 1.22624
|
||||
5 0.225 432.41 1.31579
|
||||
6 0.275 405.09 1.4223
|
||||
7 0.325 380.21 1.57565
|
||||
8 0.375 358.53 1.6386
|
||||
9 0.425 329.4 1.83125
|
||||
10 0.475 296.46 1.98311
|
||||
11 0.525 280.6 2.18681
|
||||
12 0.575 287.99 2.03327
|
||||
13 0.625 322.78 1.85243
|
||||
14 0.675 359.65 1.64226
|
||||
15 0.725 384.02 1.52497
|
||||
16 0.775 401.92 1.43309
|
||||
17 0.825 424.1 1.31983
|
||||
18 0.875 446.85 1.21977
|
||||
19 0.925 472.63 1.13385
|
||||
20 0.975 488.45 1.04385
|
||||
29000 20 8000
|
||||
1 0.025 506.36 0.971786
|
||||
2 0.075 493.53 1.0424
|
||||
3 0.125 471.69 1.1607
|
||||
4 0.175 450.37 1.22636
|
||||
5 0.225 431.21 1.31834
|
||||
6 0.275 403.65 1.42403
|
||||
7 0.325 389.87 1.50238
|
||||
8 0.375 355.31 1.64594
|
||||
9 0.425 321.68 1.80345
|
||||
10 0.475 304.94 1.98561
|
||||
11 0.525 279.44 2.16887
|
||||
12 0.575 288.08 2.02493
|
||||
13 0.625 322.67 1.83038
|
||||
14 0.675 345.44 1.71311
|
||||
15 0.725 391.16 1.53544
|
||||
16 0.775 407.43 1.41437
|
||||
17 0.825 429.64 1.35142
|
||||
18 0.875 446.88 1.22267
|
||||
19 0.925 467.47 1.14261
|
||||
20 0.975 493.18 1.02987
|
||||
30000 20 8000
|
||||
1 0.025 507.97 0.99114
|
||||
2 0.075 495.08 1.0466
|
||||
3 0.125 471.79 1.15132
|
||||
4 0.175 444.24 1.24142
|
||||
5 0.225 428.82 1.29627
|
||||
6 0.275 406.24 1.38487
|
||||
7 0.325 387.22 1.50186
|
||||
8 0.375 354.39 1.64309
|
||||
9 0.425 326.94 1.81843
|
||||
10 0.475 305.16 1.96763
|
||||
11 0.525 279.8 2.17959
|
||||
12 0.575 288.02 2.06379
|
||||
13 0.625 322.99 1.85013
|
||||
14 0.675 355.65 1.66551
|
||||
15 0.725 375.96 1.51994
|
||||
16 0.775 406.48 1.40629
|
||||
17 0.825 425.7 1.32397
|
||||
18 0.875 450.68 1.23442
|
||||
19 0.925 473.54 1.14262
|
||||
20 0.975 493.33 1.06379
|
||||
31000 20 8000
|
||||
1 0.025 504.28 0.973416
|
||||
2 0.075 495.79 1.03358
|
||||
3 0.125 471.55 1.13384
|
||||
4 0.175 451.67 1.22764
|
||||
5 0.225 428.32 1.35323
|
||||
6 0.275 408.27 1.41926
|
||||
7 0.325 385.84 1.5459
|
||||
8 0.375 362.57 1.6383
|
||||
9 0.425 331.63 1.83061
|
||||
10 0.475 295.59 2.00543
|
||||
11 0.525 270.3 2.18229
|
||||
12 0.575 290.38 1.97736
|
||||
13 0.625 324.29 1.81677
|
||||
14 0.675 352.47 1.68734
|
||||
15 0.725 388.33 1.51703
|
||||
16 0.775 398.22 1.43808
|
||||
17 0.825 425.65 1.33351
|
||||
18 0.875 451.69 1.22168
|
||||
19 0.925 470.73 1.14677
|
||||
20 0.975 492.43 1.03862
|
||||
32000 20 8000
|
||||
1 0.025 505.15 0.981622
|
||||
2 0.075 491.86 1.0527
|
||||
3 0.125 477.18 1.11105
|
||||
4 0.175 454.69 1.18908
|
||||
5 0.225 426.81 1.33909
|
||||
6 0.275 403.47 1.43727
|
||||
7 0.325 372.21 1.58336
|
||||
8 0.375 356.15 1.6291
|
||||
9 0.425 335.07 1.74639
|
||||
10 0.475 303.11 1.97158
|
||||
11 0.525 275.23 2.14202
|
||||
12 0.575 295.29 1.99219
|
||||
13 0.625 325.97 1.82239
|
||||
14 0.675 346.94 1.71607
|
||||
15 0.725 383.4 1.55667
|
||||
16 0.775 399.73 1.47679
|
||||
17 0.825 429.81 1.34237
|
||||
18 0.875 451.66 1.2178
|
||||
19 0.925 470.78 1.12779
|
||||
20 0.975 495.49 1.04056
|
||||
33000 20 8000
|
||||
1 0.025 506.3 0.995549
|
||||
2 0.075 495.52 1.03704
|
||||
3 0.125 479.33 1.11577
|
||||
4 0.175 461.59 1.21273
|
||||
5 0.225 425.42 1.35526
|
||||
6 0.275 398.84 1.4736
|
||||
7 0.325 377.54 1.54382
|
||||
8 0.375 354.06 1.64181
|
||||
9 0.425 325 1.79787
|
||||
10 0.475 291.5 1.96186
|
||||
11 0.525 280.25 2.13367
|
||||
12 0.575 293.05 1.98663
|
||||
13 0.625 331.45 1.81891
|
||||
14 0.675 350.9 1.66016
|
||||
15 0.725 380.82 1.56024
|
||||
16 0.775 400.47 1.47654
|
||||
17 0.825 428.15 1.35571
|
||||
18 0.875 454.98 1.23873
|
||||
19 0.925 472.92 1.13425
|
||||
20 0.975 491.91 1.0324
|
||||
34000 20 7999.999999999999
|
||||
1 0.025 503.99 0.973478
|
||||
2 0.075 495.02 1.03836
|
||||
3 0.125 474.47 1.11486
|
||||
4 0.175 447.33 1.1909
|
||||
5 0.225 426.53 1.29123
|
||||
6 0.275 402.41 1.42569
|
||||
7 0.325 380 1.5129
|
||||
8 0.375 360.28 1.65317
|
||||
9 0.425 326.97 1.84957
|
||||
10 0.475 296.32 2.04071
|
||||
11 0.525 282.21 2.15445
|
||||
12 0.575 311.7 1.96688
|
||||
13 0.625 330.92 1.82476
|
||||
14 0.675 352.29 1.69769
|
||||
15 0.725 380.55 1.54897
|
||||
16 0.775 399.21 1.44011
|
||||
17 0.825 423.28 1.29535
|
||||
18 0.875 446.61 1.24278
|
||||
19 0.925 466.44 1.13076
|
||||
20 0.975 493.47 1.04889
|
||||
35000 20 8000
|
||||
1 0.025 509.36 0.98159
|
||||
2 0.075 492.04 1.04473
|
||||
3 0.125 471.66 1.13058
|
||||
4 0.175 454.96 1.22598
|
||||
5 0.225 429.71 1.32158
|
||||
6 0.275 405.22 1.42212
|
||||
7 0.325 386.29 1.49908
|
||||
8 0.375 366.28 1.63568
|
||||
9 0.425 327.3 1.81544
|
||||
10 0.475 300.26 1.95371
|
||||
11 0.525 273.61 2.1394
|
||||
12 0.575 297.94 1.9704
|
||||
13 0.625 330.39 1.79359
|
||||
14 0.675 353.29 1.6494
|
||||
15 0.725 367.97 1.58059
|
||||
16 0.775 399.79 1.42628
|
||||
17 0.825 418.09 1.36531
|
||||
18 0.875 449.67 1.26453
|
||||
19 0.925 474.15 1.14318
|
||||
20 0.975 492.02 1.05355
|
||||
36000 20 8000
|
||||
1 0.025 503.66 0.97284
|
||||
2 0.075 491.48 1.0331
|
||||
3 0.125 466.92 1.14362
|
||||
4 0.175 448.55 1.22102
|
||||
5 0.225 426.43 1.32048
|
||||
6 0.275 409.61 1.40871
|
||||
7 0.325 389.34 1.48166
|
||||
8 0.375 359.81 1.6416
|
||||
9 0.425 330.43 1.7908
|
||||
10 0.475 304.62 1.97214
|
||||
11 0.525 287.37 2.15716
|
||||
12 0.575 301.97 2.00151
|
||||
13 0.625 328.45 1.81346
|
||||
14 0.675 349.7 1.68179
|
||||
15 0.725 378.28 1.54225
|
||||
16 0.775 394.88 1.42134
|
||||
17 0.825 419.4 1.32315
|
||||
18 0.875 448.46 1.21237
|
||||
19 0.925 472.21 1.13442
|
||||
20 0.975 488.43 1.04061
|
||||
37000 20 8000
|
||||
1 0.025 504.77 0.994896
|
||||
2 0.075 501.36 1.02238
|
||||
3 0.125 473.99 1.14728
|
||||
4 0.175 444.9 1.25756
|
||||
5 0.225 422.79 1.36663
|
||||
6 0.275 408.81 1.41777
|
||||
7 0.325 383.13 1.56853
|
||||
8 0.375 354.18 1.66336
|
||||
9 0.425 331.63 1.73954
|
||||
10 0.475 307.94 1.8677
|
||||
11 0.525 276.95 2.09923
|
||||
12 0.575 295.03 1.96608
|
||||
13 0.625 321.16 1.82682
|
||||
14 0.675 356.6 1.62709
|
||||
15 0.725 378.32 1.53219
|
||||
16 0.775 397.1 1.45551
|
||||
17 0.825 428.25 1.32664
|
||||
18 0.875 452.1 1.25633
|
||||
19 0.925 470.96 1.15807
|
||||
20 0.975 490.03 1.07276
|
||||
38000 20 7999.999999999999
|
||||
1 0.025 505.7 0.968918
|
||||
2 0.075 492.16 1.01256
|
||||
3 0.125 479.06 1.11221
|
||||
4 0.175 444.1 1.22833
|
||||
5 0.225 414.54 1.36114
|
||||
6 0.275 396.5 1.45426
|
||||
7 0.325 381.7 1.48405
|
||||
8 0.375 358.58 1.62848
|
||||
9 0.425 334.32 1.75733
|
||||
10 0.475 310.16 1.90008
|
||||
11 0.525 282.67 2.16854
|
||||
12 0.575 298.65 2.08588
|
||||
13 0.625 325.79 1.8458
|
||||
14 0.675 360.49 1.64005
|
||||
15 0.725 379.69 1.59707
|
||||
16 0.775 401.95 1.44507
|
||||
17 0.825 426.88 1.32181
|
||||
18 0.875 447.6 1.2393
|
||||
19 0.925 471.47 1.13648
|
||||
20 0.975 487.99 1.04018
|
||||
39000 20 7999.999999999999
|
||||
1 0.025 507.45 0.982718
|
||||
2 0.075 495.99 1.04627
|
||||
3 0.125 470.64 1.13494
|
||||
4 0.175 446.64 1.24686
|
||||
5 0.225 424.79 1.36084
|
||||
6 0.275 404.62 1.46496
|
||||
7 0.325 387.85 1.5066
|
||||
8 0.375 356.92 1.6585
|
||||
9 0.425 334.06 1.77262
|
||||
10 0.475 300.9 1.92502
|
||||
11 0.525 280.91 2.13194
|
||||
12 0.575 299.51 1.93518
|
||||
13 0.625 320.37 1.82256
|
||||
14 0.675 345.61 1.68324
|
||||
15 0.725 377.54 1.50918
|
||||
16 0.775 403.98 1.43814
|
||||
17 0.825 423.79 1.36107
|
||||
18 0.875 448.09 1.22575
|
||||
19 0.925 475.99 1.13262
|
||||
20 0.975 494.35 1.03704
|
||||
40000 20 8000.000000000002
|
||||
1 0.025 501.38 0.980165
|
||||
2 0.075 490.38 1.04038
|
||||
3 0.125 471.64 1.09321
|
||||
4 0.175 447.15 1.20684
|
||||
5 0.225 424.91 1.33421
|
||||
6 0.275 401.01 1.42752
|
||||
7 0.325 385.38 1.53096
|
||||
8 0.375 359.56 1.63337
|
||||
9 0.425 334.08 1.8033
|
||||
10 0.475 301.54 2.00277
|
||||
11 0.525 281.38 2.15122
|
||||
12 0.575 313.63 1.92646
|
||||
13 0.625 336.61 1.80366
|
||||
14 0.675 351.97 1.71083
|
||||
15 0.725 373.26 1.55935
|
||||
16 0.775 396.46 1.44152
|
||||
17 0.825 418.84 1.34615
|
||||
18 0.875 448.25 1.20745
|
||||
19 0.925 472.84 1.10142
|
||||
20 0.975 489.73 1.02147
|
||||
41000 20 7999.999999999998
|
||||
1 0.025 503.69 0.988203
|
||||
2 0.075 495.79 1.03796
|
||||
3 0.125 477.48 1.14233
|
||||
4 0.175 447.4 1.22538
|
||||
5 0.225 425.93 1.3375
|
||||
6 0.275 399.03 1.44593
|
||||
7 0.325 380.49 1.5076
|
||||
8 0.375 359.01 1.58514
|
||||
9 0.425 332.13 1.73818
|
||||
10 0.475 305.33 1.95216
|
||||
11 0.525 277.49 2.17219
|
||||
12 0.575 297.09 1.92961
|
||||
13 0.625 331.02 1.78649
|
||||
14 0.675 356.51 1.6502
|
||||
15 0.725 373.23 1.56506
|
||||
16 0.775 398.7 1.47281
|
||||
17 0.825 426.53 1.36717
|
||||
18 0.875 452.12 1.24134
|
||||
19 0.925 468.92 1.14014
|
||||
20 0.975 492.11 1.05378
|
||||
File diff suppressed because it is too large
Load Diff
@ -1,423 +0,0 @@
|
||||
# Spatial-averaged data for fix 2 and group all
|
||||
# Timestep Number-of-bins
|
||||
# Bin Coord Ncount v_temp
|
||||
12000 20
|
||||
1 0.025 325.72 1.64967
|
||||
2 0.075 336.14 1.57143
|
||||
3 0.125 351.41 1.49028
|
||||
4 0.175 367.23 1.4008
|
||||
5 0.225 377.25 1.34905
|
||||
6 0.275 393.92 1.28404
|
||||
7 0.325 416.16 1.25562
|
||||
8 0.375 428.61 1.18506
|
||||
9 0.425 449.84 1.15109
|
||||
10 0.475 454.33 1.10504
|
||||
11 0.525 467.94 1.05574
|
||||
12 0.575 453.82 1.09824
|
||||
13 0.625 441.72 1.17681
|
||||
14 0.675 432.8 1.20909
|
||||
15 0.725 420.69 1.26321
|
||||
16 0.775 408.18 1.28995
|
||||
17 0.825 388.16 1.35218
|
||||
18 0.875 380.44 1.40476
|
||||
19 0.925 362.52 1.49131
|
||||
20 0.975 343.12 1.54069
|
||||
13000 20
|
||||
1 0.025 326.93 1.62447
|
||||
2 0.075 328.85 1.59067
|
||||
3 0.125 346.53 1.49534
|
||||
4 0.175 369.58 1.39919
|
||||
5 0.225 381.8 1.37081
|
||||
6 0.275 397.21 1.32621
|
||||
7 0.325 416.63 1.25081
|
||||
8 0.375 435.66 1.20685
|
||||
9 0.425 444.3 1.15261
|
||||
10 0.475 455.21 1.12613
|
||||
11 0.525 469.46 1.06947
|
||||
12 0.575 460.88 1.10122
|
||||
13 0.625 446.13 1.14406
|
||||
14 0.675 431.57 1.17892
|
||||
15 0.725 420.25 1.25139
|
||||
16 0.775 411.92 1.29256
|
||||
17 0.825 393.91 1.3768
|
||||
18 0.875 380.05 1.40528
|
||||
19 0.925 353.51 1.47243
|
||||
20 0.975 329.62 1.58025
|
||||
14000 20
|
||||
1 0.025 315.39 1.62487
|
||||
2 0.075 329.43 1.58213
|
||||
3 0.125 348.35 1.48816
|
||||
4 0.175 373.05 1.41791
|
||||
5 0.225 390.09 1.36277
|
||||
6 0.275 405.06 1.33215
|
||||
7 0.325 425.46 1.24497
|
||||
8 0.375 435.29 1.20194
|
||||
9 0.425 445.06 1.17194
|
||||
10 0.475 459.46 1.11335
|
||||
11 0.525 464.07 1.06615
|
||||
12 0.575 455.49 1.11039
|
||||
13 0.625 443.66 1.12801
|
||||
14 0.675 436.65 1.18062
|
||||
15 0.725 422.64 1.2226
|
||||
16 0.775 406.1 1.29796
|
||||
17 0.825 394.03 1.33208
|
||||
18 0.875 367.95 1.42318
|
||||
19 0.925 353.93 1.50536
|
||||
20 0.975 328.84 1.58079
|
||||
15000 20
|
||||
1 0.025 311.5 1.63113
|
||||
2 0.075 340.21 1.56057
|
||||
3 0.125 355.35 1.48443
|
||||
4 0.175 382.66 1.41121
|
||||
5 0.225 394.26 1.32897
|
||||
6 0.275 400.94 1.28839
|
||||
7 0.325 411.78 1.24902
|
||||
8 0.375 434.87 1.19611
|
||||
9 0.425 446.35 1.13648
|
||||
10 0.475 461.45 1.07446
|
||||
11 0.525 461.34 1.06674
|
||||
12 0.575 459.07 1.10103
|
||||
13 0.625 446.19 1.14572
|
||||
14 0.675 435.97 1.1623
|
||||
15 0.725 422.58 1.23366
|
||||
16 0.775 409.35 1.25602
|
||||
17 0.825 383.41 1.32522
|
||||
18 0.875 363.76 1.38237
|
||||
19 0.925 351.8 1.43596
|
||||
20 0.975 327.16 1.55515
|
||||
16000 20
|
||||
1 0.025 317.06 1.6253
|
||||
2 0.075 332.77 1.5555
|
||||
3 0.125 360.65 1.45467
|
||||
4 0.175 386.55 1.35133
|
||||
5 0.225 396.31 1.33146
|
||||
6 0.275 404.64 1.32491
|
||||
7 0.325 412.63 1.27369
|
||||
8 0.375 436.76 1.17996
|
||||
9 0.425 450.64 1.1196
|
||||
10 0.475 455.68 1.10583
|
||||
11 0.525 458.29 1.05545
|
||||
12 0.575 457.2 1.07045
|
||||
13 0.625 446.7 1.12193
|
||||
14 0.675 430.91 1.17483
|
||||
15 0.725 417.07 1.21866
|
||||
16 0.775 405.2 1.28002
|
||||
17 0.825 391.98 1.30686
|
||||
18 0.875 380.9 1.35056
|
||||
19 0.925 346.54 1.45051
|
||||
20 0.975 311.52 1.61127
|
||||
17000 20
|
||||
1 0.025 322.65 1.59635
|
||||
2 0.075 334.55 1.51093
|
||||
3 0.125 366.63 1.43268
|
||||
4 0.175 376.34 1.37509
|
||||
5 0.225 385.74 1.32906
|
||||
6 0.275 407.31 1.28187
|
||||
7 0.325 412.93 1.24268
|
||||
8 0.375 427.54 1.18816
|
||||
9 0.425 443.8 1.13546
|
||||
10 0.475 468.4 1.09447
|
||||
11 0.525 461.55 1.06145
|
||||
12 0.575 452.26 1.08333
|
||||
13 0.625 445.05 1.12301
|
||||
14 0.675 431.68 1.15201
|
||||
15 0.725 420.66 1.20679
|
||||
16 0.775 398.93 1.27609
|
||||
17 0.825 380.75 1.33594
|
||||
18 0.875 385.16 1.35078
|
||||
19 0.925 352.25 1.44493
|
||||
20 0.975 325.82 1.55642
|
||||
18000 20
|
||||
1 0.025 311.29 1.67434
|
||||
2 0.075 336.43 1.52801
|
||||
3 0.125 357.54 1.48577
|
||||
4 0.175 375.81 1.3984
|
||||
5 0.225 385.52 1.3574
|
||||
6 0.275 404.85 1.2797
|
||||
7 0.325 420.67 1.21478
|
||||
8 0.375 434.84 1.15935
|
||||
9 0.425 438.74 1.11868
|
||||
10 0.475 450.87 1.10732
|
||||
11 0.525 456.93 1.0503
|
||||
12 0.575 454.31 1.08751
|
||||
13 0.625 447.68 1.13485
|
||||
14 0.675 433.48 1.1882
|
||||
15 0.725 425.3 1.2486
|
||||
16 0.775 405.55 1.29208
|
||||
17 0.825 387.18 1.34142
|
||||
18 0.875 369.97 1.37561
|
||||
19 0.925 358.64 1.47414
|
||||
20 0.975 344.4 1.53819
|
||||
19000 20
|
||||
1 0.025 324.37 1.58311
|
||||
2 0.075 337.6 1.51044
|
||||
3 0.125 357.95 1.44619
|
||||
4 0.175 361.06 1.4015
|
||||
5 0.225 382.24 1.34526
|
||||
6 0.275 401.55 1.29526
|
||||
7 0.325 421.25 1.24305
|
||||
8 0.375 432.6 1.18384
|
||||
9 0.425 447.98 1.13928
|
||||
10 0.475 462.78 1.09575
|
||||
11 0.525 466.42 1.0576
|
||||
12 0.575 460.93 1.09741
|
||||
13 0.625 448 1.14828
|
||||
14 0.675 434.07 1.19009
|
||||
15 0.725 421.12 1.23345
|
||||
16 0.775 399.99 1.31268
|
||||
17 0.825 383.47 1.33878
|
||||
18 0.875 361.46 1.42117
|
||||
19 0.925 354.9 1.47103
|
||||
20 0.975 340.26 1.50858
|
||||
20000 20
|
||||
1 0.025 313.72 1.6487
|
||||
2 0.075 336.75 1.52299
|
||||
3 0.125 353.35 1.4565
|
||||
4 0.175 378.45 1.36805
|
||||
5 0.225 390.44 1.36083
|
||||
6 0.275 398.78 1.34945
|
||||
7 0.325 406.73 1.25621
|
||||
8 0.375 430.41 1.20402
|
||||
9 0.425 449.75 1.13024
|
||||
10 0.475 460 1.08389
|
||||
11 0.525 470.27 1.03254
|
||||
12 0.575 461.44 1.08428
|
||||
13 0.625 446.79 1.13334
|
||||
14 0.675 425.82 1.17642
|
||||
15 0.725 412.13 1.2395
|
||||
16 0.775 408.79 1.31104
|
||||
17 0.825 387.5 1.37126
|
||||
18 0.875 365.82 1.45392
|
||||
19 0.925 359.15 1.44959
|
||||
20 0.975 343.91 1.52986
|
||||
21000 20
|
||||
1 0.025 320.25 1.6191
|
||||
2 0.075 336.13 1.5036
|
||||
3 0.125 356.61 1.50164
|
||||
4 0.175 368.32 1.38292
|
||||
5 0.225 386.26 1.33927
|
||||
6 0.275 401.16 1.34834
|
||||
7 0.325 414.64 1.28787
|
||||
8 0.375 425.83 1.22321
|
||||
9 0.425 450.17 1.13796
|
||||
10 0.475 464.68 1.0782
|
||||
11 0.525 478.24 1.04231
|
||||
12 0.575 461.9 1.07149
|
||||
13 0.625 448.18 1.13139
|
||||
14 0.675 428.79 1.2153
|
||||
15 0.725 413.97 1.24794
|
||||
16 0.775 394.45 1.30746
|
||||
17 0.825 386.11 1.35095
|
||||
18 0.875 375.14 1.37882
|
||||
19 0.925 357.28 1.45878
|
||||
20 0.975 331.89 1.52785
|
||||
22000 20
|
||||
1 0.025 320.37 1.62992
|
||||
2 0.075 333.02 1.55128
|
||||
3 0.125 344.37 1.44442
|
||||
4 0.175 366.15 1.38662
|
||||
5 0.225 380.29 1.36242
|
||||
6 0.275 397.18 1.30156
|
||||
7 0.325 423.48 1.22345
|
||||
8 0.375 438.63 1.16675
|
||||
9 0.425 433.24 1.16884
|
||||
10 0.475 455.79 1.07352
|
||||
11 0.525 475.95 1.03163
|
||||
12 0.575 464.5 1.08064
|
||||
13 0.625 446.7 1.14632
|
||||
14 0.675 438.63 1.18898
|
||||
15 0.725 422.72 1.23815
|
||||
16 0.775 405.99 1.31619
|
||||
17 0.825 379.47 1.40815
|
||||
18 0.875 368 1.43814
|
||||
19 0.925 364.13 1.48984
|
||||
20 0.975 341.39 1.59912
|
||||
23000 20
|
||||
1 0.025 325.44 1.60244
|
||||
2 0.075 335.36 1.55857
|
||||
3 0.125 345.55 1.49968
|
||||
4 0.175 357.83 1.47404
|
||||
5 0.225 390.25 1.39591
|
||||
6 0.275 415.92 1.2887
|
||||
7 0.325 421.66 1.24595
|
||||
8 0.375 433.91 1.17563
|
||||
9 0.425 447.52 1.14089
|
||||
10 0.475 468.95 1.06559
|
||||
11 0.525 478.79 1.04163
|
||||
12 0.575 464.42 1.1004
|
||||
13 0.625 450.97 1.15181
|
||||
14 0.675 434.72 1.18376
|
||||
15 0.725 416.63 1.25514
|
||||
16 0.775 394.6 1.29624
|
||||
17 0.825 376.66 1.3826
|
||||
18 0.875 366.76 1.38565
|
||||
19 0.925 346.71 1.49467
|
||||
20 0.975 327.35 1.58476
|
||||
24000 20
|
||||
1 0.025 330.21 1.606
|
||||
2 0.075 333.3 1.59105
|
||||
3 0.125 351.29 1.47358
|
||||
4 0.175 364.89 1.41907
|
||||
5 0.225 382.78 1.35585
|
||||
6 0.275 410.56 1.25973
|
||||
7 0.325 420.32 1.23086
|
||||
8 0.375 432.54 1.17746
|
||||
9 0.425 449.32 1.1115
|
||||
10 0.475 462.75 1.05462
|
||||
11 0.525 469.36 1.05271
|
||||
12 0.575 466.72 1.05664
|
||||
13 0.625 456.66 1.1164
|
||||
14 0.675 434.41 1.20663
|
||||
15 0.725 415.75 1.25433
|
||||
16 0.775 397.42 1.32091
|
||||
17 0.825 379.97 1.39402
|
||||
18 0.875 370.84 1.41237
|
||||
19 0.925 346.42 1.49635
|
||||
20 0.975 324.49 1.59137
|
||||
25000 20
|
||||
1 0.025 318.4 1.62872
|
||||
2 0.075 328.59 1.57486
|
||||
3 0.125 351.33 1.47595
|
||||
4 0.175 371.95 1.41797
|
||||
5 0.225 391.28 1.36043
|
||||
6 0.275 403.08 1.28398
|
||||
7 0.325 419.93 1.20229
|
||||
8 0.375 437.64 1.17621
|
||||
9 0.425 447.94 1.12521
|
||||
10 0.475 464.74 1.08712
|
||||
11 0.525 469.5 1.05418
|
||||
12 0.575 458.54 1.08099
|
||||
13 0.625 442.02 1.13498
|
||||
14 0.675 433.2 1.18596
|
||||
15 0.725 419.23 1.23539
|
||||
16 0.775 397.05 1.32264
|
||||
17 0.825 385.88 1.35514
|
||||
18 0.875 375.73 1.38265
|
||||
19 0.925 349.77 1.51549
|
||||
20 0.975 334.2 1.57718
|
||||
26000 20
|
||||
1 0.025 307.76 1.61816
|
||||
2 0.075 335.86 1.53527
|
||||
3 0.125 349.95 1.50998
|
||||
4 0.175 376.36 1.40133
|
||||
5 0.225 394.11 1.33504
|
||||
6 0.275 407.91 1.26943
|
||||
7 0.325 425.05 1.21677
|
||||
8 0.375 435.63 1.17553
|
||||
9 0.425 448.78 1.11418
|
||||
10 0.475 463.5 1.07816
|
||||
11 0.525 470.27 1.05075
|
||||
12 0.575 460.47 1.07669
|
||||
13 0.625 437.9 1.14479
|
||||
14 0.675 431.91 1.18037
|
||||
15 0.725 414.22 1.25406
|
||||
16 0.775 402 1.2881
|
||||
17 0.825 391.85 1.35238
|
||||
18 0.875 360.6 1.41575
|
||||
19 0.925 347.03 1.46573
|
||||
20 0.975 338.84 1.52199
|
||||
27000 20
|
||||
1 0.025 319.27 1.62165
|
||||
2 0.075 331.03 1.54185
|
||||
3 0.125 358.09 1.45185
|
||||
4 0.175 378.55 1.35791
|
||||
5 0.225 398.82 1.30363
|
||||
6 0.275 407.08 1.26087
|
||||
7 0.325 422.56 1.20838
|
||||
8 0.375 430.66 1.16356
|
||||
9 0.425 451.49 1.10503
|
||||
10 0.475 462.83 1.06674
|
||||
11 0.525 463.99 1.05389
|
||||
12 0.575 451.29 1.08789
|
||||
13 0.625 445.63 1.1482
|
||||
14 0.675 425.44 1.1947
|
||||
15 0.725 419.86 1.24214
|
||||
16 0.775 403.68 1.30287
|
||||
17 0.825 387.88 1.33637
|
||||
18 0.875 373.51 1.38336
|
||||
19 0.925 342.96 1.45443
|
||||
20 0.975 325.38 1.54167
|
||||
28000 20
|
||||
1 0.025 317.13 1.65552
|
||||
2 0.075 334.94 1.52515
|
||||
3 0.125 355.63 1.42914
|
||||
4 0.175 384.57 1.30534
|
||||
5 0.225 398.73 1.31776
|
||||
6 0.275 408.42 1.20798
|
||||
7 0.325 418.97 1.20015
|
||||
8 0.375 433.01 1.15746
|
||||
9 0.425 448.54 1.13361
|
||||
10 0.475 457.08 1.08417
|
||||
11 0.525 459.47 1.04915
|
||||
12 0.575 451.96 1.11723
|
||||
13 0.625 441.42 1.14282
|
||||
14 0.675 433.27 1.19591
|
||||
15 0.725 421.95 1.22752
|
||||
16 0.775 402.02 1.28563
|
||||
17 0.825 377.29 1.37178
|
||||
18 0.875 367.18 1.42641
|
||||
19 0.925 348.88 1.46729
|
||||
20 0.975 339.54 1.56004
|
||||
29000 20
|
||||
1 0.025 315.2 1.59355
|
||||
2 0.075 340.85 1.52259
|
||||
3 0.125 365.44 1.47495
|
||||
4 0.175 383.47 1.36231
|
||||
5 0.225 404.02 1.30424
|
||||
6 0.275 421.45 1.22747
|
||||
7 0.325 422.98 1.23362
|
||||
8 0.375 432.41 1.18915
|
||||
9 0.425 444.49 1.12834
|
||||
10 0.475 456.55 1.11099
|
||||
11 0.525 456.36 1.07884
|
||||
12 0.575 456.87 1.11769
|
||||
13 0.625 449.47 1.13001
|
||||
14 0.675 433.42 1.17867
|
||||
15 0.725 417.92 1.22338
|
||||
16 0.775 396.21 1.29975
|
||||
17 0.825 374.77 1.35437
|
||||
18 0.875 369.46 1.40491
|
||||
19 0.925 345.34 1.4422
|
||||
20 0.975 313.32 1.59329
|
||||
30000 20
|
||||
1 0.025 324.48 1.62185
|
||||
2 0.075 335.84 1.52267
|
||||
3 0.125 360.22 1.41331
|
||||
4 0.175 385.34 1.31177
|
||||
5 0.225 393.42 1.30704
|
||||
6 0.275 415.26 1.24766
|
||||
7 0.325 427.87 1.218
|
||||
8 0.375 433.34 1.18322
|
||||
9 0.425 441.77 1.12999
|
||||
10 0.475 455.06 1.07443
|
||||
11 0.525 465.81 1.04844
|
||||
12 0.575 454.41 1.08694
|
||||
