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Merge branch 'develop' into mdi-expand

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Steve Plimpton
2022-03-22 08:39:24 -06:00
parent 6555c7302d 649e8a27b3
commit eb44b6b1fa
991 changed files with 208940 additions and 395848 deletions
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144
examples/PACKAGES/atc/drift_diffusion/in.convective_pulse
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@ -1,72 +1,72 @@
# DESCRIPTION: haynes-schockley
echo both
units metal
variable V equal 5000.0
variable n0 equal 0.085
variable dn equal 2.0*${n0}
variable dt equal 0.0005
variable s equal 10
timestep ${dt}
atom_style atomic
lattice fcc 1.0
region simRegion block -50 50 0 1 0 1
boundary f p p
create_box 1 simRegion
mass 1 1.0 # need to keep this
atom_modify sort 0 1
# ID group atc PhysicsType ParameterFile
fix AtC all atc convective_drift_diffusion Cu_cddm.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create 100 1 1 simRegion f p p
fix_modify AtC material all Cu
fix_modify AtC mesh create_nodeset lbc -50.0 -50.0 -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc 50.0 50.0 -INF INF -INF INF
# fix a temperature
fix_modify AtC initial temperature all 300.0
#fix_modify AtC initial electron_temperature all 300.0
fix_modify AtC fix electron_temperature all 300.
#fix_modify AtC initial electron_temperature all gaussian 0 0 0 1 0 0 5.0 300. 300.
fix_modify AtC initial electron_density all gaussian 0 0 0 1 0 0 5.0 ${dn} ${n0}
#fix_modify AtC fix electron_density all ${n0}
# isolate system:
# diffusion: dn/dx = 0
# drift : n = 0
fix_modify AtC fix electron_density lbc ${n0}
fix_modify AtC fix electron_density rbc ${n0}
fix_modify AtC fix temperature lbc 300.0
fix_modify AtC fix temperature rbc 300.0
fix_modify AtC fix electron_temperature lbc 300.0
fix_modify AtC fix electron_temperature rbc 300.0
fix_modify AtC fix electric_potential all 0.
fix_modify AtC extrinsic electron_integration implicit
# electron velocity
fix_modify AtC initial electron_velocity x all 0.
#fix_modify AtC fix electron_velocity x all 0.
fix_modify AtC initial electron_velocity y all 0.
fix_modify AtC fix electron_velocity y all 0
fix_modify AtC initial electron_velocity z all 0.
fix_modify AtC fix electron_velocity z all 0.
# f_AtC:1 thermal energy, 2 avg T, 3 electron energy, 4 avg Te, 5 total n
thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4] f_AtC[5]
thermo_modify format 1 %5i format 2 %7.2g
fix_modify AtC output convective_pulseFE $s text binary
thermo $s
#run 100
# free electric field and allow shielding
fix_modify AtC unfix electric_potential all
fix_modify AtC fix electric_potential lbc -$V
fix_modify AtC fix electric_potential rbc 0
fix_modify AtC source electric_potential all ${n0}
fix_modify AtC extrinsic electron_integration implicit 10
run 100
# DESCRIPTION: haynes-schockley
echo both
units metal
variable V equal 5000.0
variable n0 equal 0.085
variable dn equal 2.0*${n0}
variable dt equal 0.0005
variable s equal 10
timestep ${dt}
atom_style atomic
lattice fcc 1.0
region simRegion block -50 50 0 1 0 1
boundary f p p
create_box 1 simRegion
mass 1 1.0 # need to keep this
atom_modify sort 0 1
# ID group atc PhysicsType ParameterFile
fix AtC all atc convective_drift_diffusion Cu_cddm.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create 100 1 1 simRegion f p p
fix_modify AtC material all Cu
fix_modify AtC mesh create_nodeset lbc -50.0 -50.0 -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc 50.0 50.0 -INF INF -INF INF
# fix a temperature
fix_modify AtC initial temperature all 300.0
#fix_modify AtC initial electron_temperature all 300.0
fix_modify AtC fix electron_temperature all 300.
#fix_modify AtC initial electron_temperature all gaussian 0 0 0 1 0 0 5.0 300. 300.
fix_modify AtC initial electron_density all gaussian 0 0 0 1 0 0 5.0 ${dn} ${n0}
#fix_modify AtC fix electron_density all ${n0}
# isolate system:
# diffusion: dn/dx = 0
# drift : n = 0
fix_modify AtC fix electron_density lbc ${n0}
fix_modify AtC fix electron_density rbc ${n0}
fix_modify AtC fix temperature lbc 300.0
fix_modify AtC fix temperature rbc 300.0
fix_modify AtC fix electron_temperature lbc 300.0
fix_modify AtC fix electron_temperature rbc 300.0
fix_modify AtC fix electric_potential all 0.
fix_modify AtC extrinsic electron_integration implicit
# electron velocity
fix_modify AtC initial electron_velocity x all 0.
#fix_modify AtC fix electron_velocity x all 0.
fix_modify AtC initial electron_velocity y all 0.
fix_modify AtC fix electron_velocity y all 0
fix_modify AtC initial electron_velocity z all 0.
fix_modify AtC fix electron_velocity z all 0.
# f_AtC:1 thermal energy, 2 avg T, 3 electron energy, 4 avg Te, 5 total n
thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4] f_AtC[5]
thermo_modify format 1 %5i format 2 %7.2g
fix_modify AtC output convective_pulseFE $s text binary
thermo $s
#run 100
# free electric field and allow shielding
fix_modify AtC unfix electric_potential all
fix_modify AtC fix electric_potential lbc -$V
fix_modify AtC fix electric_potential rbc 0
fix_modify AtC source electric_potential all ${n0}
fix_modify AtC extrinsic electron_integration implicit 10
run 100

132
examples/PACKAGES/atc/drift_diffusion/in.ddm_schrodinger
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@ -1,66 +1,66 @@
# needs description
# DESCRIPTION: haynes-schockley
# poisson eqn for E-field: epsilon phi,xx = -e (n - p + N_D - N_A)
# w/ E = phi,x
echo both
units metal
variable dt equal 0.0000001
variable s equal 1
variable L equal 10.0
variable N equal 40
variable T equal 30000.0
variable E equal 0.5
timestep ${dt}
atom_style atomic
lattice fcc 1.0
region simRegion block 0 $L 0 1 0 1
boundary f p p
create_box 1 simRegion
mass 1 1.0 # need to keep this
atom_modify sort 0 1
# ID group atc PhysicsType ParameterFile
fix AtC all atc drift_diffusion-schrodinger Si_ddm_schrodinger.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create $N 1 1 simRegion f p p
variable a equal $L-0.1
variable b equal $L+0.1
fix_modify AtC mesh create_nodeset lbc -0.1 0.1 -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc $a $b -INF INF -INF INF
# ics/bcs : density consistent with wave function
fix_modify AtC initial temperature all 300.0
fix_modify AtC fix temperature all 300.0
fix_modify AtC initial electron_temperature all $T
fix_modify AtC fix electron_temperature all $T
fix_modify AtC initial electron_density all 0.0
#fix_modify AtC fix electron_density lbc 0
#fix_modify AtC fix electron_density rbc 0
fix_modify AtC initial electric_potential all 0.0
fix_modify AtC initial electron_wavefunction all 0.0
fix_modify AtC fix electron_wavefunction lbc 0
fix_modify AtC fix electron_wavefunction rbc 0
thermo $s
# f_AtC:1 thermal energy, 2 avg T, 3 electron energy, 4 avg Te, 5 total n
thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4] f_AtC[5]
thermo_modify format 1 %5i format 2 %7.2g
fix_modify AtC output ddm_schrodingerFE $s text
fix_modify AtC extrinsic electron_integration implicit 1
fix_modify AtC extrinsic schrodinger_poisson_solver self_consistency 1 # 100
fix_modify AtC unfix electric_potential all
# ends zero
fix_modify AtC fix electric_potential lbc 0
fix_modify AtC fix electric_potential rbc 0
run 1
# ends from gradient
fix_modify AtC fix electric_potential lbc linear 0 0 0 $E 0 0 0
fix_modify AtC fix electric_potential rbc linear 0 0 0 $E 0 0 0
run 1
# needs description
# DESCRIPTION: haynes-schockley
# poisson eqn for E-field: epsilon phi,xx = -e (n - p + N_D - N_A)
# w/ E = phi,x
echo both
units metal
variable dt equal 0.0000001
variable s equal 1
variable L equal 10.0
variable N equal 40
variable T equal 30000.0
variable E equal 0.5
timestep ${dt}
atom_style atomic
lattice fcc 1.0
region simRegion block 0 $L 0 1 0 1
boundary f p p
create_box 1 simRegion
mass 1 1.0 # need to keep this
atom_modify sort 0 1
# ID group atc PhysicsType ParameterFile
fix AtC all atc drift_diffusion-schrodinger Si_ddm_schrodinger.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create $N 1 1 simRegion f p p
variable a equal $L-0.1
variable b equal $L+0.1
fix_modify AtC mesh create_nodeset lbc -0.1 0.1 -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc $a $b -INF INF -INF INF
# ics/bcs : density consistent with wave function
fix_modify AtC initial temperature all 300.0
fix_modify AtC fix temperature all 300.0
fix_modify AtC initial electron_temperature all $T
fix_modify AtC fix electron_temperature all $T
fix_modify AtC initial electron_density all 0.0
#fix_modify AtC fix electron_density lbc 0
#fix_modify AtC fix electron_density rbc 0
fix_modify AtC initial electric_potential all 0.0
fix_modify AtC initial electron_wavefunction all 0.0
fix_modify AtC fix electron_wavefunction lbc 0
fix_modify AtC fix electron_wavefunction rbc 0
thermo $s
# f_AtC:1 thermal energy, 2 avg T, 3 electron energy, 4 avg Te, 5 total n
thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4] f_AtC[5]
thermo_modify format 1 %5i format 2 %7.2g
fix_modify AtC output ddm_schrodingerFE $s text
fix_modify AtC extrinsic electron_integration implicit 1
fix_modify AtC extrinsic schrodinger_poisson_solver self_consistency 1 # 100
fix_modify AtC unfix electric_potential all
# ends zero
fix_modify AtC fix electric_potential lbc 0
fix_modify AtC fix electric_potential rbc 0
run 1
# ends from gradient
fix_modify AtC fix electric_potential lbc linear 0 0 0 $E 0 0 0
fix_modify AtC fix electric_potential rbc linear 0 0 0 $E 0 0 0
run 1

150
examples/PACKAGES/atc/drift_diffusion/in.finite_well
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@ -1,75 +1,75 @@
#needs description
echo both
units metal
variable E equal 0.1
variable L equal 10.0
#variable N equal 100
variable N equal 80
variable T equal 1000
variable n0 equal 0.0001
variable dn equal 2.0*${n0}
variable dt equal 0.0000001
variable s equal 1
timestep ${dt}
atom_style atomic
lattice fcc 1.0
variable a equal 0.5*$L
region simRegion block -$a $a 0 1 0 1
boundary f p p
create_box 1 simRegion
mass 1 1.0 # need to keep this
atom_modify sort 0 1
# ID group atc PhysicsType ParameterFile
fix AtC all atc drift_diffusion-schrodinger SiGe_ddm_schrodinger.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create $N 1 1 simRegion f p p
variable a equal 0.2*$L+0.001
fix_modify AtC mesh create_elementset well -$a $a -INF INF -INF INF
fix_modify AtC mesh create_nodeset well -$a $a -INF INF -INF INF
fix_modify AtC material well Ge
variable b equal $a-0.002
fix_modify AtC mesh create_nodeset lbc -$a -$b -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc $b $a -INF INF -INF INF
# ics/bcs
fix_modify AtC initial temperature all 300.0
fix_modify AtC fix temperature all 300.0
#
fix_modify AtC initial electron_temperature all $T
fix_modify AtC fix electron_temperature all $T
#
fix_modify AtC initial electron_density all 0.0
#fix_modify AtC fix electron_density all -0.001
#fix_modify AtC fix electron_density well 0.002
#
fix_modify AtC initial electric_potential all 0.0
#fix_modify AtC fix electric_potential lbc 0.5
#fix_modify AtC fix electric_potential rbc 0.5
fix_modify AtC fix electric_potential lbc 0.0
fix_modify AtC fix electric_potential rbc 0.0
#
fix_modify AtC initial electron_wavefunction all 0.0
fix_modify AtC fix electron_wavefunction lbc 0.0
fix_modify AtC fix electron_wavefunction rbc 0.0
thermo $s
# f_AtC:1 thermal energy, 2 avg T, 3 electron energy, 4 avg Te, 5 total n
thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4] f_AtC[5]
thermo_modify format 1 %5i format 2 %7.2g
fix_modify AtC output finite_wellFE $s text
fix_modify AtC extrinsic electron_integration implicit 3
fix_modify AtC extrinsic schrodinger_poisson_solver self_consistency 3 # 30
variable m equal 1*$s
# (A) no field
run $m
# (B) fixed boundary field
fix_modify AtC fix electric_potential lbc linear 0 0 0 $E 0 0 1
fix_modify AtC fix electric_potential rbc linear 0 0 0 $E 0 0 1
run $m
#needs description
echo both
units metal
variable E equal 0.1
variable L equal 10.0
#variable N equal 100
variable N equal 80
variable T equal 1000
variable n0 equal 0.0001
variable dn equal 2.0*${n0}
variable dt equal 0.0000001
variable s equal 1
timestep ${dt}
atom_style atomic
lattice fcc 1.0
variable a equal 0.5*$L
region simRegion block -$a $a 0 1 0 1
boundary f p p
create_box 1 simRegion
mass 1 1.0 # need to keep this
atom_modify sort 0 1
# ID group atc PhysicsType ParameterFile
fix AtC all atc drift_diffusion-schrodinger SiGe_ddm_schrodinger.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create $N 1 1 simRegion f p p
variable a equal 0.2*$L+0.001
fix_modify AtC mesh create_elementset well -$a $a -INF INF -INF INF
fix_modify AtC mesh create_nodeset well -$a $a -INF INF -INF INF
fix_modify AtC material well Ge
variable b equal $a-0.002
fix_modify AtC mesh create_nodeset lbc -$a -$b -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc $b $a -INF INF -INF INF
# ics/bcs
fix_modify AtC initial temperature all 300.0
fix_modify AtC fix temperature all 300.0
#
fix_modify AtC initial electron_temperature all $T
fix_modify AtC fix electron_temperature all $T
#
fix_modify AtC initial electron_density all 0.0
#fix_modify AtC fix electron_density all -0.001
#fix_modify AtC fix electron_density well 0.002
#
fix_modify AtC initial electric_potential all 0.0
#fix_modify AtC fix electric_potential lbc 0.5
#fix_modify AtC fix electric_potential rbc 0.5
fix_modify AtC fix electric_potential lbc 0.0
fix_modify AtC fix electric_potential rbc 0.0
#
fix_modify AtC initial electron_wavefunction all 0.0
fix_modify AtC fix electron_wavefunction lbc 0.0
fix_modify AtC fix electron_wavefunction rbc 0.0
thermo $s
# f_AtC:1 thermal energy, 2 avg T, 3 electron energy, 4 avg Te, 5 total n
thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4] f_AtC[5]
thermo_modify format 1 %5i format 2 %7.2g
fix_modify AtC output finite_wellFE $s text
fix_modify AtC extrinsic electron_integration implicit 3
fix_modify AtC extrinsic schrodinger_poisson_solver self_consistency 3 # 30
variable m equal 1*$s
# (A) no field
run $m
# (B) fixed boundary field
fix_modify AtC fix electric_potential lbc linear 0 0 0 $E 0 0 1
fix_modify AtC fix electric_potential rbc linear 0 0 0 $E 0 0 1
run $m

130
examples/PACKAGES/atc/drift_diffusion/in.no_atoms_ddm
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@ -1,65 +1,65 @@
# needs description
# DESCRIPTION: haynes-schockley
# continuity eqn: n,t = J,x + (G-R) = D n,xx + mu (n E),x + G - 1/tau (n - n_0)
# w/ J = D n,x + mu n phi,x
# poisson eqn for E-field: epsilon phi,xx = -e (n - p + N_D - N_A)
# w/ E = phi,x
# NOTE: does not conserve electrons even with fixed E field and zero mobility
# if J=0 --> n,x = mu/D n phi,x
echo both
units metal
variable E equal 10.0
variable n0 equal 0.0001
variable dn equal 2.0*${n0}
variable dt equal 0.0000001
timestep ${dt}
atom_style atomic
lattice fcc 1.0
region simRegion block -50 50 0 1 0 1
boundary f p p
create_box 1 simRegion
mass 1 1.0 # need to keep this
atom_modify sort 0 1
# ID group atc PhysicsType ParameterFile
fix AtC all atc drift_diffusion Si_ddm.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create 100 1 1 simRegion f p p
fix_modify AtC mesh create_nodeset lbc -50.1 -49.9 -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc 49.9 50.1 -INF INF -INF INF
# fix a temperature
fix_modify AtC initial temperature all 300.0
fix_modify AtC initial electron_temperature all 300.0
fix_modify AtC initial electron_density all gaussian 0 0 0 1 0 0 5.0 ${dn} ${n0}
# isolate system:
# diffusion: dn/dx = 0
# drift : n = 0
fix_modify AtC fix electron_density lbc ${n0}
fix_modify AtC fix electron_density rbc ${n0}
fix_modify AtC fix electric_potential all linear 0 0 0 $E 0 0 1
variable perm equal 0.06
variable nD equal 1.0e-4
fix_modify AtC source electric_potential all ${nD}
variable s equal 10
thermo $s
# f_AtC:1 thermal energy, 2 avg T, 3 electron energy, 4 avg Te, 5 total n
thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4] f_AtC[5]
thermo_modify format 1 %5i format 2 %7.2g
fix_modify AtC output no_atoms_ddmFE $s text
fix_modify AtC extrinsic electron_integration implicit
run 40
# free electric field and allow shielding
fix_modify AtC unfix electric_potential all
fix_modify AtC fix electric_potential lbc linear 0 0 0 $E 0 0 1
fix_modify AtC fix electric_potential rbc linear 0 0 0 $E 0 0 1
fix_modify AtC extrinsic electron_integration implicit 10
run 40
# needs description
# DESCRIPTION: haynes-schockley
# continuity eqn: n,t = J,x + (G-R) = D n,xx + mu (n E),x + G - 1/tau (n - n_0)
# w/ J = D n,x + mu n phi,x
# poisson eqn for E-field: epsilon phi,xx = -e (n - p + N_D - N_A)
# w/ E = phi,x
# NOTE: does not conserve electrons even with fixed E field and zero mobility
# if J=0 --> n,x = mu/D n phi,x
echo both
units metal
variable E equal 10.0
variable n0 equal 0.0001
variable dn equal 2.0*${n0}
variable dt equal 0.0000001
timestep ${dt}
atom_style atomic
lattice fcc 1.0
region simRegion block -50 50 0 1 0 1
boundary f p p
create_box 1 simRegion
mass 1 1.0 # need to keep this
atom_modify sort 0 1
# ID group atc PhysicsType ParameterFile
fix AtC all atc drift_diffusion Si_ddm.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create 100 1 1 simRegion f p p
fix_modify AtC mesh create_nodeset lbc -50.1 -49.9 -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc 49.9 50.1 -INF INF -INF INF
# fix a temperature
fix_modify AtC initial temperature all 300.0
fix_modify AtC initial electron_temperature all 300.0
fix_modify AtC initial electron_density all gaussian 0 0 0 1 0 0 5.0 ${dn} ${n0}
# isolate system:
# diffusion: dn/dx = 0
# drift : n = 0
fix_modify AtC fix electron_density lbc ${n0}
fix_modify AtC fix electron_density rbc ${n0}
fix_modify AtC fix electric_potential all linear 0 0 0 $E 0 0 1
variable perm equal 0.06
variable nD equal 1.0e-4
fix_modify AtC source electric_potential all ${nD}
variable s equal 10
thermo $s
# f_AtC:1 thermal energy, 2 avg T, 3 electron energy, 4 avg Te, 5 total n
thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4] f_AtC[5]
thermo_modify format 1 %5i format 2 %7.2g
fix_modify AtC output no_atoms_ddmFE $s text
fix_modify AtC extrinsic electron_integration implicit
run 40
# free electric field and allow shielding
fix_modify AtC unfix electric_potential all
fix_modify AtC fix electric_potential lbc linear 0 0 0 $E 0 0 1
fix_modify AtC fix electric_potential rbc linear 0 0 0 $E 0 0 1
fix_modify AtC extrinsic electron_integration implicit 10
run 40

158
examples/PACKAGES/atc/drift_diffusion/in.null_material_ddm
View File

@ -1,79 +1,79 @@
# needs description
#AtC drift diffusion Coupling
# DESCRIPTION:
# electric potential solved over whole domain
# all others only over the lower half
# temperature is fixed over whole domain
# NOTE the vacuum can fully masked out by making the material
# have null electron_density in Ar_ddm.mat
echo both
units metal
variable s equal 100
variable T equal 20
variable n equal 0.000004
variable tol equal 0.1
variable W equal 1000
atom_style atomic
lattice fcc 5.405 origin 0.25 0.25 0.25
region FE block -8 8 -6 6 0 3
region MD block -7 7 -6 0 0 3
region FREE block -4 4 -6 0 0 3
boundary f f p
# create atoms
create_box 1 FE
mass 1 39.95
atom_modify sort 0 1
timestep 0.002
thermo $s
# ID group atc PhysicsType ParameterFile
fix AtC all atc drift_diffusion Ar_ddm.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create 4 4 1 FE f f p
variable a equal $W+${tol}
fix_modify AtC mesh create_elementset wire -$a $a -INF ${tol} -INF INF
fix_modify AtC mesh create_elementset gap -$a $a -${tol} INF -INF INF
# void is the complement of the wire nodeset
variable a equal $W-${tol}
fix_modify AtC mesh create_nodeset void -$a $a ${tol} INF -INF INF
fix_modify AtC mesh output null_material_ddmMESH binary
fix_modify AtC control thermal none
# fix a temperature
fix_modify AtC initial temperature all $T
fix_modify AtC initial electron_temperature all $T
fix_modify AtC initial electron_density all $n
fix_modify AtC initial electric_potential all 0.0
fix_modify AtC initial temperature void 0.0
fix_modify AtC initial electron_density void 0.0
fix_modify AtC initial electric_potential void 0.0
# create vacuum
fix_modify AtC material gap Vacuum
thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4]
fix_modify AtC output null_material_ddmFE $s full_text binary
fix_modify AtC extrinsic electron_integration implicit
#
fix_modify AtC mesh create_nodeset lbc -8.1 -7.9 -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc 7.9 8.1 -INF INF -INF INF
fix_modify AtC fix electron_temperature lbc $T
fix_modify AtC fix electron_temperature rbc $T
fix_modify AtC fix electron_density lbc $n
fix_modify AtC fix electric_potential lbc 0.0
variable m equal $s*10
run $m
# needs description
#AtC drift diffusion Coupling
# DESCRIPTION:
# electric potential solved over whole domain
# all others only over the lower half
# temperature is fixed over whole domain
# NOTE the vacuum can fully masked out by making the material
# have null electron_density in Ar_ddm.mat
echo both
units metal
variable s equal 100
variable T equal 20
variable n equal 0.000004
variable tol equal 0.1
variable W equal 1000
atom_style atomic
lattice fcc 5.405 origin 0.25 0.25 0.25
region FE block -8 8 -6 6 0 3
region MD block -7 7 -6 0 0 3
region FREE block -4 4 -6 0 0 3
boundary f f p
# create atoms
create_box 1 FE
mass 1 39.95
atom_modify sort 0 1
timestep 0.002
thermo $s
# ID group atc PhysicsType ParameterFile
fix AtC all atc drift_diffusion Ar_ddm.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create 4 4 1 FE f f p
variable a equal $W+${tol}
fix_modify AtC mesh create_elementset wire -$a $a -INF ${tol} -INF INF
fix_modify AtC mesh create_elementset gap -$a $a -${tol} INF -INF INF
# void is the complement of the wire nodeset
variable a equal $W-${tol}
fix_modify AtC mesh create_nodeset void -$a $a ${tol} INF -INF INF
fix_modify AtC mesh output null_material_ddmMESH binary
fix_modify AtC control thermal none
# fix a temperature
fix_modify AtC initial temperature all $T
fix_modify AtC initial electron_temperature all $T
fix_modify AtC initial electron_density all $n
fix_modify AtC initial electric_potential all 0.0
fix_modify AtC initial temperature void 0.0
fix_modify AtC initial electron_density void 0.0
fix_modify AtC initial electric_potential void 0.0
# create vacuum
fix_modify AtC material gap Vacuum
thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4]
fix_modify AtC output null_material_ddmFE $s full_text binary
fix_modify AtC extrinsic electron_integration implicit
#
fix_modify AtC mesh create_nodeset lbc -8.1 -7.9 -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc 7.9 8.1 -INF INF -INF INF
fix_modify AtC fix electron_temperature lbc $T
fix_modify AtC fix electron_temperature rbc $T
fix_modify AtC fix electron_density lbc $n
fix_modify AtC fix electric_potential lbc 0.0
variable m equal $s*10
run $m

