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- deleted old doc
- renamed new doc files
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julient31
2019-05-20 21:48:05 -06:00
parent 5f2f7d1575
commit e90eed9120
13 changed files with 1 additions and 15445 deletions
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15009
examples/SPIN/dipole_spin/Fe_Mishin2006.eam.alloy
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examples/SPIN/dipole_spin/Fe_Mishin2006.eam.alloy Symbolic link
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../iron/Fe_Mishin2006.eam.alloy

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examples/SPIN/dipole_spin/in.spin.iron_ewald → examples/SPIN/dipole_spin/in.spin.iron_dipole_ewald
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examples/SPIN/dipole_spin/in.spin.iron_pppm → examples/SPIN/dipole_spin/in.spin.iron_dipole_pppm
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examples/SPIN/pppm_spin/Co_PurjaPun_2012.eam.alloy
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../cobalt_fcc/Co_PurjaPun_2012.eam.alloy

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examples/SPIN/pppm_spin/data.2
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RANDOM INITIALIZATION FOR STOCKMAYER FLUID
2 atoms
1 atom types
-3.0 3.0 xlo xhi
-3.0 3.0 ylo yhi
-3.0 3.0 zlo zhi
#30.0 30.0 0.0 xy xz yz
Atoms
1 1 1.73 0.0 0.0 0.0 0.0 0.0 1.0
2 1 1.73 0.0 2.5 0.0 0.0 0.0 1.0

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examples/SPIN/pppm_spin/exchange_fit_hcp_co/exchange_fit.py
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#Program fitting the exchange interaction
#Model curve: Bethe-Slater function
import numpy as np, pylab, tkinter
import matplotlib.pyplot as plt
from scipy.optimize import curve_fit
from decimal import *
print("Loop begin")
#Definition of the Bethe-Slater function
def func(x,a,b,c):
return 4*a*((x/c)**2)*(1-b*(x/c)**2)*np.exp(-(x/c)**2)
#Exchange coeff table (data to fit)
rdata, Jdata = np.loadtxt('exchange_hcp_co.dat', usecols=(0,1), unpack=True)
plt.plot(rdata, Jdata, 'b-', label='data')
#Perform the fit
popt, pcov = curve_fit(func, rdata, Jdata, bounds=(0, [500.,5.,5.]))
plt.plot(rdata, func(rdata, *popt), 'r--', label='fit')
#Print the fitted params
print("Parameters: a={:.10} (in meV), b={:.10} (adim), c={:.10} (in Ang)".format(*popt))
#Ploting the result
plt.xlabel('r_ij')
pylab.xlim([0,6.5])
plt.ylabel('J_ij')
plt.legend()
plt.show()
print("Loop end")

9
examples/SPIN/pppm_spin/exchange_fit_hcp_co/exchange_hcp_co.dat
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2.25569176882662 73.37931034482759
2.3817863397548162 47.99999999999999
2.4518388791593697 34.39080459770115
2.507880910683012 31.816091954022987
2.5359019264448337 28.137931034482747
2.5779334500875657 25.011494252873554
2.6339754816112086 19.126436781609186
2.760070052539404 13.241379310344826
3.5446584938704033 6.068965517241367

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examples/SPIN/pppm_spin/in.dipole.pppm_dipole
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# 3d Lennard-Jones melt
units lj
#atom_style charge
atom_style hybrid sphere dipole
processors * 1 1
lattice fcc 0.8442
#region box block 0 10 0 10 0 10
region box block 0 5 0 5 0 5
create_box 3 box
create_atoms 1 box
mass * 1.0
region long block 3 6 0 10 0 10
set region long type 2
set group all dipole/random 98934 0.75
#set type 1:2 charge 0.0
velocity all create 1.0 87287
#pair_style lj/long/coul/long long off 2.5
#pair_coeff * * 1.0 1.0 2.5
#pair_coeff * 2 1.0 1.0 5.0
pair_style lj/cut/dipole/long 3.0
pair_coeff * * 0.0 0.0
#kspace_style pppm/disp 1.0e-4
#kspace_style pppm/dipole 1.0e-4
kspace_style ewald/dipole 1.0e-4
#kspace_modify compute yes gewald 0.1
neighbor 0.3 bin
neigh_modify every 2 delay 4 check yes
group fast type 1
group slow type 2
fix 0 all balance 20 1.0 shift x 5 1.0 &
weight group 2 fast 1.0 slow 2.0 weight time 0.66
fix 1 all nve
#dump id all atom 50 dump.melt
#dump 2 all image 25 image.*.jpg type type &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
#thermo 50
thermo 1
#run 500
run 5