13 0.625 444.04 1.15679
|
||||
14 0.675 432.36 1.18503
|
||||
15 0.725 422.91 1.22934
|
||||
16 0.775 391.34 1.31983
|
||||
17 0.825 384.3 1.37946
|
||||
18 0.875 369.77 1.40996
|
||||
19 0.925 340.76 1.47343
|
||||
20 0.975 321.7 1.53491
|
||||
31000 20
|
||||
1 0.025 312.63 1.61684
|
||||
2 0.075 332.75 1.51557
|
||||
3 0.125 365.72 1.4045
|
||||
4 0.175 391.06 1.34269
|
||||
5 0.225 401.07 1.28523
|
||||
6 0.275 401.64 1.26224
|
||||
7 0.325 421.37 1.24702
|
||||
8 0.375 438.98 1.18125
|
||||
9 0.425 448.02 1.13722
|
||||
10 0.475 461.03 1.101
|
||||
11 0.525 473.07 1.04227
|
||||
12 0.575 457.88 1.07795
|
||||
13 0.625 446.31 1.14042
|
||||
14 0.675 433.75 1.16932
|
||||
15 0.725 410.41 1.25175
|
||||
16 0.775 389.58 1.29215
|
||||
17 0.825 377.56 1.35425
|
||||
18 0.875 360.08 1.42641
|
||||
19 0.925 347.69 1.47437
|
||||
20 0.975 329.4 1.5529
|
||||
@ -1,843 +0,0 @@
|
||||
# Spatial-averaged data for fix 2 and group all
|
||||
# Timestep Number-of-bins
|
||||
# Bin Coord Ncount v_temp
|
||||
2000 20
|
||||
1 0.025 408.19 1.23094
|
||||
2 0.075 408.64 1.28547
|
||||
3 0.125 402.61 1.31096
|
||||
4 0.175 399.07 1.34667
|
||||
5 0.225 401.91 1.3233
|
||||
6 0.275 407.13 1.30466
|
||||
7 0.325 402.81 1.33426
|
||||
8 0.375 398.84 1.39823
|
||||
9 0.425 403.7 1.38538
|
||||
10 0.475 394.63 1.40398
|
||||
11 0.525 379.14 1.49064
|
||||
12 0.575 388.25 1.42761
|
||||
13 0.625 397.15 1.40794
|
||||
14 0.675 397.51 1.38329
|
||||
15 0.725 405.96 1.3403
|
||||
16 0.775 402 1.34272
|
||||
17 0.825 399.95 1.35834
|
||||
18 0.875 397.38 1.33209
|
||||
19 0.925 397.59 1.32846
|
||||
20 0.975 407.54 1.29748
|
||||
3000 20
|
||||
1 0.025 439.11 1.18126
|
||||
2 0.075 431.31 1.23972
|
||||
3 0.125 415.45 1.33353
|
||||
4 0.175 410.98 1.33609
|
||||
5 0.225 410.85 1.33499
|
||||
6 0.275 402.98 1.36129
|
||||
7 0.325 402.98 1.35413
|
||||
8 0.375 396 1.40962
|
||||
9 0.425 388.02 1.4152
|
||||
10 0.475 364.5 1.48249
|
||||
11 0.525 349.37 1.5884
|
||||
12 0.575 363.96 1.51626
|
||||
13 0.625 374.78 1.44185
|
||||
14 0.675 374.66 1.39171
|
||||
15 0.725 397.21 1.33262
|
||||
16 0.775 408.14 1.3466
|
||||
17 0.825 405.26 1.32541
|
||||
18 0.875 417.88 1.29207
|
||||
19 0.925 420.74 1.30128
|
||||
20 0.975 425.82 1.26506
|
||||
4000 20
|
||||
1 0.025 458.1 1.11989
|
||||
2 0.075 442.59 1.19037
|
||||
3 0.125 421.91 1.2786
|
||||
4 0.175 413.54 1.30989
|
||||
5 0.225 421.66 1.30544
|
||||
6 0.275 405.34 1.33082
|
||||
7 0.325 390.98 1.37382
|
||||
8 0.375 381.29 1.39754
|
||||
9 0.425 371.63 1.46937
|
||||
10 0.475 349.14 1.60137
|
||||
11 0.525 321.19 1.75166
|
||||
12 0.575 351.69 1.5907
|
||||
13 0.625 376.09 1.51591
|
||||
14 0.675 382.84 1.46283
|
||||
15 0.725 398.02 1.39733
|
||||
16 0.775 405.73 1.36226
|
||||
17 0.825 414.41 1.32542
|
||||
18 0.875 418.58 1.29152
|
||||
19 0.925 430.96 1.24851
|
||||
20 0.975 444.31 1.19226
|
||||
5000 20
|
||||
1 0.025 464.38 1.11971
|
||||
2 0.075 449.49 1.17582
|
||||
3 0.125 437.54 1.24449
|
||||
4 0.175 432.27 1.26161
|
||||
5 0.225 414.51 1.34413
|
||||
6 0.275 403.81 1.39217
|
||||
7 0.325 400.68 1.38781
|
||||
8 0.375 381.32 1.48424
|
||||
9 0.425 366.54 1.55976
|
||||
10 0.475 339.84 1.65015
|
||||
11 0.525 314.87 1.80832
|
||||
12 0.575 335.17 1.66079
|
||||
13 0.625 354.15 1.52298
|
||||
14 0.675 373.09 1.47285
|
||||
15 0.725 388.27 1.40274
|
||||
16 0.775 402.75 1.35614
|
||||
17 0.825 416.77 1.27844
|
||||
18 0.875 426.65 1.28447
|
||||
19 0.925 437.37 1.21971
|
||||
20 0.975 460.53 1.16891
|
||||
6000 20
|
||||
1 0.025 477.79 1.07138
|
||||
2 0.075 463.61 1.14115
|
||||
3 0.125 442.69 1.21507
|
||||
4 0.175 430.3 1.26827
|
||||
5 0.225 420.24 1.30748
|
||||
6 0.275 399.59 1.38073
|
||||
7 0.325 398.29 1.42137
|
||||
8 0.375 382.27 1.46754
|
||||
9 0.425 355.24 1.59727
|
||||
10 0.475 326.88 1.74182
|
||||
11 0.525 310.62 1.89724
|
||||
12 0.575 316.85 1.76669
|
||||
13 0.625 342.76 1.64659
|
||||
14 0.675 369.14 1.53832
|
||||
15 0.725 388.27 1.44001
|
||||
16 0.775 406.82 1.37819
|
||||
17 0.825 422.25 1.33123
|
||||
18 0.875 435.95 1.26146
|
||||
19 0.925 449.93 1.19376
|
||||
20 0.975 460.51 1.13057
|
||||
7000 20
|
||||
1 0.025 488.18 1.0373
|
||||
2 0.075 470.37 1.10519
|
||||
3 0.125 443.36 1.20722
|
||||
4 0.175 435.37 1.26553
|
||||
5 0.225 426.31 1.31093
|
||||
6 0.275 405.18 1.43091
|
||||
7 0.325 387.67 1.45743
|
||||
8 0.375 379.81 1.49047
|
||||
9 0.425 352.41 1.61721
|
||||
10 0.475 315.06 1.77476
|
||||
11 0.525 302.37 1.94483
|
||||
12 0.575 307.9 1.88394
|
||||
13 0.625 338.8 1.6864
|
||||
14 0.675 366.12 1.57193
|
||||
15 0.725 381.74 1.45382
|
||||
16 0.775 403.74 1.39846
|
||||
17 0.825 429.37 1.31364
|
||||
18 0.875 443.37 1.22401
|
||||
19 0.925 450.8 1.21206
|
||||
20 0.975 472.07 1.09677
|
||||
8000 20
|
||||
1 0.025 490.53 1.03918
|
||||
2 0.075 475.5 1.09852
|
||||
3 0.125 450.53 1.20924
|
||||
4 0.175 440.45 1.26306
|
||||
5 0.225 424.99 1.32063
|
||||
6 0.275 416.4 1.37795
|
||||
7 0.325 392.71 1.45664
|
||||
8 0.375 369.57 1.55868
|
||||
9 0.425 340.58 1.69566
|
||||
10 0.475 310.51 1.82773
|
||||
11 0.525 290.63 2.03311
|
||||
12 0.575 303.08 1.86013
|
||||
13 0.625 338.35 1.67357
|
||||
14 0.675 365.2 1.57201
|
||||
15 0.725 385.64 1.47216
|
||||
16 0.775 408.61 1.36367
|
||||
17 0.825 426.01 1.32799
|
||||
18 0.875 435.64 1.27383
|
||||
19 0.925 459.04 1.18076
|
||||
20 0.975 476.03 1.09128
|
||||
9000 20
|
||||
1 0.025 493.66 1.01785
|
||||
2 0.075 475.36 1.09064
|
||||
3 0.125 456.41 1.17998
|
||||
4 0.175 438.35 1.24876
|
||||
5 0.225 425.48 1.32749
|
||||
6 0.275 408.77 1.39366
|
||||
7 0.325 391.89 1.49337
|
||||
8 0.375 367.99 1.5315
|
||||
9 0.425 342.16 1.66355
|
||||
10 0.475 308.44 1.85595
|
||||
11 0.525 289.5 2.1012
|
||||
12 0.575 310.94 1.86623
|
||||
13 0.625 330.85 1.74731
|
||||
14 0.675 352.26 1.61026
|
||||
15 0.725 387.52 1.49891
|
||||
16 0.775 412.22 1.41324
|
||||
17 0.825 423 1.32256
|
||||
18 0.875 440.12 1.24547
|
||||
19 0.925 461.13 1.14324
|
||||
20 0.975 483.95 1.06894
|
||||
10000 20
|
||||
1 0.025 493.44 1.00485
|
||||
2 0.075 479.96 1.08166
|
||||
3 0.125 458.49 1.17006
|
||||
4 0.175 439.98 1.27607
|
||||
5 0.225 425.46 1.32928
|
||||
6 0.275 405.36 1.41098
|
||||
7 0.325 394.95 1.47586
|
||||
8 0.375 366.38 1.61175
|
||||
9 0.425 344.7 1.66117
|
||||
10 0.475 308.49 1.88533
|
||||
11 0.525 288.96 2.0408
|
||||
12 0.575 303.38 1.9296
|
||||
13 0.625 324.75 1.77887
|
||||
14 0.675 346.84 1.70411
|
||||
15 0.725 374.03 1.53935
|
||||
16 0.775 398.67 1.43526
|
||||
17 0.825 429.68 1.3243
|
||||
18 0.875 451.59 1.22954
|
||||
19 0.925 476.04 1.12003
|
||||
20 0.975 488.85 1.04248
|
||||
11000 20
|
||||
1 0.025 500.02 0.997544
|
||||
2 0.075 485.51 1.04291
|
||||
3 0.125 460.78 1.17538
|
||||
4 0.175 443.12 1.25016
|
||||
5 0.225 425.44 1.32948
|
||||
6 0.275 404.7 1.40602
|
||||
7 0.325 384.58 1.49241
|
||||
8 0.375 362.42 1.605
|
||||
9 0.425 344.94 1.68023
|
||||
10 0.475 310.53 1.86199
|
||||
11 0.525 289.61 2.04817
|
||||
12 0.575 309.18 1.91119
|
||||
13 0.625 323.92 1.78764
|
||||
14 0.675 340.12 1.71022
|
||||
15 0.725 372.38 1.54664
|
||||
16 0.775 402.53 1.42487
|
||||
17 0.825 425.82 1.36593
|
||||
18 0.875 456.39 1.21746
|
||||
19 0.925 474.16 1.14909
|
||||
20 0.975 483.85 1.07061
|
||||
12000 20
|
||||
1 0.025 499.8 0.994909
|
||||
2 0.075 482.54 1.07207
|
||||
3 0.125 467.01 1.13936
|
||||
4 0.175 452.48 1.20563
|
||||
5 0.225 419.33 1.31739
|
||||
6 0.275 408.57 1.41738
|
||||
7 0.325 384.74 1.53218
|
||||
8 0.375 359.77 1.64898
|
||||
9 0.425 339.04 1.7564
|
||||
10 0.475 308.53 1.92345
|
||||
11 0.525 287.81 2.09824
|
||||
12 0.575 304.68 1.90702
|
||||
13 0.625 333.35 1.79157
|
||||
14 0.675 351.59 1.6893
|
||||
15 0.725 371.57 1.5772
|
||||
16 0.775 400.64 1.41488
|
||||
17 0.825 420.33 1.31099
|
||||
18 0.875 451.4 1.19304
|
||||
19 0.925 471.69 1.12948
|
||||
20 0.975 485.13 1.04746
|
||||
13000 20
|
||||
1 0.025 503.64 0.988261
|
||||
2 0.075 486.85 1.08391
|
||||
3 0.125 469.73 1.16146
|
||||
4 0.175 449.92 1.24118
|
||||
5 0.225 428.54 1.30744
|
||||
6 0.275 401 1.41827
|
||||
7 0.325 384.38 1.51763
|
||||
8 0.375 364.15 1.61539
|
||||
9 0.425 331.98 1.73066
|
||||
10 0.475 288.81 1.98365
|
||||
11 0.525 281.05 2.13748
|
||||
12 0.575 306.84 1.93487
|
||||
13 0.625 326.66 1.78932
|
||||
14 0.675 354.97 1.64836
|
||||
15 0.725 382.45 1.53741
|
||||
16 0.775 398.66 1.44439
|
||||
17 0.825 430.19 1.33042
|
||||
18 0.875 449.92 1.24153
|
||||
19 0.925 466.29 1.14799
|
||||
20 0.975 493.97 1.05127
|
||||
14000 20
|
||||
1 0.025 499.93 1.00299
|
||||
2 0.075 479.91 1.07624
|
||||
3 0.125 462.66 1.14654
|
||||
4 0.175 449.59 1.22449
|
||||
5 0.225 432.47 1.29814
|
||||
6 0.275 408.89 1.40939
|
||||
7 0.325 386.97 1.53853
|
||||
8 0.375 362.35 1.64813
|
||||
9 0.425 326.71 1.80818
|
||||
10 0.475 298.56 1.96655
|
||||
11 0.525 290.36 2.11313
|
||||
12 0.575 301.66 1.92621
|
||||
13 0.625 321.81 1.81123
|
||||
14 0.675 357.27 1.62549
|
||||
15 0.725 387.22 1.47994
|
||||
16 0.775 405.63 1.41
|
||||
17 0.825 424.92 1.32186
|
||||
18 0.875 444.21 1.23098
|
||||
19 0.925 472.25 1.15027
|
||||
20 0.975 486.63 1.04785
|
||||
15000 20
|
||||
1 0.025 497.49 1.01549
|
||||
2 0.075 487.97 1.07637
|
||||
3 0.125 469.45 1.14977
|
||||
4 0.175 453.19 1.2139
|
||||
5 0.225 428.71 1.29414
|
||||
6 0.275 396.96 1.4388
|
||||
7 0.325 380.03 1.5423
|
||||
8 0.375 360.6 1.60763
|
||||
9 0.425 328.13 1.79466
|
||||
10 0.475 311.21 1.9536
|
||||
11 0.525 274.64 2.13181
|
||||
12 0.575 293.97 1.96884
|
||||
13 0.625 328.7 1.81525
|
||||
14 0.675 357.56 1.64437
|
||||
15 0.725 388.69 1.50419
|
||||
16 0.775 403.67 1.4075
|
||||
17 0.825 432.44 1.29696
|
||||
18 0.875 446.86 1.23334
|
||||
19 0.925 469.06 1.1332
|
||||
20 0.975 490.67 1.06647
|
||||
16000 20
|
||||
1 0.025 496.54 0.992081
|
||||
2 0.075 483.37 1.05866
|
||||
3 0.125 468.02 1.15093
|
||||
4 0.175 450.02 1.18863
|
||||
5 0.225 429.07 1.32678
|
||||
6 0.275 400.75 1.40981
|
||||
7 0.325 386.33 1.51788
|
||||
8 0.375 357.57 1.60733
|
||||
9 0.425 330.81 1.78059
|
||||
10 0.475 304.98 1.99669
|
||||
11 0.525 277.98 2.21199
|
||||
12 0.575 298.05 2.00225
|
||||
13 0.625 325.8 1.82348
|
||||
14 0.675 355.79 1.659
|
||||
15 0.725 381.78 1.54841
|
||||
16 0.775 410.24 1.40353
|
||||
17 0.825 431.79 1.29682
|
||||
18 0.875 451.6 1.2255
|
||||
19 0.925 467.48 1.13627
|
||||
20 0.975 492.03 1.04517
|
||||
17000 20
|
||||
1 0.025 498.68 0.99871
|
||||
2 0.075 489.48 1.06155
|
||||
3 0.125 465.54 1.14933
|
||||
4 0.175 450.46 1.20878
|
||||
5 0.225 431.05 1.30516
|
||||
6 0.275 411.99 1.39266
|
||||
7 0.325 389.18 1.50508
|
||||
8 0.375 354.93 1.66282
|
||||
9 0.425 324.57 1.78592
|
||||
10 0.475 305.75 1.92511
|
||||
11 0.525 274.68 2.17876
|
||||
12 0.575 306.54 1.93387
|
||||
13 0.625 324.93 1.85355
|
||||
14 0.675 344.03 1.67816
|
||||
15 0.725 374.88 1.58249
|
||||
16 0.775 402.75 1.43992
|
||||
17 0.825 433.68 1.34283
|
||||
18 0.875 454.71 1.19427
|
||||
19 0.925 477.27 1.1262
|
||||
20 0.975 484.9 1.05365
|
||||
18000 20
|
||||
1 0.025 502.14 0.994111
|
||||
2 0.075 489.46 1.05234
|
||||
3 0.125 471.8 1.14019
|
||||
4 0.175 454.04 1.20163
|
||||
5 0.225 435.14 1.31679
|
||||
6 0.275 416.94 1.38216
|
||||
7 0.325 383.19 1.51772
|
||||
8 0.375 350.99 1.66337
|
||||
9 0.425 325.97 1.88725
|
||||
10 0.475 294.08 2.00371
|
||||
11 0.525 275.54 2.15248
|
||||
12 0.575 297.02 1.9867
|
||||
13 0.625 329.65 1.81588
|
||||
14 0.675 362.09 1.63016
|
||||
15 0.725 374.31 1.55182
|
||||
16 0.775 401.51 1.44582
|
||||
17 0.825 419.39 1.34122
|
||||
18 0.875 453.42 1.2206
|
||||
19 0.925 471.25 1.12867
|
||||
20 0.975 492.07 1.04354
|
||||
19000 20
|
||||
1 0.025 502.42 1.00164
|
||||
2 0.075 490.82 1.03559
|
||||
3 0.125 468.58 1.15264
|
||||
4 0.175 454.05 1.1984
|
||||
5 0.225 430.32 1.3128
|
||||
6 0.275 408.35 1.42214
|
||||
7 0.325 396.84 1.48762
|
||||
8 0.375 354.85 1.67448
|
||||
9 0.425 322.83 1.87735
|
||||
10 0.475 292.12 2.05836
|
||||
11 0.525 274.86 2.18629
|
||||
12 0.575 299.61 2.03723
|
||||
13 0.625 329.49 1.74092
|
||||
14 0.675 361.01 1.67602
|
||||
15 0.725 374.55 1.53803
|
||||
16 0.775 402.15 1.43119
|
||||
17 0.825 425.17 1.31141
|
||||
18 0.875 447.47 1.22989
|
||||
19 0.925 475.27 1.12274
|
||||
20 0.975 489.24 1.04129
|
||||
20000 20
|
||||
1 0.025 507.05 0.985636
|
||||
2 0.075 489.46 1.06482
|
||||
3 0.125 471.71 1.14289
|
||||
4 0.175 450.37 1.21487
|
||||
5 0.225 430.1 1.31104
|
||||
6 0.275 408.7 1.40935
|
||||
7 0.325 382.5 1.52176
|
||||
8 0.375 360.55 1.64968
|
||||
9 0.425 318.34 1.81665
|
||||
10 0.475 302.49 1.98709
|
||||
11 0.525 274.86 2.26875
|
||||
12 0.575 301.61 1.97991
|
||||
13 0.625 320.77 1.7889
|
||||
14 0.675 353.45 1.6694
|
||||
15 0.725 376.95 1.53918
|
||||
16 0.775 402.52 1.42965
|
||||
17 0.825 434.71 1.30078
|
||||
18 0.875 446.64 1.22872
|
||||
19 0.925 476.11 1.1357
|
||||
20 0.975 491.11 1.0545
|
||||
21000 20
|
||||
1 0.025 502.02 0.996975
|
||||
2 0.075 500 1.04008
|
||||
3 0.125 465.52 1.1527
|
||||
4 0.175 451.21 1.22241
|
||||
5 0.225 431.92 1.30438
|
||||
6 0.275 404.35 1.41696
|
||||
7 0.325 380.56 1.50702
|
||||
8 0.375 349.03 1.67654
|
||||
9 0.425 327.74 1.80477
|
||||
10 0.475 298.95 1.97771
|
||||
11 0.525 273.09 2.1449
|
||||
12 0.575 296.31 2.01143
|
||||
13 0.625 324.33 1.82373
|
||||
14 0.675 357.97 1.67534
|
||||
15 0.725 382.27 1.55158
|
||||
16 0.775 404.18 1.45029
|
||||
17 0.825 430.88 1.3346
|
||||
18 0.875 452.25 1.21963
|
||||
19 0.925 476.52 1.12056
|
||||
20 0.975 490.9 1.06242
|
||||
22000 20
|
||||
1 0.025 505.75 0.995055
|
||||
2 0.075 489.26 1.05466
|
||||
3 0.125 464.65 1.13693
|
||||
4 0.175 452.39 1.22259
|
||||
5 0.225 430.5 1.28915
|
||||
6 0.275 407.1 1.39622
|
||||
7 0.325 380.42 1.52274
|
||||
8 0.375 349.8 1.68785
|
||||
9 0.425 324.54 1.84631
|
||||
10 0.475 308.14 1.96006
|
||||
11 0.525 283.84 2.18714
|
||||
12 0.575 299.17 1.96998
|
||||
13 0.625 327.48 1.82272
|
||||
14 0.675 353.31 1.66948
|
||||
15 0.725 377.83 1.56207
|
||||
16 0.775 394.04 1.42083
|
||||
17 0.825 428.86 1.31178
|
||||
18 0.875 455.26 1.20674
|
||||
19 0.925 472.77 1.11081
|
||||
20 0.975 494.89 1.05391
|
||||
23000 20
|
||||
1 0.025 497.95 0.994932
|
||||
2 0.075 494.48 1.05526
|
||||
3 0.125 477.58 1.12291
|
||||
4 0.175 450.46 1.2093
|
||||
5 0.225 426.82 1.31591
|
||||
6 0.275 404.53 1.4151
|
||||
7 0.325 384.47 1.53316
|
||||
8 0.375 363.47 1.62974
|
||||
9 0.425 322 1.8461
|
||||
10 0.475 300.61 1.99473
|
||||
11 0.525 270.97 2.14953
|
||||
12 0.575 302.06 1.97712
|
||||
13 0.625 326.65 1.84056
|
||||
14 0.675 349.81 1.68226
|
||||
15 0.725 378.88 1.51982
|
||||
16 0.775 404.54 1.40091
|
||||
17 0.825 429.59 1.34441
|
||||
18 0.875 451.78 1.21689
|
||||
19 0.925 473.03 1.13568
|
||||
20 0.975 490.32 1.06191
|
||||
24000 20
|
||||
1 0.025 505.71 0.984351
|
||||
2 0.075 496.09 1.0397
|
||||
3 0.125 471.23 1.13752
|
||||
4 0.175 453.38 1.22101
|
||||
5 0.225 429.16 1.33429
|
||||
6 0.275 406.3 1.44301
|
||||
7 0.325 380.22 1.55489
|
||||
8 0.375 362.14 1.64792
|
||||
9 0.425 323.14 1.81837
|
||||
10 0.475 291.35 2.02091
|
||||
11 0.525 274.66 2.15935
|
||||
12 0.575 292.27 2.027
|
||||
13 0.625 329.24 1.81661
|
||||
14 0.675 358.32 1.6251
|
||||
15 0.725 385.73 1.51897
|
||||
16 0.775 400.85 1.4235
|
||||
17 0.825 426.67 1.33476
|
||||
18 0.875 452.21 1.23316
|
||||
19 0.925 474.84 1.14261
|
||||
20 0.975 486.49 1.07142
|
||||
25000 20
|
||||
1 0.025 504.2 0.986279
|
||||
2 0.075 492.68 1.04515
|
||||
3 0.125 472.59 1.11307
|
||||
4 0.175 458.93 1.21339
|
||||
5 0.225 427.02 1.30947
|
||||
6 0.275 397.21 1.45361
|
||||
7 0.325 378.68 1.53044
|
||||
8 0.375 353.18 1.6666
|
||||
9 0.425 336.06 1.80054
|
||||
10 0.475 286.89 2.03048
|
||||
11 0.525 276.75 2.15524
|
||||
12 0.575 301.59 1.99783
|
||||
13 0.625 336.16 1.79213
|
||||
14 0.675 364.99 1.63634
|
||||
15 0.725 374.23 1.53878
|
||||
16 0.775 406.37 1.43691
|
||||
17 0.825 422.42 1.33538
|
||||
18 0.875 452.17 1.20866
|
||||
19 0.925 468.2 1.14138
|
||||
20 0.975 489.68 1.0471
|
||||
26000 20
|
||||
1 0.025 504.86 0.983236
|
||||
2 0.075 490.99 1.03874
|
||||
3 0.125 472.38 1.14777
|
||||
4 0.175 449.66 1.23742
|
||||
5 0.225 429.84 1.31422
|
||||
6 0.275 405.77 1.42474
|
||||
7 0.325 373.27 1.54885
|
||||
8 0.375 352.38 1.68211
|
||||
9 0.425 328.67 1.79759
|
||||
10 0.475 299.24 1.98588
|
||||
11 0.525 276.79 2.13682
|
||||
12 0.575 306.51 1.94954
|
||||
13 0.625 332.41 1.79026
|
||||
14 0.675 344.74 1.71161
|
||||
15 0.725 383.2 1.52858
|
||||
16 0.775 397.32 1.44485
|
||||
17 0.825 429.88 1.33171
|
||||
18 0.875 451.72 1.21822
|
||||
19 0.925 473.58 1.13378
|
||||
20 0.975 496.79 1.03806
|
||||
27000 20
|
||||
1 0.025 505.1 0.985354
|
||||
2 0.075 495.4 1.02625
|
||||
3 0.125 470.54 1.12757
|
||||
4 0.175 454.69 1.21337
|
||||
5 0.225 433.62 1.31718
|
||||
6 0.275 398.04 1.44012
|
||||
7 0.325 373.71 1.5668
|
||||
8 0.375 357.1 1.66225
|
||||
9 0.425 332.54 1.81062
|
||||
10 0.475 298.38 1.98877
|
||||
11 0.525 280.65 2.14363
|
||||
12 0.575 305.3 1.94306
|
||||
13 0.625 328.16 1.83339
|
||||
14 0.675 351.99 1.67429
|
||||
15 0.725 368.53 1.59129
|
||||
16 0.775 407.26 1.4253
|
||||
17 0.825 429.89 1.28775
|
||||
18 0.875 445.36 1.23303
|
||||
19 0.925 474.61 1.11874
|
||||
20 0.975 489.13 1.05433
|
||||
28000 20
|
||||
1 0.025 500.8 1.00374
|
||||
2 0.075 492.02 1.04039
|
||||
3 0.125 476.36 1.12484
|
||||
4 0.175 447.94 1.21583
|
||||
5 0.225 436.48 1.31146
|
||||
6 0.275 407.24 1.42779
|
||||
7 0.325 376.75 1.56764
|
||||
8 0.375 364.69 1.63659
|
||||
9 0.425 328.19 1.81192
|
||||
10 0.475 306.23 1.94199
|
||||
11 0.525 276.65 2.14278
|
||||
12 0.575 303.07 1.98437
|
||||
13 0.625 318.25 1.81569
|
||||
14 0.675 338.44 1.71023
|
||||
15 0.725 375.6 1.55642
|
||||
16 0.775 406.82 1.41954
|
||||
17 0.825 431.49 1.30394
|
||||
18 0.875 451.83 1.21779
|
||||
19 0.925 472.29 1.14203
|
||||
20 0.975 488.86 1.05808
|
||||
29000 20
|
||||
1 0.025 500.09 0.991522
|
||||
2 0.075 490.38 1.04718
|
||||
3 0.125 472.73 1.12481
|
||||
4 0.175 448.42 1.21821
|
||||
5 0.225 433.93 1.28948
|
||||
6 0.275 401.3 1.42038
|
||||
7 0.325 378.55 1.54873
|
||||
8 0.375 357.9 1.63884
|
||||
9 0.425 332.31 1.81878
|
||||
10 0.475 304.94 1.95789
|
||||
11 0.525 287.53 2.09848
|
||||
12 0.575 310.61 1.92985
|
||||
13 0.625 323.68 1.87361
|
||||
14 0.675 346.52 1.70247
|
||||
15 0.725 377.17 1.54019
|
||||
16 0.775 400.09 1.3954
|
||||
17 0.825 423.34 1.3146
|
||||
18 0.875 449.8 1.21144
|
||||
19 0.925 472.55 1.12841
|
||||
20 0.975 488.16 1.0486
|
||||
30000 20
|
||||
1 0.025 505.29 0.985703
|
||||
2 0.075 490.39 1.06887
|
||||
3 0.125 467.85 1.12916
|
||||
4 0.175 451.18 1.20132
|
||||
5 0.225 428.53 1.29249
|
||||
6 0.275 399.4 1.40401
|
||||
7 0.325 380.24 1.50509
|
||||
8 0.375 356.5 1.64879
|
||||
9 0.425 336.95 1.79226
|
||||
10 0.475 308.06 1.88944
|
||||
11 0.525 280.66 2.1085
|
||||
12 0.575 294.78 2.0016
|
||||
13 0.625 318.8 1.85148
|
||||
14 0.675 353.24 1.69795
|
||||
15 0.725 376.42 1.58066
|
||||
16 0.775 408.33 1.42233
|
||||
17 0.825 429.01 1.31129
|
||||
18 0.875 450.54 1.2446
|
||||
19 0.925 473.76 1.14926
|
||||
20 0.975 490.07 1.06965
|
||||
31000 20
|
||||
1 0.025 498.95 0.997907
|
||||
2 0.075 488.46 1.05654
|
||||
3 0.125 473.44 1.14503
|
||||
4 0.175 452.04 1.22914
|
||||
5 0.225 429.51 1.31588
|
||||
6 0.275 410.71 1.40168
|
||||
7 0.325 385.91 1.52221
|
||||
8 0.375 346.49 1.69074
|
||||
9 0.425 328.92 1.82548
|
||||
10 0.475 313 1.9238
|
||||
11 0.525 273.97 2.14963
|
||||
12 0.575 295.55 2.00793
|
||||
13 0.625 326.42 1.79987
|
||||
14 0.675 356.19 1.66716
|
||||
15 0.725 377.76 1.5605
|
||||
16 0.775 401.7 1.40467
|
||||
17 0.825 426.96 1.31237
|
||||
18 0.875 454.88 1.20654
|
||||
19 0.925 471.46 1.13508
|
||||
20 0.975 487.68 1.05299
|
||||
32000 20
|
||||
1 0.025 497.3 0.993242
|
||||
2 0.075 495.55 1.05003
|
||||
3 0.125 475.01 1.12834
|
||||
4 0.175 455.88 1.21644
|
||||
5 0.225 433.79 1.34023
|
||||
6 0.275 410.65 1.41268
|
||||
7 0.325 384.81 1.55967
|
||||
8 0.375 352.55 1.69205
|
||||
9 0.425 316.53 1.85004
|
||||
10 0.475 302.33 2.02798
|
||||
11 0.525 272.85 2.15326
|
||||
12 0.575 300.8 1.94569
|
||||
13 0.625 325.9 1.78139
|
||||
14 0.675 353.04 1.64256
|
||||
15 0.725 377.61 1.5734
|
||||
16 0.775 402.07 1.42381
|
||||
17 0.825 431.29 1.29518
|
||||
18 0.875 449.44 1.20763
|
||||
19 0.925 475.18 1.14206
|
||||
20 0.975 487.42 1.07447
|
||||
33000 20
|
||||
1 0.025 498.7 0.99306
|
||||
2 0.075 484.1 1.05495
|
||||
3 0.125 477.67 1.10819
|
||||
4 0.175 456.03 1.19111
|
||||
5 0.225 430.71 1.30116
|
||||
6 0.275 401.3 1.40019
|
||||