182
examples/PACKAGES/atc/elastic/in.bar1d
View File

@ -1,91 +1,91 @@
# needs description
#AtC Thermal Coupling
echo both
units real
atom_style atomic
# create domain
#lattice type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70)
lattice fcc 5.405 origin 0.25 0.25 0.25
# create atoms
region simRegion block -12 12 -3 3 -3 3
region atomRegion block -9 9 -3 3 -3 3
region mdRegion block -8 8 -3 3 -3 3
boundary f p p
create_box 1 simRegion
create_atoms 1 region mdRegion
mass 1 39.95
# specify interal/ghost atoms
region mdInternal block -6 6 -3 3 -3 3
region leftghost block -8 -6 -3 3 -3 3
region rightghost block 6 8 -3 3 -3 3
group internal region mdInternal
group Lghost region leftghost
group Rghost region rightghost
group ghosts union Lghost Rghost
# velocities have Vcm = 0
#velocity internal create 40. 87287 mom yes loop geom
pair_style lj/cut 13.5
#pair_coeff 1 1 0.010323166 3.405 13.5
pair_coeff 1 1 .238 3.405 13.5
neighbor 5. bin
neigh_modify every 10 delay 0 check no
# define layer
# ID group atc PhysicsType ParameterFile
fix AtC internal atc elastic Ar_elastic.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create 12 1 1 simRegion f p p
# initial conditions
fix_modify AtC initial displacement x all 0.0
fix_modify AtC initial displacement y all 0.0
fix_modify AtC initial displacement z all 0.0
fix_modify AtC initial velocity x all 0.0
fix_modify AtC initial velocity y all 0.0
fix_modify AtC initial velocity z all 0.0
# set node sets and bcs
# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax
fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF
fix_modify AtC fix velocity x rbc 0.00000004
fix_modify AtC fix displacement x lbc 0.
fix_modify AtC fix velocity x lbc 0.
# specify atom types
#fix_modify AtC boundary Lghost
#fix_modify AtC boundary Rghost
fix_modify AtC boundary ghosts
#fix_modify AtC output follow_ex.fe 50
fix_modify AtC internal_quadrature off
fix_modify AtC control localized_lambda on
fix_modify AtC control momentum glc_velocity
fix_modify AtC filter type exponential
fix_modify AtC filter scale 1000.0
fix_modify AtC filter on
# run to extension
#fix_modify AtC output bar1dFE 50 text
timestep 5
thermo 100
run 1000
# change nodes to fixed
fix_modify AtC fix velocity x rbc 0.
fix_modify AtC fix displacement x rbc 0.0002
fix_modify AtC output bar1dFE 500 text
# run to equilibrium
timestep 5
thermo 100
run 10000
# needs description
#AtC Thermal Coupling
echo both
units real
atom_style atomic
# create domain
#lattice type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70)
lattice fcc 5.405 origin 0.25 0.25 0.25
# create atoms
region simRegion block -12 12 -3 3 -3 3
region atomRegion block -9 9 -3 3 -3 3
region mdRegion block -8 8 -3 3 -3 3
boundary f p p
create_box 1 simRegion
create_atoms 1 region mdRegion
mass 1 39.95
# specify interal/ghost atoms
region mdInternal block -6 6 -3 3 -3 3
region leftghost block -8 -6 -3 3 -3 3
region rightghost block 6 8 -3 3 -3 3
group internal region mdInternal
group Lghost region leftghost
group Rghost region rightghost
group ghosts union Lghost Rghost
# velocities have Vcm = 0
#velocity internal create 40. 87287 mom yes loop geom
pair_style lj/cut 13.5
#pair_coeff 1 1 0.010323166 3.405 13.5
pair_coeff 1 1 .238 3.405 13.5
neighbor 5. bin
neigh_modify every 10 delay 0 check no
# define layer
# ID group atc PhysicsType ParameterFile
fix AtC internal atc elastic Ar_elastic.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create 12 1 1 simRegion f p p
# initial conditions
fix_modify AtC initial displacement x all 0.0
fix_modify AtC initial displacement y all 0.0
fix_modify AtC initial displacement z all 0.0
fix_modify AtC initial velocity x all 0.0
fix_modify AtC initial velocity y all 0.0
fix_modify AtC initial velocity z all 0.0
# set node sets and bcs
# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax
fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF
fix_modify AtC fix velocity x rbc 0.00000004
fix_modify AtC fix displacement x lbc 0.
fix_modify AtC fix velocity x lbc 0.
# specify atom types
#fix_modify AtC boundary Lghost
#fix_modify AtC boundary Rghost
fix_modify AtC boundary ghosts
#fix_modify AtC output follow_ex.fe 50
fix_modify AtC internal_quadrature off
fix_modify AtC control localized_lambda on
fix_modify AtC control momentum glc_velocity
fix_modify AtC filter type exponential
fix_modify AtC filter scale 1000.0
fix_modify AtC filter on
# run to extension
#fix_modify AtC output bar1dFE 50 text
timestep 5
thermo 100
run 1000
# change nodes to fixed
fix_modify AtC fix velocity x rbc 0.
fix_modify AtC fix displacement x rbc 0.0002
fix_modify AtC output bar1dFE 500 text
# run to equilibrium
timestep 5
thermo 100
run 10000

232
examples/PACKAGES/atc/elastic/in.bar1d_damped
View File

@ -1,116 +1,116 @@
# needs description
echo both
units metal
atom_style atomic
# create domain
#lattice type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70)
lattice fcc 5.405 origin 0.25 0.25 0.25
# create atoms
region simRegion block -12 12 -3 3 -3 3
region atomRegion block -9 9 -3 3 -3 3
region mdRegion block -8 8 -3 3 -3 3
boundary f p p
create_box 2 simRegion
create_atoms 1 region mdRegion
mass * 39.95
# specify interal/ghost atoms
region mdInternal block -6 6 -3 3 -3 3
region leftghost block -8 -6 -3 3 -3 3
region rightghost block 6 8 -3 3 -3 3
group internal region mdInternal
group Lghost region leftghost
group Rghost region rightghost
group ghosts union Lghost Rghost
# velocities have Vcm = 0
#velocity internal create 40. 87287 mom yes loop geom
pair_style lj/cut 13.5
#pair_coeff * * .238 3.405 13.5
pair_coeff * * 0.010323166 3.405 13.5
neighbor 5. bin
neigh_modify every 10 delay 0 check no
# define layer
# ID group atc PhysicsType ParameterFile
fix AtC internal atc elastic Ar_damped.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create 12 1 1 simRegion f p p
# initial conditions
fix_modify AtC initial displacement x all 0.0
fix_modify AtC initial displacement y all 0.0
fix_modify AtC initial displacement z all 0.0
fix_modify AtC initial velocity x all 0.0
fix_modify AtC initial velocity y all 0.0
fix_modify AtC initial velocity z all 0.0
variable v equal 0.00000004e3
variable n equal 1000
variable dt equal 0.005
variable u equal $v*$n*${dt}
# set node sets and bcs
# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax
fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF
fix_modify AtC fix velocity x rbc $v
fix_modify AtC fix displacement x lbc 0.
fix_modify AtC fix velocity x lbc 0.
# specify atom types
fix_modify AtC boundary ghosts
#fix_modify AtC output follow_ex.fe 50
fix_modify AtC internal_quadrature off
fix_modify AtC control localized_lambda on
fix_modify AtC control momentum glc_velocity
#fix_modify AtC filter type exponential
#fix_modify AtC filter scale 1.0
#fix_modify AtC filter on
# run to extension
timestep 0.005
thermo 100
thermo_style custom step cpu ke pe
run 0
variable pe0 equal pe
variable pe equal pe-${pe0}
thermo_style custom step cpu ke pe v_pe f_AtC[1] f_AtC[2] f_AtC[4] f_AtC[5]
run $n
fix_modify AtC output bar1d_dampedFE 500 text
dump CONFIG all custom 500 bar1d_damped.dmp id type x y z vx vy vz
# change nodes to fixed
fix_modify AtC fix velocity x rbc 0.
fix_modify AtC fix displacement x rbc $u
# run to equilibrium
thermo 100
log bar1d_damped.log
run 2000
fix_modify AtC material all cubic # M damping
run 2000
fix_modify AtC material all damped # K damping
run 2000
# ATC: CB stiffness: 7.56717 Einstein freq: 0.355649 from Ar_CauchyBorn.mat
# real to metal 1 kcal/mol = 0.04336 eV
variable kCal2eV equal 0.04336
variable fconv equal 1./0.000103643 # NOTE old routine was doing calculations in lammps units, not atc units, so this conversion is necessary for bmark to pass
#variable k equal 1.e-3 # 7.56717*${kCal2eV} NOTE <<<
#variable k equal 0.75*0.355649e3*${kCal2eV}
variable k equal 0.5*39.95*${fconv} # NOTE it was set to above, should have been 2 above, but there was a bug so this value is here for bmark
#variable g equal 0.75*0.355649e3*${kCal2eV}
variable g equal 1.e-3*${fconv} # NOTE it should be above, but there was a bug so this value is here for bmark
variable m equal 2. #0.5*39.95
fix_modify AtC boundary_dynamics damped_harmonic $k $g $m
run 2000
# needs description
echo both
units metal
atom_style atomic
# create domain
#lattice type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70)
lattice fcc 5.405 origin 0.25 0.25 0.25
# create atoms
region simRegion block -12 12 -3 3 -3 3
region atomRegion block -9 9 -3 3 -3 3
region mdRegion block -8 8 -3 3 -3 3
boundary f p p
create_box 2 simRegion
create_atoms 1 region mdRegion
mass * 39.95
# specify interal/ghost atoms
region mdInternal block -6 6 -3 3 -3 3
region leftghost block -8 -6 -3 3 -3 3
region rightghost block 6 8 -3 3 -3 3
group internal region mdInternal
group Lghost region leftghost
group Rghost region rightghost
group ghosts union Lghost Rghost
# velocities have Vcm = 0
#velocity internal create 40. 87287 mom yes loop geom
pair_style lj/cut 13.5
#pair_coeff * * .238 3.405 13.5
pair_coeff * * 0.010323166 3.405 13.5
neighbor 5. bin
neigh_modify every 10 delay 0 check no
# define layer
# ID group atc PhysicsType ParameterFile
fix AtC internal atc elastic Ar_damped.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create 12 1 1 simRegion f p p
# initial conditions
fix_modify AtC initial displacement x all 0.0
fix_modify AtC initial displacement y all 0.0
fix_modify AtC initial displacement z all 0.0
fix_modify AtC initial velocity x all 0.0
fix_modify AtC initial velocity y all 0.0
fix_modify AtC initial velocity z all 0.0
variable v equal 0.00000004e3
variable n equal 1000
variable dt equal 0.005
variable u equal $v*$n*${dt}
# set node sets and bcs
# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax
fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF
fix_modify AtC fix velocity x rbc $v
fix_modify AtC fix displacement x lbc 0.
fix_modify AtC fix velocity x lbc 0.
# specify atom types
fix_modify AtC boundary ghosts
#fix_modify AtC output follow_ex.fe 50
fix_modify AtC internal_quadrature off
fix_modify AtC control localized_lambda on
fix_modify AtC control momentum glc_velocity
#fix_modify AtC filter type exponential
#fix_modify AtC filter scale 1.0
#fix_modify AtC filter on
# run to extension
timestep 0.005
thermo 100
thermo_style custom step cpu ke pe
run 0
variable pe0 equal pe
variable pe equal pe-${pe0}
thermo_style custom step cpu ke pe v_pe f_AtC[1] f_AtC[2] f_AtC[4] f_AtC[5]
run $n
fix_modify AtC output bar1d_dampedFE 500 text
dump CONFIG all custom 500 bar1d_damped.dmp id type x y z vx vy vz
# change nodes to fixed
fix_modify AtC fix velocity x rbc 0.
fix_modify AtC fix displacement x rbc $u
# run to equilibrium
thermo 100
log bar1d_damped.log
run 2000
fix_modify AtC material all cubic # M damping
run 2000
fix_modify AtC material all damped # K damping
run 2000
# ATC: CB stiffness: 7.56717 Einstein freq: 0.355649 from Ar_CauchyBorn.mat
# real to metal 1 kcal/mol = 0.04336 eV
variable kCal2eV equal 0.04336
variable fconv equal 1./0.000103643 # NOTE old routine was doing calculations in lammps units, not atc units, so this conversion is necessary for bmark to pass
#variable k equal 1.e-3 # 7.56717*${kCal2eV} NOTE <<<
#variable k equal 0.75*0.355649e3*${kCal2eV}
variable k equal 0.5*39.95*${fconv} # NOTE it was set to above, should have been 2 above, but there was a bug so this value is here for bmark
#variable g equal 0.75*0.355649e3*${kCal2eV}
variable g equal 1.e-3*${fconv} # NOTE it should be above, but there was a bug so this value is here for bmark
variable m equal 2. #0.5*39.95
fix_modify AtC boundary_dynamics damped_harmonic $k $g $m
run 2000

196
examples/PACKAGES/atc/elastic/in.bar1d_flux
View File

@ -1,98 +1,98 @@
# needs description
#AtC Thermal Coupling
echo both
units real
atom_style atomic
# create domain
#lattice type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70)
lattice fcc 5.2582305 origin 0.25 0.25 0.25
# create atoms
region simRegion block -12 12 -3 3 -3 3
region atomRegion block -9 9 -3 3 -3 3
region mdRegion block -8 8 -3 3 -3 3
boundary f p p
create_box 1 simRegion
create_atoms 1 region mdRegion
mass 1 39.95
# specify interal/ghost atoms
region mdInternal block -6 6 -3 3 -3 3
region leftghost block -8 -6 -3 3 -3 3
region rightghost block 6 8 -3 3 -3 3
group internal region mdInternal
group Lghost region leftghost
group Rghost region rightghost
group ghosts union Lghost Rghost
# velocities have Vcm = 0
#velocity internal create 40. 87287 mom yes loop geom
pair_style lj/cut 13.
#pair_coeff 1 1 0.010323166 3.405 13.
pair_coeff 1 1 .2381 3.405 13.
neighbor 5. bin
neigh_modify every 10 delay 0 check no
# define layer
# ID group atc PhysicsType ParameterFile
fix AtC internal atc elastic Ar_elastic.mat
#fix_modify AtC boundary Lghost
#fix_modify AtC boundary Rghost
fix_modify AtC boundary ghosts
# ID part keywords nx ny nz region
fix_modify AtC mesh create 12 1 1 simRegion f p p
fix_modify AtC mesh create_faceset obndy box -6.0 6.0 -INF INF -INF INF outward
# initial conditions
fix_modify AtC initial displacement x all 0.0
fix_modify AtC initial displacement y all 0.0
fix_modify AtC initial displacement z all 0.0
fix_modify AtC initial velocity x all 0.0
fix_modify AtC initial velocity y all 0.0
fix_modify AtC initial velocity z all 0.0
# set node sets and bcs
# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax
fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF
fix_modify AtC fix velocity x rbc 0.00000004
#fix_modify AtC fix velocity x rbc 0.
#fix_modify AtC fix displacement x rbc 0.
fix_modify AtC fix displacement x lbc 0.
fix_modify AtC fix velocity x lbc 0.
#fix_modify AtC output follow_ex.fe 50
fix_modify AtC internal_quadrature off
#fix_modify AtC control lumped_lambda_solve on
#fix_modify AtC momentum control glc_velocity
#fix_modify AtC momentum control flux faceset obndy
fix_modify AtC control momentum flux interpolate
#fix_modify AtC filter scale 1000.0
# run to extension
compute myTemp internal temp
compute atomStress internal stress/atom NULL
compute avgStress internal reduce sum c_atomStress[1] c_atomStress[2] c_atomStress[3]
variable myPres equal -(c_avgStress[1]+c_avgStress[2]+c_avgStress[3])/(3*vol)
thermo_style custom step c_myTemp v_myPres pe
fix_modify AtC output bar1d_fluxFE 10 text
timestep 5
thermo 100
run 1000
# change nodes to fixed
fix_modify AtC fix velocity x rbc 0.
fix_modify AtC fix displacement x rbc 0.0002
fix_modify AtC output bar1d_fluxFE 500 text
# run to equilibrium
timestep 5
thermo 100
run 10000
# needs description
#AtC Thermal Coupling
echo both
units real
atom_style atomic
# create domain
#lattice type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70)
lattice fcc 5.2582305 origin 0.25 0.25 0.25
# create atoms
region simRegion block -12 12 -3 3 -3 3
region atomRegion block -9 9 -3 3 -3 3
region mdRegion block -8 8 -3 3 -3 3
boundary f p p
create_box 1 simRegion
create_atoms 1 region mdRegion
mass 1 39.95
# specify interal/ghost atoms
region mdInternal block -6 6 -3 3 -3 3
region leftghost block -8 -6 -3 3 -3 3
region rightghost block 6 8 -3 3 -3 3
group internal region mdInternal
group Lghost region leftghost
group Rghost region rightghost
group ghosts union Lghost Rghost
# velocities have Vcm = 0
#velocity internal create 40. 87287 mom yes loop geom
pair_style lj/cut 13.
#pair_coeff 1 1 0.010323166 3.405 13.
pair_coeff 1 1 .2381 3.405 13.
neighbor 5. bin
neigh_modify every 10 delay 0 check no
# define layer
# ID group atc PhysicsType ParameterFile
fix AtC internal atc elastic Ar_elastic.mat
#fix_modify AtC boundary Lghost
#fix_modify AtC boundary Rghost
fix_modify AtC boundary ghosts
# ID part keywords nx ny nz region
fix_modify AtC mesh create 12 1 1 simRegion f p p
fix_modify AtC mesh create_faceset obndy box -6.0 6.0 -INF INF -INF INF outward
# initial conditions
fix_modify AtC initial displacement x all 0.0
fix_modify AtC initial displacement y all 0.0
fix_modify AtC initial displacement z all 0.0
fix_modify AtC initial velocity x all 0.0
fix_modify AtC initial velocity y all 0.0
fix_modify AtC initial velocity z all 0.0
# set node sets and bcs
# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax
fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF
fix_modify AtC fix velocity x rbc 0.00000004
#fix_modify AtC fix velocity x rbc 0.
#fix_modify AtC fix displacement x rbc 0.
fix_modify AtC fix displacement x lbc 0.
fix_modify AtC fix velocity x lbc 0.
#fix_modify AtC output follow_ex.fe 50
fix_modify AtC internal_quadrature off
#fix_modify AtC control lumped_lambda_solve on
#fix_modify AtC momentum control glc_velocity
#fix_modify AtC momentum control flux faceset obndy
fix_modify AtC control momentum flux interpolate
#fix_modify AtC filter scale 1000.0
# run to extension
compute myTemp internal temp
compute atomStress internal stress/atom NULL
compute avgStress internal reduce sum c_atomStress[1] c_atomStress[2] c_atomStress[3]
variable myPres equal -(c_avgStress[1]+c_avgStress[2]+c_avgStress[3])/(3*vol)
thermo_style custom step c_myTemp v_myPres pe
fix_modify AtC output bar1d_fluxFE 10 text
timestep 5
thermo 100
run 1000
# change nodes to fixed
fix_modify AtC fix velocity x rbc 0.
fix_modify AtC fix displacement x rbc 0.0002
fix_modify AtC output bar1d_fluxFE 500 text
# run to equilibrium
timestep 5
thermo 100
run 10000

198
examples/PACKAGES/atc/elastic/in.bar1d_frac_step
View File

@ -1,99 +1,99 @@
# needs description
#AtC Elastic Coupling
echo both
units real
atom_style atomic
# create domain
#lattice type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70)
lattice fcc 5.2582305 origin 0.25 0.25 0.25
# create atoms
region simRegion block -12 12 -3 3 -3 3
region atomRegion block -8 8 -3 3 -3 3
region mdRegion block -6 6 -3 3 -3 3
boundary f p p
create_box 1 simRegion
create_atoms 1 region atomRegion
mass 1 39.95
# specify interal/ghost atoms
region mdInternal block -6 6 -3 3 -3 3
region leftghost block -8 -6 -3 3 -3 3
region rightghost block 6 8 -3 3 -3 3
group internal region mdInternal
group Lghost region leftghost
group Rghost region rightghost
group ghosts union Lghost Rghost
pair_style lj/cut 13.
#pair_coeff 1 1 0.010323166 3.405 13.5
pair_coeff 1 1 .2381 3.405 13.
neighbor 5. bin
neigh_modify every 10 delay 0 check no
# define layer
# ID group atc PhysicsType ParameterFile
fix AtC internal atc elastic Ar_elastic.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create 12 1 1 simRegion f p p
# initial conditions
fix_modify AtC initial displacement x all 0.0
fix_modify AtC initial displacement y all 0.0
fix_modify AtC initial displacement z all 0.0
fix_modify AtC initial velocity x all 0.0
fix_modify AtC initial velocity y all 0.0
fix_modify AtC initial velocity z all 0.0
fix_modify AtC time_integration fractional_step
fix_modify AtC internal_atom_integrate off
fix iNVE internal nve
# set node sets and bcs
# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax
fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF
fix_modify AtC fix velocity x rbc 0.00000004
fix_modify AtC fix displacement x lbc 0.
fix_modify AtC fix velocity x lbc 0.
# specify atom types
#fix_modify AtC boundary Lghost
#fix_modify AtC boundary Rghost
fix_modify AtC boundary ghosts
fix_modify AtC internal_quadrature off
fix_modify AtC control localized_lambda on
fix_modify AtC control momentum flux interpolate
#fix_modify AtC control momentum hoover # tested in this mode
#fix_modify AtC filter type exponential
#fix_modify AtC filter scale 1000.0
#fix_modify AtC filter on
# run to extension
#fix_modify AtC output bar1d_frac_step_initFE 50 text binary
#dump D1 all atom 50 bar1d_frac_step_init.dmp
timestep 5
thermo 100
run 1000
# reset time
fix_modify AtC reset_time 0.
reset_timestep 0
# change nodes to fixed
fix_modify AtC fix velocity x rbc 0.
fix_modify AtC fix displacement x rbc 0.0002
fix_modify AtC output bar1d_frac_stepFE 500 text #binary
#fix_modify AtC output index step
#undump D1
#dump D1 all atom 500 bar1d_frac_step.dmp
# run to equilibrium
timestep 5
thermo 100
run 5000
# needs description
#AtC Elastic Coupling
echo both
units real
atom_style atomic
# create domain
#lattice type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70)
lattice fcc 5.2582305 origin 0.25 0.25 0.25
# create atoms
region simRegion block -12 12 -3 3 -3 3
region atomRegion block -8 8 -3 3 -3 3
region mdRegion block -6 6 -3 3 -3 3
boundary f p p
create_box 1 simRegion
create_atoms 1 region atomRegion
mass 1 39.95
# specify interal/ghost atoms
region mdInternal block -6 6 -3 3 -3 3
region leftghost block -8 -6 -3 3 -3 3
region rightghost block 6 8 -3 3 -3 3
group internal region mdInternal
group Lghost region leftghost
group Rghost region rightghost
group ghosts union Lghost Rghost
pair_style lj/cut 13.
#pair_coeff 1 1 0.010323166 3.405 13.5
pair_coeff 1 1 .2381 3.405 13.
neighbor 5. bin
neigh_modify every 10 delay 0 check no
# define layer
# ID group atc PhysicsType ParameterFile
fix AtC internal atc elastic Ar_elastic.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create 12 1 1 simRegion f p p
# initial conditions
fix_modify AtC initial displacement x all 0.0
fix_modify AtC initial displacement y all 0.0
fix_modify AtC initial displacement z all 0.0
fix_modify AtC initial velocity x all 0.0
fix_modify AtC initial velocity y all 0.0
fix_modify AtC initial velocity z all 0.0
fix_modify AtC time_integration fractional_step
fix_modify AtC internal_atom_integrate off
fix iNVE internal nve
# set node sets and bcs
# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax
fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF
fix_modify AtC fix velocity x rbc 0.00000004
fix_modify AtC fix displacement x lbc 0.
fix_modify AtC fix velocity x lbc 0.
# specify atom types
#fix_modify AtC boundary Lghost
#fix_modify AtC boundary Rghost
fix_modify AtC boundary ghosts
fix_modify AtC internal_quadrature off
fix_modify AtC control localized_lambda on
fix_modify AtC control momentum flux interpolate
#fix_modify AtC control momentum hoover # tested in this mode
#fix_modify AtC filter type exponential
#fix_modify AtC filter scale 1000.0
#fix_modify AtC filter on
# run to extension
#fix_modify AtC output bar1d_frac_step_initFE 50 text binary
#dump D1 all atom 50 bar1d_frac_step_init.dmp
timestep 5
thermo 100
run 1000
# reset time
fix_modify AtC reset_time 0.
reset_timestep 0
# change nodes to fixed
fix_modify AtC fix velocity x rbc 0.
fix_modify AtC fix displacement x rbc 0.0002
fix_modify AtC output bar1d_frac_stepFE 500 text #binary
#fix_modify AtC output index step
#undump D1
#dump D1 all atom 500 bar1d_frac_step.dmp
# run to equilibrium
timestep 5
thermo 100
run 5000

