error in create atom region

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1

hello dear
i want to simulate water and nano fluid cu in a fcc lattice…water is base fluid and cu is a region (sphere or box)in the center of lattice (between water)

molecules are in the range of 1000 to 1500 and cu atoms are about 400 to 500

when it runs it shows this error
:ERROR: Invalid atom type in create_atoms command (…/create_atoms.cpp:55)
group hydrogen type 1
748 atoms in group hydrogen
group Water type 1 2
1122 atoms in group Water
group cu type 3
0 atoms in group cu
group oxygen type 2
374 atoms in group oxygen

Cu

lattice fcc " 3. 610"
Lattice spacing in x,y,z = 3 3 3
region Cu sphere 0 0 0 7 units box
create_atoms 3 region Cu
ERROR: Invalid atom type in create_atoms command (…/create_atoms.cpp:55)

this is my input script:

modified

units real
dimension 3
boundary p p p

atom_style full
bond_style harmonic
angle_style harmonic
kspace_style pppm 1.0e-4
#kspace_modify force/disp/real …
#kspace_mdofiy force/disp/kspace …

Atom Definition

Water

read_data water.data

group hydrogen type 1
group Water type 1 2
group cu type 3
group oxygen type 2

Cu

lattice fcc " 3. 610"
region Cu sphere 0 0 0 7 units box
create_atoms 3 region Cu

set group oxygen charge -1.040
set group hydrogen charge .520
set group cu charge 0.000

pair interaction

#sigma=3.157 epsilon=0.1521

pair_style hybrid eam lj/cut/coul/long 0.1521 3.157 lj/cut 3.157
pair_coeff 1 1 lj/cut/coul/long 0.0460 0.4000 # 108.0e-21 32.0e-11
pair_coeff 1 2 lj/cut/coul/long 0.0836 1.7753
pair_coeff 1 3 lj/cut 3.157 0.1521
pair_coeff 2 2 lj/cut/coul/long 0 0 # 0.1521 3.157
pair_coeff 2 3 lj/cut 3.157 0.1521
pair_coeff 3 3 eam cu.eam

bond_coeff 1 33.5315 3.3572
angle_coeff 1 2.181383 331.52

setting

fix 1 Water nvt temp 300.0 300.0 0.01

---------- compute ---------------------

#compute Tliq water temp
#compute Tpar water temp/partial
#compute heat/flux
#compute temp/profile or compute 1 all temp
#compute peatom all pe/atom
#compute keatom all ke/atom

---------- Relaxation ---------------------

min_style fire
min_modify dmax 0.01 line forcezero
minimize 1.0e-15 1.0e-15 1000000 10000000

dump 1all xyz 1000final.xyz

---------- output---------------------

thermo_style custom step (temp) c_Tliq c_Tpar etotal enthalpy pe press vol
thermo 100
thermo_modify flush yes

timestep 2.0
velocity water create 300.0 34239 rot yes dist gaussian
run 60000

2

your data file must specify the number of atom types that will be used in the
simulation.

'3 atom types'

3

hello dear
thanks for your guidence.excuse me when it runs it shows this error.“cannot open eam potential file cu.” i’ve checked the error and of corse documentation .i dont know.can any body guide me.thanks
regard

Atom Definition

Water

read_data water.data

group hydrogen type 1
group Water type 1 2
group cu type 3
group oxygen type 2

Cu

lattice fcc " 3. 610"
region Cu sphere 0 0 0 7 units box
create_atoms 3 region Cu
#mass of cu 63.546
set group oxygen charge -1.040
set group hydrogen charge .520
set group cu charge 0.000

pair interaction

#sigma=3.157 epsilon=0.1521

pair_style hybrid lj/cut/coul/long 0.1521 3.157 eam lj/cut 3.157
pair_coeff 1 1 lj/cut/coul/long 0.0460 0.4000 # 108.0e-21 32.0e-11
pair_coeff 1 2 lj/cut/coul/long 0.0836 1.7753
pair_coeff 1 3 lj/cut 3.157 0.1521
pair_coeff 2 2 lj/cut/coul/long 0 0 # 0.1521 3.157
pair_coeff 2 3 lj/cut 3.157 0.1521
pair_coeff 3 3 eam cu

bond_coeff 1 33.5315 3.3572
angle_coeff 1 2.181383 331.52

setting

fix 1 Water nvt temp 300.0 300.0 0.01

---------- compute ---------------------

#compute Tliq water temp
#compute Tpar water temp/partial
#compute heat/flux
#compute temp/profile or compute 1 all temp
#compute peatom all pe/atom
#compute keatom all ke/atom