7 0.325 379.84 1.53695
|
||||
8 0.375 348.43 1.66976
|
||||
9 0.425 319.72 1.78537
|
||||
10 0.475 304.12 1.98665
|
||||
11 0.525 282.2 2.15122
|
||||
12 0.575 300.19 2.00112
|
||||
13 0.625 326 1.83475
|
||||
14 0.675 359.6 1.71865
|
||||
15 0.725 373.35 1.58302
|
||||
16 0.775 403.99 1.43418
|
||||
17 0.825 438.48 1.28281
|
||||
18 0.875 452.16 1.23982
|
||||
19 0.925 474.44 1.14438
|
||||
20 0.975 488.97 1.05512
|
||||
34000 20
|
||||
1 0.025 498.84 0.999218
|
||||
2 0.075 490.37 1.05551
|
||||
3 0.125 474.57 1.10448
|
||||
4 0.175 458.82 1.19533
|
||||
5 0.225 433.81 1.2994
|
||||
6 0.275 399.29 1.45103
|
||||
7 0.325 372.36 1.57931
|
||||
8 0.375 357.53 1.66622
|
||||
9 0.425 330.9 1.82
|
||||
10 0.475 300.52 1.9526
|
||||
11 0.525 283.48 2.16858
|
||||
12 0.575 298.31 2.00109
|
||||
13 0.625 324.4 1.86763
|
||||
14 0.675 356.56 1.66589
|
||||
15 0.725 378.33 1.54503
|
||||
16 0.775 402.14 1.42876
|
||||
17 0.825 427.19 1.29336
|
||||
18 0.875 454.05 1.21058
|
||||
19 0.925 471.27 1.13019
|
||||
20 0.975 487.26 1.03595
|
||||
35000 20
|
||||
1 0.025 503.09 0.981854
|
||||
2 0.075 491.52 1.04171
|
||||
3 0.125 468.83 1.14213
|
||||
4 0.175 449.28 1.22792
|
||||
5 0.225 426.61 1.33015
|
||||
6 0.275 397.29 1.45446
|
||||
7 0.325 380.22 1.50557
|
||||
8 0.375 358.44 1.65204
|
||||
9 0.425 322.17 1.81553
|
||||
10 0.475 300.01 1.94598
|
||||
11 0.525 277.14 2.23624
|
||||
12 0.575 300.5 1.96859
|
||||
13 0.625 321.66 1.83017
|
||||
14 0.675 356.45 1.6751
|
||||
15 0.725 379.61 1.56163
|
||||
16 0.775 408.27 1.44994
|
||||
17 0.825 433.01 1.30949
|
||||
18 0.875 449.72 1.20516
|
||||
19 0.925 479.63 1.12035
|
||||
20 0.975 496.55 1.03065
|
||||
36000 20
|
||||
1 0.025 508.98 0.973654
|
||||
2 0.075 491.27 1.06484
|
||||
3 0.125 470.48 1.15269
|
||||
4 0.175 441.17 1.27333
|
||||
5 0.225 424.33 1.34342
|
||||
6 0.275 398.87 1.43191
|
||||
7 0.325 385.85 1.52299
|
||||
8 0.375 355.79 1.65819
|
||||
9 0.425 333.05 1.80628
|
||||
10 0.475 299.52 1.97245
|
||||
11 0.525 281.27 2.16233
|
||||
12 0.575 296.49 2.00554
|
||||
13 0.625 319.69 1.8411
|
||||
14 0.675 353.62 1.67747
|
||||
15 0.725 376.37 1.56099
|
||||
16 0.775 406.02 1.41604
|
||||
17 0.825 431.6 1.30323
|
||||
18 0.875 456.19 1.19013
|
||||
19 0.925 471.45 1.10501
|
||||
20 0.975 497.99 1.02785
|
||||
37000 20
|
||||
1 0.025 506.28 0.967865
|
||||
2 0.075 487.66 1.06251
|
||||
3 0.125 469.65 1.17643
|
||||
4 0.175 440.95 1.27608
|
||||
5 0.225 414.43 1.38263
|
||||
6 0.275 400.32 1.45539
|
||||
7 0.325 390.41 1.51394
|
||||
8 0.375 354.58 1.67399
|
||||
9 0.425 324.34 1.82799
|
||||
10 0.475 299.66 1.90733
|
||||
11 0.525 290.36 2.11314
|
||||
12 0.575 291.1 2.01129
|
||||
13 0.625 326.89 1.77625
|
||||
14 0.675 358.51 1.64469
|
||||
15 0.725 369.84 1.56721
|
||||
16 0.775 408.25 1.42178
|
||||
17 0.825 430.89 1.30807
|
||||
18 0.875 452.54 1.20669
|
||||
19 0.925 483.2 1.09077
|
||||
20 0.975 500.14 1.02256
|
||||
38000 20
|
||||
1 0.025 509.23 0.97086
|
||||
2 0.075 490.56 1.0399
|
||||
3 0.125 458.55 1.16873
|
||||
4 0.175 438.57 1.27037
|
||||
5 0.225 418.64 1.38351
|
||||
6 0.275 396.52 1.44719
|
||||
7 0.325 379.45 1.52783
|
||||
8 0.375 356.99 1.65986
|
||||
9 0.425 328.84 1.76326
|
||||
10 0.475 305.8 1.9175
|
||||
11 0.525 284.48 2.13982
|
||||
12 0.575 304.21 2.00019
|
||||
13 0.625 324.83 1.8291
|
||||
14 0.675 348.04 1.71444
|
||||
15 0.725 384.55 1.54598
|
||||
16 0.775 406.8 1.41278
|
||||
17 0.825 437.24 1.29628
|
||||
18 0.875 459.87 1.18139
|
||||
19 0.925 472.92 1.08656
|
||||
20 0.975 493.91 1.04277
|
||||
39000 20
|
||||
1 0.025 505.83 1.00563
|
||||
2 0.075 487.5 1.06419
|
||||
3 0.125 462.51 1.16717
|
||||
4 0.175 443.87 1.29406
|
||||
5 0.225 421.08 1.35249
|
||||
6 0.275 401.24 1.43267
|
||||
7 0.325 376.19 1.5924
|
||||
8 0.375 345.31 1.66879
|
||||
9 0.425 325.44 1.74705
|
||||
10 0.475 301.64 1.91892
|
||||
11 0.525 284.49 2.11906
|
||||
12 0.575 297.3 1.99897
|
||||
13 0.625 319.27 1.79583
|
||||
14 0.675 357.16 1.63078
|
||||
15 0.725 382.77 1.54495
|
||||
16 0.775 407.59 1.40974
|
||||
17 0.825 436.57 1.31302
|
||||
18 0.875 463.27 1.19801
|
||||
19 0.925 481.13 1.10427
|
||||
20 0.975 499.84 1.02472
|
||||
40000 20
|
||||
1 0.025 494.98 0.999162
|
||||
2 0.075 484.9 1.05726
|
||||
3 0.125 474.6 1.12553
|
||||
4 0.175 447.61 1.25742
|
||||
5 0.225 421.14 1.32375
|
||||
6 0.275 395.9 1.42853
|
||||
7 0.325 372.57 1.59773
|
||||
8 0.375 357.77 1.67008
|
||||
9 0.425 328.92 1.81981
|
||||
10 0.475 299.98 2.06643
|
||||
11 0.525 280.3 2.1764
|
||||
12 0.575 295.9 2.00865
|
||||
13 0.625 324.86 1.83372
|
||||
14 0.675 367.54 1.58994
|
||||
15 0.725 390.83 1.48393
|
||||
16 0.775 407.2 1.4381
|
||||
17 0.825 426.09 1.28159
|
||||
18 0.875 457.38 1.19313
|
||||
19 0.925 476.84 1.08455
|
||||
20 0.975 494.69 1.01132
|
||||
41000 20
|
||||
1 0.025 504.28 0.993682
|
||||
2 0.075 485.15 1.07807
|
||||
3 0.125 469.32 1.15207
|
||||
4 0.175 454.45 1.216
|
||||
5 0.225 424.94 1.37143
|
||||
6 0.275 397.59 1.47379
|
||||
7 0.325 377.72 1.56347
|
||||
8 0.375 342.22 1.64781
|
||||
9 0.425 324.1 1.80277
|
||||
10 0.475 293.87 2.02367
|
||||
11 0.525 280.93 2.13449
|
||||
12 0.575 289.81 2.00446
|
||||
13 0.625 321.62 1.8231
|
||||
14 0.675 360.42 1.67296
|
||||
15 0.725 391.51 1.5234
|
||||
16 0.775 412.98 1.40015
|
||||
17 0.825 439.35 1.29886
|
||||
18 0.875 459.21 1.21081
|
||||
19 0.925 474.56 1.1222
|
||||
20 0.975 495.97 1.04918
|
||||
27
examples/PACKAGES/electrode/README
Normal file
27
examples/PACKAGES/electrode/README
Normal file
@ -0,0 +1,27 @@
|
||||
These examples demonstrate the use of the ELECTRODE package for constant potential molecular dynamics.
|
||||
|
||||
planar/
|
||||
au-vac.data -- gold electrodes with vacuum
|
||||
in.planar* -- comparison of gold electrodes with vacuum to theoretical capacitance of planar capacitor
|
||||
-- 5x, further labeled by long-range solver (ewald / pppm) and boundary correction (ew2d / ew3dc / ffield)
|
||||
-- the pppm-ew2d combination would not give correct results and will throw an error if selected
|
||||
test.sh -- run all in.planar files and check charge at 1.2V and %difference from theoretical (last column)
|
||||
|
||||
graph-il/
|
||||
graph-il.data -- graphene electrodes with electrolyte (coarse-grained BMIm-PF6)
|
||||
in.conp -- reference run at constant potential
|
||||
in.etypes -- type-based smart neighborlists
|
||||
in.ffield -- finite field method with fully periodic cell
|
||||
in.ramp -- equal-style ramping potential difference
|
||||
in.conq -- constrained electrode total charges
|
||||
in.conq2 -- constrained electrode total charges via dynamically-set potentials
|
||||
in.thermo -- thermalize electrolyte with thermopotentiostat instead of NVT
|
||||
|
||||
au-aq/
|
||||
au-aq.data -- gold electrodes with electrolyte (SPC water + NaCl)
|
||||
in.ffield -- finite field method with fully periodic cell
|
||||
in.tf -- Thomas-Fermi metallicity model with more delocalized charges
|
||||
|
||||
# future work:
|
||||
# in.cylinder -- comparison of carbon nanotube to theoretical induced charge for charge near circular conductor
|
||||
|
||||
1
examples/PACKAGES/electrode/au-aq/.gitignore
vendored
Normal file
1
examples/PACKAGES/electrode/au-aq/.gitignore
vendored
Normal file
@ -0,0 +1 @@
|
||||
log.lammps*
|
||||
26130
examples/PACKAGES/electrode/au-aq/data.au-aq
Normal file
26130
examples/PACKAGES/electrode/au-aq/data.au-aq
Normal file
File diff suppressed because it is too large
Load Diff
11
examples/PACKAGES/electrode/au-aq/in.ffield
Normal file
11
examples/PACKAGES/electrode/au-aq/in.ffield
Normal file
@ -0,0 +1,11 @@
|
||||
# electrodes with constant potential using finite field
|
||||
# for z-periodic gold-saline electrochemical cell
|
||||
|
||||
boundary p p p # ffield uses periodic z-boundary and no slab
|
||||
include settings.mod # styles, groups, computes and fixes
|
||||
|
||||
fix conp bot electrode/conp -1.0 1.805132 couple top 1.0 symm on ffield yes etypes 6*7
|
||||
|
||||
thermo 50
|
||||
thermo_style custom step temp c_ctemp epair etotal c_qtop c_qbot c_qztop c_qzbot
|
||||
run 500
|
||||
15
examples/PACKAGES/electrode/au-aq/in.tf
Normal file
15
examples/PACKAGES/electrode/au-aq/in.tf
Normal file
@ -0,0 +1,15 @@
|
||||
# electrodes with constant potential using finite field
|
||||
# for z-periodic gold-saline electrochemical cell
|
||||
# using Thomas-Fermi metallicity model: electrode q and qz will be
|
||||
# smaller because of more delocalized charge
|
||||
|
||||
boundary p p p # ffield uses periodic z-boundary and no slab
|
||||
include settings.mod # styles, groups, computes and fixes
|
||||
|
||||
fix conp bot electrode/conp -1.0 1.805132 couple top 1.0 symm on ffield yes etypes 6*7
|
||||
fix_modify conp tf 6 1.0 18.1715745
|
||||
fix_modify conp tf 7 1.0 18.1715745
|
||||
|
||||
thermo 50
|
||||
thermo_style custom step temp c_ctemp epair etotal c_qtop c_qbot c_qztop c_qzbot
|
||||
run 500
|
||||
@ -0,0 +1,150 @@
|
||||
LAMMPS (24 Mar 2022)
|
||||
# electrodes with constant potential using finite field
|
||||
# for z-periodic gold-saline electrochemical cell
|
||||
|
||||
boundary p p p # ffield uses periodic z-boundary and no slab
|
||||
include settings.mod # styles, groups, computes and fixes
|
||||
units real
|
||||
# distribute electrode atoms among all processors:
|
||||
if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2"
|
||||
|
||||
atom_style full
|
||||
pair_style lj/cut/coul/long 15
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
kspace_style pppm/electrode 1e-7
|
||||
|
||||
read_data "data.au-aq"
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (36.629993 36.629993 107.95213)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
9798 atoms
|
||||
reading velocities ...
|
||||
9798 velocities
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
scanning angles ...
|
||||
1 = max angles/atom
|
||||
reading bonds ...
|
||||
4320 bonds
|
||||
reading angles ...
|
||||
2160 angles
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.002 seconds
|
||||
read_data CPU = 0.051 seconds
|
||||
|
||||
group bot type 6
|
||||
1620 atoms in group bot
|
||||
group top type 7
|
||||
1620 atoms in group top
|
||||
|
||||
group SPC type 1 2 3
|
||||
6480 atoms in group SPC
|
||||
group electrolyte type 1 2 3 4 5
|
||||
6558 atoms in group electrolyte
|
||||
|
||||
fix nvt electrolyte nvt temp 298.0 298.0 241
|
||||
fix shake SPC shake 1e-4 20 0 b 1 2 a 1
|
||||
0 = # of size 2 clusters
|
||||
0 = # of size 3 clusters
|
||||
0 = # of size 4 clusters
|
||||
2160 = # of frozen angles
|
||||
find clusters CPU = 0.002 seconds
|
||||
|
||||
variable q atom q
|
||||
variable qz atom q*(z-lz/2)
|
||||
compute qtop top reduce sum v_q
|
||||
compute qbot bot reduce sum v_q
|
||||
compute qztop top reduce sum v_qz
|
||||
compute qzbot bot reduce sum v_qz
|
||||
compute ctemp electrolyte temp
|
||||
|
||||
|
||||
fix conp bot electrode/conp -1.0 1.805132 couple top 1.0 symm on ffield yes etypes 6*7
|
||||
3240 atoms in group conp_group
|
||||
|
||||
thermo 50
|
||||
thermo_style custom step temp c_ctemp epair etotal c_qtop c_qbot c_qztop c_qzbot
|
||||
run 500
|
||||
PPPM/electrode initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
G vector (1/distance) = 0.24017705
|
||||
grid = 54 54 120
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 3.6312561e-05
|
||||
estimated relative force accuracy = 1.093542e-07
|
||||
using double precision MKL FFT
|
||||
3d grid and FFT values/proc = 472567 349920
|
||||
generated 21 of 21 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 17
|
||||
ghost atom cutoff = 17
|
||||
binsize = 8.5, bins = 5 5 13
|
||||
3 neighbor lists, perpetual/occasional/extra = 2 1 0
|
||||
(1) pair lj/cut/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
(2) fix electrode/conp, occasional, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) fix electrode/conp, perpetual, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 194.6 | 194.6 | 194.6 Mbytes
|
||||
Step Temp c_ctemp E_pair TotEng c_qtop c_qbot c_qztop c_qzbot
|
||||
0 171.61215 298.06731 -39212.819 -35306.164 4.1391573 -4.1391573 78.718381 131.56372
|
||||
50 147.03139 255.37383 -39870.139 -36523.051 4.1312167 -4.1312167 78.563872 131.30255
|
||||
100 149.89027 260.33932 -39878.859 -36466.689 4.0217834 -4.0217834 76.482548 127.82573
|
||||
150 151.7382 263.54893 -39873.178 -36418.942 4.0469977 -4.0469977 76.967548 128.59855
|
||||
200 151.7508 263.57081 -39827.015 -36372.492 4.1830375 -4.1830375 79.554159 132.93925
|
||||
250 152.61146 265.06566 -39791.293 -36317.177 4.1835865 -4.1835865 79.56665 132.97185
|
||||
300 153.51486 266.63475 -39751.841 -36257.16 4.1571861 -4.1571861 79.061431 132.12905
|
||||
350 156.35115 271.561 -39754.955 -36195.708 4.3498059 -4.3498059 82.720202 138.28678
|
||||
400 156.26118 271.40474 -39690.781 -36133.582 4.3444079 -4.3444079 82.619396 138.11873
|
||||
450 158.54164 275.36558 -39681.083 -36071.97 4.2020488 -4.2020488 79.912674 133.55185
|
||||
500 161.40138 280.33258 -39684.185 -36009.972 4.3021924 -4.3021924 81.807527 136.7464
|
||||
Loop time of 246.197 on 1 procs for 500 steps with 9798 atoms
|
||||
|
||||
Performance: 0.175 ns/day, 136.776 hours/ns, 2.031 timesteps/s
|
||||
356.3% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 105.64 | 105.64 | 105.64 | 0.0 | 42.91
|
||||
Bond | 0.0010592 | 0.0010592 | 0.0010592 | 0.0 | 0.00
|
||||
Kspace | 37.643 | 37.643 | 37.643 | 0.0 | 15.29
|
||||
Neigh | 5.8827 | 5.8827 | 5.8827 | 0.0 | 2.39
|
||||
Comm | 0.18181 | 0.18181 | 0.18181 | 0.0 | 0.07
|
||||
Output | 0.0055762 | 0.0055762 | 0.0055762 | 0.0 | 0.00
|
||||
Modify | 96.78 | 96.78 | 96.78 | 0.0 | 39.31
|
||||
Other | | 0.06346 | | | 0.03
|
||||
|
||||
Nlocal: 9798 ave 9798 max 9798 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 31695 ave 31695 max 31695 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 8.25614e+06 ave 8.25614e+06 max 8.25614e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 8256142
|
||||
Ave neighs/atom = 842.63544
|
||||
Ave special neighs/atom = 1.3227189
|
||||
Neighbor list builds = 22
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:19:39
|
||||
@ -0,0 +1,151 @@
|
||||
LAMMPS (24 Mar 2022)
|
||||
# electrodes with constant potential using finite field
|
||||
# for z-periodic gold-saline electrochemical cell
|
||||
|
||||
boundary p p p # ffield uses periodic z-boundary and no slab
|
||||
include settings.mod # styles, groups, computes and fixes
|
||||
units real
|
||||
# distribute electrode atoms among all processors:
|
||||
if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2"
|
||||
processors * * 2
|
||||
|
||||
atom_style full
|
||||
pair_style lj/cut/coul/long 15
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
kspace_style pppm/electrode 1e-7
|
||||
|
||||
read_data "data.au-aq"
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (36.629993 36.629993 107.95213)
|
||||
2 by 1 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
9798 atoms
|
||||
reading velocities ...
|
||||
9798 velocities
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
scanning angles ...
|
||||
1 = max angles/atom
|
||||
reading bonds ...
|
||||
4320 bonds
|
||||
reading angles ...
|
||||
2160 angles
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.002 seconds
|
||||
read_data CPU = 0.149 seconds
|
||||
|
||||
group bot type 6
|
||||
1620 atoms in group bot
|
||||
group top type 7
|
||||
1620 atoms in group top
|
||||
|
||||
group SPC type 1 2 3
|
||||
6480 atoms in group SPC
|
||||
group electrolyte type 1 2 3 4 5
|
||||
6558 atoms in group electrolyte
|
||||
|
||||
fix nvt electrolyte nvt temp 298.0 298.0 241
|
||||
fix shake SPC shake 1e-4 20 0 b 1 2 a 1
|
||||
0 = # of size 2 clusters
|
||||
0 = # of size 3 clusters
|
||||
0 = # of size 4 clusters
|
||||
2160 = # of frozen angles
|
||||
find clusters CPU = 0.003 seconds
|
||||
|
||||
variable q atom q
|
||||
variable qz atom q*(z-lz/2)
|
||||
compute qtop top reduce sum v_q
|
||||
compute qbot bot reduce sum v_q
|
||||
compute qztop top reduce sum v_qz
|
||||
compute qzbot bot reduce sum v_qz
|
||||
compute ctemp electrolyte temp
|
||||
|
||||
|
||||
fix conp bot electrode/conp -1.0 1.805132 couple top 1.0 symm on ffield yes etypes 6*7
|
||||
3240 atoms in group conp_group
|
||||
|
||||
thermo 50
|
||||
thermo_style custom step temp c_ctemp epair etotal c_qtop c_qbot c_qztop c_qzbot
|
||||
run 500
|
||||
PPPM/electrode initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
G vector (1/distance) = 0.24017705
|
||||
grid = 54 54 120
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 3.6312561e-05
|
||||
estimated relative force accuracy = 1.093542e-07
|
||||
using double precision MKL FFT
|
||||
3d grid and FFT values/proc = 138958 87480
|
||||
generated 21 of 21 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 17
|
||||
ghost atom cutoff = 17
|
||||
binsize = 8.5, bins = 5 5 13
|
||||
3 neighbor lists, perpetual/occasional/extra = 2 1 0
|
||||
(1) pair lj/cut/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
(2) fix electrode/conp, occasional, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) fix electrode/conp, perpetual, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 118.1 | 120.6 | 123.1 Mbytes
|
||||
Step Temp c_ctemp E_pair TotEng c_qtop c_qbot c_qztop c_qzbot
|
||||
0 171.61215 298.06731 -39212.819 -35306.164 4.1391573 -4.1391573 78.718381 131.56372
|
||||
50 147.03139 255.37383 -39870.139 -36523.051 4.1312167 -4.1312167 78.563872 131.30255
|
||||
100 149.89027 260.33932 -39878.859 -36466.689 4.0217834 -4.0217834 76.482548 127.82573
|
||||
150 151.7382 263.54893 -39873.178 -36418.942 4.0469977 -4.0469977 76.967548 128.59855
|
||||
200 151.7508 263.57081 -39827.015 -36372.492 4.1830375 -4.1830375 79.554159 132.93925
|
||||
250 152.61146 265.06566 -39791.293 -36317.177 4.1835865 -4.1835865 79.56665 132.97185
|
||||
300 153.51486 266.63475 -39751.841 -36257.16 4.1571861 -4.1571861 79.061431 132.12905
|
||||
350 156.35115 271.561 -39754.955 -36195.708 4.3498059 -4.3498059 82.7202 138.28678
|
||||
400 156.26118 271.40474 -39690.781 -36133.582 4.3444079 -4.3444079 82.619398 138.11873
|
||||
450 158.54163 275.36558 -39681.083 -36071.97 4.2020488 -4.2020488 79.912675 133.55185
|
||||
500 161.40138 280.33257 -39684.185 -36009.972 4.3021924 -4.3021924 81.807527 136.7464
|
||||
Loop time of 111.902 on 4 procs for 500 steps with 9798 atoms
|
||||
|
||||
Performance: 0.386 ns/day, 62.168 hours/ns, 4.468 timesteps/s
|
||||
97.2% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 21.816 | 31.136 | 40.866 | 166.5 | 27.82
|
||||
Bond | 0.00073413 | 0.00080346 | 0.00084203 | 0.0 | 0.00
|
||||
Kspace | 29.546 | 39.137 | 48.326 | 146.4 | 34.97
|
||||
Neigh | 2.5867 | 2.5872 | 2.5877 | 0.0 | 2.31
|
||||
Comm | 0.33289 | 0.33603 | 0.33791 | 0.3 | 0.30
|
||||
Output | 0.0022537 | 0.0030028 | 0.005192 | 2.3 | 0.00
|
||||
Modify | 38.498 | 38.635 | 38.77 | 2.2 | 34.53
|
||||
Other | | 0.06679 | | | 0.06
|
||||
|
||||
Nlocal: 2449.5 ave 2908 max 2012 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 19345.5 ave 20244 max 18492 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 2.06404e+06 ave 2.7528e+06 max 1.40672e+06 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 8256142
|
||||
Ave neighs/atom = 842.63544
|
||||
Ave special neighs/atom = 1.3227189
|
||||
Neighbor list builds = 22
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:07:48
|
||||
154
examples/PACKAGES/electrode/au-aq/log.26Apr2022.au-aq-tf.g++.1
Normal file
154
examples/PACKAGES/electrode/au-aq/log.26Apr2022.au-aq-tf.g++.1
Normal file
@ -0,0 +1,154 @@
|
||||
LAMMPS (24 Mar 2022)
|
||||
# electrodes with constant potential using finite field
|
||||
# for z-periodic gold-saline electrochemical cell
|
||||
# using Thomas-Fermi metallicity model: electrode q and qz will be
|
||||
# smaller because of more delocalized charge
|
||||
|
||||
boundary p p p # ffield uses periodic z-boundary and no slab
|
||||
include settings.mod # styles, groups, computes and fixes
|
||||
units real
|
||||
# distribute electrode atoms among all processors:
|
||||
if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2"
|
||||
|
||||
atom_style full
|
||||
pair_style lj/cut/coul/long 15
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
kspace_style pppm/electrode 1e-7
|
||||
|
||||
read_data "data.au-aq"
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (36.629993 36.629993 107.95213)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
9798 atoms
|
||||
reading velocities ...