202
examples/PACKAGES/atc/elastic/in.bar1d_ghost_flux
View File

@ -1,101 +1,101 @@
# Computes elastic waves propagating in and out of a finite temperature region
#AtC ThermoElastic Coupling
echo both
units real
atom_style atomic
# create domain
#lattice type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70)
lattice fcc 5.2582305 origin 0.25 0.25 0.25
region simRegion block -12 12 -3 3 -3 3
region mdRegion block -8 8 -3 3 -3 3
boundary f p p
create_box 1 simRegion
create_atoms 1 region mdRegion
mass 1 39.95
# specify interal/ghost atoms
region mdInternal block -6 6 -3 3 -3 3
region leftghost block -8 -6 -3 3 -3 3
region rightghost block 6 8 -3 3 -3 3
group internal region mdInternal
group Lghost region leftghost
group Rghost region rightghost
group ghosts union Lghost Rghost
# velocities have Vcm = 0, NOTE next for lines commented out for restart
pair_style lj/cut 13.
#pair_coeff 1 1 0.010323166 3.405 13.
pair_coeff 1 1 .2381 3.405 13.
neighbor 5. bin
neigh_modify every 10 delay 0 check no
# define layer
# ID group atc PhysicsType ParameterFile
fix AtC internal atc elastic Ar_elastic.mat
fix_modify AtC boundary ghosts
# ID part keywords nx ny nz region
fix_modify AtC mesh create 12 1 1 simRegion f p p
fix_modify AtC mesh create_faceset obndy box -6.0 6.0 -INF INF -INF INF outward
fix_modify AtC internal_quadrature off
fix_modify AtC internal_atom_integrate off
fix iNVE internal nve
# initial conditions
fix_modify AtC initial displacement x all 0.0
fix_modify AtC fix displacement y all 0.0
fix_modify AtC fix displacement z all 0.0
fix_modify AtC initial velocity x all 0.0
fix_modify AtC fix velocity y all 0.0
fix_modify AtC fix velocity z all 0.0
# set node sets and bcs
# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax
fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF
#fix_modify AtC fix velocity x rbc 0.
#fix_modify AtC fix displacement x rbc 0.
fix_modify AtC fix displacement x lbc 0.
fix_modify AtC fix velocity x lbc 0.
# turn on multiscale
fix_modify AtC control momentum ghost_flux
# new boundary conditions
fix_modify AtC fix velocity x rbc 0.00000004
#fix_modify AtC output follow_ex.fe 50
#fix_modify AtC localized_lambda on
#fix_modify AtC momentum control glc_velocity
#fix_modify AtC momentum control flux faceset obndy
#fix_modify AtC control momentum flux
#fix_modify AtC control momentum ghost_flux
#fix_modify AtC filter scale 1000.0
# run to extension
compute myTemp internal temp
compute atomStress internal stress/atom NULL
compute avgStress internal reduce sum c_atomStress[1] c_atomStress[2] c_atomStress[3]
variable myPres equal -(c_avgStress[1]+c_avgStress[2]+c_avgStress[3])/(3*vol)
thermo_style custom step c_myTemp v_myPres pe
fix_modify AtC output bar1d_ghost_fluxFE 500 text
#dump D1 all atom 100 bar1d_ghost_flux.dmp
timestep 5
thermo 100
run 1000
# change nodes to fixed
fix_modify AtC unfix velocity x rbc
#fix_modify AtC fix displacement x rbc 0.0002
#fix_modify AtC output bar1d_fluxFE 500 text binary
# run to equilibrium
timestep 5
thermo 100
run 3000
# Computes elastic waves propagating in and out of a finite temperature region
#AtC ThermoElastic Coupling
echo both
units real
atom_style atomic
# create domain
#lattice type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70)
lattice fcc 5.2582305 origin 0.25 0.25 0.25
region simRegion block -12 12 -3 3 -3 3
region mdRegion block -8 8 -3 3 -3 3
boundary f p p
create_box 1 simRegion
create_atoms 1 region mdRegion
mass 1 39.95
# specify interal/ghost atoms
region mdInternal block -6 6 -3 3 -3 3
region leftghost block -8 -6 -3 3 -3 3
region rightghost block 6 8 -3 3 -3 3
group internal region mdInternal
group Lghost region leftghost
group Rghost region rightghost
group ghosts union Lghost Rghost
# velocities have Vcm = 0, NOTE next for lines commented out for restart
pair_style lj/cut 13.
#pair_coeff 1 1 0.010323166 3.405 13.
pair_coeff 1 1 .2381 3.405 13.
neighbor 5. bin
neigh_modify every 10 delay 0 check no
# define layer
# ID group atc PhysicsType ParameterFile
fix AtC internal atc elastic Ar_elastic.mat
fix_modify AtC boundary ghosts
# ID part keywords nx ny nz region
fix_modify AtC mesh create 12 1 1 simRegion f p p
fix_modify AtC mesh create_faceset obndy box -6.0 6.0 -INF INF -INF INF outward
fix_modify AtC internal_quadrature off
fix_modify AtC internal_atom_integrate off
fix iNVE internal nve
# initial conditions
fix_modify AtC initial displacement x all 0.0
fix_modify AtC fix displacement y all 0.0
fix_modify AtC fix displacement z all 0.0
fix_modify AtC initial velocity x all 0.0
fix_modify AtC fix velocity y all 0.0
fix_modify AtC fix velocity z all 0.0
# set node sets and bcs
# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax
fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF
#fix_modify AtC fix velocity x rbc 0.
#fix_modify AtC fix displacement x rbc 0.
fix_modify AtC fix displacement x lbc 0.
fix_modify AtC fix velocity x lbc 0.
# turn on multiscale
fix_modify AtC control momentum ghost_flux
# new boundary conditions
fix_modify AtC fix velocity x rbc 0.00000004
#fix_modify AtC output follow_ex.fe 50
#fix_modify AtC localized_lambda on
#fix_modify AtC momentum control glc_velocity
#fix_modify AtC momentum control flux faceset obndy
#fix_modify AtC control momentum flux
#fix_modify AtC control momentum ghost_flux
#fix_modify AtC filter scale 1000.0
# run to extension
compute myTemp internal temp
compute atomStress internal stress/atom NULL
compute avgStress internal reduce sum c_atomStress[1] c_atomStress[2] c_atomStress[3]
variable myPres equal -(c_avgStress[1]+c_avgStress[2]+c_avgStress[3])/(3*vol)
thermo_style custom step c_myTemp v_myPres pe
fix_modify AtC output bar1d_ghost_fluxFE 500 text
#dump D1 all atom 100 bar1d_ghost_flux.dmp
timestep 5
thermo 100
run 1000
# change nodes to fixed
fix_modify AtC unfix velocity x rbc
#fix_modify AtC fix displacement x rbc 0.0002
#fix_modify AtC output bar1d_fluxFE 500 text binary
# run to equilibrium
timestep 5
thermo 100
run 3000

278
examples/PACKAGES/atc/elastic/in.bar1d_thermo_elastic
View File

@ -1,139 +1,139 @@
# Computes elastic waves propagating in and out of a finite temperature region
#AtC ThermoElastic Coupling
echo both
units real
atom_style atomic
# create domain
#lattice type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70)
lattice fcc 5.2582305 origin 0.25 0.25 0.25
# NOTE following 3 lines added for restart
boundary f p p
pair_style lj/cut 13.
read_data temp.init
region simRegion block -12 12 -3 3 -3 3
# create atoms, NOTE commented out for restart
#region mdRegion block -8 8 -3 3 -3 3
#boundary f p p
#region mdBox block -9 9 -3 3 -3 3
#create_box 1 mdBox
#create_atoms 1 region mdRegion
#mass 1 39.95
# specify interal/ghost atoms
region mdInternal block -6 6 -3 3 -3 3
region leftghost block -8 -6 -3 3 -3 3
region rightghost block 6 8 -3 3 -3 3
group internal region mdInternal
group Lghost region leftghost
group Rghost region rightghost
group ghosts union Lghost Rghost
# velocities have Vcm = 0, NOTE next for lines commented out for restart
#velocity internal create 40. 87287 mom yes loop geom
#pair_style lj/cut 13.
##pair_coeff 1 1 0.010323166 3.405 13.
#pair_coeff 1 1 .2381 3.405 13.
neighbor 5. bin
neigh_modify every 10 delay 0 check no
#write_restart tinit.dat
# zero initial momentum
fix AtC internal atc elastic Ar_thermo_elastic.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create 12 1 1 simRegion f p p
fix_modify AtC mesh create_faceset obndy box -6.0 6.0 -INF INF -INF INF outward
fix_modify AtC internal_quadrature off
fix_modify AtC fix displacement x all 0.
fix_modify AtC fix displacement y all 0.
fix_modify AtC fix displacement z all 0.
fix_modify AtC fix velocity x all 0.
fix_modify AtC fix velocity y all 0.
fix_modify AtC fix velocity z all 0.
fix_modify AtC control momentum glc_velocity
#fix_modify AtC output bar1d_thermo_elastic_initializeFE 1 text #binary
timestep 0
thermo 1
run 1
unfix AtC
# define layer
# ID group atc PhysicsType ParameterFile
fix AtC internal atc thermo_elastic Ar_thermo_elastic.mat
fix_modify AtC boundary ghosts
# ID part keywords nx ny nz region
fix_modify AtC mesh create 12 1 1 simRegion f p p
fix_modify AtC mesh create_faceset obndy box -6.0 6.0 -INF INF -INF INF outward
fix_modify AtC internal_quadrature off
# initial conditions
fix_modify AtC initial displacement x all 0.0
fix_modify AtC fix displacement y all 0.0
fix_modify AtC fix displacement z all 0.0
fix_modify AtC initial velocity x all 0.0
fix_modify AtC fix velocity y all 0.0
fix_modify AtC fix velocity z all 0.0
fix_modify AtC fix temperature all 20.
# set node sets and bcs
# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax
fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF
#fix_modify AtC fix velocity x rbc 0.
#fix_modify AtC fix displacement x rbc 0.
fix_modify AtC fix displacement x lbc 0.
fix_modify AtC fix velocity x lbc 0.
# rescale thermostat for initial atomic temperatures
fix_modify AtC control thermal rescale 10
fix_modify AtC control momentum ghost_flux
fix_modify AtC output bar1d_thermo_elasticFE 100 text #binary
timestep 5
thermo 100
run 1000
# free all nodes
#fix_modify AtC unfix displacement x all
#fix_modify AtC unfix velocity x all
fix_modify AtC unfix temperature all
# new boundary conditions
fix_modify AtC fix velocity x rbc 0.00000004
fix_modify AtC fix temperature lbc 20.
#fix_modify AtC output follow_ex.fe 50
#fix_modify AtC localized_lambda on
#fix_modify AtC momentum control glc_velocity
#fix_modify AtC momentum control flux faceset obndy
#fix_modify AtC control momentum flux
#fix_modify AtC control momentum ghost_flux
fix_modify AtC control thermal flux
#fix_modify AtC filter scale 1000.0
# run to extension
compute myTemp internal temp
compute atomStress internal stress/atom NULL
compute avgStress internal reduce sum c_atomStress[1] c_atomStress[2] c_atomStress[3]
variable myPres equal -(c_avgStress[1]+c_avgStress[2]+c_avgStress[3])/(3*vol)
thermo_style custom step c_myTemp v_myPres pe
fix_modify AtC output bar1d_thermo_elasticFE 500 text
#dump D1 all custom 100 bar1d_thermo_elastic.dmp id type x y z vx vy vz
timestep 5
thermo 100
run 1000
# change nodes to fixed
fix_modify AtC unfix velocity x rbc 0.
#fix_modify AtC fix displacement x rbc 0.0002
#fix_modify AtC output bar1d_fluxFE 500 text binary
# run to equilibrium
timestep 5
thermo 100
run 3000
# Computes elastic waves propagating in and out of a finite temperature region
#AtC ThermoElastic Coupling
echo both
units real
atom_style atomic
# create domain
#lattice type reduced density rho* = 4*(sigma/a)^3, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70)
lattice fcc 5.2582305 origin 0.25 0.25 0.25
# NOTE following 3 lines added for restart
boundary f p p
pair_style lj/cut 13.
read_data temp.init
region simRegion block -12 12 -3 3 -3 3
# create atoms, NOTE commented out for restart
#region mdRegion block -8 8 -3 3 -3 3
#boundary f p p
#region mdBox block -9 9 -3 3 -3 3
#create_box 1 mdBox
#create_atoms 1 region mdRegion
#mass 1 39.95
# specify interal/ghost atoms
region mdInternal block -6 6 -3 3 -3 3
region leftghost block -8 -6 -3 3 -3 3
region rightghost block 6 8 -3 3 -3 3
group internal region mdInternal
group Lghost region leftghost
group Rghost region rightghost
group ghosts union Lghost Rghost
# velocities have Vcm = 0, NOTE next for lines commented out for restart
#velocity internal create 40. 87287 mom yes loop geom
#pair_style lj/cut 13.
##pair_coeff 1 1 0.010323166 3.405 13.
#pair_coeff 1 1 .2381 3.405 13.
neighbor 5. bin
neigh_modify every 10 delay 0 check no
#write_restart tinit.dat
# zero initial momentum
fix AtC internal atc elastic Ar_thermo_elastic.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create 12 1 1 simRegion f p p
fix_modify AtC mesh create_faceset obndy box -6.0 6.0 -INF INF -INF INF outward
fix_modify AtC internal_quadrature off
fix_modify AtC fix displacement x all 0.
fix_modify AtC fix displacement y all 0.
fix_modify AtC fix displacement z all 0.
fix_modify AtC fix velocity x all 0.
fix_modify AtC fix velocity y all 0.
fix_modify AtC fix velocity z all 0.
fix_modify AtC control momentum glc_velocity
#fix_modify AtC output bar1d_thermo_elastic_initializeFE 1 text #binary
timestep 0
thermo 1
run 1
unfix AtC
# define layer
# ID group atc PhysicsType ParameterFile
fix AtC internal atc thermo_elastic Ar_thermo_elastic.mat
fix_modify AtC boundary ghosts
# ID part keywords nx ny nz region
fix_modify AtC mesh create 12 1 1 simRegion f p p
fix_modify AtC mesh create_faceset obndy box -6.0 6.0 -INF INF -INF INF outward
fix_modify AtC internal_quadrature off
# initial conditions
fix_modify AtC initial displacement x all 0.0
fix_modify AtC fix displacement y all 0.0
fix_modify AtC fix displacement z all 0.0
fix_modify AtC initial velocity x all 0.0
fix_modify AtC fix velocity y all 0.0
fix_modify AtC fix velocity z all 0.0
fix_modify AtC fix temperature all 20.
# set node sets and bcs
# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax
fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF
#fix_modify AtC fix velocity x rbc 0.
#fix_modify AtC fix displacement x rbc 0.
fix_modify AtC fix displacement x lbc 0.
fix_modify AtC fix velocity x lbc 0.
# rescale thermostat for initial atomic temperatures
fix_modify AtC control thermal rescale 10
fix_modify AtC control momentum ghost_flux
fix_modify AtC output bar1d_thermo_elasticFE 100 text #binary
timestep 5
thermo 100
run 1000
# free all nodes
#fix_modify AtC unfix displacement x all
#fix_modify AtC unfix velocity x all
fix_modify AtC unfix temperature all
# new boundary conditions
fix_modify AtC fix velocity x rbc 0.00000004
fix_modify AtC fix temperature lbc 20.
#fix_modify AtC output follow_ex.fe 50
#fix_modify AtC localized_lambda on
#fix_modify AtC momentum control glc_velocity
#fix_modify AtC momentum control flux faceset obndy
#fix_modify AtC control momentum flux
#fix_modify AtC control momentum ghost_flux
fix_modify AtC control thermal flux
#fix_modify AtC filter scale 1000.0
# run to extension
compute myTemp internal temp
compute atomStress internal stress/atom NULL
compute avgStress internal reduce sum c_atomStress[1] c_atomStress[2] c_atomStress[3]
variable myPres equal -(c_avgStress[1]+c_avgStress[2]+c_avgStress[3])/(3*vol)
thermo_style custom step c_myTemp v_myPres pe
fix_modify AtC output bar1d_thermo_elasticFE 500 text
#dump D1 all custom 100 bar1d_thermo_elastic.dmp id type x y z vx vy vz
timestep 5
thermo 100
run 1000
# change nodes to fixed
fix_modify AtC unfix velocity x rbc 0.
#fix_modify AtC fix displacement x rbc 0.0002
#fix_modify AtC output bar1d_fluxFE 500 text binary
# run to equilibrium
timestep 5
thermo 100
run 3000

160
examples/PACKAGES/atc/elastic/in.eam_energy
View File

@ -1,80 +1,80 @@
echo both
units metal
atom_style atomic
atom_modify map hash
boundary p p p
variable l equal 3
variable l2 equal 0.5*$l
variable L equal 10
variable L2 equal 0.5*$L
variable h equal $L
lattice fcc 4.08 origin 0.25 0.25 0.25
region BOX block -${l2} ${l2} -${L2} ${L2} -${l2} ${l2}
create_box 1 BOX
create_atoms 1 region BOX
pair_style eam
pair_coeff * * Au_u3.eam
mass * 196.97
### NOTE change to CB -linear
fix PP all atc field Au_elastic.mat
fix_modify PP mesh create 1 $h 1 BOX p f p
fix_modify PP fields add displacement velocity potential_energy cauchy_born_energy # kinetic_energy
fix_modify PP gradients add displacement
fix_modify PP set reference_potential_energy
fix_modify PP output counter step
fix_modify PP output eam_energyPP 1 text
fix ATC all atc elastic Au_elastic.mat
fix_modify ATC mesh create 1 $h 1 BOX p f p
fix_modify ATC internal_quadrature off
fix_modify ATC control momentum none
#fix_modify ATC consistent_fe_initialization on
fix_modify ATC output counter step
fix_modify ATC output eam_energyFE 1 text binary
fix_modify ATC material all Au_cubic
dump CONFIG all custom 1 eam_energy.dmp id type x y z
thermo 1
timestep 0 # 1.e-20 # 0
variable e0 equal pe
variable L0 equal ly
run 0
variable pe equal pe-${e0}
variable dL equal ly-${L0}
variable strain equal v_dL/${L0}
variable x equal y[1]
variable x2 equal y[2]
variable v equal vy[1]
thermo_style custom step etotal v_pe ke f_ATC[1] f_ATC[2] v_x v_v v_x2 ly v_dL v_strain
thermo_modify format 2 %15.8g
###############################################################################
log eam_energy.log
run 1
velocity all set 0 0.1 0 units box
fix_modify ATC fix velocity y all 0.1
run 1
velocity all set 0 0.2 0 units box
fix_modify ATC fix velocity y all 0.2
run 1
velocity all set 0 0.3 0 units box
fix_modify ATC fix velocity y all 0.3
run 1
change_box all y scale 1.01 remap
fix_modify ATC fix displacement y all linear 0 0 0 0 0.01 0 0
run 1
change_box all y scale 1.01 remap
fix_modify ATC fix displacement y all linear 0 0 0 0 0.0201 0 0
run 1
change_box all y scale 1.01 remap
fix_modify ATC fix displacement y all linear 0 0 0 0 0.030301 0 0
run 1
echo both
units metal
atom_style atomic
atom_modify map hash
boundary p p p
variable l equal 3
variable l2 equal 0.5*$l
variable L equal 10
variable L2 equal 0.5*$L
variable h equal $L
lattice fcc 4.08 origin 0.25 0.25 0.25
region BOX block -${l2} ${l2} -${L2} ${L2} -${l2} ${l2}
create_box 1 BOX
create_atoms 1 region BOX
pair_style eam
pair_coeff * * Au_u3.eam
mass * 196.97
### NOTE change to CB -linear
fix PP all atc field Au_elastic.mat
fix_modify PP mesh create 1 $h 1 BOX p f p
fix_modify PP fields add displacement velocity potential_energy cauchy_born_energy # kinetic_energy
fix_modify PP gradients add displacement
fix_modify PP set reference_potential_energy
fix_modify PP output counter step
fix_modify PP output eam_energyPP 1 text
fix ATC all atc elastic Au_elastic.mat
fix_modify ATC mesh create 1 $h 1 BOX p f p
fix_modify ATC internal_quadrature off
fix_modify ATC control momentum none
#fix_modify ATC consistent_fe_initialization on
fix_modify ATC output counter step
fix_modify ATC output eam_energyFE 1 text binary
fix_modify ATC material all Au_cubic
dump CONFIG all custom 1 eam_energy.dmp id type x y z
thermo 1
timestep 0 # 1.e-20 # 0
variable e0 equal pe
variable L0 equal ly
run 0
variable pe equal pe-${e0}
variable dL equal ly-${L0}
variable strain equal v_dL/${L0}
variable x equal y[1]
variable x2 equal y[2]
variable v equal vy[1]
thermo_style custom step etotal v_pe ke f_ATC[1] f_ATC[2] v_x v_v v_x2 ly v_dL v_strain
thermo_modify format 2 %15.8g
###############################################################################
log eam_energy.log
run 1
velocity all set 0 0.1 0 units box
fix_modify ATC fix velocity y all 0.1
run 1
velocity all set 0 0.2 0 units box
fix_modify ATC fix velocity y all 0.2
run 1
velocity all set 0 0.3 0 units box
fix_modify ATC fix velocity y all 0.3
run 1
change_box all y scale 1.01 remap
fix_modify ATC fix displacement y all linear 0 0 0 0 0.01 0 0
run 1
change_box all y scale 1.01 remap
fix_modify ATC fix displacement y all linear 0 0 0 0 0.0201 0 0
run 1
change_box all y scale 1.01 remap
fix_modify ATC fix displacement y all linear 0 0 0 0 0.030301 0 0
run 1

