Commit JT 010318 (before APS)

examples/SPIN/cobalt_hcp/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")

examples/SPIN/cobalt_hcp/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

examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp

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+# fcc cobalt in a 3d periodic box
+
+clear 
+units metal
+atom_style spin
+
+dimension 3
+boundary p p p
+
+# check why?
+atom_modify map array 
+
+#lattice hcp 2.5071 2.5071 4.0695
+lattice hcp 2.5071
+region box block 0.0 5.0 0.0 5.0 0.0 5.0
+create_box 1 box
+create_atoms 1 box
+
+# setting mass, mag. moments, and interactions for cobalt
+
+mass		1 58.93
+
+set group all spin/random 31 1.72
+velocity all create 100 4928459 rot yes dist gaussian
+
+#pair_style hybrid/overlay eam/alloy pair/spin/exchange 4.0 pair/spin/soc/neel 4.0
+pair_style hybrid/overlay eam/alloy pair/spin/exchange 4.0
+pair_coeff * * eam/alloy ../examples/SPIN/cobalt_hcp/Co_PurjaPun_2012.eam.alloy Co
+pair_coeff * * pair/spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567
+#pair_coeff * * pair/spin/soc/neel neel 4.0 0.0048 0.234 1.168 2.6905 0.705 0.652  
+
+neighbor 0.1 bin
+neigh_modify every 10 check yes delay 20
+
+fix 1 all force/spin zeeman 0.01 0.0 0.0 1.0
+fix 2 all langevin/spin 0.0 0.0 21
+
+fix 3 all integration/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]
+variable mag_force equal f_1
+
+thermo_style    custom step time v_magnorm v_emag temp etotal
+thermo          10
+
+dump 1 all custom 50 dump_cobalt.lammpstrj type x y z spx spy spz
+
+run 1000
+