Commit JT 033020

- modified all spin pairs (match nve)
- correct doc min_modify
- correct code max norm (square values)
- added draft nvt validation

examples/SPIN/test_problems/validation_nve/in.spin.iron-nve

@@ -0,0 +1,49 @@
+# bcc iron 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 	bcc 2.8665
+region 		box block 0.0 3.0 0.0 3.0 0.0 3.0
+create_box 	1 box
+create_atoms 	1 box
+
+# setting mass, mag. moments, and interactions for bcc iron
+
+mass		1 55.845
+set 		group all spin/random 31 2.2
+velocity 	all create 100 4928459 rot yes dist gaussian
+
+pair_style 	hybrid/overlay eam/alloy spin/exchange 3.5
+pair_coeff 	* * eam/alloy Fe_Mishin2006.eam.alloy Fe
+pair_coeff 	* * spin/exchange exchange 3.4 0.02726 0.2171 1.841
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0
+fix 		2 all langevin/spin 0.0 0.00 21
+fix 		3 all nve/spin lattice moving
+timestep	0.0001
+
+# compute and output options
+
+compute 	out_mag    all spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo_style    custom step time v_tmag temp v_emag ke pe etotal
+thermo          200
+
+run 		100000

examples/SPIN/test_problems/validation_nve/plot_nve.py

@@ -0,0 +1,46 @@
+#!/usr/bin/env python3
+
+import numpy as np, pylab, tkinter
+import matplotlib.pyplot as plt
+from scipy.optimize import curve_fit
+from decimal import *
+import sys, string, os
+
+
+argv = sys.argv
+if len(argv) != 3:
+  print("Syntax: ./plot_precession.py res_lammps.dat")
+  sys.exit()
+
+dirname   = os.path.join(os.getcwd(), "Feb_07")
+lammps_file = sys.argv[1]
+llg_file = sys.argv[2]
+
+t,tmag,temp,e_mag,e_kin,e_pot,e_tot = np.loadtxt(lammps_file,skiprows=0, usecols=(1,2,3,4,5,6,7),unpack=True)
+
+fig = plt.figure(figsize=(8,8))
+ax1  = plt.subplot(3,1,1)
+ax2  = plt.subplot(3,1,2)
+ax3  = plt.subplot(3,1,3)
+
+ax1.plot(t, e_tot, 'k-', label='Total energy')
+ax1.plot(t, e_pot, 'r-', label='Potential energy')
+ax1.set_ylabel("E (eV)")
+ax1.legend(loc=3)
+
+ax2.plot(t, e_kin, 'b-', label='Kinetic energy')
+ax2.plot(t, e_mag, 'g-', label='Magnetic energy')
+ax2.set_ylabel("E (eV)")
+ax2.legend(loc=3)
+
+ax3.plot(t, temp, 'b--', label='Latt. temperature')
+ax3.plot(t, tmag, 'r--', label='Spin temperature')
+ax3.set_ylabel("T (K)")
+ax3.legend(loc=3)
+
+plt.xlabel('Time (in ps)')
+plt.legend()
+plt.show()
+
+fig.savefig(os.path.join(os.getcwd(), "nve_spin_lattice.pdf"), bbox_inches="tight")
+plt.close(fig)

examples/SPIN/test_problems/validation_nve/run-test-nve.sh

@@ -0,0 +1,16 @@
+#!/bin/bash
+
+# clean old res
+rm res_*.dat
+
+# compute Lammps 
+./../../../../src/lmp_serial \
+  -in in.spin.iron-nve 
+in="$(grep -n Step log.lammps | awk -F ':' '{print $1}')"
+en="$(grep -n Loop log.lammps | awk -F ':' '{print $1}')"
+in="$(echo "$in+1" | bc -l)"
+en="$(echo "$en-$in" | bc -l)"
+tail -n +$in log.lammps | head -n $en > res_lammps.dat
+
+# plot results
+python3 -m plot_nve.py res_lammps.dat res_llg.dat

examples/SPIN/test_problems/validation_nve/test-spin-precession.in

@@ -0,0 +1,39 @@
+#LAMMPS in.run 
+ 
+units           metal
+atom_style      spin
+atom_modify     map array
+boundary        f f f 
+
+read_data	two_spins.data
+
+pair_style      spin/exchange 3.1
+pair_coeff	* * exchange 3.1 11.254 0.0 1.0
+
+group bead      type 1  
+ 
+variable        H equal 0.0
+variable        Kan equal 0.0
+variable        Temperature equal 0.0 
+variable        RUN equal 30000
+
+fix             1 all nve/spin lattice no
+fix             2 all precession/spin zeeman ${H} 0.0 0.0 1.0 anisotropy ${Kan} 0.0 0.0 1.0
+fix_modify      2 energy yes
+fix             3 all langevin/spin ${Temperature} 0.01 12345
+
+compute		out_mag    all spin
+compute		out_pe     all pe
+
+variable	magx      equal c_out_mag[1]
+variable	magy      equal c_out_mag[2]
+variable	magz      equal c_out_mag[3]
+variable	magnorm   equal c_out_mag[4]
+variable	emag      equal c_out_mag[5]
+
+thermo_style    custom step time v_magx v_magy v_magz v_emag pe etotal
+thermo          10
+
+timestep	0.0001
+
+run             ${RUN}