148
examples/PACKAGES/atc/elastic/in.electron_density
View File

@ -1,74 +1,74 @@
# needs description
echo both
units metal
# PARAMETERS-----------------------------
variable s equal 1
variable L equal 10
variable e equal 4
variable E equal 0.0001
variable V equal $E*$L
# END -----------------------------------
atom_style atomic
lattice diamond 1.0
boundary f p p
region box block -$L $L 0 1 0 1
create_box 1 box
group box region box
atom_modify sort 0 1
timestep 0.0
mass * 12.01
# coupling
### NOTE ATC: material cnt does not provide all interfaces for charge_density physics and will be treated as null
fix AtC box atc electrostatic-equilibrium CNT.mat
fix_modify AtC internal_quadrature off
#fix_modify AtC atom_weight constant internal 1.0 NOTE penultimate is a group
fix_modify AtC atom_weight constant box 1.0
fix_modify AtC omit atomic_charge
fix_modify AtC mesh create $e 1 1 box f p p
#fix_modify AtC control momentum flux
fix_modify AtC mesh create_elementset all -INF INF -INF INF -INF INF
# bcs/ics conditions
fix_modify AtC fix displacement x all 0.0
fix_modify AtC fix displacement y all 0.0
fix_modify AtC fix displacement z all 0.0
fix_modify AtC fix velocity x all 0.0
fix_modify AtC fix velocity y all 0.0
fix_modify AtC fix velocity z all 0.0
fix_modify AtC mesh create_nodeset lbc -10 -10 INF INF INF INF
fix_modify AtC mesh create_nodeset rbc 10 10 INF INF INF INF
fix_modify AtC fix electric_potential lbc linear 0 0 0 $E 0 0 $V
fix_modify AtC fix electric_potential rbc linear 0 0 0 $E 0 0 $V
# run
thermo_style custom step cpu etotal ke
thermo $s
fix_modify AtC output electron_densityFE $s text
fix_modify AtC output index step
log electron_density.log
# run default material
print "default material - table linear"
run $s
# run CNT1 material
print "CNT1 material - analytical linear"
fix_modify AtC material all CNT1
run $s
# run CNT2 material
print "CNT2 material - analytical exponetial"
fix_modify AtC material all CNT2
run $s
# run CNT material
print "CNT material - table DOS"
fix_modify AtC material all CNT
#variable E equal 10*$E
#fix_modify AtC fix electric_potential lbc linear 0 0 0 $E 0 0 $V
#fix_modify AtC fix electric_potential rbc linear 0 0 0 $E 0 0 $V
run $s
# needs description
echo both
units metal
# PARAMETERS-----------------------------
variable s equal 1
variable L equal 10
variable e equal 4
variable E equal 0.0001
variable V equal $E*$L
# END -----------------------------------
atom_style atomic
lattice diamond 1.0
boundary f p p
region box block -$L $L 0 1 0 1
create_box 1 box
group box region box
atom_modify sort 0 1
timestep 0.0
mass * 12.01
# coupling
### NOTE ATC: material cnt does not provide all interfaces for charge_density physics and will be treated as null
fix AtC box atc electrostatic-equilibrium CNT.mat
fix_modify AtC internal_quadrature off
#fix_modify AtC atom_weight constant internal 1.0 NOTE penultimate is a group
fix_modify AtC atom_weight constant box 1.0
fix_modify AtC omit atomic_charge
fix_modify AtC mesh create $e 1 1 box f p p
#fix_modify AtC control momentum flux
fix_modify AtC mesh create_elementset all -INF INF -INF INF -INF INF
# bcs/ics conditions
fix_modify AtC fix displacement x all 0.0
fix_modify AtC fix displacement y all 0.0
fix_modify AtC fix displacement z all 0.0
fix_modify AtC fix velocity x all 0.0
fix_modify AtC fix velocity y all 0.0
fix_modify AtC fix velocity z all 0.0
fix_modify AtC mesh create_nodeset lbc -10 -10 INF INF INF INF
fix_modify AtC mesh create_nodeset rbc 10 10 INF INF INF INF
fix_modify AtC fix electric_potential lbc linear 0 0 0 $E 0 0 $V
fix_modify AtC fix electric_potential rbc linear 0 0 0 $E 0 0 $V
# run
thermo_style custom step cpu etotal ke
thermo $s
fix_modify AtC output electron_densityFE $s text
fix_modify AtC output index step
log electron_density.log
# run default material
print "default material - table linear"
run $s
# run CNT1 material
print "CNT1 material - analytical linear"
fix_modify AtC material all CNT1
run $s
# run CNT2 material
print "CNT2 material - analytical exponetial"
fix_modify AtC material all CNT2
run $s
# run CNT material
print "CNT material - table DOS"
fix_modify AtC material all CNT
#variable E equal 10*$E
#fix_modify AtC fix electric_potential lbc linear 0 0 0 $E 0 0 $V
#fix_modify AtC fix electric_potential rbc linear 0 0 0 $E 0 0 $V
run $s

112
examples/PACKAGES/atc/mesh/in.gaussianIC1d_hex
View File

@ -1,56 +1,56 @@
echo both
units real
atom_style atomic
lattice fcc 5.405 origin 0.25 0.25 0.25
region mdRegion block -12 12 -3 3 -3 3
region mdInternal block -10 10 -3 3 -3 3
# create atoms
boundary f p p
create_box 1 mdRegion
create_atoms 1 region mdRegion
mass 1 39.95
pair_style lj/cut 13.5
pair_coeff 1 1 .238 3.405 13.5
# specify interal/ghost atoms
group internal region mdInternal
velocity internal create 40 87287 mom yes loop geom # <<< NOTE
neighbor 5. bin
neigh_modify every 10 delay 0 check no
# ID group atc PhysicsType ParameterFile
fix AtC internal atc two_temperature Ar_ttm.mat
fix_modify AtC mesh read gaussianIC1d_hex.mesh
# fix a temperature
fix_modify AtC fix temperature all 20.0
fix_modify AtC initial temperature all 20.0
fix_modify AtC initial electron_temperature all gaussian 0 0 0 1 0 0 5 20 20
fix_modify AtC fix electron_temperature all gaussian 0 0 0 1 0 0 5 20 20
# turn on thermostat
fix_modify AtC extrinsic exchange off
fix_modify AtC control thermal rescale 10
# equilibrate MD field
timestep 5.0
thermo 10
#output
fix_modify AtC output gaussianIC1d_hexFE 10 text
# change thermostat
fix_modify AtC unfix temperature all
fix_modify AtC unfix electron_temperature all
fix_modify AtC control thermal flux
fix_modify AtC extrinsic exchange on
fix_modify AtC extrinsic electron_integration explicit 10
# run with FE
thermo_style custom step temp pe f_AtC[2] f_AtC[4]
reset_timestep 0
run 100 # 400
echo both
units real
atom_style atomic
lattice fcc 5.405 origin 0.25 0.25 0.25
region mdRegion block -12 12 -3 3 -3 3
region mdInternal block -10 10 -3 3 -3 3
# create atoms
boundary f p p
create_box 1 mdRegion
create_atoms 1 region mdRegion
mass 1 39.95
pair_style lj/cut 13.5
pair_coeff 1 1 .238 3.405 13.5
# specify interal/ghost atoms
group internal region mdInternal
velocity internal create 40 87287 mom yes loop geom # <<< NOTE
neighbor 5. bin
neigh_modify every 10 delay 0 check no
# ID group atc PhysicsType ParameterFile
fix AtC internal atc two_temperature Ar_ttm.mat
fix_modify AtC mesh read gaussianIC1d_hex.mesh
# fix a temperature
fix_modify AtC fix temperature all 20.0
fix_modify AtC initial temperature all 20.0
fix_modify AtC initial electron_temperature all gaussian 0 0 0 1 0 0 5 20 20
fix_modify AtC fix electron_temperature all gaussian 0 0 0 1 0 0 5 20 20
# turn on thermostat
fix_modify AtC extrinsic exchange off
fix_modify AtC control thermal rescale 10
# equilibrate MD field
timestep 5.0
thermo 10
#output
fix_modify AtC output gaussianIC1d_hexFE 10 text
# change thermostat
fix_modify AtC unfix temperature all
fix_modify AtC unfix electron_temperature all
fix_modify AtC control thermal flux
fix_modify AtC extrinsic exchange on
fix_modify AtC extrinsic electron_integration explicit 10
# run with FE
thermo_style custom step temp pe f_AtC[2] f_AtC[4]
reset_timestep 0
run 100 # 400

138
examples/PACKAGES/atc/mesh/in.gaussianIC2d_hex
View File

@ -1,69 +1,69 @@
echo both
units real
atom_style atomic
variable L equal 12
variable l2 equal 6
variable l equal 4
variable w equal 2
lattice fcc 5.405 origin 0.25 0.25 0.25
region mdRegion cylinder z 0. 0. ${l2} -$w $w
region mdInternal cylinder z 0. 0. $l -$w $w
boundary f f f
pair_style lj/cut 13.5
read_data circle_temp.init
fix ZWALLS all wall/reflect zlo EDGE zhi EDGE
mass 1 39.95
pair_coeff 1 1 .238 3.405 13.5
group internal region mdInternal
group ghost subtract all internal
fix AtC internal atc two_temperature Ar_ttm.mat
# computational geometry
fix_modify AtC mesh read gaussianIC2d_hex.mesh
#fix_modify AtC mesh read gaussianIC2d_hex.exo
#fix_modify AtC mesh read gaussianIC2d_hex2.exo
#fix_modify AtC mesh read gaussianIC2d_hex2.mesh
fix_modify AtC mesh write parsed_gaussianIC2d_hex.mesh
fix_modify AtC mesh output gaussianIC2d_hexMESH
fix_modify AtC boundary ghost
# numerical parameters
fix_modify AtC time_integration fractional_step
fix_modify AtC internal_quadrature off
# initial conditions
fix_modify AtC fix temperature all 20.0
# NOTE this is only gaussian in x
fix_modify AtC fix electron_temperature all gaussian 0 0 0 1 0 0 5 20 20
# thermostat
fix_modify AtC control thermal rescale 10
fix_modify AtC extrinsic exchange off
# run to equilibrate
thermo_style custom step temp pe f_AtC[2] f_AtC[4]
timestep 1.0
thermo 10
run 400
# boundary conditions
fix_modify AtC unfix temperature all
fix_modify AtC unfix electron_temperature all
fix_modify AtC fix temperature 11 20.0
fix_modify AtC fix temperature 12 20.0
# numerical parameters
fix_modify AtC extrinsic electron_integration explicit 10
# thermostat
fix_modify AtC control thermal flux
fix_modify AtC extrinsic exchange on
# output
fix_modify AtC output gaussianIC2d_hexFE 10 full_text binary
dump D1 all atom 10 gaussianIC2d_hex.dmp
# relax the system
run 1000
echo both
units real
atom_style atomic
variable L equal 12
variable l2 equal 6
variable l equal 4
variable w equal 2
lattice fcc 5.405 origin 0.25 0.25 0.25
region mdRegion cylinder z 0. 0. ${l2} -$w $w
region mdInternal cylinder z 0. 0. $l -$w $w
boundary f f f
pair_style lj/cut 13.5
read_data circle_temp.init
fix ZWALLS all wall/reflect zlo EDGE zhi EDGE
mass 1 39.95
pair_coeff 1 1 .238 3.405 13.5
group internal region mdInternal
group ghost subtract all internal
fix AtC internal atc two_temperature Ar_ttm.mat
# computational geometry
fix_modify AtC mesh read gaussianIC2d_hex.mesh
#fix_modify AtC mesh read gaussianIC2d_hex.exo
#fix_modify AtC mesh read gaussianIC2d_hex2.exo
#fix_modify AtC mesh read gaussianIC2d_hex2.mesh
fix_modify AtC mesh write parsed_gaussianIC2d_hex.mesh
fix_modify AtC mesh output gaussianIC2d_hexMESH
fix_modify AtC boundary ghost
# numerical parameters
fix_modify AtC time_integration fractional_step
fix_modify AtC internal_quadrature off
# initial conditions
fix_modify AtC fix temperature all 20.0
# NOTE this is only gaussian in x
fix_modify AtC fix electron_temperature all gaussian 0 0 0 1 0 0 5 20 20
# thermostat
fix_modify AtC control thermal rescale 10
fix_modify AtC extrinsic exchange off
# run to equilibrate
thermo_style custom step temp pe f_AtC[2] f_AtC[4]
timestep 1.0
thermo 10
run 400
# boundary conditions
fix_modify AtC unfix temperature all
fix_modify AtC unfix electron_temperature all
fix_modify AtC fix temperature 11 20.0
fix_modify AtC fix temperature 12 20.0
# numerical parameters
fix_modify AtC extrinsic electron_integration explicit 10
# thermostat
fix_modify AtC control thermal flux
fix_modify AtC extrinsic exchange on
# output
fix_modify AtC output gaussianIC2d_hexFE 10 full_text binary
dump D1 all atom 10 gaussianIC2d_hex.dmp
# relax the system
run 1000

74
examples/PACKAGES/atc/mesh/in.gaussianIC2d_hex20_uniform
View File

@ -1,37 +1,37 @@
echo both
units real
atom_style atomic
variable L equal 12
variable l2 equal 6
variable l equal 4
variable w equal 2
lattice fcc 5.405 origin 0.25 0.25 0.25
region mdInternal block -$l $l -$l $l -$w $w
boundary f f f # p
pair_style lj/cut 13.5
read_data temp.init
fix ZWALLS all wall/reflect zlo EDGE zhi EDGE
mass 1 39.95
pair_coeff 1 1 .238 3.405 13.5
group internal region mdInternal
fix AtC internal atc two_temperature Ar_ttm.mat
fix_modify AtC mesh read gaussianIC2d_hex20_uniform.mesh
fix_modify AtC output gaussianIC2d_hex20_uniformFE 10 full_text
fix_modify AtC initial temperature all 20.0
# NOTE this is only gaussian in x
fix_modify AtC initial electron_temperature all gaussian 0 0 0 1 0 0 5 20 20
fix_modify AtC fix temperature 11 20.0
fix_modify AtC fix temperature 12 20.0
fix_modify AtC control thermal flux
fix_modify AtC extrinsic exchange on
fix_modify AtC extrinsic electron_integration explicit 10
thermo_style custom step temp pe f_AtC[2] f_AtC[4]
timestep 1.0
thermo 10
run 100
echo both
units real
atom_style atomic
variable L equal 12
variable l2 equal 6
variable l equal 4
variable w equal 2
lattice fcc 5.405 origin 0.25 0.25 0.25
region mdInternal block -$l $l -$l $l -$w $w
boundary f f f # p
pair_style lj/cut 13.5
read_data temp.init
fix ZWALLS all wall/reflect zlo EDGE zhi EDGE
mass 1 39.95
pair_coeff 1 1 .238 3.405 13.5
group internal region mdInternal
fix AtC internal atc two_temperature Ar_ttm.mat
fix_modify AtC mesh read gaussianIC2d_hex20_uniform.mesh
fix_modify AtC output gaussianIC2d_hex20_uniformFE 10 full_text
fix_modify AtC initial temperature all 20.0
# NOTE this is only gaussian in x
fix_modify AtC initial electron_temperature all gaussian 0 0 0 1 0 0 5 20 20
fix_modify AtC fix temperature 11 20.0
fix_modify AtC fix temperature 12 20.0
fix_modify AtC control thermal flux
fix_modify AtC extrinsic exchange on
fix_modify AtC extrinsic electron_integration explicit 10
thermo_style custom step temp pe f_AtC[2] f_AtC[4]
timestep 1.0
thermo 10
run 100

74
examples/PACKAGES/atc/mesh/in.gaussianIC2d_hex27_uniform
View File

@ -1,37 +1,37 @@
echo both
units real
atom_style atomic
variable L equal 12
variable l2 equal 6
variable l equal 4
variable w equal 2
lattice fcc 5.405 origin 0.25 0.25 0.25
region mdInternal block -$l $l -$l $l -$w $w
boundary f f f # p
pair_style lj/cut 13.5
read_data temp.init
fix ZWALLS all wall/reflect zlo EDGE zhi EDGE
mass 1 39.95
pair_coeff 1 1 .238 3.405 13.5
group internal region mdInternal
fix AtC internal atc two_temperature Ar_ttm.mat
fix_modify AtC mesh read gaussianIC2d_hex27_uniform.mesh
fix_modify AtC output gaussianIC2d_hex27_uniformFE 10 full_text
fix_modify AtC initial temperature all 20.0
# NOTE this is only gaussian in x
fix_modify AtC initial electron_temperature all gaussian 0 0 0 1 0 0 5 20 20
fix_modify AtC fix temperature 11 20.0
fix_modify AtC fix temperature 12 20.0
fix_modify AtC control thermal flux
fix_modify AtC extrinsic exchange on
fix_modify AtC extrinsic electron_integration explicit 10
thermo_style custom step temp pe f_AtC[2] f_AtC[4]
timestep 1.0
thermo 10
run 100
echo both
units real
atom_style atomic
variable L equal 12
variable l2 equal 6
variable l equal 4
variable w equal 2
lattice fcc 5.405 origin 0.25 0.25 0.25
region mdInternal block -$l $l -$l $l -$w $w
boundary f f f # p
pair_style lj/cut 13.5
read_data temp.init
fix ZWALLS all wall/reflect zlo EDGE zhi EDGE
mass 1 39.95
pair_coeff 1 1 .238 3.405 13.5
group internal region mdInternal
fix AtC internal atc two_temperature Ar_ttm.mat
fix_modify AtC mesh read gaussianIC2d_hex27_uniform.mesh
fix_modify AtC output gaussianIC2d_hex27_uniformFE 10 full_text
fix_modify AtC initial temperature all 20.0
# NOTE this is only gaussian in x
fix_modify AtC initial electron_temperature all gaussian 0 0 0 1 0 0 5 20 20
fix_modify AtC fix temperature 11 20.0
fix_modify AtC fix temperature 12 20.0
fix_modify AtC control thermal flux
fix_modify AtC extrinsic exchange on
fix_modify AtC extrinsic electron_integration explicit 10
thermo_style custom step temp pe f_AtC[2] f_AtC[4]
timestep 1.0
thermo 10
run 100

80
examples/PACKAGES/atc/mesh/in.gaussianIC2d_tet
View File

@ -1,40 +1,40 @@
echo both
units real
atom_style atomic
variable L equal 12
variable l2 equal 6
variable l equal 4
variable w equal 2
lattice fcc 5.405 origin 0.25 0.25 0.25
region mdInternal block -$l $l -$l $l -$w $w
boundary f f f # p
pair_style lj/cut 13.5
read_data temp.init
fix ZWALLS all wall/reflect zlo EDGE zhi EDGE
mass 1 39.95
pair_coeff 1 1 .238 3.405 13.5
group internal region mdInternal
fix AtC internal atc two_temperature Ar_ttm.mat
fix_modify AtC mesh read gaussianIC2d_tet.mesh
#fix_modify AtC mesh read gaussianIC2d_tet.exo
fix_modify AtC mesh write parsed_gaussianIC2d_tet.mesh
fix_modify AtC mesh output parsed_gaussianIC2d_tetMESH
fix_modify AtC output gaussianIC2d_tetFE 10 full_text
fix_modify AtC initial temperature all 20.0
# NOTE this is only gaussian in x
fix_modify AtC initial electron_temperature all gaussian 0 0 0 1 0 0 5 20 20
fix_modify AtC fix temperature 11 20.0
fix_modify AtC fix temperature 12 20.0
fix_modify AtC control thermal flux
fix_modify AtC extrinsic exchange on
fix_modify AtC extrinsic electron_integration explicit 10
thermo_style custom step temp pe f_AtC[2] f_AtC[4]
timestep 1.0
thermo 10
run 100
echo both
units real
atom_style atomic
variable L equal 12
variable l2 equal 6
variable l equal 4
variable w equal 2
lattice fcc 5.405 origin 0.25 0.25 0.25
region mdInternal block -$l $l -$l $l -$w $w
boundary f f f # p
pair_style lj/cut 13.5
read_data temp.init
fix ZWALLS all wall/reflect zlo EDGE zhi EDGE
mass 1 39.95
pair_coeff 1 1 .238 3.405 13.5
group internal region mdInternal
fix AtC internal atc two_temperature Ar_ttm.mat
fix_modify AtC mesh read gaussianIC2d_tet.mesh
#fix_modify AtC mesh read gaussianIC2d_tet.exo
fix_modify AtC mesh write parsed_gaussianIC2d_tet.mesh
fix_modify AtC mesh output parsed_gaussianIC2d_tetMESH
fix_modify AtC output gaussianIC2d_tetFE 10 full_text
fix_modify AtC initial temperature all 20.0
# NOTE this is only gaussian in x
fix_modify AtC initial electron_temperature all gaussian 0 0 0 1 0 0 5 20 20
fix_modify AtC fix temperature 11 20.0
fix_modify AtC fix temperature 12 20.0
fix_modify AtC control thermal flux
fix_modify AtC extrinsic exchange on
fix_modify AtC extrinsic electron_integration explicit 10
thermo_style custom step temp pe f_AtC[2] f_AtC[4]
timestep 1.0
thermo 10
run 100

64
examples/PACKAGES/atc/mesh/in.kernel2d_hex
View File

@ -1,32 +1,32 @@
echo both
units real
atom_style atomic
# correct mass density = 1.0120
# NOTE the mesh is not currently periodic, so the density estimate is off by a factor of 2
variable L equal 6
variable w equal 2
lattice fcc 5.405 origin 0.25 0.25 0.25
region BOX block -$L $L -$L $L -$w $w
boundary f f p
create_box 1 BOX
create_atoms 1 region BOX
mass 1 39.95
pair_style lj/cut 13.5
pair_coeff 1 1 .238 3.405 13.5
group internal region BOX
fix AtC internal atc hardy
fix_modify AtC kernel quartic_cylinder 5.0
fix_modify AtC mesh read gaussianIC2d_hex.mesh
fix_modify AtC fields add mass_density
fix_modify AtC output kernel2d_hexFE 1 full_text binary
#dump CONFIG all custom 1 kernel2d_hexMD.dmp id type x y z
thermo_style custom step cpu temp
timestep 0.0
thermo 1
run 2
echo both
units real
atom_style atomic
# correct mass density = 1.0120
# NOTE the mesh is not currently periodic, so the density estimate is off by a factor of 2
variable L equal 6
variable w equal 2
lattice fcc 5.405 origin 0.25 0.25 0.25
region BOX block -$L $L -$L $L -$w $w
boundary f f p
create_box 1 BOX
create_atoms 1 region BOX
mass 1 39.95
pair_style lj/cut 13.5
pair_coeff 1 1 .238 3.405 13.5
group internal region BOX
fix AtC internal atc hardy
fix_modify AtC kernel quartic_cylinder 5.0
fix_modify AtC mesh read gaussianIC2d_hex.mesh
fix_modify AtC fields add mass_density
fix_modify AtC output kernel2d_hexFE 1 full_text binary
#dump CONFIG all custom 1 kernel2d_hexMD.dmp id type x y z
thermo_style custom step cpu temp
timestep 0.0
thermo 1
run 2

56
examples/PACKAGES/atc/mesh/in.kernel2d_tet
View File

@ -1,28 +1,28 @@
echo both
units real
atom_style atomic
variable L equal 6
variable w equal 2
lattice fcc 5.405 origin 0.25 0.25 0.25
region BOX block -$L $L -$L $L -$w $w
boundary f f p
create_box 1 BOX
create_atoms 1 region BOX
mass 1 39.95
pair_style lj/cut 13.5
pair_coeff 1 1 .238 3.405 13.5
group internal region BOX
fix AtC internal atc hardy
fix_modify AtC kernel quartic_sphere 5.0
fix_modify AtC mesh read gaussianIC2d_tet.mesh
fix_modify AtC fields add mass_density
fix_modify AtC output kernel2d_tetFE 1 full_text binary
thermo_style custom step cpu temp
timestep 0.0
thermo 1
run 2
echo both
units real
atom_style atomic
variable L equal 6
variable w equal 2
lattice fcc 5.405 origin 0.25 0.25 0.25
region BOX block -$L $L -$L $L -$w $w
boundary f f p
create_box 1 BOX
create_atoms 1 region BOX
mass 1 39.95
pair_style lj/cut 13.5
pair_coeff 1 1 .238 3.405 13.5
group internal region BOX
fix AtC internal atc hardy
fix_modify AtC kernel quartic_sphere 5.0
fix_modify AtC mesh read gaussianIC2d_tet.mesh
fix_modify AtC fields add mass_density
fix_modify AtC output kernel2d_tetFE 1 full_text binary
thermo_style custom step cpu temp
timestep 0.0
thermo 1
run 2

58
examples/PACKAGES/atc/mesh/in.mesh2d_tet
View File

@ -1,29 +1,29 @@
echo both
units real
atom_style atomic
variable L equal 6
variable w equal 2
lattice fcc 5.405 origin 0.25 0.25 0.25
region BOX block -$L $L -$L $L -$w $w
boundary f f p
create_box 1 BOX
create_atoms 1 region BOX
mass 1 39.95
pair_style lj/cut 13.5
pair_coeff 1 1 .238 3.405 13.5
group internal region BOX
fix AtC internal atc field
fix_modify AtC mesh read gaussianIC2d_tet.mesh
fix_modify AtC fields add mass_density
fix_modify AtC output mesh2d_tetFE 1 full_text binary
dump CONFIG all custom 10 mesh2d_tet.dmp id type x y z
thermo_style custom step cpu temp
timestep 0.0
thermo 1
run 2
echo both
units real
atom_style atomic
variable L equal 6
variable w equal 2
lattice fcc 5.405 origin 0.25 0.25 0.25
region BOX block -$L $L -$L $L -$w $w
boundary f f p
create_box 1 BOX
create_atoms 1 region BOX
mass 1 39.95
pair_style lj/cut 13.5
pair_coeff 1 1 .238 3.405 13.5
group internal region BOX
fix AtC internal atc field
fix_modify AtC mesh read gaussianIC2d_tet.mesh
fix_modify AtC fields add mass_density
fix_modify AtC output mesh2d_tetFE 1 full_text binary
dump CONFIG all custom 10 mesh2d_tet.dmp id type x y z
thermo_style custom step cpu temp
timestep 0.0
thermo 1
run 2

