fix shake

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)

i have read the manuel and know this that( , the two H atoms might

exert a repulsive force on each other ) should i use fix shake just for hydrogen or water.?(which fix shake should i use in my input code ?.and is this sentence true that there is no need to use "neigh_modify "when i use “fix shake”.)???
i appreciate any help
thanks
regard

atom_style full
bond_style harmonic #hybrid harmonic
angle_style harmonic #hybrid harmonic
kspace_style pppm 1.0e-5
#pair_modify mix arithmetic

read_data water.data

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

lattice fcc " 3. 615" #Cu lattice constant
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_style hybrid lj/cut/coul/long 0.1521 3.157 eam lj/cut 3.157 # 7.5

pair_coeff 1 1 lj/cut/coul/long 0.0460 0.4000 #H-H epsilon sigm # 108.0e-21 32.0e-11
pair_coeff 1 2 lj/cut/coul/long 0.0836 1.7753 #O-H epsilon sigma
pair_coeff 1 3 lj/cut 0.6589 0.2117 #H-Cu epsilon sigma
pair_coeff 2 2 lj/cut/coul/long 0.1521 3.157 #O-O epsilon sigma # 0 0
pair_coeff 2 3 lj/cut 1.198 1.587 #O-Cu epsilon sigma
pair_coeff 3 3 eam cu.eam #Cu-Cu

for cu-cu bond sigma=.227 epsilon(Lj)=.583 ev # sigma=2.34 epsilon=9.4512 kcal/mol

bond_coeff 1 450 0.9572 #O-H
angle_coeff 1 55 104.52 #H-O-H

++++++++++++++++setting+++++++++++++++++++++

neighbor 2 bin
#neigh_modify delay 0 every 1 check yes #Unlike “fix rigid”, there is no need to use "neigh_modify

exclude" if you use “fix shake”

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

compute 1 all temp
#compute heat/flux
compute peatom all pe/atom
compute keatom all ke/atom

dump 1 all custom 10000 dump.equilibrium. xs ys zs vx vy vz

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

thermo 100
thermo_style custom step etotal enthalpy pe press ke

velocity all create 373.0 4928459 rot yes dist gaussian #23482341
fix 1 2 water npt temp 300 300 100 iso 0 0 1000
fix water shake 1.0e-4 200 0 b 1 a 1
fix 1 all shake 1e-6 500 0 m 1.0 #for hydrogen

hello dear

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

when i run it shows this error"couldn’t find group id"

i also have read the manuel.and defined the group in input code (group hydrogen type 1 …)

does anybody know the error?

i appreciate any help
thanks
regard

atom_style full
bond_style harmonic
angle_style harmonic
kspace_style pppm 1.0e-5
#pair_modify mix arithmetic

read_data water.data

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

lattice fcc " 3. 615" #Cu lattice constant
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_style hybrid lj/cut/coul/long 0.1521 3.157 eam lj/cut 3.157 # 7.5

pair_coeff 1 1 lj/cut/coul/long 0.0460 0.4000 #H-H epsilon sigm # 108.0e-21 32.0e-11
pair_coeff 1 2 lj/cut/coul/long 0.0836 1.7753 #O-H epsilon sigma
pair_coeff 1 3 lj/cut 0.6589 0.2117 #H-Cu epsilon sigma
pair_coeff 2 2 lj/cut/coul/long 0.1521 3.157 #O-O epsilon sigma # 0 0
pair_coeff 2 3 lj/cut 1.198 1.587 #O-Cu epsilon sigma
pair_coeff 3 3 eam cu.eam #Cu-Cu

for cu-cu bond sigma=.227 epsilon(Lj)=.583 ev # sigma=2.34 epsilon=9.4512 kcal/mol

bond_coeff 1 450 0.9572 #O-H
angle_coeff 1 55 104.52 #H-O-H

++++++++++++++++setting+++++++++++++++++++++

neighbor 2 bin
#neigh_modify delay 0 every 1 check yes #Unlike “fix rigid”, there is no need to use "neigh_modify

exclude" if you use “fix shake”