|
||||
9798 velocities
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
scanning angles ...
|
||||
1 = max angles/atom
|
||||
reading bonds ...
|
||||
4320 bonds
|
||||
reading angles ...
|
||||
2160 angles
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.010 seconds
|
||||
read_data CPU = 0.115 seconds
|
||||
|
||||
group bot type 6
|
||||
1620 atoms in group bot
|
||||
group top type 7
|
||||
1620 atoms in group top
|
||||
|
||||
group SPC type 1 2 3
|
||||
6480 atoms in group SPC
|
||||
group electrolyte type 1 2 3 4 5
|
||||
6558 atoms in group electrolyte
|
||||
|
||||
fix nvt electrolyte nvt temp 298.0 298.0 241
|
||||
fix shake SPC shake 1e-4 20 0 b 1 2 a 1
|
||||
0 = # of size 2 clusters
|
||||
0 = # of size 3 clusters
|
||||
0 = # of size 4 clusters
|
||||
2160 = # of frozen angles
|
||||
find clusters CPU = 0.010 seconds
|
||||
|
||||
variable q atom q
|
||||
variable qz atom q*(z-lz/2)
|
||||
compute qtop top reduce sum v_q
|
||||
compute qbot bot reduce sum v_q
|
||||
compute qztop top reduce sum v_qz
|
||||
compute qzbot bot reduce sum v_qz
|
||||
compute ctemp electrolyte temp
|
||||
|
||||
|
||||
fix conp bot electrode/conp -1.0 1.805132 couple top 1.0 symm on ffield yes etypes 6*7
|
||||
3240 atoms in group conp_group
|
||||
fix_modify conp tf 6 1.0 18.1715745
|
||||
fix_modify conp tf 7 1.0 18.1715745
|
||||
|
||||
thermo 50
|
||||
thermo_style custom step temp c_ctemp epair etotal c_qtop c_qbot c_qztop c_qzbot
|
||||
run 500
|
||||
PPPM/electrode initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
G vector (1/distance) = 0.24017705
|
||||
grid = 54 54 120
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 3.6312561e-05
|
||||
estimated relative force accuracy = 1.093542e-07
|
||||
using double precision MKL FFT
|
||||
3d grid and FFT values/proc = 472567 349920
|
||||
generated 21 of 21 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 17
|
||||
ghost atom cutoff = 17
|
||||
binsize = 8.5, bins = 5 5 13
|
||||
3 neighbor lists, perpetual/occasional/extra = 2 1 0
|
||||
(1) pair lj/cut/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
(2) fix electrode/conp, occasional, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) fix electrode/conp, perpetual, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 194.6 | 194.6 | 194.6 Mbytes
|
||||
Step Temp c_ctemp E_pair TotEng c_qtop c_qbot c_qztop c_qzbot
|
||||
0 171.61215 298.06731 -39190.106 -35283.45 4.0804484 -4.0804484 79.075127 131.20697
|
||||
50 147.14308 255.56782 -39849.964 -36500.334 3.9990346 -3.9990346 77.497181 128.57759
|
||||
100 149.94935 260.44194 -39857.533 -36444.019 3.8613914 -3.8613914 74.82985 124.15315
|
||||
150 151.95924 263.93285 -39855.567 -36396.299 3.8677064 -3.8677064 74.957279 124.33201
|
||||
200 151.66737 263.42591 -39802.585 -36349.961 3.99842 -3.99842 77.491015 128.54496
|
||||
250 152.36874 264.64408 -39763.306 -36294.716 3.9925863 -3.9925863 77.379445 128.37226
|
||||
300 153.83916 267.19802 -39737.075 -36235.012 3.94995 -3.94995 76.553896 127.00395
|
||||
350 155.88897 270.75827 -39722.265 -36173.539 4.0598524 -4.0598524 78.679643 130.5394
|
||||
400 156.51993 271.85415 -39674.759 -36111.669 4.1312899 -4.1312899 80.060369 132.83599
|
||||
450 160.21339 278.26919 -39697.962 -36050.793 3.9068098 -3.9068098 75.713484 125.59216
|
||||
500 161.63639 280.74075 -39669.412 -35989.849 3.9261656 -3.9261656 76.0806 126.22255
|
||||
Loop time of 280.183 on 1 procs for 500 steps with 9798 atoms
|
||||
|
||||
Performance: 0.154 ns/day, 155.657 hours/ns, 1.785 timesteps/s
|
||||
341.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 119.69 | 119.69 | 119.69 | 0.0 | 42.72
|
||||
Bond | 0.0010952 | 0.0010952 | 0.0010952 | 0.0 | 0.00
|
||||
Kspace | 42.137 | 42.137 | 42.137 | 0.0 | 15.04
|
||||
Neigh | 6.5403 | 6.5403 | 6.5403 | 0.0 | 2.33
|
||||
Comm | 0.19411 | 0.19411 | 0.19411 | 0.0 | 0.07
|
||||
Output | 0.0053644 | 0.0053644 | 0.0053644 | 0.0 | 0.00
|
||||
Modify | 111.54 | 111.54 | 111.54 | 0.0 | 39.81
|
||||
Other | | 0.07244 | | | 0.03
|
||||
|
||||
Nlocal: 9798 ave 9798 max 9798 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 31718 ave 31718 max 31718 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 8.25685e+06 ave 8.25685e+06 max 8.25685e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 8256852
|
||||
Ave neighs/atom = 842.7079
|
||||
Ave special neighs/atom = 1.3227189
|
||||
Neighbor list builds = 23
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:21:11
|
||||
155
examples/PACKAGES/electrode/au-aq/log.26Apr2022.au-aq-tf.g++.4
Normal file
155
examples/PACKAGES/electrode/au-aq/log.26Apr2022.au-aq-tf.g++.4
Normal file
@ -0,0 +1,155 @@
|
||||
LAMMPS (24 Mar 2022)
|
||||
# electrodes with constant potential using finite field
|
||||
# for z-periodic gold-saline electrochemical cell
|
||||
# using Thomas-Fermi metallicity model: electrode q and qz will be
|
||||
# smaller because of more delocalized charge
|
||||
|
||||
boundary p p p # ffield uses periodic z-boundary and no slab
|
||||
include settings.mod # styles, groups, computes and fixes
|
||||
units real
|
||||
# distribute electrode atoms among all processors:
|
||||
if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2"
|
||||
processors * * 2
|
||||
|
||||
atom_style full
|
||||
pair_style lj/cut/coul/long 15
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
kspace_style pppm/electrode 1e-7
|
||||
|
||||
read_data "data.au-aq"
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (36.629993 36.629993 107.95213)
|
||||
2 by 1 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
9798 atoms
|
||||
reading velocities ...
|
||||
9798 velocities
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
scanning angles ...
|
||||
1 = max angles/atom
|
||||
reading bonds ...
|
||||
4320 bonds
|
||||
reading angles ...
|
||||
2160 angles
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.002 seconds
|
||||
read_data CPU = 0.091 seconds
|
||||
|
||||
group bot type 6
|
||||
1620 atoms in group bot
|
||||
group top type 7
|
||||
1620 atoms in group top
|
||||
|
||||
group SPC type 1 2 3
|
||||
6480 atoms in group SPC
|
||||
group electrolyte type 1 2 3 4 5
|
||||
6558 atoms in group electrolyte
|
||||
|
||||
fix nvt electrolyte nvt temp 298.0 298.0 241
|
||||
fix shake SPC shake 1e-4 20 0 b 1 2 a 1
|
||||
0 = # of size 2 clusters
|
||||
0 = # of size 3 clusters
|
||||
0 = # of size 4 clusters
|
||||
2160 = # of frozen angles
|
||||
find clusters CPU = 0.001 seconds
|
||||
|
||||
variable q atom q
|
||||
variable qz atom q*(z-lz/2)
|
||||
compute qtop top reduce sum v_q
|
||||
compute qbot bot reduce sum v_q
|
||||
compute qztop top reduce sum v_qz
|
||||
compute qzbot bot reduce sum v_qz
|
||||
compute ctemp electrolyte temp
|
||||
|
||||
|
||||
fix conp bot electrode/conp -1.0 1.805132 couple top 1.0 symm on ffield yes etypes 6*7
|
||||
3240 atoms in group conp_group
|
||||
fix_modify conp tf 6 1.0 18.1715745
|
||||
fix_modify conp tf 7 1.0 18.1715745
|
||||
|
||||
thermo 50
|
||||
thermo_style custom step temp c_ctemp epair etotal c_qtop c_qbot c_qztop c_qzbot
|
||||
run 500
|
||||
PPPM/electrode initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
G vector (1/distance) = 0.24017705
|
||||
grid = 54 54 120
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 3.6312561e-05
|
||||
estimated relative force accuracy = 1.093542e-07
|
||||
using double precision MKL FFT
|
||||
3d grid and FFT values/proc = 138958 87480
|
||||
generated 21 of 21 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 17
|
||||
ghost atom cutoff = 17
|
||||
binsize = 8.5, bins = 5 5 13
|
||||
3 neighbor lists, perpetual/occasional/extra = 2 1 0
|
||||
(1) pair lj/cut/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
(2) fix electrode/conp, occasional, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) fix electrode/conp, perpetual, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 118.1 | 120.6 | 123.1 Mbytes
|
||||
Step Temp c_ctemp E_pair TotEng c_qtop c_qbot c_qztop c_qzbot
|
||||
0 171.61215 298.06731 -39190.106 -35283.45 4.0804484 -4.0804484 79.075127 131.20697
|
||||
50 147.14308 255.56782 -39849.964 -36500.334 3.9990346 -3.9990346 77.497181 128.57759
|
||||
100 149.94935 260.44194 -39857.533 -36444.019 3.8613914 -3.8613914 74.82985 124.15315
|
||||
150 151.95924 263.93285 -39855.567 -36396.299 3.8677064 -3.8677064 74.957279 124.33201
|
||||
200 151.66737 263.42591 -39802.585 -36349.961 3.99842 -3.99842 77.491015 128.54496
|
||||
250 152.36874 264.64408 -39763.306 -36294.716 3.9925863 -3.9925863 77.379445 128.37226
|
||||
300 153.83916 267.19802 -39737.075 -36235.012 3.94995 -3.94995 76.553896 127.00395
|
||||
350 155.88897 270.75827 -39722.265 -36173.539 4.0598524 -4.0598524 78.679643 130.5394
|
||||
400 156.51993 271.85415 -39674.759 -36111.669 4.1312899 -4.1312899 80.060369 132.83599
|
||||
450 160.21339 278.26919 -39697.962 -36050.793 3.9068098 -3.9068098 75.713485 125.59216
|
||||
500 161.63639 280.74075 -39669.412 -35989.849 3.9261654 -3.9261654 76.080597 126.22255
|
||||
Loop time of 110.716 on 4 procs for 500 steps with 9798 atoms
|
||||
|
||||
Performance: 0.390 ns/day, 61.509 hours/ns, 4.516 timesteps/s
|
||||
97.2% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 21.17 | 30.449 | 39.65 | 164.9 | 27.50
|
||||
Bond | 0.0007313 | 0.00077537 | 0.00081477 | 0.0 | 0.00
|
||||
Kspace | 29.854 | 38.911 | 48.058 | 143.8 | 35.14
|
||||
Neigh | 2.7206 | 2.7213 | 2.722 | 0.0 | 2.46
|
||||
Comm | 0.33023 | 0.33225 | 0.33384 | 0.2 | 0.30
|
||||
Output | 0.0024528 | 0.0027565 | 0.0035754 | 0.9 | 0.00
|
||||
Modify | 38.091 | 38.233 | 38.365 | 2.1 | 34.53
|
||||
Other | | 0.06636 | | | 0.06
|
||||
|
||||
Nlocal: 2449.5 ave 2908 max 2017 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 19351.2 ave 20266 max 18479 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 2.06421e+06 ave 2.7551e+06 max 1.40237e+06 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 8256853
|
||||
Ave neighs/atom = 842.708
|
||||
Ave special neighs/atom = 1.3227189
|
||||
Neighbor list builds = 23
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:08:22
|
||||
29
examples/PACKAGES/electrode/au-aq/settings.mod
Normal file
29
examples/PACKAGES/electrode/au-aq/settings.mod
Normal file
@ -0,0 +1,29 @@
|
||||
units real
|
||||
# distribute electrode atoms among all processors:
|
||||
if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2"
|
||||
|
||||
atom_style full
|
||||
pair_style lj/cut/coul/long 15
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
kspace_style pppm/electrode 1e-7
|
||||
|
||||
read_data "data.au-aq"
|
||||
|
||||
group bot type 6
|
||||
group top type 7
|
||||
|
||||
group SPC type 1 2 3
|
||||
group electrolyte type 1 2 3 4 5
|
||||
|
||||
fix nvt electrolyte nvt temp 298.0 298.0 241
|
||||
fix shake SPC shake 1e-4 20 0 b 1 2 a 1
|
||||
|
||||
variable q atom q
|
||||
variable qz atom q*(z-lz/2)
|
||||
compute qtop top reduce sum v_q
|
||||
compute qbot bot reduce sum v_q
|
||||
compute qztop top reduce sum v_qz
|
||||
compute qzbot bot reduce sum v_qz
|
||||
compute ctemp electrolyte temp
|
||||
|
||||
1
examples/PACKAGES/electrode/graph-il/.gitignore
vendored
Normal file
1
examples/PACKAGES/electrode/graph-il/.gitignore
vendored
Normal file
@ -0,0 +1 @@
|
||||
log.lammps*
|
||||
4783
examples/PACKAGES/electrode/graph-il/data.graph-il
Normal file
4783
examples/PACKAGES/electrode/graph-il/data.graph-il
Normal file
File diff suppressed because it is too large
Load Diff
12
examples/PACKAGES/electrode/graph-il/in.conp
Normal file
12
examples/PACKAGES/electrode/graph-il/in.conp
Normal file
@ -0,0 +1,12 @@
|
||||
# electrodes with constant potential
|
||||
# for graphene-ionic liquid supercapacitor
|
||||
|
||||
boundary p p f # slab calculation
|
||||
include settings.mod # styles, groups, computes and fixes
|
||||
kspace_modify slab 3.0
|
||||
|
||||
fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on
|
||||
|
||||
thermo 50
|
||||
thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop
|
||||
run 500
|
||||
18
examples/PACKAGES/electrode/graph-il/in.conq
Normal file
18
examples/PACKAGES/electrode/graph-il/in.conq
Normal file
@ -0,0 +1,18 @@
|
||||
# electrodes with constrained total charges
|
||||
# for graphene-ionic liquid supercapacitor
|
||||
|
||||
boundary p p f # slab calculation
|
||||
include settings.mod # styles, groups, computes and fixes
|
||||
kspace_modify slab 3.0
|
||||
|
||||
fix conq bot electrode/conq -1.0 1.979 couple top 1.0 etypes 5 # conq doesn't take symm option
|
||||
|
||||
# ask fix conq to output electrode potentials to internal variables
|
||||
variable vbot internal 0.0
|
||||
variable vtop internal 0.0
|
||||
fix_modify conq set v bot vbot
|
||||
fix_modify conq set v top vtop
|
||||
|
||||
thermo 50
|
||||
thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop v_vbot v_vtop
|
||||
run 500
|
||||
35
examples/PACKAGES/electrode/graph-il/in.conq2
Normal file
35
examples/PACKAGES/electrode/graph-il/in.conq2
Normal file
@ -0,0 +1,35 @@
|
||||
# electrodes with constrained total charges imposed from dynamically computed potentials
|
||||
# for graphene-ionic liquid supercapacitor
|
||||
|
||||
boundary p p f # slab calculation
|
||||
include settings.mod # styles, groups, computes and fixes
|
||||
kspace_modify slab 3.0
|
||||
|
||||
fix conp bot electrode/conp v_vbot 1.979 couple top v_vtop etypes 5
|
||||
|
||||
# get the four entries of electrode elastance matrix
|
||||
variable me00 internal 0.0
|
||||
variable me01 internal 0.0
|
||||
variable me10 internal 0.0
|
||||
variable me11 internal 0.0
|
||||
fix_modify conp set me bot bot me00
|
||||
fix_modify conp set me bot top me01
|
||||
fix_modify conp set me top bot me10
|
||||
fix_modify conp set me top top me11
|
||||
|
||||
# get the 0V charges (qsb), and excess charge required to reach preset total charges
|
||||
variable qsb_bot internal 0.0
|
||||
variable qsb_top internal 0.0
|
||||
fix_modify conp set qsb bot qsb_bot
|
||||
fix_modify conp set qsb top qsb_top
|
||||
variable qex_bot equal -1.0-v_qsb_bot # difference between desired and 0V charge
|
||||
variable qex_top equal 1.0-v_qsb_top # difference between desired and 0V charge
|
||||
|
||||
# calculate imposed potential as elastance * excess charge
|
||||
# note: fix will wait until the run setup to look for its potential variables
|
||||
variable vbot equal v_me00*v_qex_bot+v_me01*v_qex_top
|
||||
variable vtop equal v_me10*v_qex_bot+v_me11*v_qex_top
|
||||
|
||||
thermo 50
|
||||
thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop v_vbot v_vtop
|
||||
run 500
|
||||
12
examples/PACKAGES/electrode/graph-il/in.etypes
Normal file
12
examples/PACKAGES/electrode/graph-il/in.etypes
Normal file
@ -0,0 +1,12 @@
|
||||
# electrodes with constant potential and smart neighborlists
|
||||
# for graphene-ionic liquid supercapacitor
|
||||
|
||||
boundary p p f # slab calculation
|
||||
include settings.mod # styles, groups, computes and fixes
|
||||
kspace_modify slab 3.0
|
||||
|
||||
fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on etypes 5
|
||||
|
||||
thermo 50
|
||||
thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop
|
||||
run 500
|
||||
11
examples/PACKAGES/electrode/graph-il/in.ffield
Normal file
11
examples/PACKAGES/electrode/graph-il/in.ffield
Normal file
@ -0,0 +1,11 @@
|
||||
# electrodes with constant potential using finite field
|
||||
# for z-periodic graphene-ionic liquid supercapacitor
|
||||
|
||||
boundary p p p # ffield uses periodic z-boundary and no slab
|
||||
include settings.mod # styles, groups, computes and fixes
|
||||
|
||||
fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on etypes 5 ffield yes
|
||||
|
||||
thermo 50
|
||||
thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop
|
||||
run 500
|
||||
13
examples/PACKAGES/electrode/graph-il/in.ramp
Normal file
13
examples/PACKAGES/electrode/graph-il/in.ramp
Normal file
@ -0,0 +1,13 @@
|
||||
# electrodes with equal-style ramped (electrode-)constant potential
|
||||
# for graphene-ionic liquid supercapacitor
|
||||
|
||||
boundary p p f # slab calculation
|
||||
include settings.mod # styles, groups, computes and fixes
|
||||
kspace_modify slab 3.0
|
||||
|
||||
variable v equal ramp(2,4)
|
||||
fix conp bot electrode/conp 0.0 1.979 couple top v_v symm on etypes 5
|
||||
|
||||
thermo 50
|
||||
thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop v_v
|
||||
run 500
|
||||
19
examples/PACKAGES/electrode/graph-il/in.thermo
Normal file
19
examples/PACKAGES/electrode/graph-il/in.thermo
Normal file
@ -0,0 +1,19 @@
|
||||
# electrodes with thermopotentiostat
|
||||
# for graphene-ionic liquid supercapacitor
|
||||
|
||||
boundary p p f # slab calculation
|
||||
include settings.mod # styles, groups, computes and fixes
|
||||
kspace_modify slab 3.0
|
||||
|
||||
unfix nvt # remove NVT thermostat included from "settings.mod"
|
||||
fix conpthermo bot electrode/thermo -1.0 1.979 couple top 1.0 etypes 5 temp 500 100 7 # temp tau rng
|
||||
# to compare to regular constant potential, switch previous line to this:
|
||||
#fix conp bot electrode/conp -1.0 1.979 couple top 1.0 etypes 5 symm on
|
||||
fix nve electrolyte nve
|
||||
|
||||
# note ionic liquid does not reach 500K immediately
|
||||
# because its thermal response time is finite
|
||||
# run this about 10k steps (10ps) to reach preset temperature
|
||||
thermo 50
|
||||
thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop
|
||||
run 500
|
||||
@ -0,0 +1,142 @@
|
||||
LAMMPS (24 Mar 2022)
|
||||
# electrodes with constant potential
|
||||
# for graphene-ionic liquid supercapacitor
|
||||
|
||||
boundary p p f # slab calculation
|
||||
include settings.mod # styles, groups, computes and fixes
|
||||
# set boundary in main script because ffield is periodic
|
||||
units real
|
||||
# distribute electrode atoms among all processors:
|
||||
if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2"
|
||||
|
||||
atom_style full
|
||||
pair_style lj/cut/coul/long 16
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
kspace_style pppm/electrode 1e-7
|
||||
# kspace_modify in main script because ffield is periodic
|
||||
|
||||
read_data "data.graph-il"
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 -68) to (32.2 34.4 68)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
3776 atoms
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
scanning angles ...
|
||||
1 = max angles/atom
|
||||
reading bonds ...
|
||||
640 bonds
|
||||
reading angles ...
|
||||
320 angles
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.001 seconds
|
||||
read_data CPU = 0.036 seconds
|
||||
|
||||
group bot molecule 641
|
||||
416 atoms in group bot
|
||||
group top molecule 642
|
||||
416 atoms in group top
|
||||
|
||||
group bmi type 1 2 3
|
||||
960 atoms in group bmi
|
||||
group electrolyte type 1 2 3 4
|
||||
1280 atoms in group electrolyte
|
||||
|
||||
fix nvt electrolyte nvt temp 500.0 500.0 100
|
||||
fix shake bmi shake 1e-4 20 0 b 1 2 a 1
|
||||
0 = # of size 2 clusters
|
||||
0 = # of size 3 clusters
|
||||
0 = # of size 4 clusters
|
||||
320 = # of frozen angles
|
||||
find clusters CPU = 0.001 seconds
|
||||
|
||||
variable q atom q
|
||||
compute qtop top reduce sum v_q
|
||||
compute qbot bot reduce sum v_q
|
||||
compute ctemp electrolyte temp
|
||||
kspace_modify slab 3.0
|
||||
|
||||
fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on
|
||||
832 atoms in group conp_group
|
||||
|
||||
thermo 50
|
||||
thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop
|
||||
run 500
|
||||
PPPM/electrode initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
G vector (1/distance) = 0.20904498
|
||||
grid = 32 32 200
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 3.7023506e-05
|
||||
estimated relative force accuracy = 1.1149519e-07
|
||||
using double precision MKL FFT
|
||||
3d grid and FFT values/proc = 307242 204800
|
||||
generated 10 of 10 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 18
|
||||
ghost atom cutoff = 18
|
||||
binsize = 9, bins = 4 4 16
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair lj/cut/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
(2) fix electrode/conp, perpetual, copy from (1)
|
||||
attributes: half, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 57.15 | 57.15 | 57.15 Mbytes
|
||||
Step Temp c_ctemp E_pair TotEng c_qbot c_qtop
|
||||
0 0 0 25137191 25137191 0.0085142912 -0.0085142912
|
||||
50 17.83755 64.26354 25137031 25137214 0.0045923944 -0.0045923944
|
||||
100 48.393682 174.34846 25136774 25137273 -0.009514517 0.009514517
|
||||
150 70.421272 253.7075 25136655 25137380 -0.033017005 0.033017005
|
||||
200 82.204844 296.16031 25136667 25137514 -0.063668175 0.063668175
|
||||
250 87.54223 315.38937 25136757 25137659 -0.096776257 0.096776257
|
||||
300 91.704746 330.38571 25136865 25137810 -0.1283784 0.1283784
|
||||
350 100.36017 361.56871 25136934 25137968 -0.15649799 0.15649799
|
||||
400 111.37575 401.25467 25136986 25138133 -0.18065435 0.18065435
|
||||
450 121.79848 438.80476 25137043 25138298 -0.19979365 0.19979365
|
||||
500 126.95916 457.39718 25137145 25138453 -0.21037535 0.21037535
|
||||
Loop time of 103.439 on 1 procs for 500 steps with 3776 atoms
|
||||
|
||||
Performance: 0.418 ns/day, 57.466 hours/ns, 4.834 timesteps/s
|
||||
393.6% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 19.309 | 19.309 | 19.309 | 0.0 | 18.67
|
||||
Bond | 0.0018867 | 0.0018867 | 0.0018867 | 0.0 | 0.00
|
||||
Kspace | 23.047 | 23.047 | 23.047 | 0.0 | 22.28
|
||||
Neigh | 0.25707 | 0.25707 | 0.25707 | 0.0 | 0.25
|
||||
Comm | 0.070734 | 0.070734 | 0.070734 | 0.0 | 0.07
|
||||
Output | 0.0023085 | 0.0023085 | 0.0023085 | 0.0 | 0.00
|
||||
Modify | 60.73 | 60.73 | 60.73 | 0.0 | 58.71
|
||||
Other | | 0.01994 | | | 0.02
|
||||
|
||||
Nlocal: 3776 ave 3776 max 3776 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 12509 ave 12509 max 12509 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 1.72633e+06 ave 1.72633e+06 max 1.72633e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1726328
|
||||
Ave neighs/atom = 457.18432
|
||||
Ave special neighs/atom = 0.50847458
|
||||
Neighbor list builds = 7
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:03:10
|
||||
@ -0,0 +1,143 @@
|
||||
LAMMPS (24 Mar 2022)
|
||||
# electrodes with constant potential
|
||||
# for graphene-ionic liquid supercapacitor
|
||||
|
||||
boundary p p f # slab calculation
|
||||
include settings.mod # styles, groups, computes and fixes
|
||||
# set boundary in main script because ffield is periodic
|
||||
units real
|
||||
# distribute electrode atoms among all processors:
|
||||
if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2"
|
||||
processors * * 2
|
||||
|
||||
atom_style full
|
||||
pair_style lj/cut/coul/long 16
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
kspace_style pppm/electrode 1e-7
|
||||
# kspace_modify in main script because ffield is periodic
|
||||
|
||||
read_data "data.graph-il"
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 -68) to (32.2 34.4 68)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
3776 atoms
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
scanning angles ...
|
||||
1 = max angles/atom
|
||||
reading bonds ...
|
||||
640 bonds
|
||||
reading angles ...