202
examples/PACKAGES/atc/mesh/in.semicircle
View File

@ -1,101 +1,101 @@
# this input can be used to generate the benchmark for in.gaussianIC2d_hex_uniform
echo both
units real
atom_style atomic
variable l equal 8
variable g equal 2
variable lg equal $l+$g
variable w equal 2
lattice fcc 5.405 origin 0.25 0.25 0.25
boundary f f f
# region to create atoms
region bigCyl cylinder z 0. 0. ${lg} -$w $w
region offsetPlane block -${lg} $g -${lg} ${lg} -$w $w
region mdRegion intersect 2 bigCyl offsetPlane
#create_box 1 mdRegion
pair_style lj/cut 13.5
read_data semicircle.init
# region for internal atoms
region mdInternalCyl cylinder z 0. 0. $l -$w $w
region leftHalfPlane block INF 0. INF INF INF INF
region mdInternal intersect 2 mdInternalCyl leftHalfPlane
# region for coupling ghosts
region rightHalfPlane block 0. INF INF INF INF INF
region mdGhost union 2 rightHalfPlane mdInternal side out
#create_atoms 1 region mdRegion
#create_atoms 1 region mdInternal
#create_atoms 2 region mdGhost
#region outerGhost intersect 2 rightHalfPlane mdRegion
#create_atoms 3 region outerGhost
#pair_style lj/cut 13.5
fix ZWALLS all wall/reflect zlo EDGE zhi EDGE
#mass 1 39.95
#pair_coeff 1 1 .238 3.405 13.5
group internal region mdInternal
group ghost region mdGhost
#velocity internal create 40 102486 mom yes rot yes dist gaussian
#write_restart semicircle_init.rst
# ATC commands
fix AtC internal atc thermal Ar_ttm.mat
fix_modify AtC boundary ghost
fix_modify AtC mesh read semicircle.mesh f f p
fix_modify AtC mesh nodeset_to_elementset 2 hole min
fix_modify AtC internal_quadrature off
fix_modify AtC time_integration fractional_step
# initial conditions
fix_modify AtC fix temperature all 20.
fix_modify AtC control thermal rescale 10
fix_modify AtC control tolerance 1.e-14 # tolerance needed to produce consistent parallel and serial results
# initial output
#fix_modify AtC mesh output semicircle_mesh
#fix_modify AtC output semicircle_init 100 text binary
#dump D1 all atom 100 semicircle_init.dmp
# run
timestep 5.0
thermo 100
run 500
# boundary conditions
fix_modify AtC unfix temperature all
fix_modify AtC fix temperature 1 20.
fix_modify AtC control thermal flux
fix_modify AtC control localized_lambda on
# NOTE appears to be a problem with the temporal ramp function
variable delta_t equal 1000*5.
fix_modify AtC source temperature hole temporal_ramp 0. 0.0000000001 ${delta_t}
# equilibrate filter
fix_modify AtC filter type exponential
fix_modify AtC filter scale 1000.
fix_modify AtC filter on
# equilibration output
fix_modify AtC output semicircleFE 100 full_text #binary
#undump D1
#dump D1 all atom 100 semicircle_equil.dmp
# run
fix_modify AtC reset_time 0.
reset_timestep 0
thermo 100
run 1000
# heat source
# NOTE second run omitted as it causes diffs in parallel execution after just one timestep, not sure why
#fix_modify AtC source temperature hole 0.0000000001
#fix_modify AtC output semicircleFE 1 full_text #binary
#undump D1
#dump D1 all atom 100 semicircle.dmp
#run 1#000
# this input can be used to generate the benchmark for in.gaussianIC2d_hex_uniform
echo both
units real
atom_style atomic
variable l equal 8
variable g equal 2
variable lg equal $l+$g
variable w equal 2
lattice fcc 5.405 origin 0.25 0.25 0.25
boundary f f f
# region to create atoms
region bigCyl cylinder z 0. 0. ${lg} -$w $w
region offsetPlane block -${lg} $g -${lg} ${lg} -$w $w
region mdRegion intersect 2 bigCyl offsetPlane
#create_box 1 mdRegion
pair_style lj/cut 13.5
read_data semicircle.init
# region for internal atoms
region mdInternalCyl cylinder z 0. 0. $l -$w $w
region leftHalfPlane block INF 0. INF INF INF INF
region mdInternal intersect 2 mdInternalCyl leftHalfPlane
# region for coupling ghosts
region rightHalfPlane block 0. INF INF INF INF INF
region mdGhost union 2 rightHalfPlane mdInternal side out
#create_atoms 1 region mdRegion
#create_atoms 1 region mdInternal
#create_atoms 2 region mdGhost
#region outerGhost intersect 2 rightHalfPlane mdRegion
#create_atoms 3 region outerGhost
#pair_style lj/cut 13.5
fix ZWALLS all wall/reflect zlo EDGE zhi EDGE
#mass 1 39.95
#pair_coeff 1 1 .238 3.405 13.5
group internal region mdInternal
group ghost region mdGhost
#velocity internal create 40 102486 mom yes rot yes dist gaussian
#write_restart semicircle_init.rst
# ATC commands
fix AtC internal atc thermal Ar_ttm.mat
fix_modify AtC boundary ghost
fix_modify AtC mesh read semicircle.mesh f f p
fix_modify AtC mesh nodeset_to_elementset 2 hole min
fix_modify AtC internal_quadrature off
fix_modify AtC time_integration fractional_step
# initial conditions
fix_modify AtC fix temperature all 20.
fix_modify AtC control thermal rescale 10
fix_modify AtC control tolerance 1.e-14 # tolerance needed to produce consistent parallel and serial results
# initial output
#fix_modify AtC mesh output semicircle_mesh
#fix_modify AtC output semicircle_init 100 text binary
#dump D1 all atom 100 semicircle_init.dmp
# run
timestep 5.0
thermo 100
run 500
# boundary conditions
fix_modify AtC unfix temperature all
fix_modify AtC fix temperature 1 20.
fix_modify AtC control thermal flux
fix_modify AtC control localized_lambda on
# NOTE appears to be a problem with the temporal ramp function
variable delta_t equal 1000*5.
fix_modify AtC source temperature hole temporal_ramp 0. 0.0000000001 ${delta_t}
# equilibrate filter
fix_modify AtC filter type exponential
fix_modify AtC filter scale 1000.
fix_modify AtC filter on
# equilibration output
fix_modify AtC output semicircleFE 100 full_text #binary
#undump D1
#dump D1 all atom 100 semicircle_equil.dmp
# run
fix_modify AtC reset_time 0.
reset_timestep 0
thermo 100
run 1000
# heat source
# NOTE second run omitted as it causes diffs in parallel execution after just one timestep, not sure why
#fix_modify AtC source temperature hole 0.0000000001
#fix_modify AtC output semicircleFE 1 full_text #binary
#undump D1
#dump D1 all atom 100 semicircle.dmp
#run 1#000

112
examples/PACKAGES/atc/thermal/in.no_atoms
View File

@ -1,56 +1,56 @@
# needs description
#AtC thermal Coupling
#
echo both
units real
atom_style atomic
lattice fcc 5.405 origin 0.25 0.25 0.25
region feRegion block -10 10 -1 1 -1 1
boundary f p p
create_box 1 feRegion
mass 1 39.95 # need to keep this
atom_modify sort 0 1
region dummyRegion block -100 -99 -1 1 -1 1
group dummy region dummyRegion
# ID group atc PhysicsType ParameterFile
fix AtC dummy atc thermal Ar_thermal.mat
timestep 5.0
# ID part keywords nx ny nz region
fix_modify AtC mesh create 10 1 1 feRegion f p p
# fix end temperatures and an internal source
fix_modify AtC initial temperature all 20.0
fix_modify AtC source temperature all 0.0000000000632
fix_modify AtC mesh create_nodeset lbc -10.1 -9.9 -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc 9.9 10.1 -INF INF -INF INF
fix_modify AtC fix temperature lbc 20.
fix_modify AtC fix temperature rbc 20.
fix_modify AtC mesh create_elementset middle -4.1 4.1 -INF INF -INF INF
fix_modify AtC material middle Ar2
thermo_style custom step cpu f_AtC[1] f_AtC[2]
fix_modify AtC output no_atomsFE 1000 text binary
thermo 100
run 10000
fix_modify AtC remove_source temperature all
fix_modify AtC unfix temperature rbc
fix_modify AtC fix temperature all 20.
run 1
fix_modify AtC unfix temperature all
reset_timestep 0
# fix one end temperature and the a source at the other
fix_modify AtC fix temperature lbc 20.
fix_modify AtC mesh create_faceset rbcFace plane x 10.0
fix_modify AtC fix_flux temperature rbcFace 0.000000001
fix_modify AtC output no_atoms_flux_FE 1000 text binary # NOTE not used
thermo 100
run 10000
# needs description
#AtC thermal Coupling
#
echo both
units real
atom_style atomic
lattice fcc 5.405 origin 0.25 0.25 0.25
region feRegion block -10 10 -1 1 -1 1
boundary f p p
create_box 1 feRegion
mass 1 39.95 # need to keep this
atom_modify sort 0 1
region dummyRegion block -100 -99 -1 1 -1 1
group dummy region dummyRegion
# ID group atc PhysicsType ParameterFile
fix AtC dummy atc thermal Ar_thermal.mat
timestep 5.0
# ID part keywords nx ny nz region
fix_modify AtC mesh create 10 1 1 feRegion f p p
# fix end temperatures and an internal source
fix_modify AtC initial temperature all 20.0
fix_modify AtC source temperature all 0.0000000000632
fix_modify AtC mesh create_nodeset lbc -10.1 -9.9 -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc 9.9 10.1 -INF INF -INF INF
fix_modify AtC fix temperature lbc 20.
fix_modify AtC fix temperature rbc 20.
fix_modify AtC mesh create_elementset middle -4.1 4.1 -INF INF -INF INF
fix_modify AtC material middle Ar2
thermo_style custom step cpu f_AtC[1] f_AtC[2]
fix_modify AtC output no_atomsFE 1000 text binary
thermo 100
run 10000
fix_modify AtC remove_source temperature all
fix_modify AtC unfix temperature rbc
fix_modify AtC fix temperature all 20.
run 1
fix_modify AtC unfix temperature all
reset_timestep 0
# fix one end temperature and the a source at the other
fix_modify AtC fix temperature lbc 20.
fix_modify AtC mesh create_faceset rbcFace plane x 10.0
fix_modify AtC fix_flux temperature rbcFace 0.000000001
fix_modify AtC output no_atoms_flux_FE 1000 text binary # NOTE not used
thermo 100
run 10000

174
examples/PACKAGES/atc/two_temperature/in.cutout
View File

@ -1,87 +1,87 @@
# needs description
#AtC Two temperature Coupling
# DESCRIPTION:
# delete elements from the mesh
# heating and then relaxation
echo both
units metal
variable INF equal 1000
variable T equal 20
atom_style atomic
lattice fcc 5.405 origin 0.25 0.25 0.25
region FE block -8 8 -6 6 0 3
region MD block -7 7 -6 0 0 3
region FREE block -4 4 -6 0 0 3
boundary f f p
# create atoms
#create_box 1 FE
#create_atoms 1 region MD
#group internal region FREE
#mass 1 39.95
#read_data cutout.data
#pair_coeff * * .238 3.405 13.5
#velocity internal create 40 87287 mom yes loop geom
#fix NVE internal nve
#thermo 100
#dump CONFIG all atom 100 cutout.dump
##run 1000
#unfix NVE
#write_restart cutout.rst
pair_style lj/cut 13.5
read_data cutout.init
group internal region FREE
group ghost subtract all internal
timestep 0.002
thermo 20
# allow initial state to relax
fix NVT internal nvt temp $T $T 10 drag 0.2
fix RESCALE internal temp/rescale 25 $T $T 0.05 1.0
run 200
unfix RESCALE
run 800
unfix NVT
# ID group atc PhysicsType ParameterFile
fix AtC internal atc two_temperature Ar_ttm.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create 8 6 1 FE f f p
fix_modify AtC mesh create_elementset wire -4 4 -INF 0 -INF INF
fix_modify AtC mesh create_nodeset gap -4 4 -0 INF -INF INF
fix_modify AtC mesh create_elementset gap -4 4 -0 INF -INF INF
fix_modify AtC mesh delete_elements gap
fix_modify AtC mesh create_faceset bndy box -4 4 -INF 0 -INF INF
fix_modify AtC control thermal flux faceset bndy
# fix a temperature
fix_modify AtC initial temperature all 20.0
fix_modify AtC initial electron_temperature all 30.0
fix_modify AtC initial temperature gap 0.0
# relaxation
thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4]
fix_modify AtC output cutoutFE 10 text
fix_modify AtC extrinsic electron_integration implicit
# heating
fix_modify AtC mesh create_nodeset lbc -8 -8 -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc 8 8 -INF INF -INF INF
fix_modify AtC fix electron_temperature lbc 20.
fix_modify AtC fix electron_temperature rbc 20.
fix_modify AtC source electron_temperature wire 0.001
run 200
# relaxation
fix_modify AtC remove_source electron_temperature wire
run 200
# needs description
#AtC Two temperature Coupling
# DESCRIPTION:
# delete elements from the mesh
# heating and then relaxation
echo both
units metal
variable INF equal 1000
variable T equal 20
atom_style atomic
lattice fcc 5.405 origin 0.25 0.25 0.25
region FE block -8 8 -6 6 0 3
region MD block -7 7 -6 0 0 3
region FREE block -4 4 -6 0 0 3
boundary f f p
# create atoms
#create_box 1 FE
#create_atoms 1 region MD
#group internal region FREE
#mass 1 39.95
#read_data cutout.data
#pair_coeff * * .238 3.405 13.5
#velocity internal create 40 87287 mom yes loop geom
#fix NVE internal nve
#thermo 100
#dump CONFIG all atom 100 cutout.dump
##run 1000
#unfix NVE
#write_restart cutout.rst
pair_style lj/cut 13.5
read_data cutout.init
group internal region FREE
group ghost subtract all internal
timestep 0.002
thermo 20
# allow initial state to relax
fix NVT internal nvt temp $T $T 10 drag 0.2
fix RESCALE internal temp/rescale 25 $T $T 0.05 1.0
run 200
unfix RESCALE
run 800
unfix NVT
# ID group atc PhysicsType ParameterFile
fix AtC internal atc two_temperature Ar_ttm.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create 8 6 1 FE f f p
fix_modify AtC mesh create_elementset wire -4 4 -INF 0 -INF INF
fix_modify AtC mesh create_nodeset gap -4 4 -0 INF -INF INF
fix_modify AtC mesh create_elementset gap -4 4 -0 INF -INF INF
fix_modify AtC mesh delete_elements gap
fix_modify AtC mesh create_faceset bndy box -4 4 -INF 0 -INF INF
fix_modify AtC control thermal flux faceset bndy
# fix a temperature
fix_modify AtC initial temperature all 20.0
fix_modify AtC initial electron_temperature all 30.0
fix_modify AtC initial temperature gap 0.0
# relaxation
thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4]
fix_modify AtC output cutoutFE 10 text
fix_modify AtC extrinsic electron_integration implicit
# heating
fix_modify AtC mesh create_nodeset lbc -8 -8 -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc 8 8 -INF INF -INF INF
fix_modify AtC fix electron_temperature lbc 20.
fix_modify AtC fix electron_temperature rbc 20.
fix_modify AtC source electron_temperature wire 0.001
run 200
# relaxation
fix_modify AtC remove_source electron_temperature wire
run 200

188
examples/PACKAGES/atc/two_temperature/in.gaussianIC_ttm
View File

@ -1,94 +1,94 @@
#AtC Two temperature Coupling
# DESCRIPTION:
# full overlap of MD and FE regions w/ free ends & lateral periodic bcs
# initial gaussian electron temperature profile and uniform phonon temperature
# results in fast exchange followed by slower diffusion and finally relaxation
# to equilibrium
#
echo both
units real
atom_style atomic
# create domain
#lattice type reduced density rho* = 4*(sigma/a)^3,
# where N = 4 for fcc,
# s = 3.405 A (Wagner)
# a = 5.25 A (Ashcroft & Mermin, p. 70)
# to create restart :
# write_restart temp.bin
# then : restart2data temp.bin temp.init
#if {restart}
boundary f p p
pair_style lj/cut 13.5
read_data temp.init
#endif
lattice fcc 5.405 origin 0.25 0.25 0.25
region feRegion block -10 10 -3 3 -3 3
region mdRegion block -12 12 -3 3 -3 3
region mdInternal block -10 10 -3 3 -3 3
# create atoms, NOTE commented out for restart
#if !{restart}
#boundary f p p
#create_box 1 mdRegion
#create_atoms 1 region mdRegion
#mass 1 39.95
#pair_style lj/cut 13.5
#pair_coeff 1 1 .238 3.405 13.5
#velocity internal create 40 87287 mom yes loop geom
#endif
# specify interal/ghost atoms
group internal region mdInternal
# do not define ghosts if outside fe region
#group ghost subtract all internal
neighbor 5. bin
neigh_modify every 10 delay 0 check no
# ID group atc PhysicsType ParameterFile
fix AtC internal atc two_temperature Ar_ttm.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create 10 1 1 feRegion f p p
# fix a temperature
fix_modify AtC fix temperature all 20.0
fix_modify AtC initial temperature all 20.0
fix_modify AtC initial electron_temperature all gaussian 0 0 0 1 0 0 5 20 20
fix_modify AtC fix electron_temperature all gaussian 0 0 0 1 0 0 5 20 20
# turn on thermostat
fix_modify AtC extrinsic exchange off
fix_modify AtC control thermal rescale 10
# equilibrate MD field
timestep 5.0
#timestep 0.1
thermo 10
#if !{restart}
#run 1000
#endif
# write restart file (for atoms)
#if !{restart}
#write_restart gaussianT0.dat
#endif
#output
fix_modify AtC output gaussianIC_ttmFE 10 text
# change thermostat
fix_modify AtC unfix temperature all
fix_modify AtC unfix electron_temperature all
fix_modify AtC control thermal flux
fix_modify AtC extrinsic exchange on
fix_modify AtC extrinsic electron_integration explicit 10
# run with FE
thermo_style custom step temp pe f_AtC[2] f_AtC[4]
reset_timestep 0
run 400
#AtC Two temperature Coupling
# DESCRIPTION:
# full overlap of MD and FE regions w/ free ends & lateral periodic bcs
# initial gaussian electron temperature profile and uniform phonon temperature
# results in fast exchange followed by slower diffusion and finally relaxation
# to equilibrium
#
echo both
units real
atom_style atomic
# create domain
#lattice type reduced density rho* = 4*(sigma/a)^3,
# where N = 4 for fcc,
# s = 3.405 A (Wagner)
# a = 5.25 A (Ashcroft & Mermin, p. 70)
# to create restart :
# write_restart temp.bin
# then : restart2data temp.bin temp.init
#if {restart}
boundary f p p
pair_style lj/cut 13.5
read_data temp.init
#endif
lattice fcc 5.405 origin 0.25 0.25 0.25
region feRegion block -10 10 -3 3 -3 3
region mdRegion block -12 12 -3 3 -3 3
region mdInternal block -10 10 -3 3 -3 3
# create atoms, NOTE commented out for restart
#if !{restart}
#boundary f p p
#create_box 1 mdRegion
#create_atoms 1 region mdRegion
#mass 1 39.95
#pair_style lj/cut 13.5
#pair_coeff 1 1 .238 3.405 13.5
#velocity internal create 40 87287 mom yes loop geom
#endif
# specify interal/ghost atoms
group internal region mdInternal
# do not define ghosts if outside fe region
#group ghost subtract all internal
neighbor 5. bin
neigh_modify every 10 delay 0 check no
# ID group atc PhysicsType ParameterFile
fix AtC internal atc two_temperature Ar_ttm.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create 10 1 1 feRegion f p p
# fix a temperature
fix_modify AtC fix temperature all 20.0
fix_modify AtC initial temperature all 20.0
fix_modify AtC initial electron_temperature all gaussian 0 0 0 1 0 0 5 20 20
fix_modify AtC fix electron_temperature all gaussian 0 0 0 1 0 0 5 20 20
# turn on thermostat
fix_modify AtC extrinsic exchange off
fix_modify AtC control thermal rescale 10
# equilibrate MD field
timestep 5.0
#timestep 0.1
thermo 10
#if !{restart}
#run 1000
#endif
# write restart file (for atoms)
#if !{restart}
#write_restart gaussianT0.dat
#endif
#output
fix_modify AtC output gaussianIC_ttmFE 10 text
# change thermostat
fix_modify AtC unfix temperature all
fix_modify AtC unfix electron_temperature all
fix_modify AtC control thermal flux
fix_modify AtC extrinsic exchange on
fix_modify AtC extrinsic electron_integration explicit 10
# run with FE
thermo_style custom step temp pe f_AtC[2] f_AtC[4]
reset_timestep 0
run 400

122
examples/PACKAGES/atc/two_temperature/in.no_atoms
View File

@ -1,61 +1,61 @@
# needs description
#AtC Two temperature Coupling
# DESCRIPTION:
# no atoms and FE regions with periodic boundary conditions.
# heating and then relaxation
echo both
#units real
units metal
atom_style atomic
lattice fcc 5.405 origin 0.25 0.25 0.25
region simRegion block -14 14 -3 3 -3 3
region feRegion block -12 12 -3 3 -3 3
# need to create atoms or lammps throws an error
region mdRegion block -12 12 -3 3 -3 3
boundary f p p
create_box 1 mdRegion
mass 1 39.95 # need to keep this
atom_modify sort 0 1
region dummyRegion block -100 -99 -1 1 -1 1
group dummy region dummyRegion
# ID group atc PhysicsType ParameterFile
fix AtC dummy atc two_temperature Cu_ttm.mat
timestep 0.002
thermo 20
# ID part keywords nx ny nz region
fix_modify AtC mesh create 12 1 1 feRegion f p p
# fix a temperature
fix_modify AtC initial temperature all 20.0
#fix_modify AtC initial electron_temperature all 30.0
fix_modify AtC initial electron_temperature all gaussian 0 0 0 1 0 0 5 20 20
# relaxation
thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4]
fix_modify AtC output no_atomsFE 10 text
#fix_modify AtC extrinsic electron_integration subcycle 100
fix_modify AtC extrinsic electron_integration implicit
run 400
# heating
fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF
fix_modify AtC fix electron_temperature lbc 20.
fix_modify AtC fix electron_temperature rbc 20.
#fix_modify AtC extrinsic exchange off
#fix_modify AtC fix temperature lbc 20.
#fix_modify AtC fix temperature rbc 20.
#fix_modify AtC extrinsic electron_integration lockstep
#fix_modify AtC source electron_temperature all 1000.0
fix_modify AtC source electron_temperature all 0.521981
run 400
# relaxation
fix_modify AtC remove_source electron_temperature all
run 400
# needs description
#AtC Two temperature Coupling
# DESCRIPTION:
# no atoms and FE regions with periodic boundary conditions.
# heating and then relaxation
echo both
#units real
units metal
atom_style atomic
lattice fcc 5.405 origin 0.25 0.25 0.25
region simRegion block -14 14 -3 3 -3 3
region feRegion block -12 12 -3 3 -3 3
# need to create atoms or lammps throws an error
region mdRegion block -12 12 -3 3 -3 3
boundary f p p
create_box 1 mdRegion
mass 1 39.95 # need to keep this
atom_modify sort 0 1
region dummyRegion block -100 -99 -1 1 -1 1
group dummy region dummyRegion
# ID group atc PhysicsType ParameterFile
fix AtC dummy atc two_temperature Cu_ttm.mat
timestep 0.002
thermo 20
# ID part keywords nx ny nz region
fix_modify AtC mesh create 12 1 1 feRegion f p p
# fix a temperature
fix_modify AtC initial temperature all 20.0
#fix_modify AtC initial electron_temperature all 30.0
fix_modify AtC initial electron_temperature all gaussian 0 0 0 1 0 0 5 20 20
# relaxation
thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4]
fix_modify AtC output no_atomsFE 10 text
#fix_modify AtC extrinsic electron_integration subcycle 100
fix_modify AtC extrinsic electron_integration implicit
run 400
# heating
fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF
fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF
fix_modify AtC fix electron_temperature lbc 20.
fix_modify AtC fix electron_temperature rbc 20.
#fix_modify AtC extrinsic exchange off
#fix_modify AtC fix temperature lbc 20.
#fix_modify AtC fix temperature rbc 20.
#fix_modify AtC extrinsic electron_integration lockstep
#fix_modify AtC source electron_temperature all 1000.0
fix_modify AtC source electron_temperature all 0.521981
run 400
# relaxation
fix_modify AtC remove_source electron_temperature all
run 400