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examples/SPIN/pppm_spin/in.spin.2
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# two magnetic atoms in a 3d box
clear
units metal
atom_style spin
dimension 3
#boundary p p p
atom_modify map array
read_data ../examples/SPIN/pppm_spin/data.2
mass 1 58.93
#set group all spin/random 31 1.72
#velocity all create 100 4928459 rot yes dist gaussian
pair_style spin/dipolar/cut 4.0
pair_coeff * * long 2.6
#pair_style hybrid/overlay spin/exchange 4.0 spin/dipolar/long 8.0
#pair_style hybrid/overlay eam/alloy spin/exchange 4.0 spin/dipolar/long 8.0
#pair_style hybrid/overlay eam/alloy spin/exchange 4.0 spin/dipolar/long/qsymp 8.0
#pair_coeff * * eam/alloy ../examples/SPIN/pppm_spin/Co_PurjaPun_2012.eam.alloy Co
#pair_coeff * * spin/exchange exchange 4.0 0.1 1.135028015e-05 1.064568567
#pair_coeff * * spin/dipolar/long long 8.0
#neighbor 0.1 bin
#neigh_modify every 10 check yes delay 20
neighbor 0.3 bin
neigh_modify delay 0
#neigh_modify every 1 delay 10 check yes page 100000000 one 10000000
#kspace_style pppm/dipole/spin 1.0e-4
#kspace_style ewald/dipole/spin 1.0e-4
#kspace_modify compute yes
#kspace_modify compute yes gewald 0.1
fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0
fix 2 all langevin/spin 0.0 0.0 21
#fix 3 all nve/spin lattice yes
fix 3 all nve/spin lattice no
timestep 0.0001
thermo_style custom step temp pe ke etotal press
thermo_modify format float %20.16g
thermo 1
#compute peratom all pe/atom
#compute pe all reduce sum c_peratom
#thermo_style custom step temp pe c_pe
#compute peratom2 all stress/atom
#compute peratom2 all stress/atom NULL
#compute p all reduce sum c_peratom2[1] c_peratom2[2] c_peratom2[3] c_peratom2[4] c_peratom2[5] c_peratom2[6]
#variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
#variable pxx equal -c_p[1]/vol
#variable pyy equal -c_p[2]/vol
#variable pzz equal -c_p[3]/vol
#variable pxy equal -c_p[4]/vol
#variable pxz equal -c_p[5]/vol
#variable pyz equal -c_p[6]/vol
#thermo_style custom step temp etotal pe c_pe press v_press pxx v_pxx pyy v_pyy pzz v_pzz pxy v_pxy pxz v_pxz pyz v_pyz
#thermo_style custom step etotal pe press v_press v_pxx v_pyy v_pzz v_pxy v_pxz v_pyz
#thermo_style custom step temp etotal press v_press
compute outsp all property/atom spx spy spz sp fmx fmy fmz
dump 1 all custom 1 dump.equil id type x y z c_outsp[1] c_outsp[2] c_outsp[3]
#c_outsp[5] c_outsp[6] c_outsp[7]
#dump_modify 1 format line "%d %d %20.15g %20.15g %20.15g %20.15g %20.15g %20.15g" scale yes
#pair_modify compute no
run 1