---------- Relaxation ---------------------

min_style fire
min_modify dmax 0.01 line forcezero
minimize 1.0e-15 1.0e-15 1000000 10000000

dump 1all xyz 1000final.xyz

---------- output---------------------

thermo_style custom step (temp) c_Tliq c_Tpar etotal enthalpy pe press vol
thermo 100
thermo_modify flush yes

timestep 2.0
velocity water create 300.0 34239 rot yes dist gaussian
run 60000

1122 atoms
748 bonds
374 angles
0 dihedrals
0 impropers

3 atom types
1 bond types
1 angle types
0 dihedral types
0 improper types

-12.498 12.43 xlo xhi
-12.397 12.45 ylo yhi
-12.304 12.371 zlo zhi

Masses

1 1.008
2 15.9994
3 63.546

Atoms

1 1 2 -0.834 -8.832 -2.418 3.404
2 1 1 0.417 -9.276 -2.049 2.601
3 1 1 0.417 -9.408 -2.121 4.127
4 2 2 -0.834 -6.467 -7.624 8.391
5 2 1 0.417 -6.422 -7.276 9.298
6 2 1 0.417 -5.908 -8.412 8.461
7 3 2 -0.834 -4.176 1.311 8.832
8 3 1 0.417 -3.867 0.848 9.612
9 3 1 0.417 -3.495 1.993 8.567
10 4 2 -0.834 -8.714 3.818 -11.19

4

LAMMPS happens to have an extensive documentation. It is a really helpful and I
am sure that you will find that it can help you proceed further in your
simulation work.

If you have not found it already, it is on the website of LAMMPS
http://lammps.sandia.gov/

Pierre

5

And use -echo screen on your command line
when you launch LAMMPS. Then it will be
clear which line of the input script the error
refers to and as Pierre says, the manual will
help you figure out the problem.

Steve

6

hello dear
i want to simulate water and nano fluid cu in a fcc lattice…water is base fluid and cu is a region (sphere or box)in the center of lattice (between water)

when it runs it shows this error
"cannot open eam potential file cu "
thanks
regard

this is my input script:

units real
dimension 3
boundary p p p

atom_style full
bond_style harmonic
angle_style harmonic
kspace_style pppm 1.0e-4
#kspace_modify force/disp/real …
#kspace_mdofiy force/disp/kspace …

Atom Definition

Water

read_data water.data

group hydrogen type 1
group Water type 1 2
group cu type 3
group oxygen type 2

Cu

lattice fcc " 3. 610"
region Cu sphere 0 0 0 7 units box
create_atoms 3 region Cu

set group oxygen charge -1.040
set group hydrogen charge .520
set group cu charge 0.000

pair interaction

#sigma=3.157 epsilon=0.1521

pair_style hybrid eam lj/cut/coul/long 0.1521 3.157 lj/cut 3.157
pair_coeff 1 1 lj/cut/coul/long 0.0460 0.4000 # 108.0e-21 32.0e-11
pair_coeff 1 2 lj/cut/coul/long 0.0836 1.7753
pair_coeff 1 3 lj/cut 3.157 0.1521
pair_coeff 2 2 lj/cut/coul/long 0 0 # 0.1521 3.157
pair_coeff 2 3 lj/cut 3.157 0.1521
pair_coeff 3 3 eam cu.eam

bond_coeff 1 33.5315 3.3572
angle_coeff 1 2.181383 331.52

setting

fix 1 Water nvt temp 300.0 300.0 0.01

---------- compute ---------------------

#compute Tliq water temp
#compute Tpar water temp/partial
#compute heat/flux
#compute temp/profile or compute 1 all temp
#compute peatom all pe/atom
#compute keatom all ke/atom

---------- Relaxation ---------------------

min_style fire
min_modify dmax 0.01 line forcezero
minimize 1.0e-15 1.0e-15 1000000 10000000

dump 1all xyz 1000final.xyz

---------- output---------------------

thermo_style custom step (temp) c_Tliq c_Tpar etotal enthalpy pe press vol
thermo 100
thermo_modify flush yes

timestep 2.0
velocity water create 300.0 34239 rot yes dist gaussian
run 60000

7

hello dear
i used echo screen and this is my log.(should i specify a file which contain potential or …for cu like data file?)
i dont know what should i do.please guide
thanks
regard

LAMMPS (12 Apr 2013)

modified

units real
echo screen
2 = max bonds/atom
1 = max angles/atom
orthogonal box = (-12.498 -12.397 -12.304) to (12.43 12.45 12.371)
1 by 1 by 1 MPI processor grid
1122 atoms
748 bonds
374 angles
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
748 atoms in group hydrogen
1122 atoms in group Water
0 atoms in group cu
374 atoms in group oxygen
Lattice spacing in x,y,z = 3 3 3
Created 201 atoms
374 settings made for charge
748 settings made for charge
0 settings made for charge

pair_style hybrid lj/cut/coul/long 0.1521 3.157 eam lj/cut 3.157
pair_coeff 1 1 lj/cut/coul/long 0.0460 0.4000 # 108.0e-21 32.0e-11
pair_coeff 1 2 lj/cut/coul/long 0.0836 1.7753
pair_coeff 1 3 lj/cut 3.157 0.1521
pair_coeff 2 2 lj/cut/coul/long 0 0 # 0.1521 3.157
pair_coeff 2 3 lj/cut 3.157 0.1521
pair_coeff 3 3 eam cu

error on proc 0 :"cannot open eam potential file cu " (…/pair-eam.cpp:445)

8

Do you have a file named “cu”? Is it
in the directory where you are running from?

Steve