132
examples/PACKAGES/atc/two_temperature/in.uniform_exchange
View File

@ -1,66 +1,66 @@
#AtC Two temperature Coupling
# DESCRIPTION:
# full overlap of MD and FE regions with full periodic boundary conditions.
# initial electron and phonon temperatures are different and then allowed to
# relax.
#
units real
atom_style atomic
boundary p p p
# create domain
#lattice type reduced density rho* = 4*(sigma/a)^3,
# where N = 4 for fcc,
# s = 3.405 A (Wagner)
# a = 5.25 A (Ashcroft & Mermin, p. 70)
lattice fcc 5.405 origin 0.25 0.25 0.25
pair_style lj/cut 13.5
read_data uniform_exchange.init
region simRegion block -12 12 -3 3 -3 3
region feRegion block -12 12 -3 3 -3 3
# create atoms
region mdRegion block -12 12 -3 3 -3 3
# specify interal/ghost atoms
region mdInternal block -12 12 -3 3 -3 3
group internal region mdInternal
neighbor 5. bin
neigh_modify every 10 delay 0 check no
# ID group atc PhysicsType ParameterFile
fix AtC internal atc two_temperature Ar_ttm.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create 4 1 1 feRegion p p p
# fix a temperature
fix_modify AtC fix temperature all 20.0
fix_modify AtC fix electron_temperature all 30.0
timestep 5.0
# output
thermo_style custom step pe temp f_AtC[2] f_AtC[4]
thermo 10
# equilibrate MD field
fix_modify AtC control thermal rescale 13
run 500
# relax
fix_modify AtC output uniform_exchangeFE 100 text
fix_modify AtC filter type exponential
fix_modify AtC filter scale 5.0e2
fix_modify AtC filter on
fix_modify AtC unfix temperature all
fix_modify AtC unfix electron_temperature all
fix_modify AtC control thermal flux
# run with FE
run 5000
#AtC Two temperature Coupling
# DESCRIPTION:
# full overlap of MD and FE regions with full periodic boundary conditions.
# initial electron and phonon temperatures are different and then allowed to
# relax.
#
units real
atom_style atomic
boundary p p p
# create domain
#lattice type reduced density rho* = 4*(sigma/a)^3,
# where N = 4 for fcc,
# s = 3.405 A (Wagner)
# a = 5.25 A (Ashcroft & Mermin, p. 70)
lattice fcc 5.405 origin 0.25 0.25 0.25
pair_style lj/cut 13.5
read_data uniform_exchange.init
region simRegion block -12 12 -3 3 -3 3
region feRegion block -12 12 -3 3 -3 3
# create atoms
region mdRegion block -12 12 -3 3 -3 3
# specify interal/ghost atoms
region mdInternal block -12 12 -3 3 -3 3
group internal region mdInternal
neighbor 5. bin
neigh_modify every 10 delay 0 check no
# ID group atc PhysicsType ParameterFile
fix AtC internal atc two_temperature Ar_ttm.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create 4 1 1 feRegion p p p
# fix a temperature
fix_modify AtC fix temperature all 20.0
fix_modify AtC fix electron_temperature all 30.0
timestep 5.0
# output
thermo_style custom step pe temp f_AtC[2] f_AtC[4]
thermo 10
# equilibrate MD field
fix_modify AtC control thermal rescale 13
run 500
# relax
fix_modify AtC output uniform_exchangeFE 100 text
fix_modify AtC filter type exponential
fix_modify AtC filter scale 5.0e2
fix_modify AtC filter on
fix_modify AtC unfix temperature all
fix_modify AtC unfix electron_temperature all
fix_modify AtC control thermal flux
# run with FE
run 5000

238
examples/PACKAGES/eff/Auger-Adamantane/data.adamantane
View File

@ -1,119 +1,119 @@
Created by AJB
102 atoms
3 atom types
-500.0 500.0 xlo xhi
-500.0 500.0 ylo yhi
-500.0 500.0 zlo zhi
Masses
1 12.01070 # C nuclei
2 1.000794 # H nuclei
3 1.000000 # electron
Atoms
1 1 6.00 0 0.000000 0.223271 2.836177 0.99547
2 1 6.00 0 0.000000 -0.611326 1.278041 3.303884
3 1 6.00 0 0.000000 -0.645795 -1.544681 2.608294
4 1 6.00 0 0.000000 -2.509122 -1.980433 0.419368
5 1 6.00 0 0.000000 -1.674732 -0.422977 -1.889518
6 1 6.00 0 0.000000 -1.640226 2.39965 -1.193097
7 1 6.00 0 0.000000 2.018681 -2.373515 1.79163
8 1 6.00 0 0.000000 2.887596 2.006776 0.178976
9 1 6.00 0 0.000000 0.98999 -1.251962 -2.705445
10 1 6.00 0 0.000000 2.853997 -0.815965 -0.517029
11 2 1.00 0 0.000000 -3.029741 -0.739677 -3.479893
12 2 1.00 0 0.000000 -4.456466 -1.425024 1.003463
13 2 1.00 0 0.000000 -2.581253 -4.027951 -0.074795
14 2 1.00 0 0.000000 -1.252983 -2.67657 4.28622
15 2 1.00 0 0.000000 -2.524731 1.891635 3.93955
16 2 1.00 0 0.000000 0.703394 1.61118 4.917143
17 2 1.00 0 0.000000 0.247516 4.887701 1.501501
18 2 1.00 0 0.000000 2.027034 -4.428006 1.321731
19 2 1.00 0 0.000000 3.379737 -2.105382 3.378244
20 2 1.00 0 0.000000 4.790758 -1.418428 -1.109855
21 2 1.00 0 0.000000 -1.077541 3.552194 -2.865467
22 2 1.00 0 0.000000 -3.572149 3.033181 -0.63782
23 2 1.00 0 0.000000 1.599389 -0.164293 -4.40463
24 2 1.00 0 0.000000 0.980069 -3.286423 -3.255167
25 2 1.00 0 0.000000 4.264224 2.353276 1.736734
26 2 1.00 0 0.000000 3.530575 3.152347 -1.469016
27 3 0.00 1 0.332948 0.223271 2.836177 0.99547
28 3 0.00 -1 0.332948 0.223271 2.836177 0.99547
29 3 0.00 1 0.332948 -0.611326 1.278041 3.303884
30 3 0.00 -1 0.332948 -0.611326 1.278041 3.303884
31 3 0.00 1 0.332948 -0.645795 -1.544681 2.608294
32 3 0.00 -1 0.332948 -0.645795 -1.544681 2.608294
33 3 0.00 1 0.332948 -2.509122 -1.980433 0.419368
34 3 0.00 -1 0.332948 -2.509122 -1.980433 0.419368
35 3 0.00 1 0.332948 -1.674732 -0.422977 -1.889518
36 3 0.00 -1 0.332948 -1.674732 -0.422977 -1.889518
37 3 0.00 1 0.332948 -1.640226 2.39965 -1.193097
38 3 0.00 -1 0.332948 -1.640226 2.39965 -1.193097
39 3 0.00 1 0.332948 2.018681 -2.373515 1.79163
40 3 0.00 -1 0.332948 2.018681 -2.373515 1.79163
41 3 0.00 1 0.332948 2.887596 2.006776 0.178976
42 3 0.00 -1 0.332948 2.887596 2.006776 0.178976
43 3 0.00 1 0.332948 0.98999 -1.251962 -2.705445
44 3 0.00 -1 0.332948 0.98999 -1.251962 -2.705445
45 3 0.00 1 0.332948 2.853997 -0.815965 -0.517029
46 3 0.00 -1 0.332948 2.853997 -0.815965 -0.517029
47 3 0.00 1 1.258000 -0.194028 2.057109 2.149677
48 3 0.00 -1 1.258000 -0.194028 2.057109 2.149677
49 3 0.00 1 1.258000 -0.628561 -0.13332 2.956089
50 3 0.00 -1 1.258000 -0.628561 -0.13332 2.956089
51 3 0.00 1 1.258000 -1.577458 -1.762557 1.513831
52 3 0.00 -1 1.258000 -1.577458 -1.762557 1.513831
53 3 0.00 1 1.258000 -2.091927 -1.201705 -0.735075
54 3 0.00 -1 1.258000 -2.091927 -1.201705 -0.735075
55 3 0.00 1 1.258000 -0.708477 2.617913 -0.098814
56 3 0.00 -1 1.258000 -0.708477 2.617913 -0.098814
57 3 0.00 1 1.258000 -1.657479 0.988336 -1.541308
58 3 0.00 -1 1.258000 -1.657479 0.988336 -1.541308
59 3 0.00 1 1.258000 0.686443 -1.959098 2.199962
60 3 0.00 -1 1.258000 0.686443 -1.959098 2.199962
61 3 0.00 1 1.258000 1.555434 2.421476 0.587223
62 3 0.00 -1 1.258000 1.555434 2.421476 0.587223
63 3 0.00 1 1.258000 -0.342371 -0.83747 -2.297482
64 3 0.00 -1 1.258000 -0.342371 -0.83747 -2.297482
65 3 0.00 1 1.258000 2.436339 -1.59474 0.637301
66 3 0.00 -1 1.258000 2.436339 -1.59474 0.637301
67 3 0.00 1 1.258000 2.870796 0.595405 -0.169027
68 3 0.00 -1 1.258000 2.870796 0.595405 -0.169027
69 3 0.00 1 1.258000 1.921993 -1.033964 -1.611237
70 3 0.00 -1 1.258000 1.921993 -1.033964 -1.611237
71 3 0.00 1 1.543000 -2.632724 -0.646884 -3.013913
72 3 0.00 -1 1.543000 -2.632724 -0.646884 -3.013913
73 3 0.00 1 1.543000 -3.885894 -1.587759 0.832324
74 3 0.00 -1 1.543000 -3.885894 -1.587759 0.832324
75 3 0.00 1 1.543000 -2.560118 -3.428028 0.069995
76 3 0.00 -1 1.543000 -2.560118 -3.428028 0.069995
77 3 0.00 1 1.543000 -1.075077 -2.344927 3.794588
78 3 0.00 -1 1.543000 -1.075077 -2.344927 3.794588
79 3 0.00 1 1.543000 -1.964103 1.711852 3.7533
80 3 0.00 -1 1.543000 -1.964103 1.711852 3.7533
81 3 0.00 1 1.543000 0.318181 1.513571 4.444458
82 3 0.00 -1 1.543000 0.318181 1.513571 4.444458
83 3 0.00 1 1.543000 0.240412 4.286604 1.353234
84 3 0.00 -1 1.543000 0.240412 4.286604 1.353234
85 3 0.00 1 1.543000 2.024586 -3.82604 1.459412
86 3 0.00 -1 1.543000 2.024586 -3.82604 1.459412
87 3 0.00 1 1.543000 2.980948 -2.183945 2.913367
88 3 0.00 -1 1.543000 2.980948 -2.183945 2.913367
89 3 0.00 1 1.543000 4.223287 -1.241907 -0.936157
90 3 0.00 -1 1.543000 4.223287 -1.241907 -0.936157
91 3 0.00 1 1.543000 -1.242407 3.214498 -2.375463
92 3 0.00 -1 1.543000 -1.242407 3.214498 -2.375463
93 3 0.00 1 1.543000 -3.006096 2.847556 -0.800517
94 3 0.00 -1 1.543000 -3.006096 2.847556 -0.800517
95 3 0.00 1 1.543000 1.420835 -0.48298 -3.906769
96 3 0.00 -1 1.543000 1.420835 -0.48298 -3.906769
97 3 0.00 1 1.543000 0.982976 -2.690326 -3.094098
98 3 0.00 -1 1.543000 0.982976 -2.690326 -3.094098
99 3 0.00 1 1.543000 3.860872 2.251751 1.280311
100 3 0.00 -1 1.543000 3.860872 2.251751 1.280311
101 3 0.00 1 1.543000 3.342182 2.816694 -0.986155
102 3 0.00 -1 1.543000 3.342182 2.816694 -0.986155
Created by AJB
102 atoms
3 atom types
-500.0 500.0 xlo xhi
-500.0 500.0 ylo yhi
-500.0 500.0 zlo zhi
Masses
1 12.01070 # C nuclei
2 1.000794 # H nuclei
3 1.000000 # electron
Atoms
1 1 6.00 0 0.000000 0.223271 2.836177 0.99547
2 1 6.00 0 0.000000 -0.611326 1.278041 3.303884
3 1 6.00 0 0.000000 -0.645795 -1.544681 2.608294
4 1 6.00 0 0.000000 -2.509122 -1.980433 0.419368
5 1 6.00 0 0.000000 -1.674732 -0.422977 -1.889518
6 1 6.00 0 0.000000 -1.640226 2.39965 -1.193097
7 1 6.00 0 0.000000 2.018681 -2.373515 1.79163
8 1 6.00 0 0.000000 2.887596 2.006776 0.178976
9 1 6.00 0 0.000000 0.98999 -1.251962 -2.705445
10 1 6.00 0 0.000000 2.853997 -0.815965 -0.517029
11 2 1.00 0 0.000000 -3.029741 -0.739677 -3.479893
12 2 1.00 0 0.000000 -4.456466 -1.425024 1.003463
13 2 1.00 0 0.000000 -2.581253 -4.027951 -0.074795
14 2 1.00 0 0.000000 -1.252983 -2.67657 4.28622
15 2 1.00 0 0.000000 -2.524731 1.891635 3.93955
16 2 1.00 0 0.000000 0.703394 1.61118 4.917143
17 2 1.00 0 0.000000 0.247516 4.887701 1.501501
18 2 1.00 0 0.000000 2.027034 -4.428006 1.321731
19 2 1.00 0 0.000000 3.379737 -2.105382 3.378244
20 2 1.00 0 0.000000 4.790758 -1.418428 -1.109855
21 2 1.00 0 0.000000 -1.077541 3.552194 -2.865467
22 2 1.00 0 0.000000 -3.572149 3.033181 -0.63782
23 2 1.00 0 0.000000 1.599389 -0.164293 -4.40463
24 2 1.00 0 0.000000 0.980069 -3.286423 -3.255167
25 2 1.00 0 0.000000 4.264224 2.353276 1.736734
26 2 1.00 0 0.000000 3.530575 3.152347 -1.469016
27 3 0.00 1 0.332948 0.223271 2.836177 0.99547
28 3 0.00 -1 0.332948 0.223271 2.836177 0.99547
29 3 0.00 1 0.332948 -0.611326 1.278041 3.303884
30 3 0.00 -1 0.332948 -0.611326 1.278041 3.303884
31 3 0.00 1 0.332948 -0.645795 -1.544681 2.608294
32 3 0.00 -1 0.332948 -0.645795 -1.544681 2.608294
33 3 0.00 1 0.332948 -2.509122 -1.980433 0.419368
34 3 0.00 -1 0.332948 -2.509122 -1.980433 0.419368
35 3 0.00 1 0.332948 -1.674732 -0.422977 -1.889518
36 3 0.00 -1 0.332948 -1.674732 -0.422977 -1.889518
37 3 0.00 1 0.332948 -1.640226 2.39965 -1.193097
38 3 0.00 -1 0.332948 -1.640226 2.39965 -1.193097
39 3 0.00 1 0.332948 2.018681 -2.373515 1.79163
40 3 0.00 -1 0.332948 2.018681 -2.373515 1.79163
41 3 0.00 1 0.332948 2.887596 2.006776 0.178976
42 3 0.00 -1 0.332948 2.887596 2.006776 0.178976
43 3 0.00 1 0.332948 0.98999 -1.251962 -2.705445
44 3 0.00 -1 0.332948 0.98999 -1.251962 -2.705445
45 3 0.00 1 0.332948 2.853997 -0.815965 -0.517029
46 3 0.00 -1 0.332948 2.853997 -0.815965 -0.517029
47 3 0.00 1 1.258000 -0.194028 2.057109 2.149677
48 3 0.00 -1 1.258000 -0.194028 2.057109 2.149677
49 3 0.00 1 1.258000 -0.628561 -0.13332 2.956089
50 3 0.00 -1 1.258000 -0.628561 -0.13332 2.956089
51 3 0.00 1 1.258000 -1.577458 -1.762557 1.513831
52 3 0.00 -1 1.258000 -1.577458 -1.762557 1.513831
53 3 0.00 1 1.258000 -2.091927 -1.201705 -0.735075
54 3 0.00 -1 1.258000 -2.091927 -1.201705 -0.735075
55 3 0.00 1 1.258000 -0.708477 2.617913 -0.098814
56 3 0.00 -1 1.258000 -0.708477 2.617913 -0.098814
57 3 0.00 1 1.258000 -1.657479 0.988336 -1.541308
58 3 0.00 -1 1.258000 -1.657479 0.988336 -1.541308
59 3 0.00 1 1.258000 0.686443 -1.959098 2.199962
60 3 0.00 -1 1.258000 0.686443 -1.959098 2.199962
61 3 0.00 1 1.258000 1.555434 2.421476 0.587223
62 3 0.00 -1 1.258000 1.555434 2.421476 0.587223
63 3 0.00 1 1.258000 -0.342371 -0.83747 -2.297482
64 3 0.00 -1 1.258000 -0.342371 -0.83747 -2.297482
65 3 0.00 1 1.258000 2.436339 -1.59474 0.637301
66 3 0.00 -1 1.258000 2.436339 -1.59474 0.637301
67 3 0.00 1 1.258000 2.870796 0.595405 -0.169027
68 3 0.00 -1 1.258000 2.870796 0.595405 -0.169027
69 3 0.00 1 1.258000 1.921993 -1.033964 -1.611237
70 3 0.00 -1 1.258000 1.921993 -1.033964 -1.611237
71 3 0.00 1 1.543000 -2.632724 -0.646884 -3.013913
72 3 0.00 -1 1.543000 -2.632724 -0.646884 -3.013913
73 3 0.00 1 1.543000 -3.885894 -1.587759 0.832324
74 3 0.00 -1 1.543000 -3.885894 -1.587759 0.832324
75 3 0.00 1 1.543000 -2.560118 -3.428028 0.069995
76 3 0.00 -1 1.543000 -2.560118 -3.428028 0.069995
77 3 0.00 1 1.543000 -1.075077 -2.344927 3.794588
78 3 0.00 -1 1.543000 -1.075077 -2.344927 3.794588
79 3 0.00 1 1.543000 -1.964103 1.711852 3.7533
80 3 0.00 -1 1.543000 -1.964103 1.711852 3.7533
81 3 0.00 1 1.543000 0.318181 1.513571 4.444458
82 3 0.00 -1 1.543000 0.318181 1.513571 4.444458
83 3 0.00 1 1.543000 0.240412 4.286604 1.353234
84 3 0.00 -1 1.543000 0.240412 4.286604 1.353234
85 3 0.00 1 1.543000 2.024586 -3.82604 1.459412
86 3 0.00 -1 1.543000 2.024586 -3.82604 1.459412
87 3 0.00 1 1.543000 2.980948 -2.183945 2.913367
88 3 0.00 -1 1.543000 2.980948 -2.183945 2.913367
89 3 0.00 1 1.543000 4.223287 -1.241907 -0.936157
90 3 0.00 -1 1.543000 4.223287 -1.241907 -0.936157
91 3 0.00 1 1.543000 -1.242407 3.214498 -2.375463
92 3 0.00 -1 1.543000 -1.242407 3.214498 -2.375463
93 3 0.00 1 1.543000 -3.006096 2.847556 -0.800517
94 3 0.00 -1 1.543000 -3.006096 2.847556 -0.800517
95 3 0.00 1 1.543000 1.420835 -0.48298 -3.906769
96 3 0.00 -1 1.543000 1.420835 -0.48298 -3.906769
97 3 0.00 1 1.543000 0.982976 -2.690326 -3.094098
98 3 0.00 -1 1.543000 0.982976 -2.690326 -3.094098
99 3 0.00 1 1.543000 3.860872 2.251751 1.280311
100 3 0.00 -1 1.543000 3.860872 2.251751 1.280311
101 3 0.00 1 1.543000 3.342182 2.816694 -0.986155
102 3 0.00 -1 1.543000 3.342182 2.816694 -0.986155