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examples/SPIN/pppm_spin/in.spin.cut_comp
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# bcc iron in a 3d periodic box
clear
units metal
atom_style spin
dimension 3
boundary p p p
atom_modify map array
lattice bcc 2.8665
region box block 0.0 5.0 0.0 5.0 0.0 5.0
create_box 1 box
create_atoms 1 box
mass 1 58.93
#set group all spin 2.2 0.0 0.0 1.0
set group all spin/random 31 2.2
#pair_style spin/dipolar/cut 5.0
#pair_coeff * * long 5.0
pair_style spin/dipolar/long 4.0
pair_coeff * * long 4.0
#neighbor 0.1 bin
#neigh_modify every 10 check yes delay 20
neighbor 0.3 bin
neigh_modify delay 0
#neigh_modify every 1 delay 10 check yes page 100000000 one 10000000
#kspace_style pppm/dipole/spin 1.0e-4
#kspace_style ewald/dipole/spin 1.0e-4
#kspace_modify compute yes
#kspace_modify compute yes gewald 0.1
fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0
fix 2 all langevin/spin 0.0 0.0 21
#fix 3 all nve/spin lattice yes
fix 3 all nve/spin lattice no
timestep 0.0001
thermo_style custom step temp pe ke etotal press
thermo_modify format float %20.16g
thermo 50
compute outsp all property/atom spx spy spz sp fmx fmy fmz
dump 50 all custom 1 dump.equil id type x y z c_outsp[1] c_outsp[2] c_outsp[3]
#c_outsp[5] c_outsp[6] c_outsp[7]
#dump_modify 1 format line "%d %d %20.15g %20.15g %20.15g %20.15g %20.15g %20.15g" scale yes
run 10000

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examples/SPIN/pppm_spin/in.spin.ewald_spin
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# hcp cobalt in a 3d periodic box
clear
units metal
atom_style spin
dimension 3
boundary p p p
# necessary for the serial algorithm (sametag)
atom_modify map array
lattice hcp 2.5071
region box block 0.0 8.0 0.0 8.0 0.0 8.0
create_box 1 box
create_atoms 1 box
# setting mass, mag. moments, and interactions for hcp cobalt
mass 1 58.93
set group all spin/random 31 1.72
#set group all spin 1.72 0.0 0.0 1.0
#velocity all create 100 4928459 rot yes dist gaussian
#pair_style hybrid/overlay eam/alloy spin/exchange 4.0 spin/dipolar/long 8.0
#pair_style hybrid/overlay eam/alloy spin/exchange 4.0 spin/long/qsymp 8.0
#pair_style hybrid/overlay eam/alloy spin/exchange 4.0
#pair_coeff * * eam/alloy ../examples/SPIN/pppm_spin/Co_PurjaPun_2012.eam.alloy Co
#pair_coeff * * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567
#pair_coeff * * spin/long/qsymp long 8.0
pair_style spin/dipolar/long 8.0
pair_coeff * * long 8.0
neighbor 0.1 bin
neigh_modify every 10 check yes delay 20
kspace_style ewald/dipole/spin 1.0e-4
#kspace_modify mesh 32 32 32
#fix 1 all precession/spin zeeman 1.0 0.0 0.0 1.0
fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0
fix 2 all langevin/spin 0.0 0.0 21
#fix 3 all nve/spin lattice yes
fix 3 all nve/spin lattice no
timestep 0.001
compute out_mag all compute/spin
compute out_pe all pe
compute out_ke all ke
compute out_temp all temp
variable magz equal c_out_mag[3]
variable magnorm equal c_out_mag[4]
variable emag equal c_out_mag[5]
variable tmag equal c_out_mag[6]
thermo_style custom step time v_magnorm v_tmag temp v_emag ke pe etotal
#thermo_style custom step time v_magnorm v_emag temp etotal
thermo 10
compute outsp all property/atom spx spy spz sp fmx fmy fmz
dump 100 all custom 1 dump_cobalt_hcp.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
#run 20000
run 1000