|
||||
320 angles
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.001 seconds
|
||||
read_data CPU = 0.014 seconds
|
||||
|
||||
group bot molecule 641
|
||||
416 atoms in group bot
|
||||
group top molecule 642
|
||||
416 atoms in group top
|
||||
|
||||
group bmi type 1 2 3
|
||||
960 atoms in group bmi
|
||||
group electrolyte type 1 2 3 4
|
||||
1280 atoms in group electrolyte
|
||||
|
||||
fix nvt electrolyte nvt temp 500.0 500.0 100
|
||||
fix shake bmi shake 1e-4 20 0 b 1 2 a 1
|
||||
0 = # of size 2 clusters
|
||||
0 = # of size 3 clusters
|
||||
0 = # of size 4 clusters
|
||||
320 = # of frozen angles
|
||||
find clusters CPU = 0.001 seconds
|
||||
|
||||
variable q atom q
|
||||
compute qtop top reduce sum v_q
|
||||
compute qbot bot reduce sum v_q
|
||||
compute ctemp electrolyte temp
|
||||
kspace_modify slab 3.0
|
||||
|
||||
fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on
|
||||
832 atoms in group conp_group
|
||||
|
||||
thermo 50
|
||||
thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop
|
||||
run 500
|
||||
PPPM/electrode initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
G vector (1/distance) = 0.20904498
|
||||
grid = 32 32 200
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 3.7023506e-05
|
||||
estimated relative force accuracy = 1.1149519e-07
|
||||
using double precision MKL FFT
|
||||
3d grid and FFT values/proc = 151593 85504
|
||||
generated 10 of 10 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 18
|
||||
ghost atom cutoff = 18
|
||||
binsize = 9, bins = 4 4 16
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair lj/cut/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
(2) fix electrode/conp, perpetual, copy from (1)
|
||||
attributes: half, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 23.13 | 26.96 | 30.79 Mbytes
|
||||
Step Temp c_ctemp E_pair TotEng c_qbot c_qtop
|
||||
0 0 0 25137191 25137191 0.0085142912 -0.0085142912
|
||||
50 17.83755 64.26354 25137031 25137214 0.0045923944 -0.0045923944
|
||||
100 48.393682 174.34846 25136774 25137273 -0.009514517 0.009514517
|
||||
150 70.421272 253.7075 25136655 25137380 -0.033017005 0.033017005
|
||||
200 82.204844 296.16031 25136667 25137514 -0.063668175 0.063668175
|
||||
250 87.54223 315.38937 25136757 25137659 -0.096776257 0.096776257
|
||||
300 91.704746 330.38571 25136865 25137810 -0.1283784 0.1283784
|
||||
350 100.36017 361.56871 25136934 25137968 -0.15649799 0.15649799
|
||||
400 111.37575 401.25467 25136986 25138133 -0.18065435 0.18065435
|
||||
450 121.79848 438.80476 25137043 25138298 -0.19979365 0.19979365
|
||||
500 126.95916 457.39718 25137145 25138453 -0.21037535 0.21037535
|
||||
Loop time of 49.6656 on 4 procs for 500 steps with 3776 atoms
|
||||
|
||||
Performance: 0.870 ns/day, 27.592 hours/ns, 10.067 timesteps/s
|
||||
95.1% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 5.968 | 6.1677 | 6.382 | 6.5 | 12.42
|
||||
Bond | 0.00071151 | 0.00078617 | 0.00090387 | 0.0 | 0.00
|
||||
Kspace | 17.345 | 17.558 | 17.755 | 3.8 | 35.35
|
||||
Neigh | 0.10939 | 0.10945 | 0.10948 | 0.0 | 0.22
|
||||
Comm | 0.15295 | 0.15474 | 0.15699 | 0.4 | 0.31
|
||||
Output | 0.00074458 | 0.0010336 | 0.0018799 | 1.5 | 0.00
|
||||
Modify | 25.634 | 25.641 | 25.645 | 0.1 | 51.63
|
||||
Other | | 0.03276 | | | 0.07
|
||||
|
||||
Nlocal: 944 ave 951 max 941 min
|
||||
Histogram: 1 2 0 0 0 0 0 0 0 1
|
||||
Nghost: 5923.25 ave 5941 max 5906 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
Neighs: 431582 ave 442090 max 419903 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 1726328
|
||||
Ave neighs/atom = 457.18432
|
||||
Ave special neighs/atom = 0.50847458
|
||||
Neighbor list builds = 7
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:01:11
|
||||
@ -0,0 +1,153 @@
|
||||
LAMMPS (24 Mar 2022)
|
||||
# electrodes with constrained total charges
|
||||
# for graphene-ionic liquid supercapacitor
|
||||
|
||||
boundary p p f # slab calculation
|
||||
include settings.mod # styles, groups, computes and fixes
|
||||
# set boundary in main script because ffield is periodic
|
||||
units real
|
||||
# distribute electrode atoms among all processors:
|
||||
if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2"
|
||||
|
||||
atom_style full
|
||||
pair_style lj/cut/coul/long 16
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
kspace_style pppm/electrode 1e-7
|
||||
# kspace_modify in main script because ffield is periodic
|
||||
|
||||
read_data "data.graph-il"
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 -68) to (32.2 34.4 68)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
3776 atoms
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
scanning angles ...
|
||||
1 = max angles/atom
|
||||
reading bonds ...
|
||||
640 bonds
|
||||
reading angles ...
|
||||
320 angles
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.001 seconds
|
||||
read_data CPU = 0.012 seconds
|
||||
|
||||
group bot molecule 641
|
||||
416 atoms in group bot
|
||||
group top molecule 642
|
||||
416 atoms in group top
|
||||
|
||||
group bmi type 1 2 3
|
||||
960 atoms in group bmi
|
||||
group electrolyte type 1 2 3 4
|
||||
1280 atoms in group electrolyte
|
||||
|
||||
fix nvt electrolyte nvt temp 500.0 500.0 100
|
||||
fix shake bmi shake 1e-4 20 0 b 1 2 a 1
|
||||
0 = # of size 2 clusters
|
||||
0 = # of size 3 clusters
|
||||
0 = # of size 4 clusters
|
||||
320 = # of frozen angles
|
||||
find clusters CPU = 0.000 seconds
|
||||
|
||||
variable q atom q
|
||||
compute qtop top reduce sum v_q
|
||||
compute qbot bot reduce sum v_q
|
||||
compute ctemp electrolyte temp
|
||||
kspace_modify slab 3.0
|
||||
|
||||
fix conq bot electrode/conq -1.0 1.979 couple top 1.0 etypes 5 # conq doesn't take symm option
|
||||
832 atoms in group conp_group
|
||||
|
||||
# ask fix conq to output electrode potentials to internal variables
|
||||
variable vbot internal 0.0
|
||||
variable vtop internal 0.0
|
||||
fix_modify conq set v bot vbot
|
||||
fix_modify conq set v top vtop
|
||||
|
||||
thermo 50
|
||||
thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop v_vbot v_vtop
|
||||
run 500
|
||||
PPPM/electrode initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
G vector (1/distance) = 0.20904498
|
||||
grid = 32 32 200
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 3.7023506e-05
|
||||
estimated relative force accuracy = 1.1149519e-07
|
||||
using double precision MKL FFT
|
||||
3d grid and FFT values/proc = 307242 204800
|
||||
generated 10 of 10 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 18
|
||||
ghost atom cutoff = 18
|
||||
binsize = 9, bins = 4 4 16
|
||||
3 neighbor lists, perpetual/occasional/extra = 2 1 0
|
||||
(1) pair lj/cut/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
(2) fix electrode/conq, occasional, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) fix electrode/conq, perpetual, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 56.89 | 56.89 | 56.89 Mbytes
|
||||
Step Temp c_ctemp E_pair TotEng c_qbot c_qtop v_vbot v_vtop
|
||||
0 0 0 25136984 25136984 -1 1 -9.931852 10.097344
|
||||
50 20.206425 72.797911 25136825 25137033 -1 1 -9.4359366 9.5964514
|
||||
100 55.931663 201.50563 25136587 25137163 -1 1 -8.0440112 8.1861787
|
||||
150 81.389273 293.22204 25136533 25137371 -1 1 -6.1113109 6.2267114
|
||||
200 92.867946 334.57639 25136646 25137603 -1 1 -4.1857807 4.2740694
|
||||
250 97.518304 351.33028 25136809 25137814 -1 1 -2.8383703 2.9101475
|
||||
300 102.36577 368.79431 25136933 25137987 -1 1 -2.3831643 2.4461115
|
||||
350 113.66597 409.50566 25136960 25138131 -1 1 -2.7083563 2.7457811
|
||||
400 122.8443 442.57252 25136991 25138256 -1 1 -3.4311003 3.3941657
|
||||
450 128.63713 463.44243 25137048 25138373 -1 1 -4.132871 3.9852959
|
||||
500 131.18361 472.61665 25137142 25138493 -1 1 -4.5104095 4.2567261
|
||||
Loop time of 48.9361 on 1 procs for 500 steps with 3776 atoms
|
||||
|
||||
Performance: 0.883 ns/day, 27.187 hours/ns, 10.217 timesteps/s
|
||||
393.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 17.652 | 17.652 | 17.652 | 0.0 | 36.07
|
||||
Bond | 0.0010418 | 0.0010418 | 0.0010418 | 0.0 | 0.00
|
||||
Kspace | 16.566 | 16.566 | 16.566 | 0.0 | 33.85
|
||||
Neigh | 0.21584 | 0.21584 | 0.21584 | 0.0 | 0.44
|
||||
Comm | 0.04167 | 0.04167 | 0.04167 | 0.0 | 0.09
|
||||
Output | 0.0014585 | 0.0014585 | 0.0014585 | 0.0 | 0.00
|
||||
Modify | 14.445 | 14.445 | 14.445 | 0.0 | 29.52
|
||||
Other | | 0.0134 | | | 0.03
|
||||
|
||||
Nlocal: 3776 ave 3776 max 3776 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 12510 ave 12510 max 12510 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 1.72559e+06 ave 1.72559e+06 max 1.72559e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1725588
|
||||
Ave neighs/atom = 456.98835
|
||||
Ave special neighs/atom = 0.50847458
|
||||
Neighbor list builds = 6
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:01:43
|
||||
@ -0,0 +1,154 @@
|
||||
LAMMPS (24 Mar 2022)
|
||||
# electrodes with constrained total charges
|
||||
# for graphene-ionic liquid supercapacitor
|
||||
|
||||
boundary p p f # slab calculation
|
||||
include settings.mod # styles, groups, computes and fixes
|
||||
# set boundary in main script because ffield is periodic
|
||||
units real
|
||||
# distribute electrode atoms among all processors:
|
||||
if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2"
|
||||
processors * * 2
|
||||
|
||||
atom_style full
|
||||
pair_style lj/cut/coul/long 16
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
kspace_style pppm/electrode 1e-7
|
||||
# kspace_modify in main script because ffield is periodic
|
||||
|
||||
read_data "data.graph-il"
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 -68) to (32.2 34.4 68)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
3776 atoms
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
scanning angles ...
|
||||
1 = max angles/atom
|
||||
reading bonds ...
|
||||
640 bonds
|
||||
reading angles ...
|
||||
320 angles
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.001 seconds
|
||||
read_data CPU = 0.020 seconds
|
||||
|
||||
group bot molecule 641
|
||||
416 atoms in group bot
|
||||
group top molecule 642
|
||||
416 atoms in group top
|
||||
|
||||
group bmi type 1 2 3
|
||||
960 atoms in group bmi
|
||||
group electrolyte type 1 2 3 4
|
||||
1280 atoms in group electrolyte
|
||||
|
||||
fix nvt electrolyte nvt temp 500.0 500.0 100
|
||||
fix shake bmi shake 1e-4 20 0 b 1 2 a 1
|
||||
0 = # of size 2 clusters
|
||||
0 = # of size 3 clusters
|
||||
0 = # of size 4 clusters
|
||||
320 = # of frozen angles
|
||||
find clusters CPU = 0.001 seconds
|
||||
|
||||
variable q atom q
|
||||
compute qtop top reduce sum v_q
|
||||
compute qbot bot reduce sum v_q
|
||||
compute ctemp electrolyte temp
|
||||
kspace_modify slab 3.0
|
||||
|
||||
fix conq bot electrode/conq -1.0 1.979 couple top 1.0 etypes 5 # conq doesn't take symm option
|
||||
832 atoms in group conp_group
|
||||
|
||||
# ask fix conq to output electrode potentials to internal variables
|
||||
variable vbot internal 0.0
|
||||
variable vtop internal 0.0
|
||||
fix_modify conq set v bot vbot
|
||||
fix_modify conq set v top vtop
|
||||
|
||||
thermo 50
|
||||
thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop v_vbot v_vtop
|
||||
run 500
|
||||
PPPM/electrode initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
G vector (1/distance) = 0.20904498
|
||||
grid = 32 32 200
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 3.7023506e-05
|
||||
estimated relative force accuracy = 1.1149519e-07
|
||||
using double precision MKL FFT
|
||||
3d grid and FFT values/proc = 151593 85504
|
||||
generated 10 of 10 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 18
|
||||
ghost atom cutoff = 18
|
||||
binsize = 9, bins = 4 4 16
|
||||
3 neighbor lists, perpetual/occasional/extra = 2 1 0
|
||||
(1) pair lj/cut/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
(2) fix electrode/conq, occasional, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) fix electrode/conq, perpetual, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 23.63 | 27.46 | 31.29 Mbytes
|
||||
Step Temp c_ctemp E_pair TotEng c_qbot c_qtop v_vbot v_vtop
|
||||
0 0 0 25136984 25136984 -1 1 -9.931852 10.097344
|
||||
50 20.206425 72.797911 25136825 25137033 -1 1 -9.4359366 9.5964514
|
||||
100 55.931663 201.50563 25136587 25137163 -1 1 -8.0440112 8.1861787
|
||||
150 81.389273 293.22204 25136533 25137371 -1 1 -6.1113109 6.2267114
|
||||
200 92.867946 334.57639 25136646 25137603 -1 1 -4.1857807 4.2740694
|
||||
250 97.518304 351.33028 25136809 25137814 -1 1 -2.8383703 2.9101475
|
||||
300 102.36577 368.79431 25136933 25137987 -1 1 -2.3831643 2.4461115
|
||||
350 113.66597 409.50566 25136960 25138131 -1 1 -2.7083563 2.7457811
|
||||
400 122.8443 442.57252 25136991 25138256 -1 1 -3.4311003 3.3941657
|
||||
450 128.63713 463.44243 25137048 25138373 -1 1 -4.132871 3.9852959
|
||||
500 131.18361 472.61665 25137142 25138493 -1 1 -4.5104095 4.2567261
|
||||
Loop time of 28.8336 on 4 procs for 500 steps with 3776 atoms
|
||||
|
||||
Performance: 1.498 ns/day, 16.019 hours/ns, 17.341 timesteps/s
|
||||
94.1% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 5.7721 | 5.9353 | 6.144 | 6.0 | 20.58
|
||||
Bond | 0.00057855 | 0.00067043 | 0.00074793 | 0.0 | 0.00
|
||||
Kspace | 13.485 | 13.694 | 13.857 | 4.0 | 47.49
|
||||
Neigh | 0.092021 | 0.092044 | 0.092068 | 0.0 | 0.32
|
||||
Comm | 0.11486 | 0.11638 | 0.11801 | 0.4 | 0.40
|
||||
Output | 0.00090452 | 0.001109 | 0.0017097 | 1.0 | 0.00
|
||||
Modify | 8.974 | 8.9761 | 8.978 | 0.1 | 31.13
|
||||
Other | | 0.01837 | | | 0.06
|
||||
|
||||
Nlocal: 944 ave 948 max 940 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
Nghost: 5920.5 ave 5941 max 5899 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
Neighs: 431397 ave 442329 max 421103 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 1725588
|
||||
Ave neighs/atom = 456.98835
|
||||
Ave special neighs/atom = 0.50847458
|
||||
Neighbor list builds = 6
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:51
|
||||
@ -0,0 +1,170 @@
|
||||
LAMMPS (24 Mar 2022)
|
||||
# electrodes with constrained total charges imposed from dynamically computed potentials
|
||||
# for graphene-ionic liquid supercapacitor
|
||||
|
||||
boundary p p f # slab calculation
|
||||
include settings.mod # styles, groups, computes and fixes
|
||||
# set boundary in main script because ffield is periodic
|
||||
units real
|
||||
# distribute electrode atoms among all processors:
|
||||
if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2"
|
||||
|
||||
atom_style full
|
||||
pair_style lj/cut/coul/long 16
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
kspace_style pppm/electrode 1e-7
|
||||
# kspace_modify in main script because ffield is periodic
|
||||
|
||||
read_data "data.graph-il"
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 -68) to (32.2 34.4 68)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
3776 atoms
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
scanning angles ...
|
||||
1 = max angles/atom
|
||||
reading bonds ...
|
||||
640 bonds
|
||||
reading angles ...
|
||||
320 angles
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.001 seconds
|
||||
read_data CPU = 0.031 seconds
|
||||
|
||||
group bot molecule 641
|
||||
416 atoms in group bot
|
||||
group top molecule 642
|
||||
416 atoms in group top
|
||||
|
||||
group bmi type 1 2 3
|
||||
960 atoms in group bmi
|
||||
group electrolyte type 1 2 3 4
|
||||
1280 atoms in group electrolyte
|
||||
|
||||
fix nvt electrolyte nvt temp 500.0 500.0 100
|
||||
fix shake bmi shake 1e-4 20 0 b 1 2 a 1
|
||||
0 = # of size 2 clusters
|
||||
0 = # of size 3 clusters
|
||||
0 = # of size 4 clusters
|
||||
320 = # of frozen angles
|
||||
find clusters CPU = 0.001 seconds
|
||||
|
||||
variable q atom q
|
||||
compute qtop top reduce sum v_q
|
||||
compute qbot bot reduce sum v_q
|
||||
compute ctemp electrolyte temp
|
||||
kspace_modify slab 3.0
|
||||
|
||||
fix conp bot electrode/conp v_vbot 1.979 couple top v_vtop etypes 5
|
||||
832 atoms in group conp_group
|
||||
|
||||
# get the four entries of electrode elastance matrix
|
||||
variable me00 internal 0.0
|
||||
variable me01 internal 0.0
|
||||
variable me10 internal 0.0
|
||||
variable me11 internal 0.0
|
||||
fix_modify conp set me bot bot me00
|
||||
fix_modify conp set me bot top me01
|
||||
fix_modify conp set me top bot me10
|
||||
fix_modify conp set me top top me11
|
||||
|
||||
# get the 0V charges (qsb), and excess charge required to reach preset total charges
|
||||
variable qsb_bot internal 0.0
|
||||
variable qsb_top internal 0.0
|
||||
fix_modify conp set qsb bot qsb_bot
|
||||
fix_modify conp set qsb top qsb_top
|
||||
variable qex_bot equal -1.0-v_qsb_bot # difference between desired and 0V charge
|
||||
variable qex_top equal 1.0-v_qsb_top # difference between desired and 0V charge
|
||||
|
||||
# calculate imposed potential as elastance * excess charge
|
||||
# note: fix will wait until the run setup to look for its potential variables
|
||||
variable vbot equal v_me00*v_qex_bot+v_me01*v_qex_top
|
||||
variable vtop equal v_me10*v_qex_bot+v_me11*v_qex_top
|
||||
|
||||
thermo 50
|
||||
thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop v_vbot v_vtop
|
||||
run 500
|
||||
PPPM/electrode initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
G vector (1/distance) = 0.20904498
|
||||
grid = 32 32 200
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 3.7023506e-05
|
||||
estimated relative force accuracy = 1.1149519e-07
|
||||
using double precision MKL FFT
|
||||
3d grid and FFT values/proc = 307242 204800
|
||||
generated 10 of 10 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 18
|
||||
ghost atom cutoff = 18
|
||||
binsize = 9, bins = 4 4 16
|
||||
3 neighbor lists, perpetual/occasional/extra = 2 1 0
|
||||
(1) pair lj/cut/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
(2) fix electrode/conp, occasional, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) fix electrode/conp, perpetual, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 56.89 | 56.89 | 56.89 Mbytes
|
||||
Step Temp c_ctemp E_pair TotEng c_qbot c_qtop v_vbot v_vtop
|
||||
0 0 0 25136984 25136984 -1 1 -9.931852 10.097344
|
||||
50 20.206425 72.797911 25136825 25137033 -1 1 -9.4359366 9.5964514
|
||||
100 55.931663 201.50563 25136587 25137163 -1 1 -8.0440112 8.1861787
|
||||
150 81.389273 293.22204 25136533 25137371 -1 1 -6.1113109 6.2267114
|
||||
200 92.867946 334.57639 25136646 25137603 -1 1 -4.1857807 4.2740694
|
||||
250 97.518304 351.33028 25136809 25137814 -1 1 -2.8383703 2.9101475
|
||||
300 102.36577 368.79431 25136933 25137987 -1 1 -2.3831643 2.4461115
|
||||
350 113.66597 409.50566 25136960 25138131 -1 1 -2.7083563 2.7457811
|
||||
400 122.8443 442.57252 25136991 25138256 -1 1 -3.4311003 3.3941657
|
||||
450 128.63713 463.44243 25137048 25138373 -1 1 -4.132871 3.9852959
|
||||
500 131.18361 472.61665 25137142 25138493 -1 1 -4.5104095 4.2567261
|
||||
Loop time of 62.9692 on 1 procs for 500 steps with 3776 atoms
|
||||
|
||||
Performance: 0.686 ns/day, 34.983 hours/ns, 7.940 timesteps/s
|
||||
393.7% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 20.307 | 20.307 | 20.307 | 0.0 | 32.25
|
||||
Bond | 0.0020074 | 0.0020074 | 0.0020074 | 0.0 | 0.00
|
||||
Kspace | 23.562 | 23.562 | 23.562 | 0.0 | 37.42
|
||||
Neigh | 0.26149 | 0.26149 | 0.26149 | 0.0 | 0.42
|
||||
Comm | 0.059436 | 0.059436 | 0.059436 | 0.0 | 0.09
|
||||
Output | 0.0023888 | 0.0023888 | 0.0023888 | 0.0 | 0.00
|
||||
Modify | 18.756 | 18.756 | 18.756 | 0.0 | 29.79
|
||||
Other | | 0.01897 | | | 0.03
|
||||
|
||||
Nlocal: 3776 ave 3776 max 3776 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 12510 ave 12510 max 12510 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 1.72559e+06 ave 1.72559e+06 max 1.72559e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1725588
|
||||
Ave neighs/atom = 456.98835
|
||||
Ave special neighs/atom = 0.50847458
|
||||
Neighbor list builds = 6
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:02:26
|
||||
@ -0,0 +1,171 @@
|
||||
LAMMPS (24 Mar 2022)
|
||||
# electrodes with constrained total charges imposed from dynamically computed potentials
|
||||
# for graphene-ionic liquid supercapacitor
|
||||
|
||||
boundary p p f # slab calculation
|
||||
include settings.mod # styles, groups, computes and fixes
|
||||
# set boundary in main script because ffield is periodic
|
||||
units real
|
||||
# distribute electrode atoms among all processors:
|
||||
if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2"
|
||||
processors * * 2
|
||||
|
||||
atom_style full
|
||||
pair_style lj/cut/coul/long 16
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
kspace_style pppm/electrode 1e-7
|
||||
# kspace_modify in main script because ffield is periodic
|
||||
|
||||
read_data "data.graph-il"
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 -68) to (32.2 34.4 68)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
3776 atoms
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
scanning angles ...
|
||||
1 = max angles/atom
|
||||
reading bonds ...
|
||||
640 bonds
|
||||
reading angles ...
|
||||
320 angles
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.001 seconds
|
||||
read_data CPU = 0.019 seconds
|
||||
|
||||
group bot molecule 641
|
||||
416 atoms in group bot
|
||||
group top molecule 642
|
||||
416 atoms in group top
|
||||
|
||||
group bmi type 1 2 3
|
||||
960 atoms in group bmi
|
||||
group electrolyte type 1 2 3 4
|
||||
1280 atoms in group electrolyte
|
||||
|
||||
fix nvt electrolyte nvt temp 500.0 500.0 100
|
||||
fix shake bmi shake 1e-4 20 0 b 1 2 a 1
|
||||
0 = # of size 2 clusters
|
||||
0 = # of size 3 clusters
|
||||
0 = # of size 4 clusters
|
||||
320 = # of frozen angles
|
||||
find clusters CPU = 0.001 seconds
|
||||
|
||||
variable q atom q
|
||||
compute qtop top reduce sum v_q
|
||||
compute qbot bot reduce sum v_q
|
||||
compute ctemp electrolyte temp
|
||||
kspace_modify slab 3.0
|
||||
|
||||
fix conp bot electrode/conp v_vbot 1.979 couple top v_vtop etypes 5
|
||||
832 atoms in group conp_group
|
||||
|
||||
# get the four entries of electrode elastance matrix
|
||||
variable me00 internal 0.0
|
||||
variable me01 internal 0.0
|
||||
variable me10 internal 0.0
|
||||
variable me11 internal 0.0
|
||||
fix_modify conp set me bot bot me00
|
||||
fix_modify conp set me bot top me01
|
||||
fix_modify conp set me top bot me10
|
||||
fix_modify conp set me top top me11
|
||||
|
||||
# get the 0V charges (qsb), and excess charge required to reach preset total charges
|
||||
variable qsb_bot internal 0.0
|
||||
variable qsb_top internal 0.0
|
||||
fix_modify conp set qsb bot qsb_bot
|
||||
fix_modify conp set qsb top qsb_top
|
||||
variable qex_bot equal -1.0-v_qsb_bot # difference between desired and 0V charge
|
||||
variable qex_top equal 1.0-v_qsb_top # difference between desired and 0V charge
|
||||
|
||||
# calculate imposed potential as elastance * excess charge
|
||||
# note: fix will wait until the run setup to look for its potential variables
|
||||
variable vbot equal v_me00*v_qex_bot+v_me01*v_qex_top
|
||||
variable vtop equal v_me10*v_qex_bot+v_me11*v_qex_top
|
||||
|
||||
thermo 50
|
||||
thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop v_vbot v_vtop
|
||||
run 500
|
||||
PPPM/electrode initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
G vector (1/distance) = 0.20904498
|
||||
grid = 32 32 200
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 3.7023506e-05
|
||||
estimated relative force accuracy = 1.1149519e-07
|
||||
using double precision MKL FFT
|
||||
3d grid and FFT values/proc = 151593 85504
|
||||
generated 10 of 10 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 18
|
||||
ghost atom cutoff = 18
|
||||
binsize = 9, bins = 4 4 16
|
||||
3 neighbor lists, perpetual/occasional/extra = 2 1 0
|
||||
(1) pair lj/cut/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
(2) fix electrode/conp, occasional, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) fix electrode/conp, perpetual, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 23.63 | 27.46 | 31.29 Mbytes
|
||||
Step Temp c_ctemp E_pair TotEng c_qbot c_qtop v_vbot v_vtop
|
||||
0 0 0 25136984 25136984 -1 1 -9.931852 10.097344
|
||||
50 20.206425 72.797911 25136825 25137033 -1 1 -9.4359366 9.5964514
|
||||
100 55.931663 201.50563 25136587 25137163 -1 1 -8.0440112 8.1861787
|
||||
150 81.389273 293.22204 25136533 25137371 -1 1 -6.1113109 6.2267114
|
||||
200 92.867946 334.57639 25136646 25137603 -1 1 -4.1857807 4.2740694
|
||||
250 97.518304 351.33028 25136809 25137814 -1 1 -2.8383703 2.9101475
|
||||
300 102.36577 368.79431 25136933 25137987 -1 1 -2.3831643 2.4461115
|
||||
350 113.66597 409.50566 25136960 25138131 -1 1 -2.7083563 2.7457811
|
||||
400 122.8443 442.57252 25136991 25138256 -1 1 -3.4311003 3.3941657
|
||||
450 128.63713 463.44243 25137048 25138373 -1 1 -4.132871 3.9852959
|
||||
500 131.18361 472.61665 25137142 25138493 -1 1 -4.5104095 4.2567261
|
||||
Loop time of 33.4031 on 4 procs for 500 steps with 3776 atoms
|
||||
|
||||
Performance: 1.293 ns/day, 18.557 hours/ns, 14.969 timesteps/s
|
||||
94.3% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 7.1262 | 7.3913 | 7.611 | 6.8 | 22.13
|
||||
Bond | 0.0007191 | 0.00079089 | 0.00087005 | 0.0 | 0.00
|
||||
Kspace | 15.139 | 15.358 | 15.623 | 4.7 | 45.98
|
||||
Neigh | 0.10374 | 0.10377 | 0.10383 | 0.0 | 0.31
|
||||
Comm | 0.14245 | 0.14353 | 0.14563 | 0.3 | 0.43
|
||||
Output | 0.0012987 | 0.0015671 | 0.0022434 | 1.0 | 0.00
|
||||
Modify | 10.381 | 10.383 | 10.384 | 0.0 | 31.08
|
||||
Other | | 0.02134 | | | 0.06
|
||||
|
||||
Nlocal: 944 ave 948 max 940 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
Nghost: 5920.5 ave 5941 max 5899 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
Neighs: 431397 ave 442329 max 421103 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 1725588
|
||||
Ave neighs/atom = 456.98835
|
||||
Ave special neighs/atom = 0.50847458
|
||||
Neighbor list builds = 6
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:01:01
|
||||
@ -0,0 +1,147 @@
|
||||
LAMMPS (24 Mar 2022)
|
||||
# electrodes with constant potential and smart neighborlists
|
||||
# for graphene-ionic liquid supercapacitor
|
||||
|
||||
boundary p p f # slab calculation
|
||||
include settings.mod # styles, groups, computes and fixes
|
||||
# set boundary in main script because ffield is periodic
|
||||
units real
|
||||
# distribute electrode atoms among all processors:
|
||||
if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2"
|
||||
|
||||
atom_style full
|
||||
pair_style lj/cut/coul/long 16
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
kspace_style pppm/electrode 1e-7
|
||||
# kspace_modify in main script because ffield is periodic
|
||||
|
||||
read_data "data.graph-il"
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 -68) to (32.2 34.4 68)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
3776 atoms
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
scanning angles ...
|
||||
1 = max angles/atom
|
||||
reading bonds ...
|
||||
640 bonds
|
||||
reading angles ...