236
examples/PACKAGES/eff/Auger-Adamantane/data.adamantane_ionized
View File

@ -1,118 +1,118 @@
Created by AJB
101 atoms
3 atom types
-50.0 50.0 xlo xhi
-50.0 50.0 ylo yhi
-50.0 50.0 zlo zhi
Masses
1 12.01070 # C nuclei
2 1.000794 # H nuclei
3 1.000000 # electron
Atoms
1 1 6.00 0 0.000000 0.224230 2.918607 1.015812
2 1 6.00 0 0.000000 -0.634450 1.314460 3.390303
3 1 6.00 0 0.000000 -0.670162 -1.590173 2.675707
4 1 6.00 0 0.000000 -2.586695 -2.037708 0.422846
5 1 6.00 0 0.000000 -1.729127 -0.435706 -1.953488
6 1 6.00 0 0.000000 -1.692867 2.468206 -1.236000
7 1 6.00 0 0.000000 2.071281 -2.442011 1.834504
8 1 6.00 0 0.000000 2.965108 2.063979 0.175607
9 1 6.00 0 0.000000 1.013015 -1.288254 -2.791737
10 1 6.00 0 0.000000 2.931847 -0.840220 -0.540904
11 2 1.00 0 0.000000 -3.237070 -0.788493 -3.724286
12 2 1.00 0 0.000000 -4.691469 -1.429253 1.056080
13 2 1.00 0 0.000000 -2.657034 -4.253233 -0.113602
14 2 1.00 0 0.000000 -1.345725 -2.850372 4.543752
15 2 1.00 0 0.000000 -2.707861 1.976434 4.071194
16 2 1.00 0 0.000000 0.794230 1.672161 5.131751
17 2 1.00 0 0.000000 0.251667 5.202465 1.579125
18 2 1.00 0 0.000000 2.074796 -4.663951 1.320307
19 2 1.00 0 0.000000 3.542471 -2.144066 3.551451
20 2 1.00 0 0.000000 5.087753 -1.511020 -1.201338
21 2 1.00 0 0.000000 -1.077021 3.711707 -3.045901
22 2 1.00 0 0.000000 -3.783389 3.148492 -0.629227
23 2 1.00 0 0.000000 1.671766 -0.104421 -4.626344
24 2 1.00 0 0.000000 0.999815 -3.491890 -3.379184
25 2 1.00 0 0.000000 4.450647 2.434018 1.865941
26 2 1.00 0 0.000000 3.654660 3.300997 -1.612081
27 3 0.00 -1 0.328405 -0.634804 1.315020 3.391634
28 3 0.00 -1 0.328107 -0.670512 -1.590826 2.676675
29 3 0.00 -1 0.328405 -2.587889 -2.038591 0.422899
30 3 0.00 -1 0.328107 -1.729909 -0.435889 -1.954405
31 3 0.00 -1 0.328405 -1.693676 2.469262 -1.236661
32 3 0.00 -1 0.328405 2.072091 -2.443067 1.835165
33 3 0.00 -1 0.328405 2.966303 2.064861 0.175553
34 3 0.00 -1 0.328405 1.013370 -1.288814 -2.793067
35 3 0.00 -1 0.328108 2.932965 -0.840567 -0.541247
36 3 0.00 -1 1.326096 -0.210743 2.123398 2.223462
37 3 0.00 -1 1.326096 -0.657351 -0.127988 3.052304
38 3 0.00 -1 1.326093 -1.646634 -1.826737 1.548546
39 3 0.00 -1 1.326095 -2.175416 -1.250260 -0.762988
40 3 0.00 -1 1.326093 -0.747076 2.708081 -0.120938
41 3 0.00 -1 1.326095 -1.722464 1.033139 -1.603613
42 3 0.00 -1 1.326092 0.713852 -2.031645 2.263933
43 3 0.00 -1 1.326092 1.613424 2.503259 0.594420
44 3 0.00 -1 1.326098 -0.351222 -0.870483 -2.392027
45 3 0.00 -1 1.326100 2.512477 -1.657113 0.657756
46 3 0.00 -1 1.326099 2.965428 0.626295 -0.182887
47 3 0.00 -1 1.326101 1.976186 -1.072464 -1.686660
48 3 0.00 -1 1.603792 -2.952851 -0.722000 -3.390526
49 3 0.00 -1 1.558563 -4.265445 -1.534526 0.932369
50 3 0.00 -1 1.558562 -2.625986 -3.810249 -0.010226
51 3 0.00 -1 1.603792 -1.218394 -2.612849 4.191661
52 3 0.00 -1 1.558507 -2.300135 1.839753 3.919625
53 3 0.00 -1 1.558620 0.522041 1.594565 4.774310
54 3 0.00 -1 1.603792 0.246496 4.772002 1.472951
55 3 0.00 -1 1.558582 2.062319 -4.217199 1.410516
56 3 0.00 -1 1.558537 3.245048 -2.186529 3.208486
57 3 0.00 -1 1.603791 4.681408 -1.384588 -1.076860
58 3 0.00 -1 1.558565 -1.184793 3.454906 -2.684898
59 3 0.00 -1 1.558559 -3.365733 3.001032 -0.737405
60 3 0.00 -1 1.558551 1.538708 -0.326106 -4.250794
61 3 0.00 -1 1.558563 0.997214 -3.055912 -3.245768
62 3 0.00 -1 1.558524 4.144833 2.349324 1.538532
63 3 0.00 -1 1.558594 3.503398 3.047996 -1.264247
64 3 0.00 1 0.328107 0.224244 2.919790 1.016104
65 3 0.00 1 0.328405 -0.634804 1.315020 3.391634
66 3 0.00 1 0.328107 -0.670512 -1.590826 2.676675
67 3 0.00 1 0.328405 -2.587889 -2.038591 0.422899
68 3 0.00 1 0.328107 -1.729909 -0.435889 -1.954405
69 3 0.00 1 0.328405 -1.693676 2.469262 -1.236661
70 3 0.00 1 0.328405 2.072091 -2.443067 1.835165
71 3 0.00 1 0.328405 2.966303 2.064861 0.175553
72 3 0.00 1 0.328405 1.013370 -1.288814 -2.793067
73 3 0.00 1 0.328108 2.932965 -0.840567 -0.541247
74 3 0.00 1 1.326096 -0.210743 2.123398 2.223462
75 3 0.00 1 1.326096 -0.657351 -0.127988 3.052304
76 3 0.00 1 1.326093 -1.646634 -1.826737 1.548546
77 3 0.00 1 1.326094 -2.175416 -1.250259 -0.762988
78 3 0.00 1 1.326094 -0.747076 2.708081 -0.120938
79 3 0.00 1 1.326096 -1.722464 1.033139 -1.603613
80 3 0.00 1 1.326092 0.713852 -2.031645 2.263933
81 3 0.00 1 1.326092 1.613424 2.503259 0.594420
82 3 0.00 1 1.326098 -0.351222 -0.870483 -2.392027
83 3 0.00 1 1.326100 2.512477 -1.657113 0.657756
84 3 0.00 1 1.326099 2.965428 0.626295 -0.182887
85 3 0.00 1 1.326101 1.976186 -1.072464 -1.686660
86 3 0.00 1 1.603792 -2.952851 -0.722000 -3.390526
87 3 0.00 1 1.558563 -4.265445 -1.534526 0.932369
88 3 0.00 1 1.558562 -2.625986 -3.810249 -0.010226
89 3 0.00 1 1.603792 -1.218394 -2.612849 4.191661
90 3 0.00 1 1.558507 -2.300135 1.839753 3.919625
91 3 0.00 1 1.558620 0.522041 1.594565 4.774310
92 3 0.00 1 1.603792 0.246496 4.772002 1.472951
93 3 0.00 1 1.558582 2.062319 -4.217199 1.410516
94 3 0.00 1 1.558537 3.245048 -2.186529 3.208486
95 3 0.00 1 1.603791 4.681408 -1.384588 -1.076860
96 3 0.00 1 1.558565 -1.184793 3.454906 -2.684898
97 3 0.00 1 1.558559 -3.365733 3.001032 -0.737405
98 3 0.00 1 1.558551 1.538708 -0.326106 -4.250794
99 3 0.00 1 1.558563 0.997214 -3.055912 -3.245768
100 3 0.00 1 1.558524 4.144833 2.349324 1.538532
101 3 0.00 1 1.558594 3.503398 3.047996 -1.264247
Created by AJB
101 atoms
3 atom types
-50.0 50.0 xlo xhi
-50.0 50.0 ylo yhi
-50.0 50.0 zlo zhi
Masses
1 12.01070 # C nuclei
2 1.000794 # H nuclei
3 1.000000 # electron
Atoms
1 1 6.00 0 0.000000 0.224230 2.918607 1.015812
2 1 6.00 0 0.000000 -0.634450 1.314460 3.390303
3 1 6.00 0 0.000000 -0.670162 -1.590173 2.675707
4 1 6.00 0 0.000000 -2.586695 -2.037708 0.422846
5 1 6.00 0 0.000000 -1.729127 -0.435706 -1.953488
6 1 6.00 0 0.000000 -1.692867 2.468206 -1.236000
7 1 6.00 0 0.000000 2.071281 -2.442011 1.834504
8 1 6.00 0 0.000000 2.965108 2.063979 0.175607
9 1 6.00 0 0.000000 1.013015 -1.288254 -2.791737
10 1 6.00 0 0.000000 2.931847 -0.840220 -0.540904
11 2 1.00 0 0.000000 -3.237070 -0.788493 -3.724286
12 2 1.00 0 0.000000 -4.691469 -1.429253 1.056080
13 2 1.00 0 0.000000 -2.657034 -4.253233 -0.113602
14 2 1.00 0 0.000000 -1.345725 -2.850372 4.543752
15 2 1.00 0 0.000000 -2.707861 1.976434 4.071194
16 2 1.00 0 0.000000 0.794230 1.672161 5.131751
17 2 1.00 0 0.000000 0.251667 5.202465 1.579125
18 2 1.00 0 0.000000 2.074796 -4.663951 1.320307
19 2 1.00 0 0.000000 3.542471 -2.144066 3.551451
20 2 1.00 0 0.000000 5.087753 -1.511020 -1.201338
21 2 1.00 0 0.000000 -1.077021 3.711707 -3.045901
22 2 1.00 0 0.000000 -3.783389 3.148492 -0.629227
23 2 1.00 0 0.000000 1.671766 -0.104421 -4.626344
24 2 1.00 0 0.000000 0.999815 -3.491890 -3.379184
25 2 1.00 0 0.000000 4.450647 2.434018 1.865941
26 2 1.00 0 0.000000 3.654660 3.300997 -1.612081
27 3 0.00 -1 0.328405 -0.634804 1.315020 3.391634
28 3 0.00 -1 0.328107 -0.670512 -1.590826 2.676675
29 3 0.00 -1 0.328405 -2.587889 -2.038591 0.422899
30 3 0.00 -1 0.328107 -1.729909 -0.435889 -1.954405
31 3 0.00 -1 0.328405 -1.693676 2.469262 -1.236661
32 3 0.00 -1 0.328405 2.072091 -2.443067 1.835165
33 3 0.00 -1 0.328405 2.966303 2.064861 0.175553
34 3 0.00 -1 0.328405 1.013370 -1.288814 -2.793067
35 3 0.00 -1 0.328108 2.932965 -0.840567 -0.541247
36 3 0.00 -1 1.326096 -0.210743 2.123398 2.223462
37 3 0.00 -1 1.326096 -0.657351 -0.127988 3.052304
38 3 0.00 -1 1.326093 -1.646634 -1.826737 1.548546
39 3 0.00 -1 1.326095 -2.175416 -1.250260 -0.762988
40 3 0.00 -1 1.326093 -0.747076 2.708081 -0.120938
41 3 0.00 -1 1.326095 -1.722464 1.033139 -1.603613
42 3 0.00 -1 1.326092 0.713852 -2.031645 2.263933
43 3 0.00 -1 1.326092 1.613424 2.503259 0.594420
44 3 0.00 -1 1.326098 -0.351222 -0.870483 -2.392027
45 3 0.00 -1 1.326100 2.512477 -1.657113 0.657756
46 3 0.00 -1 1.326099 2.965428 0.626295 -0.182887
47 3 0.00 -1 1.326101 1.976186 -1.072464 -1.686660
48 3 0.00 -1 1.603792 -2.952851 -0.722000 -3.390526
49 3 0.00 -1 1.558563 -4.265445 -1.534526 0.932369
50 3 0.00 -1 1.558562 -2.625986 -3.810249 -0.010226
51 3 0.00 -1 1.603792 -1.218394 -2.612849 4.191661
52 3 0.00 -1 1.558507 -2.300135 1.839753 3.919625
53 3 0.00 -1 1.558620 0.522041 1.594565 4.774310
54 3 0.00 -1 1.603792 0.246496 4.772002 1.472951
55 3 0.00 -1 1.558582 2.062319 -4.217199 1.410516
56 3 0.00 -1 1.558537 3.245048 -2.186529 3.208486
57 3 0.00 -1 1.603791 4.681408 -1.384588 -1.076860
58 3 0.00 -1 1.558565 -1.184793 3.454906 -2.684898
59 3 0.00 -1 1.558559 -3.365733 3.001032 -0.737405
60 3 0.00 -1 1.558551 1.538708 -0.326106 -4.250794
61 3 0.00 -1 1.558563 0.997214 -3.055912 -3.245768
62 3 0.00 -1 1.558524 4.144833 2.349324 1.538532
63 3 0.00 -1 1.558594 3.503398 3.047996 -1.264247
64 3 0.00 1 0.328107 0.224244 2.919790 1.016104
65 3 0.00 1 0.328405 -0.634804 1.315020 3.391634
66 3 0.00 1 0.328107 -0.670512 -1.590826 2.676675
67 3 0.00 1 0.328405 -2.587889 -2.038591 0.422899
68 3 0.00 1 0.328107 -1.729909 -0.435889 -1.954405
69 3 0.00 1 0.328405 -1.693676 2.469262 -1.236661
70 3 0.00 1 0.328405 2.072091 -2.443067 1.835165
71 3 0.00 1 0.328405 2.966303 2.064861 0.175553
72 3 0.00 1 0.328405 1.013370 -1.288814 -2.793067
73 3 0.00 1 0.328108 2.932965 -0.840567 -0.541247
74 3 0.00 1 1.326096 -0.210743 2.123398 2.223462
75 3 0.00 1 1.326096 -0.657351 -0.127988 3.052304
76 3 0.00 1 1.326093 -1.646634 -1.826737 1.548546
77 3 0.00 1 1.326094 -2.175416 -1.250259 -0.762988
78 3 0.00 1 1.326094 -0.747076 2.708081 -0.120938
79 3 0.00 1 1.326096 -1.722464 1.033139 -1.603613
80 3 0.00 1 1.326092 0.713852 -2.031645 2.263933
81 3 0.00 1 1.326092 1.613424 2.503259 0.594420
82 3 0.00 1 1.326098 -0.351222 -0.870483 -2.392027
83 3 0.00 1 1.326100 2.512477 -1.657113 0.657756
84 3 0.00 1 1.326099 2.965428 0.626295 -0.182887
85 3 0.00 1 1.326101 1.976186 -1.072464 -1.686660
86 3 0.00 1 1.603792 -2.952851 -0.722000 -3.390526
87 3 0.00 1 1.558563 -4.265445 -1.534526 0.932369
88 3 0.00 1 1.558562 -2.625986 -3.810249 -0.010226
89 3 0.00 1 1.603792 -1.218394 -2.612849 4.191661
90 3 0.00 1 1.558507 -2.300135 1.839753 3.919625
91 3 0.00 1 1.558620 0.522041 1.594565 4.774310
92 3 0.00 1 1.603792 0.246496 4.772002 1.472951
93 3 0.00 1 1.558582 2.062319 -4.217199 1.410516
94 3 0.00 1 1.558537 3.245048 -2.186529 3.208486
95 3 0.00 1 1.603791 4.681408 -1.384588 -1.076860
96 3 0.00 1 1.558565 -1.184793 3.454906 -2.684898
97 3 0.00 1 1.558559 -3.365733 3.001032 -0.737405
98 3 0.00 1 1.558551 1.538708 -0.326106 -4.250794
99 3 0.00 1 1.558563 0.997214 -3.055912 -3.245768
100 3 0.00 1 1.558524 4.144833 2.349324 1.538532
101 3 0.00 1 1.558594 3.503398 3.047996 -1.264247

6944
examples/PACKAGES/eff/Li-dendritic/data.Li-dendritic
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File diff suppressed because it is too large Load Diff

12012
examples/PACKAGES/entropy/Na_MendelevM_2014.eam.fs
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File diff suppressed because it is too large Load Diff

126
examples/PACKAGES/interlayer/lebedeva/2particles.in
View File

@ -1,63 +1,63 @@
# After running LAMMPS with this input script a number of dump files is created.
# To extract the data from there I used grep script:
# grep '^2 ' *cfg > LammpsResult.dat
# After that after removing some text from LammpsResult.dat,
# the data can be viewed by lebedeva00.plot
#
# Author: Zbigniew Koziol, National Center for Nuclear Research, Poland
# Email: softquake@gmail.com
# ---------- Start simulation ---------------------
clear
units metal
dimension 3
boundary f f f
atom_style atomic
# ========================== Create Atomistic Structure ===========================
region whole block 0 20 0 20 0 10
create_box 2 whole
read_data 2particles.dat add append
region graphite block INF INF INF INF 0 10 units box
group graphite type 1 2
group graphene1 type 1
group graphene2 type 2
pair_style hybrid/overlay lebedeva/z 20
pair_coeff * * none
pair_coeff 1 2 lebedeva/z CC.Lebedeva C C
mass 1 12.01 # Carbon
mass 2 12.01 # Carbon
neighbor 0.3 bin
neigh_modify delay 1 check yes
compute peratom all pe/atom
dump 1 all custom 1 dump_lebedeva_*.cfg id x y z c_peratom fx fy fz
dump_modify 1 pad 3
thermo 10
thermo_style custom step pe press temp
thermo_modify lost ignore
label STEP_LOOP
variable MYSTEP loop 0 400 pad # in degrees
variable DELTA_STEP equal 0.05
displace_atoms graphene2 move ${DELTA_STEP} ${DELTA_STEP} 0
run 1
next MYSTEP
jump SELF STEP_LOOP
print "all done"
# After running LAMMPS with this input script a number of dump files is created.
# To extract the data from there I used grep script:
# grep '^2 ' *cfg > LammpsResult.dat
# After that after removing some text from LammpsResult.dat,
# the data can be viewed by lebedeva00.plot
#
# Author: Zbigniew Koziol, National Center for Nuclear Research, Poland
# Email: softquake@gmail.com
# ---------- Start simulation ---------------------
clear
units metal
dimension 3
boundary f f f
atom_style atomic
# ========================== Create Atomistic Structure ===========================
region whole block 0 20 0 20 0 10
create_box 2 whole
read_data 2particles.dat add append
region graphite block INF INF INF INF 0 10 units box
group graphite type 1 2
group graphene1 type 1
group graphene2 type 2
pair_style hybrid/overlay lebedeva/z 20
pair_coeff * * none
pair_coeff 1 2 lebedeva/z CC.Lebedeva C C
mass 1 12.01 # Carbon
mass 2 12.01 # Carbon
neighbor 0.3 bin
neigh_modify delay 1 check yes
compute peratom all pe/atom
dump 1 all custom 1 dump_lebedeva_*.cfg id x y z c_peratom fx fy fz
dump_modify 1 pad 3
thermo 10
thermo_style custom step pe press temp
thermo_modify lost ignore
label STEP_LOOP
variable MYSTEP loop 0 400 pad # in degrees
variable DELTA_STEP equal 0.05
displace_atoms graphene2 move ${DELTA_STEP} ${DELTA_STEP} 0
run 1
next MYSTEP
jump SELF STEP_LOOP
print "all done"

31
examples/PACKAGES/latboltz/confined_colloid/in.confined_colloids
View File

@ -6,10 +6,10 @@
# 280 x 280 x 101 lattice-Boltzmann grid sites. #
# #
# This simulation is used to illustrate the simulation time of a realistic #
# implementation of the lb_fluid fix. #
# implementation of the lb/fluid fix. #
# The data file "confinedcolloids.dat" is quite large and so is not #
# included here. It can be obtained from: #
# http://www.apmaths.uwo.ca/~cdennist/confinedcolloids.dat.gz #
# http://publish.uwo.ca/~cdennist/confinedcolloids.dat.gz #
# #
# Sample output from this run can be found in the file: #
# results64.out #
@ -19,7 +19,10 @@ units micro
dimension 3
boundary p p f
atom_style molecular
read_data confinedcolloids.dat
# try to download
shell test -f confinedcolloids.dat.gz || curl -L -o confinedcolloids.dat.gz http://publish.uwo.ca/~cdennist/confinedcolloids.dat.gz
read_data confinedcolloids.dat.gz
mass * 0.00010287
@ -62,23 +65,18 @@ pair_coeff * * 0.0 0.0 1.572
pair_coeff 1 1 10.0 1.400492785 1.572
pair_modify shift yes
timestep 0.0006
timestep 0.001
#---------------------------------------------------------------------------
# Create a lattice-Boltzmann fluid covering the simulation domain.
# This fluid feels a force due to the particles specified through FluidAtoms
# (however, this fix does not explicitly apply a force back on to these
# particles...this is accomplished through the use of the viscous_lb fix).
# Use the standard LB integration scheme, a fluid density = 1.0,
# fluid viscosity = 1.0, lattice spacing dx=0.06, and mass unit, dm=0.00003.
# Use the default method to calculate the interaction force between the
# particles and the fluid. This calculation makes use of the surface area
# of the composite object represented by each particle node. Since this is
# not equal to dx*dx, it is input through the setArea keyword (i.e.
# particles of type 2 correspond to a surface area of 0.0018337299).
# Implement walls moving at speeds of 20.0 in opposite directions.
# particles...this is accomplished through the use of the lb/viscous fix).
# Use a fluid density = 1.0, fluid viscosity = 1.0, (water at STP) and a
# lattice spacing dx=0.06.
# Implement top/bottomw walls moving at speeds of 20.0 in opposite directions
#----------------------------------------------------------------------------
fix 1 FluidAtoms lb/fluid 1 1 1.0 1.0 dx 0.06 dm 0.00003 setArea 2 0.0018337299 zwall_velocity -20.0 20.0
fix 1 FluidAtoms lb/fluid 1 1.0 1.0 dx 0.06 zwall_velocity -20.0 20.0
#----------------------------------------------------------------------------
# Apply the force due to the fluid onto the FluidAtoms particles (again,
@ -105,4 +103,7 @@ fix walllo ForceAtoms wall/lj126 zlo 0.0 20.0 0.8071542386 0.906 units box
#dump ParticleTracking ForceAtoms custom 50 test.track id mol x y z vx vy vz
run 400
thermo 50
#run 400
run 100

190
examples/PACKAGES/latboltz/confined_colloid/log.09Mar22.confined_colloids.g++.4 Normal file
View File

@ -0,0 +1,190 @@
LAMMPS (17 Feb 2022)
#===========================================================================#
# System of colloidal particles under shear. #
# #
# Run consists of 10x12x4 particles, each composed of 3613 particle nodes #
# (3612 particles forming a spherical shell, and 1 central particle). #
# 280 x 280 x 101 lattice-Boltzmann grid sites. #
# #
# This simulation is used to illustrate the simulation time of a realistic #
# implementation of the lb/fluid fix. #
# The data file "confinedcolloids.dat" is quite large and so is not #
# included here. It can be obtained from: #
# http://publish.uwo.ca/~cdennist/confinedcolloids.dat.gz #
# #
# Sample output from this run can be found in the file: #
# results64.out #
#===========================================================================#
units micro
dimension 3
boundary p p f
atom_style molecular
read_data confinedcolloids.dat
Reading data file ...
orthogonal box = (0 0 0) to (16.8 16.8 6)
2 by 2 by 1 MPI processor grid
reading atoms ...
1734240 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.372 seconds
read_data CPU = 34.950 seconds
mass * 0.00010287
#----------------------------------------------------------------------------
# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing
# to ensure that the particles belonging to a given processor remain inside
# that processors lattice-Boltzmann grid.
# The arguments for neigh_modify have been set to "delay 0 every 1", again
# to ensure that the particles belonging to a given processor remain inside
# that processors lattice-Boltzmann grid. However, these values can likely
# be somewhat increased without issue. If a problem does arise (a particle
# is outside of its processors LB grid) an error message is printed and
# the simulation is terminated.
#----------------------------------------------------------------------------
neighbor 0.03 bin
neigh_modify delay 0 every 1
neigh_modify exclude type 2 2
neigh_modify exclude type 2 1
#----------------------------------------------------------------------------
# ForceAtoms are the particles at the center of each colloidal object which
# do not interact with the fluid, but are used to implement the hard-sphere
# interactions.
#----------------------------------------------------------------------------
group ForceAtoms type 1
480 atoms in group ForceAtoms
#----------------------------------------------------------------------------
# FluidAtoms are the particles representing the surface of the colloidal
# object which do interact with the fluid.
#----------------------------------------------------------------------------
group FluidAtoms type 2
1733760 atoms in group FluidAtoms
#----------------------------------------------------------------------------
# Implement a hard-sphere interaction between the particles at the center of
# each colloidal object (use a truncated and shifted Lennard-Jones
# potential).
#----------------------------------------------------------------------------
pair_style lj/cut 1.572
pair_coeff * * 0.0 0.0 1.572
pair_coeff 1 1 10.0 1.400492785 1.572
pair_modify shift yes
timestep 0.001
#---------------------------------------------------------------------------
# Create a lattice-Boltzmann fluid covering the simulation domain.
# This fluid feels a force due to the particles specified through FluidAtoms
# (however, this fix does not explicitly apply a force back on to these
# particles...this is accomplished through the use of the lb/viscous fix).
# Use a fluid density = 1.0, fluid viscosity = 1.0, (water at STP) and a
# lattice spacing dx=0.06.
# Implement top/bottomw walls moving at speeds of 20.0 in opposite directions
#----------------------------------------------------------------------------
fix 1 FluidAtoms lb/fluid 1 1.0 1.0 dx 0.06 zwall_velocity -20.0 20.0
Using a lattice-Boltzmann grid of 280 by 280 by 101 total grid points. (../fix_lb_fluid.cpp:486)
Local Grid Geometry created. (../fix_lb_fluid.cpp:1018)
#----------------------------------------------------------------------------
# Apply the force due to the fluid onto the FluidAtoms particles (again,
# these atoms represent the surface of the colloidal object, which should
# interact with the fluid).
#----------------------------------------------------------------------------
fix 2 FluidAtoms lb/viscous
#----------------------------------------------------------------------------
# Each colloidal object (spherical shell of particles and central particle)
# is specified as a separate molecule in the confinedcolloids.dat data
# file. Integrate the motion of each of these sets of particles as rigid
# objects which move and rotate together.
#----------------------------------------------------------------------------
fix 3 all rigid molecule
480 rigid bodies with 1734240 atoms
#----------------------------------------------------------------------------
# Implement a repulsive interaction between the ForceAtoms particles, and the
# upper and lower z-walls. (A truncated and shifted Lennard-Jones potential
# is used).
#----------------------------------------------------------------------------
fix wallhi ForceAtoms wall/lj126 zhi 5.88 20.0 0.8071542386 0.906 units box
fix walllo ForceAtoms wall/lj126 zlo 0.0 20.0 0.8071542386 0.906 units box
#dump ParticleTracking ForceAtoms custom 50 test.track id mol x y z vx vy vz
thermo 50
#run 400
run 100
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- fix lb/fluid command:
@Article{Denniston et al.,
author = {C. Denniston, N. Afrasiabian, M.G. Cole-Andre,F.E. Mackay, S.T.T. Ollila, T. Whitehead},
title = {LAMMPS lb/fluid fix version 2: Improved Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid}, journal = {Comp.~Phys.~Comm.},
year = 2022,
volume = 275,
pages = {108318}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.602
ghost atom cutoff = 1.602
binsize = 0.801, bins = 21 21 8
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 373.3 | 373.3 | 373.3 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 0 0 0 0
50 4511970.8 0 0 89.610701 0.21526205
100 16113793 0 0 320.0305 -0.54714356
Loop time of 2168.87 on 4 procs for 100 steps with 1734240 atoms
Performance: 3983.646 ns/day, 0.006 hours/ns, 0.046 timesteps/s
99.9% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.67377 | 0.70143 | 0.72779 | 2.5 | 0.03
Bond | 4.19e-05 | 6.0825e-05 | 7.85e-05 | 0.0 | 0.00
Neigh | 1978.7 | 1982.4 | 1985.9 | 6.3 | 91.40
Comm | 9.4132 | 12.886 | 16.538 | 78.3 | 0.59
Output | 0.0089264 | 0.016853 | 0.024638 | 4.3 | 0.00
Modify | 171.19 | 171.23 | 171.27 | 0.3 | 7.89
Other | | 1.598 | | | 0.07
Nlocal: 433560 ave 433560 max 433560 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 397888 ave 397888 max 397888 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 60 ave 60 max 60 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 240
Ave neighs/atom = 0.00013838915
Ave special neighs/atom = 0
Neighbor list builds = 16
Dangerous builds = 0
Total wall time: 0:39:00

