Commit 3486b7d5 authored by sjplimp's avatar sjplimp
Browse files 

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15663 f3b2605a-c512-4ea7-a41b-209d697bcdaa
parent 6fedf8d8

examples/neb/README

+11 −6
Original line number Diff line number Diff line 
Run these examples as:



mpirun -np 4 lmp_linux -partition 4x1 -in in.neb.hop1

mpirun -np 4 lmp_linux -partition 4x1 -in in.neb.hop2

mpirun -np 3 lmp_linux -partition 3x1 -in in.neb.sivac

mpirun -np 4 lmp_g++ -partition 4x1 -in in.neb.hop1

mpirun -np 4 lmp_g++ -partition 4x1 -in in.neb.hop2

mpirun -np 3 lmp_g++ -partition 3x1 -in in.neb.sivac



Create dump files to do visualization from via Python tools:

(see lammps/tools/README and lammps/tools/python/README

for more info on these Python scripts)

mpirun -np 8 lmp_g++ -partition 4x2 -in in.neb.hop1

mpirun -np 8 lmp_g++ -partition 4x2 -in in.neb.hop2

mpirun -np 6 lmp_g++ -partition 3x2 -in in.neb.sivac



If you uncomment the dump command lines in the input scripts, you can

create dump files to do visualization from via Python tools: (see

lammps/tools/README and lammps/tools/python/README for more info on

these Python scripts)



python ~/lammps/tools/python/neb_combine.py -o dump.hop1.combine

					    -b dump.nonneb.1

examples/neb/in.neb.hop1

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@@ -14,10 +14,13 @@ variable u uloop 20 


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

#create_box	3 box

#create_atoms	1 box

#mass		* 1.0

#write_data      initial.hop1



read_data        initial.hop1



# LJ potentials

examples/neb/in.neb.hop2

+7 −4
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@@ -15,11 +15,14 @@ variable u uloop 20 
lattice		hex 0.9

region		box block 0 20 0 11 -0.25 0.25

region		box1 block 0 20 0 10 -0.25 0.25

create_box	3 box

create_atoms	1 region box1

create_atoms	1 single 11.5 10.5 0



mass		* 1.0

#create_box	3 box

#create_atoms	1 region box1

#create_atoms	1 single 11.5 10.5 0

#mass		* 1.0

#write_data      initial.hop2



read_data        initial.hop2



# LJ potentials

examples/neb/in.neb.sivac

+10 −8
Original line number Diff line number Diff line
@@ -30,17 +30,20 @@ lattice custom $a & 
region          myreg block     0 4 &

                                0 4 &

                                0 4

create_box      1 myreg

create_atoms    1 region myreg



mass            1       28.06

#create_box      1 myreg

#create_atoms    1 region myreg

#mass            1       28.06

#write_data      initial.sivac



group Si type 1

read_data       initial.sivac



# make a vacancy



group Si type 1



group del id 300

delete_atoms group del

delete_atoms group del compress no

group vacneigh id 174 175 301 304 306 331 337

 

# choose potential
@@ -54,7 +57,7 @@ variable u uloop 20 


# only output atoms near vacancy



dump events vacneigh custom 1000 dump.neb.sivac.$u id type x y z

#dump events vacneigh custom 1000 dump.neb.sivac.$u id type x y z



# initial minimization to relax vacancy
@@ -72,5 +75,4 @@ thermo 100 
timestep        0.01

min_style	quickmin



neb		0.0 0.01 50 100 10 final final.sivac

neb		0.0 0.01 100 100 10 final final.sivac

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