|
||||
320 angles
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.001 seconds
|
||||
read_data CPU = 0.024 seconds
|
||||
|
||||
group bot molecule 641
|
||||
416 atoms in group bot
|
||||
group top molecule 642
|
||||
416 atoms in group top
|
||||
|
||||
group bmi type 1 2 3
|
||||
960 atoms in group bmi
|
||||
group electrolyte type 1 2 3 4
|
||||
1280 atoms in group electrolyte
|
||||
|
||||
fix nvt electrolyte nvt temp 500.0 500.0 100
|
||||
fix shake bmi shake 1e-4 20 0 b 1 2 a 1
|
||||
0 = # of size 2 clusters
|
||||
0 = # of size 3 clusters
|
||||
0 = # of size 4 clusters
|
||||
320 = # of frozen angles
|
||||
find clusters CPU = 0.001 seconds
|
||||
|
||||
variable q atom q
|
||||
compute qtop top reduce sum v_q
|
||||
compute qbot bot reduce sum v_q
|
||||
compute ctemp electrolyte temp
|
||||
kspace_modify slab 3.0
|
||||
|
||||
fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on etypes 5
|
||||
832 atoms in group conp_group
|
||||
|
||||
thermo 50
|
||||
thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop
|
||||
run 500
|
||||
PPPM/electrode initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
G vector (1/distance) = 0.20904498
|
||||
grid = 32 32 200
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 3.7023506e-05
|
||||
estimated relative force accuracy = 1.1149519e-07
|
||||
using double precision MKL FFT
|
||||
3d grid and FFT values/proc = 307242 204800
|
||||
generated 10 of 10 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 18
|
||||
ghost atom cutoff = 18
|
||||
binsize = 9, bins = 4 4 16
|
||||
3 neighbor lists, perpetual/occasional/extra = 2 1 0
|
||||
(1) pair lj/cut/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
(2) fix electrode/conp, occasional, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) fix electrode/conp, perpetual, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 56.89 | 56.89 | 56.89 Mbytes
|
||||
Step Temp c_ctemp E_pair TotEng c_qbot c_qtop
|
||||
0 0 0 25137191 25137191 0.0085142912 -0.0085142912
|
||||
50 17.83755 64.26354 25137031 25137214 0.0045923944 -0.0045923944
|
||||
100 48.393682 174.34846 25136774 25137273 -0.009514517 0.009514517
|
||||
150 70.421272 253.7075 25136655 25137380 -0.033017005 0.033017005
|
||||
200 82.204844 296.16031 25136667 25137514 -0.063668175 0.063668175
|
||||
250 87.54223 315.38937 25136757 25137659 -0.096776257 0.096776257
|
||||
300 91.704746 330.38571 25136865 25137810 -0.1283784 0.1283784
|
||||
350 100.36017 361.56871 25136934 25137968 -0.15649799 0.15649799
|
||||
400 111.37575 401.25467 25136986 25138133 -0.18065435 0.18065435
|
||||
450 121.79848 438.80476 25137043 25138298 -0.19979365 0.19979365
|
||||
500 126.95916 457.39718 25137145 25138453 -0.21037535 0.21037535
|
||||
Loop time of 63.497 on 1 procs for 500 steps with 3776 atoms
|
||||
|
||||
Performance: 0.680 ns/day, 35.276 hours/ns, 7.874 timesteps/s
|
||||
393.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 20.628 | 20.628 | 20.628 | 0.0 | 32.49
|
||||
Bond | 0.0019309 | 0.0019309 | 0.0019309 | 0.0 | 0.00
|
||||
Kspace | 23.61 | 23.61 | 23.61 | 0.0 | 37.18
|
||||
Neigh | 0.28156 | 0.28156 | 0.28156 | 0.0 | 0.44
|
||||
Comm | 0.061191 | 0.061191 | 0.061191 | 0.0 | 0.10
|
||||
Output | 0.0022666 | 0.0022666 | 0.0022666 | 0.0 | 0.00
|
||||
Modify | 18.891 | 18.891 | 18.891 | 0.0 | 29.75
|
||||
Other | | 0.02047 | | | 0.03
|
||||
|
||||
Nlocal: 3776 ave 3776 max 3776 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 12509 ave 12509 max 12509 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 1.72633e+06 ave 1.72633e+06 max 1.72633e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1726328
|
||||
Ave neighs/atom = 457.18432
|
||||
Ave special neighs/atom = 0.50847458
|
||||
Neighbor list builds = 7
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:02:24
|
||||
@ -0,0 +1,148 @@
|
||||
LAMMPS (24 Mar 2022)
|
||||
# electrodes with constant potential and smart neighborlists
|
||||
# for graphene-ionic liquid supercapacitor
|
||||
|
||||
boundary p p f # slab calculation
|
||||
include settings.mod # styles, groups, computes and fixes
|
||||
# set boundary in main script because ffield is periodic
|
||||
units real
|
||||
# distribute electrode atoms among all processors:
|
||||
if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2"
|
||||
processors * * 2
|
||||
|
||||
atom_style full
|
||||
pair_style lj/cut/coul/long 16
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
kspace_style pppm/electrode 1e-7
|
||||
# kspace_modify in main script because ffield is periodic
|
||||
|
||||
read_data "data.graph-il"
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 -68) to (32.2 34.4 68)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
3776 atoms
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
scanning angles ...
|
||||
1 = max angles/atom
|
||||
reading bonds ...
|
||||
640 bonds
|
||||
reading angles ...
|
||||
320 angles
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.001 seconds
|
||||
read_data CPU = 0.016 seconds
|
||||
|
||||
group bot molecule 641
|
||||
416 atoms in group bot
|
||||
group top molecule 642
|
||||
416 atoms in group top
|
||||
|
||||
group bmi type 1 2 3
|
||||
960 atoms in group bmi
|
||||
group electrolyte type 1 2 3 4
|
||||
1280 atoms in group electrolyte
|
||||
|
||||
fix nvt electrolyte nvt temp 500.0 500.0 100
|
||||
fix shake bmi shake 1e-4 20 0 b 1 2 a 1
|
||||
0 = # of size 2 clusters
|
||||
0 = # of size 3 clusters
|
||||
0 = # of size 4 clusters
|
||||
320 = # of frozen angles
|
||||
find clusters CPU = 0.001 seconds
|
||||
|
||||
variable q atom q
|
||||
compute qtop top reduce sum v_q
|
||||
compute qbot bot reduce sum v_q
|
||||
compute ctemp electrolyte temp
|
||||
kspace_modify slab 3.0
|
||||
|
||||
fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on etypes 5
|
||||
832 atoms in group conp_group
|
||||
|
||||
thermo 50
|
||||
thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop
|
||||
run 500
|
||||
PPPM/electrode initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
G vector (1/distance) = 0.20904498
|
||||
grid = 32 32 200
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 3.7023506e-05
|
||||
estimated relative force accuracy = 1.1149519e-07
|
||||
using double precision MKL FFT
|
||||
3d grid and FFT values/proc = 151593 85504
|
||||
generated 10 of 10 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 18
|
||||
ghost atom cutoff = 18
|
||||
binsize = 9, bins = 4 4 16
|
||||
3 neighbor lists, perpetual/occasional/extra = 2 1 0
|
||||
(1) pair lj/cut/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
(2) fix electrode/conp, occasional, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) fix electrode/conp, perpetual, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 23.63 | 27.46 | 31.29 Mbytes
|
||||
Step Temp c_ctemp E_pair TotEng c_qbot c_qtop
|
||||
0 0 0 25137191 25137191 0.0085142912 -0.0085142912
|
||||
50 17.83755 64.26354 25137031 25137214 0.0045923944 -0.0045923944
|
||||
100 48.393682 174.34846 25136774 25137273 -0.009514517 0.009514517
|
||||
150 70.421272 253.7075 25136655 25137380 -0.033017005 0.033017005
|
||||
200 82.204844 296.16031 25136667 25137514 -0.063668175 0.063668175
|
||||
250 87.54223 315.38937 25136757 25137659 -0.096776257 0.096776257
|
||||
300 91.704746 330.38571 25136865 25137810 -0.1283784 0.1283784
|
||||
350 100.36017 361.56871 25136934 25137968 -0.15649799 0.15649799
|
||||
400 111.37575 401.25467 25136986 25138133 -0.18065435 0.18065435
|
||||
450 121.79848 438.80476 25137043 25138298 -0.19979365 0.19979365
|
||||
500 126.95916 457.39718 25137145 25138453 -0.21037535 0.21037535
|
||||
Loop time of 30.7883 on 4 procs for 500 steps with 3776 atoms
|
||||
|
||||
Performance: 1.403 ns/day, 17.105 hours/ns, 16.240 timesteps/s
|
||||
94.1% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 6.5102 | 6.7303 | 6.9362 | 7.6 | 21.86
|
||||
Bond | 0.00064504 | 0.00071061 | 0.000779 | 0.0 | 0.00
|
||||
Kspace | 14.081 | 14.287 | 14.507 | 5.2 | 46.40
|
||||
Neigh | 0.11831 | 0.11841 | 0.11851 | 0.0 | 0.38
|
||||
Comm | 0.12216 | 0.12434 | 0.12651 | 0.6 | 0.40
|
||||
Output | 0.00083347 | 0.0010533 | 0.0017069 | 1.2 | 0.00
|
||||
Modify | 9.5052 | 9.5071 | 9.5093 | 0.1 | 30.88
|
||||
Other | | 0.01927 | | | 0.06
|
||||
|
||||
Nlocal: 944 ave 951 max 941 min
|
||||
Histogram: 1 2 0 0 0 0 0 0 0 1
|
||||
Nghost: 5923.25 ave 5941 max 5906 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
Neighs: 431582 ave 442090 max 419903 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 1726328
|
||||
Ave neighs/atom = 457.18432
|
||||
Ave special neighs/atom = 0.50847458
|
||||
Neighbor list builds = 7
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:56
|
||||
@ -0,0 +1,146 @@
|
||||
LAMMPS (24 Mar 2022)
|
||||
# electrodes with constant potential using finite field
|
||||
# for z-periodic graphene-ionic liquid supercapacitor
|
||||
|
||||
boundary p p p # ffield uses periodic z-boundary and no slab
|
||||
include settings.mod # styles, groups, computes and fixes
|
||||
# set boundary in main script because ffield is periodic
|
||||
units real
|
||||
# distribute electrode atoms among all processors:
|
||||
if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2"
|
||||
|
||||
atom_style full
|
||||
pair_style lj/cut/coul/long 16
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
kspace_style pppm/electrode 1e-7
|
||||
# kspace_modify in main script because ffield is periodic
|
||||
|
||||
read_data "data.graph-il"
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 -68) to (32.2 34.4 68)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
3776 atoms
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
scanning angles ...
|
||||
1 = max angles/atom
|
||||
reading bonds ...
|
||||
640 bonds
|
||||
reading angles ...
|
||||
320 angles
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.001 seconds
|
||||
read_data CPU = 0.022 seconds
|
||||
|
||||
group bot molecule 641
|
||||
416 atoms in group bot
|
||||
group top molecule 642
|
||||
416 atoms in group top
|
||||
|
||||
group bmi type 1 2 3
|
||||
960 atoms in group bmi
|
||||
group electrolyte type 1 2 3 4
|
||||
1280 atoms in group electrolyte
|
||||
|
||||
fix nvt electrolyte nvt temp 500.0 500.0 100
|
||||
fix shake bmi shake 1e-4 20 0 b 1 2 a 1
|
||||
0 = # of size 2 clusters
|
||||
0 = # of size 3 clusters
|
||||
0 = # of size 4 clusters
|
||||
320 = # of frozen angles
|
||||
find clusters CPU = 0.001 seconds
|
||||
|
||||
variable q atom q
|
||||
compute qtop top reduce sum v_q
|
||||
compute qbot bot reduce sum v_q
|
||||
compute ctemp electrolyte temp
|
||||
|
||||
fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on etypes 5 ffield yes
|
||||
832 atoms in group conp_group
|
||||
|
||||
thermo 50
|
||||
thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop
|
||||
run 500
|
||||
PPPM/electrode initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
G vector (1/distance) = 0.20949995
|
||||
grid = 32 32 90
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 3.5014341e-05
|
||||
estimated relative force accuracy = 1.0544465e-07
|
||||
using double precision MKL FFT
|
||||
3d grid and FFT values/proc = 147537 92160
|
||||
generated 10 of 10 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 18
|
||||
ghost atom cutoff = 18
|
||||
binsize = 9, bins = 4 4 16
|
||||
3 neighbor lists, perpetual/occasional/extra = 2 1 0
|
||||
(1) pair lj/cut/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
(2) fix electrode/conp, occasional, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) fix electrode/conp, perpetual, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 49.5 | 49.5 | 49.5 Mbytes
|
||||
Step Temp c_ctemp E_pair TotEng c_qbot c_qtop
|
||||
0 0 0 25137187 25137187 0.0085209384 -0.0085209384
|
||||
50 17.837642 64.263873 25137027 25137211 0.0045513522 -0.0045513522
|
||||
100 48.393984 174.34955 25136771 25137269 -0.0097291786 0.0097291786
|
||||
150 70.421823 253.70949 25136651 25137377 -0.033522793 0.033522793
|
||||
200 82.205535 296.1628 25136664 25137510 -0.064555648 0.064555648
|
||||
250 87.542843 315.39158 25136754 25137655 -0.098075546 0.098075546
|
||||
300 91.705733 330.38927 25136862 25137806 -0.13006751 0.13006751
|
||||
350 100.36128 361.5727 25136930 25137964 -0.15852814 0.15852814
|
||||
400 111.37586 401.25505 25136982 25138129 -0.18297207 0.18297207
|
||||
450 121.79814 438.80351 25137039 25138294 -0.2023394 0.2023394
|
||||
500 126.95882 457.39597 25137142 25138449 -0.21305221 0.21305221
|
||||
Loop time of 36.7618 on 1 procs for 500 steps with 3776 atoms
|
||||
|
||||
Performance: 1.175 ns/day, 20.423 hours/ns, 13.601 timesteps/s
|
||||
393.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 19.737 | 19.737 | 19.737 | 0.0 | 53.69
|
||||
Bond | 0.00092668 | 0.00092668 | 0.00092668 | 0.0 | 0.00
|
||||
Kspace | 6.5854 | 6.5854 | 6.5854 | 0.0 | 17.91
|
||||
Neigh | 0.33914 | 0.33914 | 0.33914 | 0.0 | 0.92
|
||||
Comm | 0.090124 | 0.090124 | 0.090124 | 0.0 | 0.25
|
||||
Output | 0.0013975 | 0.0013975 | 0.0013975 | 0.0 | 0.00
|
||||
Modify | 9.9834 | 9.9834 | 9.9834 | 0.0 | 27.16
|
||||
Other | | 0.02455 | | | 0.07
|
||||
|
||||
Nlocal: 3776 ave 3776 max 3776 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 23654 ave 23654 max 23654 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 1.86369e+06 ave 1.86369e+06 max 1.86369e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1863691
|
||||
Ave neighs/atom = 493.56224
|
||||
Ave special neighs/atom = 0.50847458
|
||||
Neighbor list builds = 7
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:01:39
|
||||
@ -0,0 +1,147 @@
|
||||
LAMMPS (24 Mar 2022)
|
||||
# electrodes with constant potential using finite field
|
||||
# for z-periodic graphene-ionic liquid supercapacitor
|
||||
|
||||
boundary p p p # ffield uses periodic z-boundary and no slab
|
||||
include settings.mod # styles, groups, computes and fixes
|
||||
# set boundary in main script because ffield is periodic
|
||||
units real
|
||||
# distribute electrode atoms among all processors:
|
||||
if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2"
|
||||
processors * * 2
|
||||
|
||||
atom_style full
|
||||
pair_style lj/cut/coul/long 16
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
kspace_style pppm/electrode 1e-7
|
||||
# kspace_modify in main script because ffield is periodic
|
||||
|
||||
read_data "data.graph-il"
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 -68) to (32.2 34.4 68)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
3776 atoms
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
scanning angles ...
|
||||
1 = max angles/atom
|
||||
reading bonds ...
|
||||
640 bonds
|
||||
reading angles ...
|
||||
320 angles
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.001 seconds
|
||||
read_data CPU = 0.016 seconds
|
||||
|
||||
group bot molecule 641
|
||||
416 atoms in group bot
|
||||
group top molecule 642
|
||||
416 atoms in group top
|
||||
|
||||
group bmi type 1 2 3
|
||||
960 atoms in group bmi
|
||||
group electrolyte type 1 2 3 4
|
||||
1280 atoms in group electrolyte
|
||||
|
||||
fix nvt electrolyte nvt temp 500.0 500.0 100
|
||||
fix shake bmi shake 1e-4 20 0 b 1 2 a 1
|
||||
0 = # of size 2 clusters
|
||||
0 = # of size 3 clusters
|
||||
0 = # of size 4 clusters
|
||||
320 = # of frozen angles
|
||||
find clusters CPU = 0.001 seconds
|
||||
|
||||
variable q atom q
|
||||
compute qtop top reduce sum v_q
|
||||
compute qbot bot reduce sum v_q
|
||||
compute ctemp electrolyte temp
|
||||
|
||||
fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on etypes 5 ffield yes
|
||||
832 atoms in group conp_group
|
||||
|
||||
thermo 50
|
||||
thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop
|
||||
run 500
|
||||
PPPM/electrode initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
G vector (1/distance) = 0.20949995
|
||||
grid = 32 32 90
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 3.5014341e-05
|
||||
estimated relative force accuracy = 1.0544465e-07
|
||||
using double precision MKL FFT
|
||||
3d grid and FFT values/proc = 46644 23552
|
||||
generated 10 of 10 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 18
|
||||
ghost atom cutoff = 18
|
||||
binsize = 9, bins = 4 4 16
|
||||
3 neighbor lists, perpetual/occasional/extra = 2 1 0
|
||||
(1) pair lj/cut/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
(2) fix electrode/conp, occasional, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) fix electrode/conp, perpetual, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 21.96 | 22.27 | 22.77 Mbytes
|
||||
Step Temp c_ctemp E_pair TotEng c_qbot c_qtop
|
||||
0 0 0 25137187 25137187 0.0085209384 -0.0085209384
|
||||
50 17.837642 64.263873 25137027 25137211 0.0045513522 -0.0045513522
|
||||
100 48.393984 174.34955 25136771 25137269 -0.0097291786 0.0097291786
|
||||
150 70.421823 253.70949 25136651 25137377 -0.033522793 0.033522793
|
||||
200 82.205535 296.1628 25136664 25137510 -0.064555648 0.064555648
|
||||
250 87.542843 315.39158 25136754 25137655 -0.098075546 0.098075546
|
||||
300 91.705733 330.38927 25136862 25137806 -0.13006751 0.13006751
|
||||
350 100.36128 361.5727 25136930 25137964 -0.15852814 0.15852814
|
||||
400 111.37586 401.25505 25136982 25138129 -0.18297207 0.18297207
|
||||
450 121.79814 438.80351 25137039 25138294 -0.2023394 0.2023394
|
||||
500 126.95882 457.39597 25137142 25138449 -0.21305221 0.21305221
|
||||
Loop time of 19.3932 on 4 procs for 500 steps with 3776 atoms
|
||||
|
||||
Performance: 2.228 ns/day, 10.774 hours/ns, 25.782 timesteps/s
|
||||
96.3% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 7.1247 | 7.6399 | 8.1323 | 13.3 | 39.39
|
||||
Bond | 0.00072445 | 0.00077581 | 0.00085933 | 0.0 | 0.00
|
||||
Kspace | 5.098 | 5.5905 | 6.1036 | 15.6 | 28.83
|
||||
Neigh | 0.145 | 0.14517 | 0.14532 | 0.0 | 0.75
|
||||
Comm | 0.24683 | 0.25127 | 0.25907 | 1.0 | 1.30
|
||||
Output | 0.00084146 | 0.0011298 | 0.0019741 | 1.5 | 0.01
|
||||
Modify | 5.6957 | 5.7129 | 5.729 | 0.6 | 29.46
|
||||
Other | | 0.05153 | | | 0.27
|
||||
|
||||
Nlocal: 944 ave 951 max 941 min
|
||||
Histogram: 1 2 0 0 0 0 0 0 0 1
|
||||
Nghost: 10122.8 ave 10136 max 10101 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||
Neighs: 465923 ave 510116 max 422901 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 1863691
|
||||
Ave neighs/atom = 493.56224
|
||||
Ave special neighs/atom = 0.50847458
|
||||
Neighbor list builds = 7
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:44
|
||||
@ -0,0 +1,148 @@
|
||||
LAMMPS (24 Mar 2022)
|
||||
# electrodes with equal-style ramped (electrode-)constant potential
|
||||
# for graphene-ionic liquid supercapacitor
|
||||
|
||||
boundary p p f # slab calculation
|
||||
include settings.mod # styles, groups, computes and fixes
|
||||
# set boundary in main script because ffield is periodic
|
||||
units real
|
||||
# distribute electrode atoms among all processors:
|
||||
if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2"
|
||||
|
||||
atom_style full
|
||||
pair_style lj/cut/coul/long 16
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
kspace_style pppm/electrode 1e-7
|
||||
# kspace_modify in main script because ffield is periodic
|
||||
|
||||
read_data "data.graph-il"
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 -68) to (32.2 34.4 68)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
3776 atoms
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
scanning angles ...
|
||||
1 = max angles/atom
|
||||
reading bonds ...
|
||||
640 bonds
|
||||
reading angles ...
|
||||
320 angles
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.001 seconds
|
||||
read_data CPU = 0.014 seconds
|
||||
|
||||
group bot molecule 641
|
||||
416 atoms in group bot
|
||||
group top molecule 642
|
||||
416 atoms in group top
|
||||
|
||||
group bmi type 1 2 3
|
||||
960 atoms in group bmi
|
||||
group electrolyte type 1 2 3 4
|
||||
1280 atoms in group electrolyte
|
||||
|
||||
fix nvt electrolyte nvt temp 500.0 500.0 100
|
||||
fix shake bmi shake 1e-4 20 0 b 1 2 a 1
|
||||
0 = # of size 2 clusters
|
||||
0 = # of size 3 clusters
|
||||
0 = # of size 4 clusters
|
||||
320 = # of frozen angles
|
||||
find clusters CPU = 0.001 seconds
|
||||
|
||||
variable q atom q
|
||||
compute qtop top reduce sum v_q
|
||||
compute qbot bot reduce sum v_q
|
||||
compute ctemp electrolyte temp
|
||||
kspace_modify slab 3.0
|
||||
|
||||
variable v equal ramp(2,4)
|
||||
fix conp bot electrode/conp 0.0 1.979 couple top v_v symm on etypes 5
|
||||
832 atoms in group conp_group
|
||||
|
||||
thermo 50
|
||||
thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop v_v
|
||||
run 500
|
||||
PPPM/electrode initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
G vector (1/distance) = 0.20904498
|
||||
grid = 32 32 200
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 3.7023506e-05
|
||||
estimated relative force accuracy = 1.1149519e-07
|
||||
using double precision MKL FFT
|
||||
3d grid and FFT values/proc = 307242 204800
|
||||
generated 10 of 10 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 18
|
||||
ghost atom cutoff = 18
|
||||
binsize = 9, bins = 4 4 16
|
||||
3 neighbor lists, perpetual/occasional/extra = 2 1 0
|
||||
(1) pair lj/cut/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
(2) fix electrode/conp, occasional, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) fix electrode/conp, perpetual, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 56.89 | 56.89 | 56.89 Mbytes
|
||||
Step Temp c_ctemp E_pair TotEng c_qbot c_qtop v_v
|
||||
0 0 0 25137191 25137191 0.0085142912 -0.0085142912 2
|
||||
50 17.839699 64.271283 25137031 25137214 -0.0067894391 0.0067894391 2.2
|
||||
100 48.411618 174.41308 25136774 25137273 -0.033422174 0.033422174 2.4
|
||||
150 70.478909 253.91515 25136654 25137380 -0.071583953 0.071583953 2.6
|
||||
200 82.322716 296.58497 25136666 25137513 -0.11962095 0.11962095 2.8
|
||||
250 87.739905 316.10153 25136754 25137658 -0.17281469 0.17281469 3
|
||||
300 91.974584 331.35786 25136861 25137808 -0.22657123 0.22657123 3.2
|
||||
350 100.73048 362.90284 25136928 25137965 -0.27817429 0.27817429 3.4
|
||||
400 111.78597 402.73256 25136977 25138129 -0.32659395 0.32659395 3.6
|
||||
450 122.14181 440.04167 25137033 25138291 -0.37054363 0.37054363 3.8
|
||||
500 127.32331 458.70912 25137133 25138444 -0.40653009 0.40653009 4
|
||||
Loop time of 50.8569 on 1 procs for 500 steps with 3776 atoms
|
||||
|
||||
Performance: 0.849 ns/day, 28.254 hours/ns, 9.831 timesteps/s
|
||||
393.5% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 18.166 | 18.166 | 18.166 | 0.0 | 35.72
|
||||
Bond | 0.00091918 | 0.00091918 | 0.00091918 | 0.0 | 0.00
|
||||
Kspace | 17.267 | 17.267 | 17.267 | 0.0 | 33.95
|
||||
Neigh | 0.27635 | 0.27635 | 0.27635 | 0.0 | 0.54
|
||||
Comm | 0.044714 | 0.044714 | 0.044714 | 0.0 | 0.09
|
||||
Output | 0.0018345 | 0.0018345 | 0.0018345 | 0.0 | 0.00
|
||||
Modify | 15.086 | 15.086 | 15.086 | 0.0 | 29.66
|
||||
Other | | 0.01409 | | | 0.03
|
||||
|
||||
Nlocal: 3776 ave 3776 max 3776 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 12511 ave 12511 max 12511 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 1.72628e+06 ave 1.72628e+06 max 1.72628e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1726280
|
||||
Ave neighs/atom = 457.17161
|
||||
Ave special neighs/atom = 0.50847458
|
||||
Neighbor list builds = 7
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:01:50
|
||||
@ -0,0 +1,149 @@
|
||||
LAMMPS (24 Mar 2022)
|
||||
# electrodes with equal-style ramped (electrode-)constant potential
|
||||
# for graphene-ionic liquid supercapacitor
|
||||
|
||||
boundary p p f # slab calculation
|
||||
include settings.mod # styles, groups, computes and fixes
|
||||
# set boundary in main script because ffield is periodic
|
||||
units real
|
||||
# distribute electrode atoms among all processors:
|
||||
if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2"
|
||||
processors * * 2
|
||||
|
||||
atom_style full
|
||||
pair_style lj/cut/coul/long 16
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
kspace_style pppm/electrode 1e-7
|
||||
# kspace_modify in main script because ffield is periodic
|
||||
|
||||
read_data "data.graph-il"
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 -68) to (32.2 34.4 68)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
3776 atoms
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
scanning angles ...
|
||||
1 = max angles/atom
|
||||
reading bonds ...
|
||||
640 bonds
|
||||
reading angles ...
|
||||
320 angles
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.001 seconds
|
||||
read_data CPU = 0.024 seconds
|
||||
|
||||
group bot molecule 641
|
||||
416 atoms in group bot
|
||||
group top molecule 642
|
||||
416 atoms in group top
|
||||
|
||||
group bmi type 1 2 3
|
||||
960 atoms in group bmi
|
||||
group electrolyte type 1 2 3 4
|
||||
1280 atoms in group electrolyte
|
||||
|
||||
fix nvt electrolyte nvt temp 500.0 500.0 100
|
||||
fix shake bmi shake 1e-4 20 0 b 1 2 a 1
|
||||
0 = # of size 2 clusters
|
||||
0 = # of size 3 clusters
|
||||
0 = # of size 4 clusters
|
||||
320 = # of frozen angles
|
||||
find clusters CPU = 0.001 seconds
|
||||
|
||||
variable q atom q
|
||||
compute qtop top reduce sum v_q
|
||||
compute qbot bot reduce sum v_q
|
||||
compute ctemp electrolyte temp
|
||||
kspace_modify slab 3.0
|
||||
|
||||
variable v equal ramp(2,4)
|
||||
fix conp bot electrode/conp 0.0 1.979 couple top v_v symm on etypes 5
|
||||
832 atoms in group conp_group
|
||||
|
||||
thermo 50
|
||||
thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop v_v
|
||||
run 500
|
||||
PPPM/electrode initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
G vector (1/distance) = 0.20904498
|
||||
grid = 32 32 200
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 3.7023506e-05
|
||||
estimated relative force accuracy = 1.1149519e-07
|
||||
using double precision MKL FFT
|
||||
3d grid and FFT values/proc = 151593 85504
|
||||
generated 10 of 10 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 18
|
||||
ghost atom cutoff = 18
|
||||
binsize = 9, bins = 4 4 16
|
||||
3 neighbor lists, perpetual/occasional/extra = 2 1 0
|
||||
(1) pair lj/cut/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
(2) fix electrode/conp, occasional, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) fix electrode/conp, perpetual, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 23.63 | 27.46 | 31.29 Mbytes
|
||||
Step Temp c_ctemp E_pair TotEng c_qbot c_qtop v_v
|
||||
0 0 0 25137191 25137191 0.0085142912 -0.0085142912 2
|
||||
50 17.839699 64.271283 25137031 25137214 -0.0067894391 0.0067894391 2.2
|
||||
100 48.411618 174.41308 25136774 25137273 -0.033422174 0.033422174 2.4
|
||||
150 70.478909 253.91515 25136654 25137380 -0.071583953 0.071583953 2.6
|
||||
200 82.322716 296.58497 25136666 25137513 -0.11962095 0.11962095 2.8
|
||||
250 87.739905 316.10153 25136754 25137658 -0.17281469 0.17281469 3
|
||||
300 91.974584 331.35786 25136861 25137808 -0.22657123 0.22657123 3.2
|
||||
350 100.73048 362.90284 25136928 25137965 -0.27817429 0.27817429 3.4
|
||||
400 111.78597 402.73256 25136977 25138129 -0.32659395 0.32659395 3.6
|
||||
450 122.14181 440.04167 25137033 25138291 -0.37054363 0.37054363 3.8
|
||||
500 127.32331 458.70912 25137133 25138444 -0.40653009 0.40653009 4
|
||||
Loop time of 31.7642 on 4 procs for 500 steps with 3776 atoms
|
||||
|
||||
Performance: 1.360 ns/day, 17.647 hours/ns, 15.741 timesteps/s
|
||||
94.1% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 6.7949 | 7.0359 | 7.3092 | 7.9 | 22.15
|
||||
Bond | 0.00069874 | 0.00073747 | 0.00077928 | 0.0 | 0.00
|
||||
Kspace | 14.375 | 14.648 | 14.89 | 5.5 | 46.12
|
||||
Neigh | 0.12057 | 0.1206 | 0.12062 | 0.0 | 0.38
|
||||
Comm | 0.13412 | 0.13439 | 0.13483 | 0.1 | 0.42
|
||||
Output | 0.0010019 | 0.0013088 | 0.0020937 | 1.3 | 0.00
|
||||
Modify | 9.8017 | 9.8025 | 9.8031 | 0.0 | 30.86
|
||||
Other | | 0.02036 | | | 0.06
|
||||
|
||||
Nlocal: 944 ave 951 max 941 min
|
||||
Histogram: 1 2 0 0 0 0 0 0 0 1
|
||||
Nghost: 5924.75 ave 5941 max 5910 min
|
||||
Histogram: 1 0 0 1 0 1 0 0 0 1
|
||||
Neighs: 431570 ave 442073 max 419253 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 1726280
|
||||
Ave neighs/atom = 457.17161
|
||||
Ave special neighs/atom = 0.50847458
|
||||
Neighbor list builds = 7
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:58
|
||||
@ -0,0 +1,154 @@
|
||||
LAMMPS (24 Mar 2022)
|
||||
# electrodes with thermopotentiostat
|
||||
# for graphene-ionic liquid supercapacitor
|
||||
|
||||
boundary p p f # slab calculation
|
||||
include settings.mod # styles, groups, computes and fixes
|
||||
# set boundary in main script because ffield is periodic
|
||||
units real
|
||||
# distribute electrode atoms among all processors:
|
||||
if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2"
|
||||
|
||||
atom_style full
|
||||
pair_style lj/cut/coul/long 16
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
kspace_style pppm/electrode 1e-7
|
||||
# kspace_modify in main script because ffield is periodic
|
||||
|
||||
read_data "data.graph-il"
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 -68) to (32.2 34.4 68)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
3776 atoms
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
scanning angles ...