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

compute 1 all temp
#compute heat/flux
compute peatom all pe/atom
compute keatom all ke/atom

dump 1 all custom 10000 dump.equilibrium. xs ys zs vx vy vz

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

thermo 100
thermo_style custom step etotal enthalpy pe press ke

velocity all create 373.0 4928459 rot yes dist gaussian #23482341
fix 1 2 water npt temp 300 300 100 iso 0 0 1000
fix water shake 1.0e-4 200 0 b 1 a 1
fix 1 all shake 1e-6 500 0 m 1.0 #for hydrogen

hello dear

I HAVE WORKED somedays to correct the error but i could’nt.it’s about fix npt and fix shake.

when i run it shows this error"couldn’t find group id"

i also have read the manuel.and defined the group in input code (group hydrogen type 1 …)

can anybody help me to modify the error?

i appreciate any help
thanks
regard

atom_style full
bond_style harmonic
angle_style harmonic

kspace_style pppm 1.0e-5
#pair_modify mix arithmetic

read_data water.data

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

lattice fcc " 3. 615" #Cu lattice constant
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_style hybrid lj/cut/coul/long 0.1521 3.157 eam lj/cut 3.157 # 7.5

pair_coeff 1 1 lj/cut/coul/long 0.0460 0.4000 #H-H epsilon sigm # 108.0e-21 32.0e-11
pair_coeff 1 2 lj/cut/coul/long 0.0836 1.7753 #O-H epsilon sigma
pair_coeff 1 3 lj/cut 0.6589 0.2117 #H-Cu epsilon sigma
pair_coeff 2 2 lj/cut/coul/long 0.1521 3.157 #O-O epsilon sigma # 0 0
pair_coeff 2 3 lj/cut 1.198 1.587 #O-Cu epsilon sigma
pair_coeff 3 3 eam cu.eam #Cu-Cu

for cu-cu bond sigma=.227 epsilon(Lj)=.583 ev # sigma=2.34 epsilon=9.4512 kcal/mol

bond_coeff 1 450 0.9572 #O-H
angle_coeff 1 55 104.52 #H-O-H

++++++++++++++++setting+++++++++++++++++++++

neighbor 2 bin

dump 1 all custom 10000 dump.equilibrium. xs ys zs vx vy vz

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

thermo 100
thermo_style custom step etotal enthalpy pe press ke

velocity all create 373.0 4928459 rot yes dist gaussian #23482341
fix 1 2 water npt temp 300 300 100 iso 0 0 1000
fix water shake 1.0e-4 200 0 b 1 a 1
fix 1 all shake 1e-6 500 0 m 1.0 #for hydrogen

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

compute 1 all temp
#compute heat/flux
compute peatom all pe/atom
compute keatom all ke/atom

Please keep in mind that all LAMMPS variables are “case sensitive”. “Water” does not equal to “water”.

Also, you have to correct your Cu lattice constant.

Ray

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)

i have read the manuel and know this that( , the two H atoms might

exert a repulsive force on each other ) should i use fix shake just for hydrogen or water?
i appreciate any help
thanks
regard

atom_style full
bond_style harmonic #hybrid harmonic
angle_style harmonic #hybrid harmonic
kspace_style pppm 1.0e-5
#pair_modify mix arithmetic

read_data water.data

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

lattice fcc " 3. 615" #Cu lattice constant
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_style hybrid lj/cut/coul/long 0.1521 3.157 eam lj/cut 3.157 # 7.5

pair_coeff 1 1 lj/cut/coul/long 0.0460 0.4000 #H-H epsilon sigm # 108.0e-21 32.0e-11
pair_coeff 1 2 lj/cut/coul/long 0.0836 1.7753 #O-H epsilon sigma
pair_coeff 1 3 lj/cut 0.6589 0.2117 #H-Cu epsilon sigma
pair_coeff 2 2 lj/cut/coul/long 0.1521 3.157 #O-O epsilon sigma # 0 0
pair_coeff 2 3 lj/cut 1.198 1.587 #O-Cu epsilon sigma
pair_coeff 3 3 eam cu.eam #Cu-Cu

for cu-cu bond sigma=.227 epsilon(Lj)=.583 ev # sigma=2.34 epsilon=9.4512 kcal/mol

bond_coeff 1 450 0.9572 #O-H
angle_coeff 1 55 104.52 #H-O-H

++++++++++++++++setting+++++++++++++++++++++

neighbor 2.0 bin
neigh_modify delay 0 every 1 check yes

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

minimization : avoid atoms overlapping

min_style fire
min_modify dmax 0.01
minimize 1.0e-10 0 100000 1000000

#(the minimization step is not necessary in this example. However

in general, it’s always a good idea to minimize the system beforehand.

fSHAKE was defined in system.in.settings. It is incompatible with “minimize”.

