create molecule

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1

Dear Lammps users
I am trying to creating molecules in a block void on a metal surface, here is my input:

units real
atom_style charge
boundary p p p

region box block -10 10 -10 10 -10 10 units box
create_box 3 box
lattice fcc 3.52
create_atoms 3 region box

region void block -10 10 -10 10 0 10 units box

region void1 block -10 10 -10 10 -10 -6 units box
region void2 union 2 void void1

delete_atoms region void2

pair_style reax/c NULL
pair_coeff * * ffield.reax H O Ni

fix eem all qeq/reax 1 0.0 10.0 1e-6 reax/c

neighbor 2 bin
neigh_modify every 10 delay 0 check no
mass 1 1.007940
mass 2 15.999400
mass 3 58.69

group nickel type 3

velocity nickel create 300 4928459 rot yes dist gaussian
fix 1 all temp/rescale 1 300 300 10.0 1.0
fix 2 all nvt temp 300.0 300.0 10.0 drag 2.0

timestep 0.1
thermo 100

run 2000

unfix 2

change_box all boundary p p f
region water block -10 10 -10 10 6 10 units box

molecule mymol water.txt
create_atoms 0 random 10 123 water mol mymol 123456

fix wall all wall/reflect zhi EDGE
group water type 1 2

velocity water create 300 4928459 dist gaussian rot yes
fix 10 water temp/rescale 1 300 300 10.0 1.0

fix 3 all nvt temp 300 300 10.0 drag 2
thermo 100
timestep 0.1
run 2000

after creating 30 atoms in water region, two lines reported and simulation stopped:

step2000-hbondchk failed: H=0 end(H)=1 str(H+1)=0
application called MPI_Abort(MPI_COMM_WORLD, -14) - process 0

i change many commands in my input several times but it reports again and again,what does it mean and how can i solve it?

Best Regard.

2

Dear Lammps users
I am trying to creating molecules in a block void on a metal surface, here
is my input:

units real
atom_style charge
boundary p p p

region box block -10 10 -10 10 -10 10 units box
create_box 3 box
lattice fcc 3.52
create_atoms 3 region box

region void block -10 10 -10 10 0 10 units box
region void1 block -10 10 -10 10 -10 -6 units box
region void2 union 2 void void1

delete_atoms region void2

pair_style reax/c NULL
pair_coeff * * ffield.reax H O Ni

fix eem all qeq/reax 1 0.0 10.0 1e-6 reax/c

neighbor 2 bin
neigh_modify every 10 delay 0 check no
mass 1 1.007940
mass 2 15.999400
mass 3 58.69

group nickel type 3

velocity nickel create 300 4928459 rot yes dist gaussian
fix 1 all temp/rescale 1 300 300 10.0 1.0
fix 2 all nvt temp 300.0 300.0 10.0 drag 2.0

timestep 0.1
thermo 100

run 2000

unfix 2

change_box all boundary p p f
region water block -10 10 -10 10 6 10 units box

molecule mymol water.txt
create_atoms 0 random 10 123 water mol mymol 123456

fix wall all wall/reflect zhi EDGE
group water type 1 2

velocity water create 300 4928459 dist gaussian rot yes
fix 10 water temp/rescale 1 300 300 10.0 1.0

fix 3 all nvt temp 300 300 10.0 drag 2
thermo 100
timestep 0.1
run 2000

after creating 30 atoms in water region, two lines reported and simulation
stopped:

step2000-hbondchk failed: H=0 end(H)=1 str(H+1)=0
application called MPI_Abort(MPI_COMM_WORLD, -14) - process 0

i change many commands in my input several times but it reports again and
again,what does it mean and how can i solve it?

i don't know exactly, but there is a serious flaw in your procedure:
placing atoms at random in a volume is likely to create overlapping
particles and next to no force field can handle this situation well.
you would have to use something like fix gcmc to properly insert
atoms/molecules and even that is not likely to work well.

a better way to build your system would be to take a previously
equilibrated water box at the desired density (or rather at slightly
higher than desired density to compensate for a safety margin), carve
out the desired volume of molecules and then merge this with your
hollow metal block (e.g. by reserving one atom type and then creating
the metal atoms after reading the water system from a data file.

you still have to very carefully choose the respective volumes to
avoid overlaps and achieve a reasonable water density (the larger the
system, the easier, of course) and start with a minimization w/o
charge equilibration to gradually relax the rather unphysical
structure at the interface.

axel.