|
||||
1 = max angles/atom
|
||||
reading bonds ...
|
||||
640 bonds
|
||||
reading angles ...
|
||||
320 angles
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.002 seconds
|
||||
read_data CPU = 0.024 seconds
|
||||
|
||||
group bot molecule 641
|
||||
416 atoms in group bot
|
||||
group top molecule 642
|
||||
416 atoms in group top
|
||||
|
||||
group bmi type 1 2 3
|
||||
960 atoms in group bmi
|
||||
group electrolyte type 1 2 3 4
|
||||
1280 atoms in group electrolyte
|
||||
|
||||
fix nvt electrolyte nvt temp 500.0 500.0 100
|
||||
fix shake bmi shake 1e-4 20 0 b 1 2 a 1
|
||||
0 = # of size 2 clusters
|
||||
0 = # of size 3 clusters
|
||||
0 = # of size 4 clusters
|
||||
320 = # of frozen angles
|
||||
find clusters CPU = 0.000 seconds
|
||||
|
||||
variable q atom q
|
||||
compute qtop top reduce sum v_q
|
||||
compute qbot bot reduce sum v_q
|
||||
compute ctemp electrolyte temp
|
||||
kspace_modify slab 3.0
|
||||
|
||||
unfix nvt # remove NVT thermostat included from "settings.mod"
|
||||
fix conpthermo bot electrode/thermo -1.0 1.979 couple top 1.0 etypes 5 temp 500 100 7 # temp tau rng
|
||||
832 atoms in group conp_group
|
||||
# to compare to regular constant potential, switch previous line to this:
|
||||
#fix conp bot electrode/conp -1.0 1.979 couple top 1.0 etypes 5 symm on
|
||||
fix nve electrolyte nve
|
||||
|
||||
# note ionic liquid does not reach 500K immediately
|
||||
# because its thermal response time is finite
|
||||
# run this about 10k steps (10ps) to reach preset temperature
|
||||
thermo 50
|
||||
thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop
|
||||
run 500
|
||||
PPPM/electrode initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
G vector (1/distance) = 0.20904498
|
||||
grid = 32 32 200
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 3.7023506e-05
|
||||
estimated relative force accuracy = 1.1149519e-07
|
||||
using double precision MKL FFT
|
||||
3d grid and FFT values/proc = 307242 204800
|
||||
generated 10 of 10 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 18
|
||||
ghost atom cutoff = 18
|
||||
binsize = 9, bins = 4 4 16
|
||||
3 neighbor lists, perpetual/occasional/extra = 2 1 0
|
||||
(1) pair lj/cut/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
(2) fix electrode/thermo, occasional, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) fix electrode/thermo, perpetual, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 56.89 | 56.89 | 56.89 Mbytes
|
||||
Step Temp c_ctemp E_pair TotEng c_qbot c_qtop
|
||||
0 0 0 25137187 25137187 0.12767613 -0.12767613
|
||||
50 16.63971 59.94807 25137031 25137203 0.11714714 -0.11714714
|
||||
100 40.785523 146.93846 25136782 25137202 0.1278358 -0.1278358
|
||||
150 53.394067 192.3634 25136654 25137204 0.080257143 -0.080257143
|
||||
200 56.419019 203.26143 25136624 25137205 0.024756489 -0.024756489
|
||||
250 54.922935 197.87147 25136640 25137205 -0.024533719 0.024533719
|
||||
300 52.884861 190.52888 25136660 25137205 -0.066341094 0.066341094
|
||||
350 52.41676 188.84244 25136666 25137206 -0.089546252 0.089546252
|
||||
400 54.366979 195.86852 25136646 25137206 -0.10239753 0.10239753
|
||||
450 54.906542 197.81241 25136642 25137208 -0.099987401 0.099987401
|
||||
500 54.33841 195.7656 25136642 25137201 -0.21295942 0.21295942
|
||||
Loop time of 49.9831 on 1 procs for 500 steps with 3776 atoms
|
||||
|
||||
Performance: 0.864 ns/day, 27.768 hours/ns, 10.003 timesteps/s
|
||||
393.3% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 17.01 | 17.01 | 17.01 | 0.0 | 34.03
|
||||
Bond | 0.0010374 | 0.0010374 | 0.0010374 | 0.0 | 0.00
|
||||
Kspace | 18.096 | 18.096 | 18.096 | 0.0 | 36.20
|
||||
Neigh | 0.1828 | 0.1828 | 0.1828 | 0.0 | 0.37
|
||||
Comm | 0.043856 | 0.043856 | 0.043856 | 0.0 | 0.09
|
||||
Output | 0.0018373 | 0.0018373 | 0.0018373 | 0.0 | 0.00
|
||||
Modify | 14.632 | 14.632 | 14.632 | 0.0 | 29.27
|
||||
Other | | 0.01548 | | | 0.03
|
||||
|
||||
Nlocal: 3776 ave 3776 max 3776 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 12504 ave 12504 max 12504 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 1.72597e+06 ave 1.72597e+06 max 1.72597e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1725966
|
||||
Ave neighs/atom = 457.08845
|
||||
Ave special neighs/atom = 0.50847458
|
||||
Neighbor list builds = 5
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:01:50
|
||||
@ -0,0 +1,155 @@
|
||||
LAMMPS (24 Mar 2022)
|
||||
# electrodes with thermopotentiostat
|
||||
# for graphene-ionic liquid supercapacitor
|
||||
|
||||
boundary p p f # slab calculation
|
||||
include settings.mod # styles, groups, computes and fixes
|
||||
# set boundary in main script because ffield is periodic
|
||||
units real
|
||||
# distribute electrode atoms among all processors:
|
||||
if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2"
|
||||
processors * * 2
|
||||
|
||||
atom_style full
|
||||
pair_style lj/cut/coul/long 16
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
kspace_style pppm/electrode 1e-7
|
||||
# kspace_modify in main script because ffield is periodic
|
||||
|
||||
read_data "data.graph-il"
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 -68) to (32.2 34.4 68)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
3776 atoms
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
scanning angles ...
|
||||
1 = max angles/atom
|
||||
reading bonds ...
|
||||
640 bonds
|
||||
reading angles ...
|
||||
320 angles
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.002 seconds
|
||||
read_data CPU = 0.025 seconds
|
||||
|
||||
group bot molecule 641
|
||||
416 atoms in group bot
|
||||
group top molecule 642
|
||||
416 atoms in group top
|
||||
|
||||
group bmi type 1 2 3
|
||||
960 atoms in group bmi
|
||||
group electrolyte type 1 2 3 4
|
||||
1280 atoms in group electrolyte
|
||||
|
||||
fix nvt electrolyte nvt temp 500.0 500.0 100
|
||||
fix shake bmi shake 1e-4 20 0 b 1 2 a 1
|
||||
0 = # of size 2 clusters
|
||||
0 = # of size 3 clusters
|
||||
0 = # of size 4 clusters
|
||||
320 = # of frozen angles
|
||||
find clusters CPU = 0.001 seconds
|
||||
|
||||
variable q atom q
|
||||
compute qtop top reduce sum v_q
|
||||
compute qbot bot reduce sum v_q
|
||||
compute ctemp electrolyte temp
|
||||
kspace_modify slab 3.0
|
||||
|
||||
unfix nvt # remove NVT thermostat included from "settings.mod"
|
||||
fix conpthermo bot electrode/thermo -1.0 1.979 couple top 1.0 etypes 5 temp 500 100 7 # temp tau rng
|
||||
832 atoms in group conp_group
|
||||
# to compare to regular constant potential, switch previous line to this:
|
||||
#fix conp bot electrode/conp -1.0 1.979 couple top 1.0 etypes 5 symm on
|
||||
fix nve electrolyte nve
|
||||
|
||||
# note ionic liquid does not reach 500K immediately
|
||||
# because its thermal response time is finite
|
||||
# run this about 10k steps (10ps) to reach preset temperature
|
||||
thermo 50
|
||||
thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop
|
||||
run 500
|
||||
PPPM/electrode initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
G vector (1/distance) = 0.20904498
|
||||
grid = 32 32 200
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 3.7023506e-05
|
||||
estimated relative force accuracy = 1.1149519e-07
|
||||
using double precision MKL FFT
|
||||
3d grid and FFT values/proc = 151593 85504
|
||||
generated 10 of 10 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 18
|
||||
ghost atom cutoff = 18
|
||||
binsize = 9, bins = 4 4 16
|
||||
3 neighbor lists, perpetual/occasional/extra = 2 1 0
|
||||
(1) pair lj/cut/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
(2) fix electrode/thermo, occasional, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) fix electrode/thermo, perpetual, skip from (1)
|
||||
attributes: half, newton on
|
||||
pair build: skip
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 23.63 | 27.46 | 31.29 Mbytes
|
||||
Step Temp c_ctemp E_pair TotEng c_qbot c_qtop
|
||||
0 0 0 25137187 25137187 0.12767613 -0.12767613
|
||||
50 16.63971 59.94807 25137031 25137203 0.11714714 -0.11714714
|
||||
100 40.785523 146.93846 25136782 25137202 0.1278358 -0.1278358
|
||||
150 53.394067 192.3634 25136654 25137204 0.080257143 -0.080257143
|
||||
200 56.419019 203.26143 25136624 25137205 0.024756489 -0.024756489
|
||||
250 54.922935 197.87147 25136640 25137205 -0.024533719 0.024533719
|
||||
300 52.884861 190.52888 25136660 25137205 -0.066341094 0.066341094
|
||||
350 52.41676 188.84244 25136666 25137206 -0.089546252 0.089546252
|
||||
400 54.366979 195.86852 25136646 25137206 -0.10239753 0.10239753
|
||||
450 54.906542 197.81241 25136642 25137208 -0.099987401 0.099987401
|
||||
500 54.33841 195.7656 25136642 25137201 -0.21295942 0.21295942
|
||||
Loop time of 27.6772 on 4 procs for 500 steps with 3776 atoms
|
||||
|
||||
Performance: 1.561 ns/day, 15.376 hours/ns, 18.065 timesteps/s
|
||||
91.7% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 4.6214 | 4.8032 | 4.9546 | 6.5 | 17.35
|
||||
Bond | 0.0005324 | 0.00060509 | 0.00069468 | 0.0 | 0.00
|
||||
Kspace | 13.883 | 14.034 | 14.216 | 3.8 | 50.71
|
||||
Neigh | 0.061704 | 0.061727 | 0.06176 | 0.0 | 0.22
|
||||
Comm | 0.10101 | 0.10374 | 0.10645 | 0.8 | 0.37
|
||||
Output | 0.00086818 | 0.0010909 | 0.001715 | 1.1 | 0.00
|
||||
Modify | 8.65 | 8.6524 | 8.6545 | 0.1 | 31.26
|
||||
Other | | 0.02055 | | | 0.07
|
||||
|
||||
Nlocal: 944 ave 951 max 940 min
|
||||
Histogram: 1 1 1 0 0 0 0 0 0 1
|
||||
Nghost: 5918.5 ave 5940 max 5899 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
Neighs: 431492 ave 442132 max 419533 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 1725966
|
||||
Ave neighs/atom = 457.08845
|
||||
Ave special neighs/atom = 0.50847458
|
||||
Neighbor list builds = 5
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:50
|
||||
27
examples/PACKAGES/electrode/graph-il/settings.mod
Normal file
27
examples/PACKAGES/electrode/graph-il/settings.mod
Normal file
@ -0,0 +1,27 @@
|
||||
# set boundary in main script because ffield is periodic
|
||||
units real
|
||||
# distribute electrode atoms among all processors:
|
||||
if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2"
|
||||
|
||||
atom_style full
|
||||
pair_style lj/cut/coul/long 16
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
kspace_style pppm/electrode 1e-7
|
||||
# kspace_modify in main script because ffield is periodic
|
||||
|
||||
read_data "data.graph-il"
|
||||
|
||||
group bot molecule 641
|
||||
group top molecule 642
|
||||
|
||||
group bmi type 1 2 3
|
||||
group electrolyte type 1 2 3 4
|
||||
|
||||
fix nvt electrolyte nvt temp 500.0 500.0 100
|
||||
fix shake bmi shake 1e-4 20 0 b 1 2 a 1
|
||||
|
||||
variable q atom q
|
||||
compute qtop top reduce sum v_q
|
||||
compute qbot bot reduce sum v_q
|
||||
compute ctemp electrolyte temp
|
||||
1
examples/PACKAGES/electrode/planar/.gitignore
vendored
Normal file
1
examples/PACKAGES/electrode/planar/.gitignore
vendored
Normal file
@ -0,0 +1 @@
|
||||
log.lammps*
|
||||
600
examples/PACKAGES/electrode/planar/data.au-vac
Normal file
600
examples/PACKAGES/electrode/planar/data.au-vac
Normal file
@ -0,0 +1,600 @@
|
||||
LAMMPS data file via write_data, version 24 Dec 2020, timestep = 0
|
||||
|
||||
288 atoms
|
||||
2 atom types
|
||||
|
||||
0.285001 25.325067 xlo xhi
|
||||
-0.368323 24.671743 ylo yhi
|
||||
-1.043333 43.303354 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 196.966553
|
||||
2 196.966553
|
||||
|
||||
Pair Coeffs # lj/cut/coul/long
|
||||
|
||||
1 0 0
|
||||
2 0 0
|
||||
|
||||
Atoms # full
|
||||
|
||||
2 1 1 -0.002921 2.086672 2.086672 8 0 0 0
|
||||
3 1 1 -0.04033 2.086672 0 10.086673 0 1 0
|
||||
5 1 1 -0.000757 4.173345 0 8 0 1 0
|
||||
6 1 1 -0.000483 6.260016 2.086672 8 0 0 0
|
||||
7 1 1 -0.02377 6.260016 0 10.086673 0 1 0
|
||||
8 1 1 -0.031311 4.173345 2.086672 10.086673 0 0 0
|
||||
9 1 1 -0.002302 8.346689 0 8 0 1 0
|
||||
12 1 1 -0.03014 8.346689 2.086672 10.086673 0 0 0
|
||||
26 1 1 -3e-05 2.086672 6.260016 8 0 0 0
|
||||
27 1 1 -0.011104 2.086672 4.173345 10.086673 0 0 0
|
||||
29 1 1 0.000807 4.173345 4.173345 8 0 0 0
|
||||
30 1 1 -0.000974 6.260016 6.260016 8 0 0 0
|
||||
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|
||||
277 2 2 -0.004414 12.520033 20.86672 32.173344 0 0 0
|
||||
278 2 2 0.017397 14.606705 22.953394 32.173344 0 0 0
|
||||
279 2 2 0.001344 14.606705 20.86672 34.260021 0 0 0
|
||||
280 2 2 0.000672 12.520033 22.953394 34.260021 0 0 0
|
||||
281 2 2 0.0252 16.693378 20.86672 32.173344 0 0 0
|
||||
284 2 2 0.001824 16.693378 22.953394 34.260021 0 0 0
|
||||
241 2 2 0.029057 25.040066 16.693378 32.173344 0 0 0
|
||||
244 2 2 0.001076 25.040066 18.780048 34.260021 0 0 0
|
||||
258 2 2 0.035183 18.780048 18.780048 32.173344 0 0 0
|
||||
259 2 2 0.0002 18.780048 16.693378 34.260021 0 0 0
|
||||
261 2 2 0.034083 20.86672 16.693378 32.173344 0 0 0
|
||||
262 2 2 0.036995 22.953394 18.780048 32.173344 0 0 0
|
||||
263 2 2 0.001484 22.953394 16.693378 34.260021 0 0 0
|
||||
264 2 2 0.00377 20.86672 18.780048 34.260021 0 0 0
|
||||
265 2 2 0.024028 25.040066 20.86672 32.173344 0 0 0
|
||||
268 2 2 0.001334 25.040066 22.953394 34.260021 0 0 0
|
||||
282 2 2 0.030927 18.780048 22.953394 32.173344 0 0 0
|
||||
283 2 2 0.002185 18.780048 20.86672 34.260021 0 0 0
|
||||
285 2 2 0.043618 20.86672 20.86672 32.173344 0 0 0
|
||||
286 2 2 0.030615 22.953394 22.953394 32.173344 0 0 0
|
||||
287 2 2 0.001068 22.953394 20.86672 34.260021 0 0 0
|
||||
288 2 2 0.001887 20.86672 22.953394 34.260021 0 0 0
|
||||
|
||||
Velocities
|
||||
|
||||
2 0 0 0
|
||||
3 0 0 0
|
||||
5 0 0 0
|
||||
6 0 0 0
|
||||
7 0 0 0
|
||||
8 0 0 0
|
||||
9 0 0 0
|
||||
12 0 0 0
|
||||
26 0 0 0
|
||||
27 0 0 0
|
||||
29 0 0 0
|
||||
30 0 0 0
|
||||
31 0 0 0
|
||||
32 0 0 0
|
||||
33 0 0 0
|
||||
36 0 0 0
|
||||
10 0 0 0
|
||||
11 0 0 0
|
||||
13 0 0 0
|
||||
14 0 0 0
|
||||
15 0 0 0
|
||||
16 0 0 0
|
||||
17 0 0 0
|
||||
20 0 0 0
|
||||
34 0 0 0
|
||||
35 0 0 0
|
||||
37 0 0 0
|
||||
38 0 0 0
|
||||
39 0 0 0
|
||||
40 0 0 0
|
||||
41 0 0 0
|
||||
44 0 0 0
|
||||
1 0 0 0
|
||||
4 0 0 0
|
||||
18 0 0 0
|
||||
19 0 0 0
|
||||
21 0 0 0
|
||||
22 0 0 0
|
||||
23 0 0 0
|
||||
24 0 0 0
|
||||
25 0 0 0
|
||||
28 0 0 0
|
||||
42 0 0 0
|
||||
43 0 0 0
|
||||
45 0 0 0
|
||||
46 0 0 0
|
||||
47 0 0 0
|
||||
48 0 0 0
|
||||
50 0 0 0
|
||||
51 0 0 0
|
||||
53 0 0 0
|
||||
54 0 0 0
|
||||
55 0 0 0
|
||||
56 0 0 0
|
||||
57 0 0 0
|
||||
60 0 0 0
|
||||
74 0 0 0
|
||||
75 0 0 0
|
||||
77 0 0 0
|
||||
78 0 0 0
|
||||
79 0 0 0
|
||||
80 0 0 0
|
||||
81 0 0 0
|
||||
84 0 0 0
|
||||
58 0 0 0
|
||||
59 0 0 0
|
||||
61 0 0 0
|
||||
62 0 0 0
|
||||
63 0 0 0
|
||||
64 0 0 0
|
||||
65 0 0 0
|
||||
68 0 0 0
|
||||
82 0 0 0
|
||||
83 0 0 0
|
||||
85 0 0 0
|
||||
86 0 0 0
|
||||
87 0 0 0
|
||||
88 0 0 0
|
||||
89 0 0 0
|
||||
92 0 0 0
|
||||
49 0 0 0
|
||||
52 0 0 0
|
||||
66 0 0 0
|
||||
67 0 0 0
|
||||
69 0 0 0
|
||||
70 0 0 0
|
||||
71 0 0 0
|
||||
72 0 0 0
|
||||
73 0 0 0
|
||||
76 0 0 0
|
||||
90 0 0 0
|
||||
91 0 0 0
|
||||
93 0 0 0
|
||||
94 0 0 0
|
||||
95 0 0 0
|
||||
96 0 0 0
|
||||
98 0 0 0
|
||||
99 0 0 0
|
||||
101 0 0 0
|
||||
102 0 0 0
|
||||
103 0 0 0
|
||||
104 0 0 0
|
||||
105 0 0 0
|
||||
108 0 0 0
|
||||
122 0 0 0
|
||||
123 0 0 0
|
||||
125 0 0 0
|
||||
126 0 0 0
|
||||
127 0 0 0
|
||||
128 0 0 0
|
||||
129 0 0 0
|
||||
132 0 0 0
|
||||
106 0 0 0
|
||||
107 0 0 0
|
||||
109 0 0 0
|
||||
110 0 0 0
|
||||
111 0 0 0
|
||||
112 0 0 0
|
||||
113 0 0 0
|
||||
116 0 0 0
|
||||
130 0 0 0
|
||||
131 0 0 0
|
||||
133 0 0 0
|
||||
134 0 0 0
|
||||
135 0 0 0
|
||||
136 0 0 0
|
||||
137 0 0 0
|
||||
140 0 0 0
|
||||
97 0 0 0
|
||||
100 0 0 0
|
||||
114 0 0 0
|
||||
115 0 0 0
|
||||
117 0 0 0
|
||||
118 0 0 0
|
||||
119 0 0 0
|
||||
120 0 0 0
|
||||
121 0 0 0
|
||||
124 0 0 0
|
||||
138 0 0 0
|
||||
139 0 0 0
|
||||
141 0 0 0
|
||||
142 0 0 0
|
||||
143 0 0 0
|
||||
144 0 0 0
|
||||
146 0 0 0
|
||||
147 0 0 0
|
||||
149 0 0 0
|
||||
150 0 0 0
|
||||
151 0 0 0
|
||||
152 0 0 0
|
||||
153 0 0 0
|
||||
156 0 0 0
|
||||
170 0 0 0
|
||||
171 0 0 0
|
||||
173 0 0 0
|
||||
174 0 0 0
|
||||
175 0 0 0
|
||||
176 0 0 0
|
||||
177 0 0 0
|
||||
180 0 0 0
|
||||
154 0 0 0
|
||||
155 0 0 0
|
||||
157 0 0 0
|
||||
158 0 0 0
|
||||
159 0 0 0
|
||||
160 0 0 0
|
||||
161 0 0 0
|
||||
164 0 0 0
|
||||
178 0 0 0
|
||||
179 0 0 0
|
||||
181 0 0 0
|
||||
182 0 0 0
|
||||
183 0 0 0
|
||||
184 0 0 0
|
||||
185 0 0 0
|
||||
188 0 0 0
|
||||
145 0 0 0
|
||||
148 0 0 0
|
||||
162 0 0 0
|
||||
163 0 0 0
|
||||
165 0 0 0
|
||||
166 0 0 0
|
||||
167 0 0 0
|
||||
168 0 0 0
|
||||
169 0 0 0
|
||||
172 0 0 0
|
||||
186 0 0 0
|
||||
187 0 0 0
|
||||
189 0 0 0
|
||||
190 0 0 0
|
||||
191 0 0 0
|
||||
192 0 0 0
|
||||
194 0 0 0
|
||||
195 0 0 0
|
||||
197 0 0 0
|
||||
198 0 0 0
|
||||
199 0 0 0
|
||||
200 0 0 0
|
||||
201 0 0 0
|
||||
204 0 0 0
|
||||
218 0 0 0
|
||||
219 0 0 0
|
||||
221 0 0 0
|
||||
222 0 0 0
|
||||
223 0 0 0
|
||||
224 0 0 0
|
||||
225 0 0 0
|
||||
228 0 0 0
|
||||
202 0 0 0
|
||||
203 0 0 0
|
||||
205 0 0 0
|
||||
206 0 0 0
|
||||
207 0 0 0
|
||||
208 0 0 0
|
||||
209 0 0 0
|
||||
212 0 0 0
|
||||
226 0 0 0
|
||||
227 0 0 0
|
||||
229 0 0 0
|
||||
230 0 0 0
|
||||
231 0 0 0
|
||||
232 0 0 0
|
||||
233 0 0 0
|
||||
236 0 0 0
|
||||
193 0 0 0
|
||||
196 0 0 0
|
||||
210 0 0 0
|
||||
211 0 0 0
|
||||
213 0 0 0
|
||||
214 0 0 0
|
||||
215 0 0 0
|
||||
216 0 0 0
|
||||
217 0 0 0
|
||||
220 0 0 0
|
||||
234 0 0 0
|
||||
235 0 0 0
|
||||
237 0 0 0
|
||||
238 0 0 0
|
||||
239 0 0 0
|
||||
240 0 0 0
|
||||
242 0 0 0
|
||||
243 0 0 0
|
||||
245 0 0 0
|
||||
246 0 0 0
|
||||
247 0 0 0
|
||||
248 0 0 0
|
||||
249 0 0 0
|
||||
252 0 0 0
|
||||
266 0 0 0
|
||||
267 0 0 0
|
||||
269 0 0 0
|
||||
270 0 0 0
|
||||
271 0 0 0
|
||||
272 0 0 0
|
||||
273 0 0 0
|
||||
276 0 0 0
|
||||
250 0 0 0
|
||||
251 0 0 0
|
||||
253 0 0 0
|
||||
254 0 0 0
|
||||
255 0 0 0
|
||||
256 0 0 0
|
||||
257 0 0 0
|
||||
260 0 0 0
|
||||
274 0 0 0
|
||||
275 0 0 0
|
||||
277 0 0 0
|
||||
278 0 0 0
|
||||
279 0 0 0
|
||||
280 0 0 0
|
||||
281 0 0 0
|
||||
284 0 0 0
|
||||
241 0 0 0
|
||||
244 0 0 0
|
||||
258 0 0 0
|
||||
259 0 0 0
|
||||
261 0 0 0
|
||||
262 0 0 0
|
||||
263 0 0 0
|
||||
264 0 0 0
|
||||
265 0 0 0
|
||||
268 0 0 0
|
||||
282 0 0 0
|
||||
283 0 0 0
|
||||
285 0 0 0
|
||||
286 0 0 0
|
||||
287 0 0 0
|
||||
288 0 0 0
|
||||
14
examples/PACKAGES/electrode/planar/in.planar-ewald-ew2d
Normal file
14
examples/PACKAGES/electrode/planar/in.planar-ewald-ew2d
Normal file
@ -0,0 +1,14 @@
|
||||
boundary p p f
|
||||
kspace_style ewald/electrode 1.0e-7
|
||||
kspace_modify slab ew2d
|
||||
|
||||
include "settings.mod" # styles, computes, groups and fixes
|
||||
|
||||
# constant potential electrodes with ramping potential difference
|
||||
fix conp bot electrode/conp 0 1.979 couple top v_v symm on
|
||||
|
||||
thermo 1
|
||||
# thermo: step, imposed potential, bottom charge, top charge, theory charge, percent deviation
|
||||
thermo_style custom step v_v c_qbot c_qtop v_qtheory v_percdev
|
||||
|
||||
run 10
|
||||
14
examples/PACKAGES/electrode/planar/in.planar-ewald-ew3dc
Normal file
14
examples/PACKAGES/electrode/planar/in.planar-ewald-ew3dc
Normal file
@ -0,0 +1,14 @@
|
||||
boundary p p f
|
||||
kspace_style ewald/electrode 1.0e-7
|
||||
kspace_modify slab 3.0 # ew3dc
|
||||
|
||||
include "settings.mod" # styles, computes, groups and fixes
|
||||
|
||||
# constant potential electrodes with ramping potential difference
|
||||
fix conp bot electrode/conp 0 1.979 couple top v_v symm on
|
||||
|
||||
thermo 1
|
||||
# thermo: step, imposed potential, bottom charge, top charge, theory charge, percent deviation
|
||||
thermo_style custom step v_v c_qbot c_qtop v_qtheory v_percdev
|
||||
|
||||
run 10
|
||||
13
examples/PACKAGES/electrode/planar/in.planar-ewald-ffield
Normal file
13
examples/PACKAGES/electrode/planar/in.planar-ewald-ffield
Normal file
@ -0,0 +1,13 @@
|
||||
boundary p p p # finite field, fully periodic
|
||||
kspace_style ewald/electrode 1.0e-7
|
||||
|
||||
include "settings.mod" # styles, computes, groups and fixes
|
||||
|
||||
# constant potential electrodes with ramping potential difference
|
||||
fix conp bot electrode/conp 0 1.979 couple top v_v symm on ffield yes
|
||||
|
||||
thermo 1
|
||||
# thermo: step, imposed potential, bottom charge, top charge, theory charge, percent deviation
|
||||
thermo_style custom step v_v c_qbot c_qtop v_qtheory v_percdev
|
||||
|
||||
run 10
|
||||
15
examples/PACKAGES/electrode/planar/in.planar-pppm-ew3dc
Normal file
15
examples/PACKAGES/electrode/planar/in.planar-pppm-ew3dc
Normal file
@ -0,0 +1,15 @@
|
||||
boundary p p f
|
||||
kspace_style pppm/electrode 1.0e-7
|
||||
kspace_modify slab 3.0
|
||||
|
||||
include "settings.mod" # styles, computes, groups and fixes
|
||||
|
||||
# constant potential electrodes with ramping potential difference
|
||||
fix conp bot electrode/conp 0 1.979 couple top v_v symm on
|
||||
|
||||
thermo 1
|
||||
# thermo: step, imposed potential, bottom charge, top charge, theory charge, percent deviation
|
||||
thermo_style custom step v_v c_qbot c_qtop v_qtheory v_percdev
|
||||
|
||||
run 10
|
||||
|
||||
13
examples/PACKAGES/electrode/planar/in.planar-pppm-ffield
Normal file
13
examples/PACKAGES/electrode/planar/in.planar-pppm-ffield
Normal file
@ -0,0 +1,13 @@
|
||||
boundary p p p # finite field, fully periodic
|
||||
kspace_style pppm/electrode 1.0e-7
|
||||
|
||||
include "settings.mod" # styles, computes, groups and fixes
|
||||
|
||||
# constant potential electrodes with ramping potential difference
|
||||
fix conp bot electrode/conp 0 1.979 couple top v_v symm on ffield yes
|
||||
|
||||
thermo 1
|
||||
# thermo: step, imposed potential, bottom charge, top charge, theory charge, percent deviation
|
||||
thermo_style custom step v_v c_qbot c_qtop v_qtheory v_percdev
|
||||
|
||||
run 10
|
||||
@ -0,0 +1,139 @@
|
||||
LAMMPS (24 Mar 2022)
|
||||
boundary p p f
|
||||
kspace_style ewald/electrode 1.0e-7
|
||||
kspace_modify slab ew2d
|
||||
|
||||
include "settings.mod" # styles, computes, groups and fixes
|
||||
# set boundary in main script because ffield is periodic
|
||||
units real
|
||||
# distribute electrode atoms among all processors:
|
||||
if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2"
|
||||
|
||||
atom_style full
|
||||
pair_style lj/cut/coul/long 14
|
||||
# kspace_style and _modify in main script to test different approaches
|
||||
|
||||
read_data "data.au-vac"
|
||||
Reading data file ...