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examples/SPIN/pppm_spin/in.spin.pppm_spin
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# hcp cobalt in a 3d periodic box
clear
units metal
atom_style spin
dimension 3
boundary p p p
# necessary for the serial algorithm (sametag)
atom_modify map array
lattice hcp 2.5071
region box block 0.0 8.0 0.0 8.0 0.0 8.0
create_box 1 box
create_atoms 1 box
# setting mass, mag. moments, and interactions for hcp cobalt
mass 1 58.93
set group all spin/random 31 1.72
#set group all spin 1.72 0.0 0.0 1.0
velocity all create 100 4928459 rot yes dist gaussian
pair_style hybrid/overlay eam/alloy spin/exchange 4.0 spin/dipolar/long 8.0
#pair_style hybrid/overlay eam/alloy spin/exchange 4.0 spin/dipolar/long/qsymp 8.0
pair_coeff * * eam/alloy ../examples/SPIN/pppm_spin/Co_PurjaPun_2012.eam.alloy Co
#pair_coeff * * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567
pair_coeff * * spin/exchange exchange 4.0 0.0 1.135028015e-05 1.064568567
#pair_coeff * * spin/dipolar/long/qsymp long 8.0
pair_coeff * * spin/dipolar/long long 8.0
neighbor 0.1 bin
neigh_modify every 10 check yes delay 20
kspace_style pppm/dipole/spin 1.0e-4
kspace_modify compute yes
#fix 1 all precession/spin zeeman 1.0 0.0 0.0 1.0
fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0
fix 2 all langevin/spin 0.0 0.0 21
fix 3 all nve/spin lattice yes
timestep 0.0001
compute out_mag all compute/spin
compute out_pe all pe
compute out_ke all ke
compute out_temp all temp
variable magz equal c_out_mag[3]
variable magnorm equal c_out_mag[4]
variable emag equal c_out_mag[5]
variable tmag equal c_out_mag[6]
thermo_style custom step time v_magnorm v_emag temp etotal
thermo_modify format float %20.16g
thermo 10
compute outsp all property/atom spx spy spz sp fmx fmy fmz
dump 100 all custom 1 dump_cobalt_hcp.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
run 20000
#run 1

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examples/SPIN/pppm_spin/in.spin.spin_dipolar_cut
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# hcp cobalt in a 3d periodic box
clear
units metal
atom_style spin
dimension 3
boundary p p p
# necessary for the serial algorithm (sametag)
atom_modify map array
lattice hcp 2.5071
region box block 0.0 8.0 0.0 8.0 0.0 8.0
create_box 1 box
create_atoms 1 box
# setting mass, mag. moments, and interactions for hcp cobalt
mass 1 58.93
set group all spin/random 31 1.72
#set group all spin 1.72 0.0 0.0 1.0
velocity all create 100 4928459 rot yes dist gaussian
pair_style hybrid/overlay eam/alloy spin/exchange 4.0 spin/dipolar/cut 8.0
#pair_style hybrid/overlay eam/alloy spin/dipolar/cut 8.0
pair_coeff * * eam/alloy ../examples/SPIN/pppm_spin/Co_PurjaPun_2012.eam.alloy Co
pair_coeff * * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567
pair_coeff * * spin/dipolar/cut long 8.0
#pair_style spin/dipolar/cut 8.0
#pair_coeff * * long 8.0
neighbor 0.1 bin
neigh_modify every 10 check yes delay 20
#fix 1 all precession/spin zeeman 1.0 0.0 0.0 1.0
fix 1 all precession/spin zeeman 0.0 0.0 0.0 1.0
fix 2 all langevin/spin 0.0 0.0 21
fix 3 all nve/spin lattice yes
#fix 3 all nve/spin lattice no
timestep 0.0001
compute out_mag all compute/spin
compute out_pe all pe
compute out_ke all ke
compute out_temp all temp
variable magz equal c_out_mag[3]
variable magnorm equal c_out_mag[4]
variable emag equal c_out_mag[5]
variable tmag equal c_out_mag[6]
thermo_style custom step time v_magnorm v_emag temp etotal
thermo_modify format float %20.16g
thermo 10
compute outsp all property/atom spx spy spz sp fmx fmy fmz
dump 100 all custom 1 dump_cobalt_hcp.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
run 20000
#run 10