#unfix fSHAKE
#minimize 1.0e-5 1.0e-7 100000 400000 )
#------------------------dump--------------------------------

dump 1 all custom 10000 dump.equilibrium. xs ys zs # vx vy vz

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

thermo 100
thermo_style custom step etotal enthalpy pe press ke
thermo_modify flush yes

#+++++++++++++++++++++++++++++++fix ++++++++++++++++++++++++++++++++
velocity all create 300.0 4928459 rot yes dist gaussian #23482341

fix 1 hydrogen shake 1e-6 500 0 m 1.0 a 1 #for hydrogen
fix 12 water npt temp 300.0 300.0 100.0 iso 0.0 0.0 1000.0

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

compute 1 all temp
#compute heat/flux
compute peatom all pe/atom
compute keatom all ke/atom
#fix 12 all thermal /conductivity 100 z 20
#fix 12

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)

i have read the manuel and know this that( , the two H atoms might

exert a repulsive force on each other ) should i use fix shake just for hydrogen or water?

i appreciate any help
thanks
regard

atom_style full
bond_style harmonic #hybrid harmonic
angle_style harmonic #hybrid harmonic
kspace_style pppm 1.0e-5
#pair_modify mix arithmetic

read_data water.data

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

lattice fcc " 3. 615" #Cu lattice constant
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_style hybrid lj/cut/coul/long 0.1521 3.157 eam lj/cut 3.157 # 7.5

pair_coeff 1 1 lj/cut/coul/long 0.0460 0.4000 #H-H epsilon sigm # 108.0e-21 32.0e-11
pair_coeff 1 2 lj/cut/coul/long 0.0836 1.7753 #O-H epsilon sigma
pair_coeff 1 3 lj/cut 0.6589 0.2117 #H-Cu epsilon sigma
pair_coeff 2 2 lj/cut/coul/long 0.1521 3.157 #O-O epsilon sigma # 0 0
pair_coeff 2 3 lj/cut 1.198 1.587 #O-Cu epsilon sigma
pair_coeff 3 3 eam cu.eam #Cu-Cu

for cu-cu bond sigma=.227 epsilon(Lj)=.583 ev # sigma=2.34 epsilon=9.4512 kcal/mol

bond_coeff 1 450 0.9572 #O-H
angle_coeff 1 55 104.52 #H-O-H

++++++++++++++++setting+++++++++++++++++++++

neighbor 2.0 bin

neigh_modify delay 0 every 1 check yes

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

minimization : avoid atoms overlapping

min_style fire
min_modify dmax 0.01
minimize 1.0e-10 0 100000 1000000

#(the minimization step is not necessary in this example. However

in general, it’s always a good idea to minimize the system beforehand.

fSHAKE was defined in system.in.settings. It is incompatible with “minimize”.

#unfix fSHAKE
#minimize 1.0e-5 1.0e-7 100000 400000 )
#------------------------dump--------------------------------

dump 1 all custom 10000 dump.equilibrium. xs ys zs # vx vy vz

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

thermo 100
thermo_style custom step etotal enthalpy pe press ke

thermo_modify flush yes

#+++++++++++++++++++++++++++++++fix ++++++++++++++++++++++++++++++++
velocity all create 300.0 4928459 rot yes dist gaussian #23482341

fix 1 hydrogen shake 1e-6 500 0 m 1.0 a 1 #for hydrogen
fix 12 water npt temp 300.0 300.0 100.0 iso 0.0 0.0 1000.0

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

compute 1 all temp
#compute heat/flux
compute peatom all pe/atom
compute keatom all ke/atom

#fix 12 all thermal /conductivity 100 z 20
#fix 12