|
||||
orthogonal box = (0.285001 -0.368323 -1.043333) to (25.325067 24.671743 43.303354)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
288 atoms
|
||||
reading velocities ...
|
||||
288 velocities
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.006 seconds
|
||||
|
||||
group bot molecule 1
|
||||
144 atoms in group bot
|
||||
group top molecule 2
|
||||
144 atoms in group top
|
||||
|
||||
# ramping potential difference
|
||||
variable v equal ramp(0,2)
|
||||
|
||||
# get electrode charges
|
||||
variable q atom q
|
||||
compute qbot bot reduce sum v_q
|
||||
compute qtop top reduce sum v_q
|
||||
|
||||
# get theoretical charges:
|
||||
# calculate distance dz between electrodes
|
||||
compute zbot bot reduce max z
|
||||
compute ztop top reduce min z
|
||||
variable dz equal c_ztop-c_zbot
|
||||
|
||||
# calculate theoretical capacitance as eps0 * area / dz
|
||||
variable eps0 equal 55.26349406/10000 # epsilon zero
|
||||
variable capac equal "v_eps0 * lx * ly / v_dz"
|
||||
|
||||
# calculate theoretical charges and deviation of constant potential charges from theory
|
||||
variable qtheory equal "v_capac * v_v"
|
||||
variable percdev equal "100 * (c_qtop - v_qtheory) / (v_qtheory + 1e-9)" # avoid divide-by-zero
|
||||
|
||||
# constant potential electrodes with ramping potential difference
|
||||
fix conp bot electrode/conp 0 1.979 couple top v_v symm on
|
||||
288 atoms in group conp_group
|
||||
|
||||
thermo 1
|
||||
# thermo: step, imposed potential, bottom charge, top charge, theory charge, percent deviation
|
||||
thermo_style custom step v_v c_qbot c_qtop v_qtheory v_percdev
|
||||
|
||||
run 10
|
||||
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
|
||||
Ewald/electrode initialization ...
|
||||
WARNING: System is not charge neutral, net charge = 0.000219 (src/kspace.cpp:327)
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
G vector (1/distance) = 0.15955673
|
||||
estimated absolute RMS force accuracy = 4.0330163e-05
|
||||
estimated relative force accuracy = 1.2145309e-07
|
||||
KSpace vectors: actual max1d max3d = 90 5 665
|
||||
kxmax kymax kzmax = 3 3 5
|
||||
generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 16
|
||||
ghost atom cutoff = 16
|
||||
binsize = 8, bins = 4 4 6
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair lj/cut/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
(2) fix electrode/conp, perpetual, copy from (1)
|
||||
attributes: half, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 15.93 | 15.93 | 15.93 Mbytes
|
||||
Step v_v c_qbot c_qtop v_qtheory v_percdev
|
||||
0 0 0 0 0 0
|
||||
1 0.2 -0.030920491 0.030920491 0.031376826 -1.4543703
|
||||
2 0.4 -0.061840982 0.061840982 0.062753652 -1.4543704
|
||||
3 0.6 -0.092761473 0.092761473 0.094130479 -1.4543704
|
||||
4 0.8 -0.12368196 0.12368196 0.1255073 -1.4543704
|
||||
5 1 -0.15460245 0.15460245 0.15688413 -1.4543704
|
||||
6 1.2 -0.18552295 0.18552295 0.18826096 -1.4543704
|
||||
7 1.4 -0.21644344 0.21644344 0.21963778 -1.4543704
|
||||
8 1.6 -0.24736393 0.24736393 0.25101461 -1.4543704
|
||||
9 1.8 -0.27828442 0.27828442 0.28239144 -1.4543704
|
||||
10 2 -0.30920491 0.30920491 0.31376826 -1.4543704
|
||||
Loop time of 0.0912872 on 1 procs for 10 steps with 288 atoms
|
||||
|
||||
Performance: 9.465 ns/day, 2.536 hours/ns, 109.544 timesteps/s
|
||||
400.1% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0086713 | 0.0086713 | 0.0086713 | 0.0 | 9.50
|
||||
Bond | 3.759e-06 | 3.759e-06 | 3.759e-06 | 0.0 | 0.00
|
||||
Kspace | 0.04575 | 0.04575 | 0.04575 | 0.0 | 50.12
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00018224 | 0.00018224 | 0.00018224 | 0.0 | 0.20
|
||||
Output | 0.0027569 | 0.0027569 | 0.0027569 | 0.0 | 3.02
|
||||
Modify | 0.03386 | 0.03386 | 0.03386 | 0.0 | 37.09
|
||||
Other | | 6.314e-05 | | | 0.07
|
||||
|
||||
Nlocal: 288 ave 288 max 288 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1170 ave 1170 max 1170 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 26496 ave 26496 max 26496 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 26496
|
||||
Ave neighs/atom = 92
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
@ -0,0 +1,140 @@
|
||||
LAMMPS (24 Mar 2022)
|
||||
boundary p p f
|
||||
kspace_style ewald/electrode 1.0e-7
|
||||
kspace_modify slab ew2d
|
||||
|
||||
include "settings.mod" # styles, computes, groups and fixes
|
||||
# set boundary in main script because ffield is periodic
|
||||
units real
|
||||
# distribute electrode atoms among all processors:
|
||||
if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2"
|
||||
processors * * 2
|
||||
|
||||
atom_style full
|
||||
pair_style lj/cut/coul/long 14
|
||||
# kspace_style and _modify in main script to test different approaches
|
||||
|
||||
read_data "data.au-vac"
|
||||
Reading data file ...
|
||||
orthogonal box = (0.285001 -0.368323 -1.043333) to (25.325067 24.671743 43.303354)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
288 atoms
|
||||
reading velocities ...
|
||||
288 velocities
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.001 seconds
|
||||
read_data CPU = 0.008 seconds
|
||||
|
||||
group bot molecule 1
|
||||
144 atoms in group bot
|
||||
group top molecule 2
|
||||
144 atoms in group top
|
||||
|
||||
# ramping potential difference
|
||||
variable v equal ramp(0,2)
|
||||
|
||||
# get electrode charges
|
||||
variable q atom q
|
||||
compute qbot bot reduce sum v_q
|
||||
compute qtop top reduce sum v_q
|
||||
|
||||
# get theoretical charges:
|
||||
# calculate distance dz between electrodes
|
||||
compute zbot bot reduce max z
|
||||
compute ztop top reduce min z
|
||||
variable dz equal c_ztop-c_zbot
|
||||
|
||||
# calculate theoretical capacitance as eps0 * area / dz
|
||||
variable eps0 equal 55.26349406/10000 # epsilon zero
|
||||
variable capac equal "v_eps0 * lx * ly / v_dz"
|
||||
|
||||
# calculate theoretical charges and deviation of constant potential charges from theory
|
||||
variable qtheory equal "v_capac * v_v"
|
||||
variable percdev equal "100 * (c_qtop - v_qtheory) / (v_qtheory + 1e-9)" # avoid divide-by-zero
|
||||
|
||||
# constant potential electrodes with ramping potential difference
|
||||
fix conp bot electrode/conp 0 1.979 couple top v_v symm on
|
||||
288 atoms in group conp_group
|
||||
|
||||
thermo 1
|
||||
# thermo: step, imposed potential, bottom charge, top charge, theory charge, percent deviation
|
||||
thermo_style custom step v_v c_qbot c_qtop v_qtheory v_percdev
|
||||
|
||||
run 10
|
||||
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
|
||||
Ewald/electrode initialization ...
|
||||
WARNING: System is not charge neutral, net charge = 0.000219 (src/kspace.cpp:327)
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
G vector (1/distance) = 0.15955673
|
||||
estimated absolute RMS force accuracy = 4.0330163e-05
|
||||
estimated relative force accuracy = 1.2145309e-07
|
||||
KSpace vectors: actual max1d max3d = 90 5 665
|
||||
kxmax kymax kzmax = 3 3 5
|
||||
generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 16
|
||||
ghost atom cutoff = 16
|
||||
binsize = 8, bins = 4 4 6
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair lj/cut/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
(2) fix electrode/conp, perpetual, copy from (1)
|
||||
attributes: half, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 15.96 | 15.96 | 15.96 Mbytes
|
||||
Step v_v c_qbot c_qtop v_qtheory v_percdev
|
||||
0 0 0 0 0 0
|
||||
1 0.2 -0.030920491 0.030920491 0.031376826 -1.4543703
|
||||
2 0.4 -0.061840982 0.061840982 0.062753652 -1.4543704
|
||||
3 0.6 -0.092761473 0.092761473 0.094130479 -1.4543704
|
||||
4 0.8 -0.12368196 0.12368196 0.1255073 -1.4543704
|
||||
5 1 -0.15460245 0.15460245 0.15688413 -1.4543704
|
||||
6 1.2 -0.18552295 0.18552295 0.18826096 -1.4543704
|
||||
7 1.4 -0.21644344 0.21644344 0.21963778 -1.4543704
|
||||
8 1.6 -0.24736393 0.24736393 0.25101461 -1.4543704
|
||||
9 1.8 -0.27828442 0.27828442 0.28239144 -1.4543704
|
||||
10 2 -0.30920491 0.30920491 0.31376826 -1.4543704
|
||||
Loop time of 0.0456609 on 4 procs for 10 steps with 288 atoms
|
||||
|
||||
Performance: 18.922 ns/day, 1.268 hours/ns, 219.006 timesteps/s
|
||||
86.7% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0019389 | 0.0024013 | 0.0030807 | 0.9 | 5.26
|
||||
Bond | 1.493e-06 | 1.7132e-06 | 1.935e-06 | 0.0 | 0.00
|
||||
Kspace | 0.016165 | 0.016695 | 0.017072 | 0.3 | 36.56
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0030891 | 0.0037595 | 0.0040145 | 0.6 | 8.23
|
||||
Output | 0.0024177 | 0.0027885 | 0.0037099 | 1.0 | 6.11
|
||||
Modify | 0.01944 | 0.019746 | 0.020327 | 0.2 | 43.24
|
||||
Other | | 0.0002691 | | | 0.59
|
||||
|
||||
Nlocal: 72 ave 72 max 72 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1062 ave 1062 max 1062 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 6624 ave 6936 max 6312 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 26496
|
||||
Ave neighs/atom = 92
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
@ -0,0 +1,139 @@
|
||||
LAMMPS (24 Mar 2022)
|
||||
boundary p p f
|
||||
kspace_style ewald/electrode 1.0e-7
|
||||
kspace_modify slab 3.0 # ew3dc
|
||||
|
||||
include "settings.mod" # styles, computes, groups and fixes
|
||||
# set boundary in main script because ffield is periodic
|
||||
units real
|
||||
# distribute electrode atoms among all processors:
|
||||
if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2"
|
||||
|
||||
atom_style full
|
||||
pair_style lj/cut/coul/long 14
|
||||
# kspace_style and _modify in main script to test different approaches
|
||||
|
||||
read_data "data.au-vac"
|
||||
Reading data file ...
|
||||
orthogonal box = (0.285001 -0.368323 -1.043333) to (25.325067 24.671743 43.303354)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
288 atoms
|
||||
reading velocities ...
|
||||
288 velocities
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.007 seconds
|
||||
|
||||
group bot molecule 1
|
||||
144 atoms in group bot
|
||||
group top molecule 2
|
||||
144 atoms in group top
|
||||
|
||||
# ramping potential difference
|
||||
variable v equal ramp(0,2)
|
||||
|
||||
# get electrode charges
|
||||
variable q atom q
|
||||
compute qbot bot reduce sum v_q
|
||||
compute qtop top reduce sum v_q
|
||||
|
||||
# get theoretical charges:
|
||||
# calculate distance dz between electrodes
|
||||
compute zbot bot reduce max z
|
||||
compute ztop top reduce min z
|
||||
variable dz equal c_ztop-c_zbot
|
||||
|
||||
# calculate theoretical capacitance as eps0 * area / dz
|
||||
variable eps0 equal 55.26349406/10000 # epsilon zero
|
||||
variable capac equal "v_eps0 * lx * ly / v_dz"
|
||||
|
||||
# calculate theoretical charges and deviation of constant potential charges from theory
|
||||
variable qtheory equal "v_capac * v_v"
|
||||
variable percdev equal "100 * (c_qtop - v_qtheory) / (v_qtheory + 1e-9)" # avoid divide-by-zero
|
||||
|
||||
# constant potential electrodes with ramping potential difference
|
||||
fix conp bot electrode/conp 0 1.979 couple top v_v symm on
|
||||
288 atoms in group conp_group
|
||||
|
||||
thermo 1
|
||||
# thermo: step, imposed potential, bottom charge, top charge, theory charge, percent deviation
|
||||
thermo_style custom step v_v c_qbot c_qtop v_qtheory v_percdev
|
||||
|
||||
run 10
|
||||
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
|
||||
Ewald/electrode initialization ...
|
||||
WARNING: System is not charge neutral, net charge = 0.000219 (src/kspace.cpp:327)
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
G vector (1/distance) = 0.15955673
|
||||
estimated absolute RMS force accuracy = 3.1187248e-05
|
||||
estimated relative force accuracy = 9.3919471e-08
|
||||
KSpace vectors: actual max1d max3d = 266 12 7812
|
||||
kxmax kymax kzmax = 3 3 12
|
||||
generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 16
|
||||
ghost atom cutoff = 16
|
||||
binsize = 8, bins = 4 4 6
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair lj/cut/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
(2) fix electrode/conp, perpetual, copy from (1)
|
||||
attributes: half, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 27.27 | 27.27 | 27.27 Mbytes
|
||||
Step v_v c_qbot c_qtop v_qtheory v_percdev
|
||||
0 0 0 0 0 0
|
||||
1 0.2 -0.030925182 0.030925182 0.031376826 -1.4394194
|
||||
2 0.4 -0.061850364 0.061850364 0.062753652 -1.4394194
|
||||
3 0.6 -0.092775546 0.092775546 0.094130479 -1.4394194
|
||||
4 0.8 -0.12370073 0.12370073 0.1255073 -1.4394195
|
||||
5 1 -0.15462591 0.15462591 0.15688413 -1.4394195
|
||||
6 1.2 -0.18555109 0.18555109 0.18826096 -1.4394195
|
||||
7 1.4 -0.21647627 0.21647627 0.21963778 -1.4394195
|
||||
8 1.6 -0.24740146 0.24740146 0.25101461 -1.4394195
|
||||
9 1.8 -0.27832664 0.27832664 0.28239144 -1.4394195
|
||||
10 2 -0.30925182 0.30925182 0.31376826 -1.4394195
|
||||
Loop time of 0.0672288 on 1 procs for 10 steps with 288 atoms
|
||||
|
||||
Performance: 12.852 ns/day, 1.867 hours/ns, 148.746 timesteps/s
|
||||
400.4% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0071442 | 0.0071442 | 0.0071442 | 0.0 | 10.63
|
||||
Bond | 2.976e-06 | 2.976e-06 | 2.976e-06 | 0.0 | 0.00
|
||||
Kspace | 0.0097903 | 0.0097903 | 0.0097903 | 0.0 | 14.56
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00023514 | 0.00023514 | 0.00023514 | 0.0 | 0.35
|
||||
Output | 0.0029795 | 0.0029795 | 0.0029795 | 0.0 | 4.43
|
||||
Modify | 0.047009 | 0.047009 | 0.047009 | 0.0 | 69.92
|
||||
Other | | 6.809e-05 | | | 0.10
|
||||
|
||||
Nlocal: 288 ave 288 max 288 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1170 ave 1170 max 1170 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 26496 ave 26496 max 26496 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 26496
|
||||
Ave neighs/atom = 92
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
@ -0,0 +1,140 @@
|
||||
LAMMPS (24 Mar 2022)
|
||||
boundary p p f
|
||||
kspace_style ewald/electrode 1.0e-7
|
||||
kspace_modify slab 3.0 # ew3dc
|
||||
|
||||
include "settings.mod" # styles, computes, groups and fixes
|
||||
# set boundary in main script because ffield is periodic
|
||||
units real
|
||||
# distribute electrode atoms among all processors:
|
||||
if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2"
|
||||
processors * * 2
|
||||
|
||||
atom_style full
|
||||
pair_style lj/cut/coul/long 14
|
||||
# kspace_style and _modify in main script to test different approaches
|
||||
|
||||
read_data "data.au-vac"
|
||||
Reading data file ...
|
||||
orthogonal box = (0.285001 -0.368323 -1.043333) to (25.325067 24.671743 43.303354)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
288 atoms
|
||||
reading velocities ...
|
||||
288 velocities
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.008 seconds
|
||||
read_data CPU = 0.123 seconds
|
||||
|
||||
group bot molecule 1
|
||||
144 atoms in group bot
|
||||
group top molecule 2
|
||||
144 atoms in group top
|
||||
|
||||
# ramping potential difference
|
||||
variable v equal ramp(0,2)
|
||||
|
||||
# get electrode charges
|
||||
variable q atom q
|
||||
compute qbot bot reduce sum v_q
|
||||
compute qtop top reduce sum v_q
|
||||
|
||||
# get theoretical charges:
|
||||
# calculate distance dz between electrodes
|
||||
compute zbot bot reduce max z
|
||||
compute ztop top reduce min z
|
||||
variable dz equal c_ztop-c_zbot
|
||||
|
||||
# calculate theoretical capacitance as eps0 * area / dz
|
||||
variable eps0 equal 55.26349406/10000 # epsilon zero
|
||||
variable capac equal "v_eps0 * lx * ly / v_dz"
|
||||
|
||||
# calculate theoretical charges and deviation of constant potential charges from theory
|
||||
variable qtheory equal "v_capac * v_v"
|
||||
variable percdev equal "100 * (c_qtop - v_qtheory) / (v_qtheory + 1e-9)" # avoid divide-by-zero
|
||||
|
||||
# constant potential electrodes with ramping potential difference
|
||||
fix conp bot electrode/conp 0 1.979 couple top v_v symm on
|
||||
288 atoms in group conp_group
|
||||
|
||||
thermo 1
|
||||
# thermo: step, imposed potential, bottom charge, top charge, theory charge, percent deviation
|
||||
thermo_style custom step v_v c_qbot c_qtop v_qtheory v_percdev
|
||||
|
||||
run 10
|
||||
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
|
||||
Ewald/electrode initialization ...
|
||||
WARNING: System is not charge neutral, net charge = 0.000219 (src/kspace.cpp:327)
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
G vector (1/distance) = 0.15955673
|
||||
estimated absolute RMS force accuracy = 3.1187248e-05
|
||||
estimated relative force accuracy = 9.3919471e-08
|
||||
KSpace vectors: actual max1d max3d = 266 12 7812
|
||||
kxmax kymax kzmax = 3 3 12
|
||||
generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 16
|
||||
ghost atom cutoff = 16
|
||||
binsize = 8, bins = 4 4 6
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair lj/cut/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
(2) fix electrode/conp, perpetual, copy from (1)
|
||||
attributes: half, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 27.31 | 27.31 | 27.31 Mbytes
|
||||
Step v_v c_qbot c_qtop v_qtheory v_percdev
|
||||
0 0 0 0 0 0
|
||||
1 0.2 -0.030925182 0.030925182 0.031376826 -1.4394194
|
||||
2 0.4 -0.061850364 0.061850364 0.062753652 -1.4394194
|
||||
3 0.6 -0.092775546 0.092775546 0.094130479 -1.4394194
|
||||
4 0.8 -0.12370073 0.12370073 0.1255073 -1.4394195
|
||||
5 1 -0.15462591 0.15462591 0.15688413 -1.4394195
|
||||
6 1.2 -0.18555109 0.18555109 0.18826096 -1.4394195
|
||||
7 1.4 -0.21647627 0.21647627 0.21963778 -1.4394195
|
||||
8 1.6 -0.24740146 0.24740146 0.25101461 -1.4394195
|
||||
9 1.8 -0.27832664 0.27832664 0.28239144 -1.4394195
|
||||
10 2 -0.30925182 0.30925182 0.31376826 -1.4394195
|
||||
Loop time of 0.0459561 on 4 procs for 10 steps with 288 atoms
|
||||
|
||||
Performance: 18.801 ns/day, 1.277 hours/ns, 217.599 timesteps/s
|
||||
95.8% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0021527 | 0.0026891 | 0.0037845 | 1.3 | 5.85
|
||||
Bond | 1.303e-06 | 1.9462e-06 | 3.206e-06 | 0.0 | 0.00
|
||||
Kspace | 0.0066254 | 0.0077509 | 0.0083577 | 0.8 | 16.87
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00285 | 0.0057275 | 0.0067088 | 2.2 | 12.46
|
||||
Output | 0.0024325 | 0.0034682 | 0.0065316 | 3.0 | 7.55
|
||||
Modify | 0.025911 | 0.025969 | 0.026007 | 0.0 | 56.51
|
||||
Other | | 0.0003494 | | | 0.76
|
||||
|
||||
Nlocal: 72 ave 72 max 72 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1062 ave 1062 max 1062 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 6624 ave 6936 max 6312 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 26496
|
||||
Ave neighs/atom = 92
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
@ -0,0 +1,138 @@
|
||||
LAMMPS (24 Mar 2022)
|
||||
boundary p p p # finite field, fully periodic
|
||||
kspace_style ewald/electrode 1.0e-7
|
||||
|
||||
include "settings.mod" # styles, computes, groups and fixes
|
||||
# set boundary in main script because ffield is periodic
|
||||
units real
|
||||
# distribute electrode atoms among all processors:
|
||||
if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2"
|
||||
|
||||
atom_style full
|
||||
pair_style lj/cut/coul/long 14
|
||||
# kspace_style and _modify in main script to test different approaches
|
||||
|
||||
read_data "data.au-vac"
|
||||
Reading data file ...
|
||||
orthogonal box = (0.285001 -0.368323 -1.043333) to (25.325067 24.671743 43.303354)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
288 atoms
|
||||
reading velocities ...
|
||||
288 velocities
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.001 seconds
|
||||
read_data CPU = 0.010 seconds
|
||||
|
||||
group bot molecule 1
|
||||
144 atoms in group bot
|
||||
group top molecule 2
|
||||
144 atoms in group top
|
||||
|
||||
# ramping potential difference
|
||||
variable v equal ramp(0,2)
|
||||
|
||||
# get electrode charges
|
||||
variable q atom q
|
||||
compute qbot bot reduce sum v_q
|
||||
compute qtop top reduce sum v_q
|
||||
|
||||
# get theoretical charges:
|
||||
# calculate distance dz between electrodes
|
||||
compute zbot bot reduce max z
|
||||
compute ztop top reduce min z
|
||||
variable dz equal c_ztop-c_zbot
|
||||
|
||||
# calculate theoretical capacitance as eps0 * area / dz
|
||||
variable eps0 equal 55.26349406/10000 # epsilon zero
|
||||
variable capac equal "v_eps0 * lx * ly / v_dz"
|
||||
|
||||
# calculate theoretical charges and deviation of constant potential charges from theory
|
||||
variable qtheory equal "v_capac * v_v"
|
||||
variable percdev equal "100 * (c_qtop - v_qtheory) / (v_qtheory + 1e-9)" # avoid divide-by-zero
|
||||
|
||||
# constant potential electrodes with ramping potential difference
|
||||
fix conp bot electrode/conp 0 1.979 couple top v_v symm on ffield yes
|
||||
288 atoms in group conp_group
|
||||
|
||||
thermo 1
|
||||
# thermo: step, imposed potential, bottom charge, top charge, theory charge, percent deviation
|
||||
thermo_style custom step v_v c_qbot c_qtop v_qtheory v_percdev
|
||||
|
||||
run 10
|
||||
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
|
||||
Ewald/electrode initialization ...
|
||||
WARNING: System is not charge neutral, net charge = 0.000219 (src/kspace.cpp:327)
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
G vector (1/distance) = 0.15955673
|
||||
estimated absolute RMS force accuracy = 4.0330163e-05
|
||||
estimated relative force accuracy = 1.2145309e-07
|
||||
KSpace vectors: actual max1d max3d = 95 5 665
|
||||
kxmax kymax kzmax = 3 3 5
|
||||
generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 16
|
||||
ghost atom cutoff = 16
|
||||
binsize = 8, bins = 4 4 6
|
||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
||||
(1) pair lj/cut/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
(2) fix electrode/conp, perpetual, copy from (1)
|
||||
attributes: half, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 16.01 | 16.01 | 16.01 Mbytes
|
||||
Step v_v c_qbot c_qtop v_qtheory v_percdev
|
||||
0 0 0 0 0 0
|
||||
1 0.2 -0.030908718 0.030908718 0.031376826 -1.491893
|
||||
2 0.4 -0.061817435 0.061817435 0.062753652 -1.491893
|
||||
3 0.6 -0.092726153 0.092726153 0.094130479 -1.491893
|
||||
4 0.8 -0.12363487 0.12363487 0.1255073 -1.491893
|
||||
5 1 -0.15454359 0.15454359 0.15688413 -1.491893
|
||||
6 1.2 -0.18545231 0.18545231 0.18826096 -1.491893
|
||||
7 1.4 -0.21636102 0.21636102 0.21963778 -1.491893
|
||||
8 1.6 -0.24726974 0.24726974 0.25101461 -1.491893
|
||||
9 1.8 -0.27817846 0.27817846 0.28239144 -1.491893
|
||||
10 2 -0.30908718 0.30908718 0.31376826 -1.491893
|
||||
Loop time of 0.0481838 on 1 procs for 10 steps with 288 atoms
|
||||
|
||||
Performance: 17.931 ns/day, 1.338 hours/ns, 207.539 timesteps/s
|
||||
390.7% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0071719 | 0.0071719 | 0.0071719 | 0.0 | 14.88
|
||||
Bond | 2.946e-06 | 2.946e-06 | 2.946e-06 | 0.0 | 0.01
|
||||
Kspace | 0.0038758 | 0.0038758 | 0.0038758 | 0.0 | 8.04
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00053561 | 0.00053561 | 0.00053561 | 0.0 | 1.11
|
||||
Output | 0.0025385 | 0.0025385 | 0.0025385 | 0.0 | 5.27
|
||||
Modify | 0.033951 | 0.033951 | 0.033951 | 0.0 | 70.46
|
||||
Other | | 0.0001075 | | | 0.22
|
||||
|
||||
Nlocal: 288 ave 288 max 288 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 2628 ave 2628 max 2628 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 26496 ave 26496 max 26496 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 26496
|
||||
Ave neighs/atom = 92
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user