ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Commit JT 020419

Browse Source 
- neb/spin implemneted
- rotational initial states to be implemented
- climbing image to be implemented
This commit is contained in:
julient31
2019-02-04 11:27:00 -07:00
parent 08b1728a96
commit 9fcd69921f
9 changed files with 754 additions and 348 deletions
Download Patch File Download Diff File Expand all files Collapse all files

64
examples/SPIN/gneb_bfo/final.iron_spin
View File

@ -1,36 +1,36 @@
32
2.2000000000000002e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
2.2000000000000002e+00 1.4332499999999999e+00 1.4332499999999999e+00 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
2.2000000000000002e+00 2.8664999999999998e+00 0.0000000000000000e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
2.2000000000000002e+00 4.2997499999999995e+00 1.4332499999999999e+00 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
2.2000000000000002e+00 5.7329999999999997e+00 0.0000000000000000e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
2.2000000000000002e+00 7.1662499999999998e+00 1.4332499999999999e+00 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
2.2000000000000002e+00 8.5994999999999990e+00 0.0000000000000000e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
2.2000000000000002e+00 1.0032750000000000e+01 1.4332499999999999e+00 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
2.2000000000000002e+00 0.0000000000000000e+00 2.8664999999999998e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
2.2000000000000002e+00 2.8664999999999998e+00 2.8664999999999998e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
2.2000000000000002e+00 5.7329999999999997e+00 2.8664999999999998e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
2.2000000000000002e+00 8.5994999999999990e+00 2.8664999999999998e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
2.2000000000000002e+00 1.4332499999999999e+00 4.2997499999999995e+00 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
2.2000000000000002e+00 4.2997499999999995e+00 4.2997499999999995e+00 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
2.2000000000000002e+00 7.1662499999999998e+00 4.2997499999999995e+00 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
2.2000000000000002e+00 1.0032750000000000e+01 4.2997499999999995e+00 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
2.2000000000000002e+00 0.0000000000000000e+00 5.7329999999999997e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
2.2000000000000002e+00 1.4332499999999999e+00 7.1662499999999998e+00 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
2.2000000000000002e+00 2.8664999999999998e+00 5.7329999999999997e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
2.2000000000000002e+00 4.2997499999999995e+00 7.1662499999999998e+00 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
2.2000000000000002e+00 5.7329999999999997e+00 5.7329999999999997e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
2.2000000000000002e+00 7.1662499999999998e+00 7.1662499999999998e+00 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
2.2000000000000002e+00 8.5994999999999990e+00 5.7329999999999997e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
2.2000000000000002e+00 1.0032750000000000e+01 7.1662499999999998e+00 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
2.2000000000000002e+00 0.0000000000000000e+00 8.5994999999999990e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
2.2000000000000002e+00 2.8664999999999998e+00 8.5994999999999990e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
2.2000000000000002e+00 5.7329999999999997e+00 8.5994999999999990e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
2.2000000000000002e+00 8.5994999999999990e+00 8.5994999999999990e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
2.2000000000000002e+00 1.4332499999999999e+00 1.0032750000000000e+01 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
2.2000000000000002e+00 4.2997499999999995e+00 1.0032750000000000e+01 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
2.2000000000000002e+00 7.1662499999999998e+00 1.0032750000000000e+01 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
2.2000000000000002e+00 1.0032750000000000e+01 1.0032750000000000e+01 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
1 2.2000000000000002e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
2 2.2000000000000002e+00 1.4332499999999999e+00 1.4332499999999999e+00 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
3 2.2000000000000002e+00 2.8664999999999998e+00 0.0000000000000000e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
4 2.2000000000000002e+00 4.2997499999999995e+00 1.4332499999999999e+00 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
5 2.2000000000000002e+00 5.7329999999999997e+00 0.0000000000000000e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
6 2.2000000000000002e+00 7.1662499999999998e+00 1.4332499999999999e+00 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
7 2.2000000000000002e+00 8.5994999999999990e+00 0.0000000000000000e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
8 2.2000000000000002e+00 1.0032750000000000e+01 1.4332499999999999e+00 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
9 2.2000000000000002e+00 0.0000000000000000e+00 2.8664999999999998e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
10 2.2000000000000002e+00 2.8664999999999998e+00 2.8664999999999998e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
11 2.2000000000000002e+00 5.7329999999999997e+00 2.8664999999999998e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
12 2.2000000000000002e+00 8.5994999999999990e+00 2.8664999999999998e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
13 2.2000000000000002e+00 1.4332499999999999e+00 4.2997499999999995e+00 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
14 2.2000000000000002e+00 4.2997499999999995e+00 4.2997499999999995e+00 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
15 2.2000000000000002e+00 7.1662499999999998e+00 4.2997499999999995e+00 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
16 2.2000000000000002e+00 1.0032750000000000e+01 4.2997499999999995e+00 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
17 2.2000000000000002e+00 0.0000000000000000e+00 5.7329999999999997e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
18 2.2000000000000002e+00 1.4332499999999999e+00 7.1662499999999998e+00 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
19 2.2000000000000002e+00 2.8664999999999998e+00 5.7329999999999997e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
20 2.2000000000000002e+00 4.2997499999999995e+00 7.1662499999999998e+00 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
21 2.2000000000000002e+00 5.7329999999999997e+00 5.7329999999999997e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
22 2.2000000000000002e+00 7.1662499999999998e+00 7.1662499999999998e+00 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
23 2.2000000000000002e+00 8.5994999999999990e+00 5.7329999999999997e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
24 2.2000000000000002e+00 1.0032750000000000e+01 7.1662499999999998e+00 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
25 2.2000000000000002e+00 0.0000000000000000e+00 8.5994999999999990e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
26 2.2000000000000002e+00 2.8664999999999998e+00 8.5994999999999990e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
27 2.2000000000000002e+00 5.7329999999999997e+00 8.5994999999999990e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
28 2.2000000000000002e+00 8.5994999999999990e+00 8.5994999999999990e+00 0.0000000000000000e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
29 2.2000000000000002e+00 1.4332499999999999e+00 1.0032750000000000e+01 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
30 2.2000000000000002e+00 4.2997499999999995e+00 1.0032750000000000e+01 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
31 2.2000000000000002e+00 7.1662499999999998e+00 1.0032750000000000e+01 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
32 2.2000000000000002e+00 1.0032750000000000e+01 1.0032750000000000e+01 1.4332499999999999e+00 -1.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00

1
examples/SPIN/gneb_bfo/in.neb.hop1
View File

@ -1,4 +1,5 @@
# 2d NEB surface simulation, hop from surface to become adatom
print "Test 1"
dimension 2
boundary p s p

82
examples/SPIN/gneb_bfo/in.neb.spin_iron
View File

@ -1,12 +1,12 @@
# 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
timestep 0.0001
#############################################################
# 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
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

4
examples/SPIN/gneb_bfo/in.spin.iron
View File

@ -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