Commit 9fcd6992 authored by julient31's avatar julient31
Browse files

Commit JT 020419 

- neb/spin implemneted
- rotational initial states to be implemented
- climbing image to be implemented
parent 08b1728a

examples/SPIN/gneb_bfo/final.iron_spin

+32 −32
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examples/SPIN/gneb_bfo/in.neb.hop1

+1 −0
Original line number Diff line number Diff line 
# 2d NEB surface simulation, hop from surface to become adatom

print "Test 1"



dimension	2

boundary	p s p

examples/SPIN/gneb_bfo/in.neb.spin_iron

+11 −71
Original line number Diff line number Diff line 
# bcc iron in a 3d periodic box

print "Test 1"



clear 

units 		metal

atom_style 	spin



dimension 	3

boundary 	p p f



atom_style 	spin



# necessary for the serial algorithm (sametag)

atom_modify 	map array
@@ -20,7 +20,7 @@ read_data ../examples/SPIN/gneb_bfo/initial.iron_spin 
# setting mass, mag. moments, and interactions for bcc iron



mass		1 55.845

set 		group all spin 2.2 -1.0 0.0 0.0

#set 		group all spin 2.2 -1.0 0.0 0.0



pair_style 	spin/exchange 3.5

pair_coeff 	* * exchange 3.4 0.02726 0.2171 1.841
@@ -28,73 +28,13 @@ pair_coeff * * 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 0.0 21

fix		2 nebatoms neb_spin 1.0 

fix 		1 all precession/spin zeeman 0.001 0.0 0.0 1.0 anisotropy 0.01 1.0 0.0 0.0 

#fix 		2 all langevin/spin 0.0 0.0 21

fix		2 all neb/spin 1.0 

#parallel ideal



min_style	quickmin

neb		0.0 0.1 1000 1000 100 final ../examples/SPIN/gneb_bfo/final.iron_spin





#############################################################



# 2d NEB surface simulation, hop from surface to become adatom





variable	u uloop 20



# create geometry with flat surface



lattice		hex 0.9

region		box block 0 20 0 10 -0.25 0.25



#create_box	3 box

#create_atoms	1 box

#mass		* 1.0

#write_data      initial.hop1



read_data        ../examples/SPIN/gneb_bfo/initial.hop1



# LJ potentials



pair_style	lj/cut 2.5

pair_coeff	* * 1.0 1.0 2.5

pair_modify	shift yes



# initial minimization to relax surface



minimize	1.0e-6 1.0e-4 1000 10000

reset_timestep	0



# define groups



region	        1 block INF INF INF 1.25 INF INF

group		lower region 1

group		mobile subtract all lower

set		group lower type 2



timestep	0.05



# group of NEB atoms - either block or single atom ID 412



region		surround block 10 18 17 20 0 0 units box

group		nebatoms region surround

#group		nebatoms id 412

set		group nebatoms type 3

group		nonneb subtract all nebatoms



fix		1 lower setforce 0.0 0.0 0.0

fix		2 nebatoms neb 1.0 parallel ideal

fix		3 all enforce2d



thermo		100



#dump		1 nebatoms atom 10 dump.neb.$u

#dump		2 nonneb atom 10 dump.nonneb.$u



# run NEB for 2000 steps or to force tolerance



min_style	quickmin

timestep	0.0001



neb		0.0 0.1 1000 1000 100 final ../examples/SPIN/gneb_bfo/final.hop1
 
#min_style	quickmin

neb/spin		0.0 0.1 1 1 1 final ../examples/SPIN/gneb_bfo/final.iron_spin

#neb/spin		0.0 0.1 1000 1000 100 final ../examples/SPIN/gneb_bfo/final.iron_spin

examples/SPIN/gneb_bfo/in.spin.iron

+2 −2
Original line number Diff line number Diff line
@@ -19,7 +19,7 @@ create_atoms 1 box 


mass		1 55.845



set 		group all spin 2.2 -1.0 0.0 0.0

set 		group all spin 2.2 1.0 0.0 0.0

#velocity 	all create 100 4928459 rot yes dist gaussian



pair_style 	spin/exchange 3.5
@@ -53,4 +53,4 @@ compute outsp all property/atom spx spy spz sp fmx fmy fmz 
dump 		100 all custom 1 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]



run 		0

write_data	final.iron_spin
 
write_data	initial.iron_spin

src/REPLICA/fix_neb_spin.cpp

+296 −185

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