41
examples/PACKAGES/latboltz/confined_colloid/results64.out
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@ -1,41 +0,0 @@
LAMMPS (22 Feb 2013)
Scanning data file ...
Reading data file ...
orthogonal box = (0 0 0) to (16.8 16.8 6)
4 by 8 by 2 MPI processor grid
1734240 atoms
Finding 1-2 1-3 1-4 neighbors ...
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
480 atoms in group ForceAtoms
1733760 atoms in group FluidAtoms
Using a lattice-Boltzmann grid of 280 by 280 by 101 total grid points. (fix_lb_fluid.cpp:341)
480 rigid bodies with 1734240 atoms
Setting up run ...
Memory usage per processor = 79.5765 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 0 0 0 0
400 65143387 608.21941 0 1902.0097 4.5858406
Loop time of 503.932 on 64 procs for 400 steps with 1734240 atoms
Pair time (%) = 0.151149 (0.0299939)
Bond time (%) = 0.000111468 (2.21197e-05)
Neigh time (%) = 308.546 (61.2278)
Comm time (%) = 88.6413 (17.5899)
Outpt time (%) = 0.00124746 (0.000247546)
Other time (%) = 106.592 (21.152)
Nlocal: 27097.5 ave 27415 max 26825 min
Histogram: 8 0 12 12 8 0 8 4 8 4
Nghost: 159582 ave 161567 max 158145 min
Histogram: 32 0 0 0 0 4 12 0 0 16
Neighs: 3.75 ave 6 max 2 min
Histogram: 16 0 16 0 0 16 0 0 0 16
Total # of neighbors = 240
Ave neighs/atom = 0.000138389
Ave special neighs/atom = 0
Neighbor list builds = 68
Dangerous builds = 0

207
examples/PACKAGES/latboltz/diffusingsphere/in.trapnewsphere Normal file
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#===========================================================================#
# Large colloidal sphere difusing around. #
# #
# In the first stage, the sphere is constructed by condensing atoms onto #
# the surface of a spherical region. There are a flag you can change to #
# either bond atoms into a spherical shell or integrate them as a rigid body#
# #
# To run this example, LAMMPS needs to be compiled with a the following #
# packages: RIGID, LATBOTLZ #
# #
# If you uncomment the "dump..." line, sample output from this run #
# can be found in the file: #
# 'dump.trapnewsphere.lammpstrj' #
# and viewed using, e.g., the VMD software. #
# #
#===========================================================================#
units nano
dimension 3
boundary p p p
region mybox block -24 24 -24 24 -24 24
# flag indicating whether sphere will be bonded or rigid, 0 or 1
variable is_bonded equal 0
# timestep for the LB run (setup uses different timesteps)
variable tstep equal 0.00025
# number of stencil points in any direction. could be 2, 3, or 4
variable stpts equal 2
if "${is_bonded} == 1" then &
"create_box 1 mybox bond/types 10 extra/bond/per/atom 12" &
else &
"create_box 1 mybox"
#----------------------------------------------------------------------------
# Create a spherical region and then fill it with atoms
#----------------------------------------------------------------------------
region mysphereinside sphere 0 0 0 4.0
#variable n_nodes equal 216
variable n_nodes equal 284
create_atoms 1 random ${n_nodes} 1234 mysphereinside units box
pair_style soft 1.0
pair_coeff * * 0.0
variable prefactor equal ramp(0,30)
fix 1 all adapt 1 pair soft a * * v_prefactor
mass * 1.0
#----------------------------------------------------------------------------
# Set up and do an initial run to push the atoms apart as the random creation
# could have them overlapping too much for stability.
#----------------------------------------------------------------------------
timestep 0.002
# Define sphere where minimum of wall potential is at r=4 so
# regions is 4 + (2/5)^(1/6) sigma
region mysphere sphere 0 0 0 5.28756
fix wall all wall/region mysphere lj93 15.0 1.5 5.28
fix 2 all nve
#dump mydump all atom 10000 dump.trapnewsphere.lammpstrj
run 20000
unfix wall
fix wall all wall/region mysphere lj93 50.0 1.5 5.68
unfix 1
#----------------------------------------------------------------------------
# Do a run to condense the atoms onto the spherical surface and anneal them
# so they will be orderly aranged onto a semi-triangular mesh on the sphere
#----------------------------------------------------------------------------
pair_style lj/cut 1.68359
#pair_coeff * * 0.002 1.5 1.68369
pair_coeff * * 0.0005 1.5 1.68369
fix 3 all langevin 1.5 0.01 100.0 5678
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
comm_modify cutoff 2.5
run 500000
minimize 0.0 1.0e-8 1000 100000
unfix wall
unfix 2
unfix 3
#----------------------------------------------------------------------------
# If bonded, bond the atoms together at something close to their current
# configuration
#----------------------------------------------------------------------------
variable total_mass equal 0.002398
variable node_mass equal "v_total_mass / v_n_nodes"
mass * ${node_mass}
if "${is_bonded} == 1" then &
"bond_style harmonic" &
"bond_coeff 1 25.0 0.869333" &
"bond_coeff 2 25.0 0.948" &
"bond_coeff 3 25.0 1.026666" &
"bond_coeff 4 25.0 1.105333" &
"bond_coeff 5 25.0 1.184" &
"bond_coeff 6 25.0 1.262666" &
"bond_coeff 7 25.0 1.341333" &
"bond_coeff 8 25.0 1.42" &
"bond_coeff 9 25.0 1.498666" &
"bond_coeff 10 25.0 1.577333" &
"create_bonds many all all 1 0.83 0.908666" &
"create_bonds many all all 2 0.908667 0.987333" &
"create_bonds many all all 3 0.987334 1.066" &
"create_bonds many all all 4 1.066001 1.144666" &
"create_bonds many all all 5 1.144667 1.223333" &
"create_bonds many all all 6 1.223334 1.302" &
"create_bonds many all all 7 1.302001 1.380666" &
"create_bonds many all all 8 1.380667 1.459333" &
"create_bonds many all all 9 1.459334 1.538" &
"create_bonds many all all 10 1.538001 1.61667"
if "${is_bonded} == 1" then &
"pair_style lj/cut 5.05108" &
"pair_coeff * * 0.5 4.5" &
else &
"pair_style lj/cut 1.2" &
"pair_coeff * * 0.0 0.0"
timestep ${tstep}
#----------------------------------------------------------------------------
# You could uncomment the following lines and then turn off the noise and
# comment out the trap (following) to instead do a run that drags the
# sphere through the fluid to measure the drag force.
#----------------------------------------------------------------------------
#variable total_force equal 8.0
#variable node_force equal "v_total_force / v_n_nodes"
#variable oscillateY equal cos(step*0.0005)/(-0.004+50*v_tstep)/v_n_nodes
#variable oscillateZ equal cos(step*0.0003)/(-0.004+50*v_tstep)/v_n_nodes
#fix drag all addforce ${node_force} v_oscillateY v_oscillateZ
#----------------------------------------------------------------------------
# Trap the sphere along x (could be done experimentally using optical
# tweezers.
#----------------------------------------------------------------------------
variable fx atom -x*4.14195/284.0
fix trap all addforce v_fx 0.0 0.0 # needs to go before fix lb/fluid and lb/viscous
#----------------------------------------------------------------------------
# Set up the lb/fluid parameters for water and at a temperature of 300 K. If
# the colloid is integrated with the rigid fix, the dof are not
# automatically calculated correctly but as this would then be a rigid
# sphere it is clear it should have 6 degrees of freedom.
#----------------------------------------------------------------------------
if "${is_bonded} == 1" then &
"fix FL all lb/fluid 1 1.0 0.0009982071 stencil ${stpts} dx 1.2 noise 300.0 181920" &
else &
"fix FL all lb/fluid 1 1.0 0.0009982071 stencil ${stpts} dx 1.2 noise 300.0 181920 dof 6"
fix 2 all lb/viscous
if "${is_bonded} == 1" then &
"fix 3 all nve" &
else &
"fix 3 all rigid group 1 all"
#equilibration run
run 10000
unfix 2
unfix FL
# data gathering run
reset_timestep 0
if "${is_bonded} == 1" then &
"fix FL all lb/fluid 1 1.0 0.0009982071 stencil ${stpts} dx 1.2 noise 300.0 181920" &
else &
"fix FL all lb/fluid 1 1.0 0.0009982071 stencil ${stpts} dx 1.2 noise 300.0 181920 dof 6"
fix 2 all lb/viscous
#----------------------------------------------------------------------------
# Create variables containing the positions/velocity of the colloids center
# of mass.
#----------------------------------------------------------------------------
variable cmx equal xcm(all,x)
variable cmy equal xcm(all,y)
variable cmz equal xcm(all,z)
variable vcmx equal vcm(all,x)
variable vcmy equal vcm(all,y)
variable vcmz equal vcm(all,z)
if "${is_bonded} == 1" then &
"variable comdatafile string trap_nb${n_nodes}_st${stpts}_dt${tstep}.out" &
else &
"variable comdatafile string trap_n${n_nodes}_st${stpts}_dt${tstep}.out"
#fix printCM all print 10 "$(step) $(f_FL) ${cmx} ${cmy} ${cmz} ${vcmx} ${vcmy} ${vcmz}" file ${comdatafile} screen no
run 10000
#run 25000000

388
examples/PACKAGES/latboltz/diffusingsphere/log.09Mar22.trapnewsphere.g++.4 Normal file
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LAMMPS (17 Feb 2022)
#===========================================================================#
# Large colloidal sphere difusing around. #
# #
# In the first stage, the sphere is constructed by condensing atoms onto #
# the surface of a spherical region. There are a flag you can change to #
# either bond atoms into a spherical shell or integrate them as a rigid body#
# #
# To run this example, LAMMPS needs to be compiled with a the following #
# packages: RIGID, LATBOTLZ #
# #
# If you uncomment the "dump..." line, sample output from this run #
# can be found in the file: #
# 'dump.trapnewsphere.lammpstrj' #
# and viewed using, e.g., the VMD software. #
# #
#===========================================================================#
units nano
dimension 3
boundary p p p
region mybox block -24 24 -24 24 -24 24
# flag indicating whether sphere will be bonded or rigid, 0 or 1
variable is_bonded equal 0
# timestep for the LB run (setup uses different timesteps)
variable tstep equal 0.00025
# number of stencil points in any direction. could be 2, 3, or 4
variable stpts equal 2
if "${is_bonded} == 1" then "create_box 1 mybox bond/types 10 extra/bond/per/atom 12" else "create_box 1 mybox"
create_box 1 mybox
Created orthogonal box = (-24 -24 -24) to (24 24 24)
1 by 2 by 2 MPI processor grid
#----------------------------------------------------------------------------
# Create a spherical region and then fill it with atoms
#----------------------------------------------------------------------------
region mysphereinside sphere 0 0 0 4.0
#variable n_nodes equal 216
variable n_nodes equal 284
create_atoms 1 random ${n_nodes} 1234 mysphereinside units box
create_atoms 1 random 284 1234 mysphereinside units box
Created 284 atoms
using box units in orthogonal box = (-24 -24 -24) to (24 24 24)
create_atoms CPU = 0.001 seconds
pair_style soft 1.0
pair_coeff * * 0.0
variable prefactor equal ramp(0,30)
fix 1 all adapt 1 pair soft a * * v_prefactor
mass * 1.0
#----------------------------------------------------------------------------
# Set up and do an initial run to push the atoms apart as the random creation
# could have them overlapping too much for stability.
#----------------------------------------------------------------------------
timestep 0.002
# Define sphere where minimum of wall potential is at r=4 so
# regions is 4 + (2/5)^(1/6) sigma
region mysphere sphere 0 0 0 5.28756
fix wall all wall/region mysphere lj93 15.0 1.5 5.28
fix 2 all nve
#dump mydump all atom 10000 dump.trapnewsphere.lammpstrj
run 20000
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.1
ghost atom cutoff = 1.1
binsize = 0.55, bins = 88 88 88
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair soft, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.944 | 3.944 | 3.944 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 0 0 0 0
20000 317.05614 618.63581 0 2476.8578 0.030715
Loop time of 0.573686 on 4 procs for 20000 steps with 284 atoms
Performance: 6024197.192 ns/day, 0.000 hours/ns, 34862.252 timesteps/s
100.0% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.062609 | 0.070036 | 0.076149 | 1.8 | 12.21
Neigh | 0.21074 | 0.2209 | 0.2305 | 1.5 | 38.51
Comm | 0.17847 | 0.19084 | 0.21153 | 3.0 | 33.26
Output | 1.74e-05 | 2.58e-05 | 5.02e-05 | 0.0 | 0.00
Modify | 0.079214 | 0.082596 | 0.085481 | 0.8 | 14.40
Other | | 0.009288 | | | 1.62
Nlocal: 71 ave 73 max 69 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Nghost: 54.75 ave 57 max 53 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Neighs: 107.25 ave 127 max 85 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Total # of neighbors = 429
Ave neighs/atom = 1.5105634
Neighbor list builds = 1996
Dangerous builds = 1993
unfix wall
fix wall all wall/region mysphere lj93 50.0 1.5 5.68
unfix 1
#----------------------------------------------------------------------------
# Do a run to condense the atoms onto the spherical surface and anneal them
# so they will be orderly aranged onto a semi-triangular mesh on the sphere
#----------------------------------------------------------------------------
pair_style lj/cut 1.68359
#pair_coeff * * 0.002 1.5 1.68369
pair_coeff * * 0.0005 1.5 1.68369
fix 3 all langevin 1.5 0.01 100.0 5678
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
comm_modify cutoff 2.5
run 500000
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.98369
ghost atom cutoff = 2.5
binsize = 0.991845, bins = 49 49 49
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.277 | 3.277 | 3.277 Mbytes
Step Temp E_pair E_mol TotEng Press
20000 317.05614 626.83186 0 2485.0538 0.034256287
520000 0.20789564 780.54747 0 781.76592 0.028916791
Loop time of 12.8226 on 4 procs for 500000 steps with 284 atoms
Performance: 6738089.440 ns/day, 0.000 hours/ns, 38993.573 timesteps/s
100.0% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.6508 | 3.1904 | 3.6443 | 20.0 | 24.88
Neigh | 0.68551 | 0.75012 | 0.80362 | 5.1 | 5.85
Comm | 3.7915 | 4.3143 | 4.922 | 19.6 | 33.65
Output | 2.26e-05 | 3.335e-05 | 6.29e-05 | 0.0 | 0.00
Modify | 3.1825 | 3.2495 | 3.3155 | 2.6 | 25.34
Other | | 1.318 | | | 10.28
Nlocal: 71 ave 74 max 69 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Nghost: 109.75 ave 113 max 105 min
Histogram: 1 0 0 0 0 1 0 0 1 1
Neighs: 613.25 ave 718 max 495 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Total # of neighbors = 2453
Ave neighs/atom = 8.6373239
Neighbor list builds = 13515
Dangerous builds = 0
minimize 0.0 1.0e-8 1000 100000
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 4.402 | 4.402 | 4.402 Mbytes
Step Temp E_pair E_mol TotEng Press
520000 0.20789564 780.54747 0 781.76592 0.028916791
520004 0.20789564 780.00993 0 781.22838 0.02889732
Loop time of 0.00296133 on 4 procs for 4 steps with 284 atoms
99.8% CPU use with 4 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
780.547473373201 780.009929329778 780.009929329778
Force two-norm initial, final = 40.166574 13.723713
Force max component initial, final = 4.2404394 1.5423956
Final line search alpha, max atom move = 6.0381565e-11 9.3132257e-11
Iterations, force evaluations = 4 69
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0009509 | 0.0010909 | 0.0014002 | 0.5 | 36.84
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0007064 | 0.0010256 | 0.0011795 | 0.6 | 34.63
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0.000204 | 0.00024405 | 0.0002982 | 0.0 | 8.24
Other | | 0.0006008 | | | 20.29
Nlocal: 71 ave 72 max 69 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 109.75 ave 113 max 107 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Neighs: 612.75 ave 726 max 504 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Total # of neighbors = 2451
Ave neighs/atom = 8.6302817
Neighbor list builds = 0
Dangerous builds = 0
unfix wall
unfix 2
unfix 3
#----------------------------------------------------------------------------
# If bonded, bond the atoms together at something close to their current
# configuration
#----------------------------------------------------------------------------
variable total_mass equal 0.002398
variable node_mass equal "v_total_mass / v_n_nodes"
mass * ${node_mass}
mass * 8.44366197183099e-06
if "${is_bonded} == 1" then "bond_style harmonic" "bond_coeff 1 25.0 0.869333" "bond_coeff 2 25.0 0.948" "bond_coeff 3 25.0 1.026666" "bond_coeff 4 25.0 1.105333" "bond_coeff 5 25.0 1.184" "bond_coeff 6 25.0 1.262666" "bond_coeff 7 25.0 1.341333" "bond_coeff 8 25.0 1.42" "bond_coeff 9 25.0 1.498666" "bond_coeff 10 25.0 1.577333" "create_bonds many all all 1 0.83 0.908666" "create_bonds many all all 2 0.908667 0.987333" "create_bonds many all all 3 0.987334 1.066" "create_bonds many all all 4 1.066001 1.144666" "create_bonds many all all 5 1.144667 1.223333" "create_bonds many all all 6 1.223334 1.302" "create_bonds many all all 7 1.302001 1.380666" "create_bonds many all all 8 1.380667 1.459333" "create_bonds many all all 9 1.459334 1.538" "create_bonds many all all 10 1.538001 1.61667"
if "${is_bonded} == 1" then "pair_style lj/cut 5.05108" "pair_coeff * * 0.5 4.5" else "pair_style lj/cut 1.2" "pair_coeff * * 0.0 0.0"
pair_style lj/cut 1.2
pair_coeff * * 0.0 0.0
timestep ${tstep}
timestep 0.00025
#----------------------------------------------------------------------------
# You could uncomment the following lines and then turn off the noise and
# comment out the trap (following) to instead do a run that drags the
# sphere through the fluid to measure the drag force.
#----------------------------------------------------------------------------
#variable total_force equal 8.0
#variable node_force equal "v_total_force / v_n_nodes"
#variable oscillateY equal cos(step*0.0005)/(-0.004+50*v_tstep)/v_n_nodes
#variable oscillateZ equal cos(step*0.0003)/(-0.004+50*v_tstep)/v_n_nodes
#fix drag all addforce ${node_force} v_oscillateY v_oscillateZ
#----------------------------------------------------------------------------
# Trap the sphere along x (could be done experimentally using optical
# tweezers.
#----------------------------------------------------------------------------
variable fx atom -x*4.14195/284.0
fix trap all addforce v_fx 0.0 0.0 # needs to go before fix lb/fluid and lb/viscous
#----------------------------------------------------------------------------
# Set up the lb/fluid parameters for water and at a temperature of 300 K. If
# the colloid is integrated with the rigid fix, the dof are not
# automatically calculated correctly but as this would then be a rigid
# sphere it is clear it should have 6 degrees of freedom.
#----------------------------------------------------------------------------
if "${is_bonded} == 1" then "fix FL all lb/fluid 1 1.0 0.0009982071 stencil ${stpts} dx 1.2 noise 300.0 181920" else "fix FL all lb/fluid 1 1.0 0.0009982071 stencil ${stpts} dx 1.2 noise 300.0 181920 dof 6"
fix FL all lb/fluid 1 1.0 0.0009982071 stencil ${stpts} dx 1.2 noise 300.0 181920 dof 6
fix FL all lb/fluid 1 1.0 0.0009982071 stencil 2 dx 1.2 noise 300.0 181920 dof 6
Using a lattice-Boltzmann grid of 40 by 40 by 40 total grid points. (../fix_lb_fluid.cpp:486)
Local Grid Geometry created. (../fix_lb_fluid.cpp:1018)
fix 2 all lb/viscous
if "${is_bonded} == 1" then "fix 3 all nve" else "fix 3 all rigid group 1 all"
fix 3 all rigid group 1 all
1 rigid bodies with 284 atoms
#equilibration run
run 10000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- fix lb/fluid command:
@Article{Denniston et al.,
author = {C. Denniston, N. Afrasiabian, M.G. Cole-Andre,F.E. Mackay, S.T.T. Ollila, T. Whitehead},
title = {LAMMPS lb/fluid fix version 2: Improved Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid}, journal = {Comp.~Phys.~Comm.},
year = 2022,
volume = 275,
pages = {108318}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 5.306 | 5.306 | 5.306 Mbytes
Step Temp E_pair E_mol TotEng Press
520004 8.9102565e-07 0 0 1.8452924e-08 6.7761632e-05
530004 3.474402 0 0 0.071954018 -0.00061159689
Loop time of 238.57 on 4 procs for 10000 steps with 284 atoms
Performance: 905.396 ns/day, 0.027 hours/ns, 41.916 timesteps/s
100.0% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.07901 | 0.086329 | 0.095378 | 2.0 | 0.04
Neigh | 0.012928 | 0.013445 | 0.013795 | 0.3 | 0.01
Comm | 0.18848 | 0.1969 | 0.20455 | 1.3 | 0.08
Output | 4.07e-05 | 5.9575e-05 | 0.0001157 | 0.0 | 0.00
Modify | 238.01 | 238.02 | 238.03 | 0.1 | 99.77
Other | | 0.2536 | | | 0.11
Nlocal: 71 ave 84 max 59 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Nghost: 110.75 ave 121 max 101 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Neighs: 243.25 ave 285 max 209 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Total # of neighbors = 973
Ave neighs/atom = 3.4260563
Neighbor list builds = 52
Dangerous builds = 0
# data gathering run
reset_timestep 0
#----------------------------------------------------------------------------
# Create variables containing the positions/velocity of the colloids center
# of mass.
#----------------------------------------------------------------------------
variable cmx equal xcm(all,x)
variable cmy equal xcm(all,y)
variable cmz equal xcm(all,z)
variable vcmx equal vcm(all,x)
variable vcmy equal vcm(all,y)
variable vcmz equal vcm(all,z)
if "${is_bonded} == 1" then "variable comdatafile string trap_nb${n_nodes}_st${stpts}_dt${tstep}.out" else "variable comdatafile string trap_n${n_nodes}_st${stpts}_dt${tstep}.out"
variable comdatafile string trap_n${n_nodes}_st${stpts}_dt${tstep}.out
variable comdatafile string trap_n284_st${stpts}_dt${tstep}.out
variable comdatafile string trap_n284_st2_dt${tstep}.out
variable comdatafile string trap_n284_st2_dt0.00025.out
#fix printCM all print 10 "$(step) $(f_FL) ${cmx} ${cmy} ${cmz} ${vcmx} ${vcmy} ${vcmz}" file ${comdatafile} screen no
run 10000
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 5.306 | 5.306 | 5.306 Mbytes
Step Temp E_pair E_mol TotEng Press
0 3.474402 0 0 0.071954018 0.00181615
10000 2.6284662 0 0 0.054434894 0.00098091301
Loop time of 237.772 on 4 procs for 10000 steps with 284 atoms
Performance: 908.435 ns/day, 0.026 hours/ns, 42.057 timesteps/s
100.0% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.079283 | 0.087287 | 0.095198 | 2.6 | 0.04
Neigh | 0.0133 | 0.013789 | 0.014439 | 0.3 | 0.01
Comm | 0.18949 | 0.1975 | 0.20661 | 1.8 | 0.08
Output | 2.88e-05 | 4.3675e-05 | 8.58e-05 | 0.0 | 0.00
Modify | 237.21 | 237.22 | 237.22 | 0.0 | 99.77
Other | | 0.253 | | | 0.11
Nlocal: 71 ave 87 max 54 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Nghost: 110 ave 125 max 100 min
Histogram: 1 1 0 0 1 0 0 0 0 1
Neighs: 243.25 ave 264 max 207 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Total # of neighbors = 973
Ave neighs/atom = 3.4260563
Neighbor list builds = 53
Dangerous builds = 0
#run 25000000
Total wall time: 0:08:09

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examples/PACKAGES/latboltz/dragforce/defaultgamma_drag.out
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#===========================================================================#
# Drag force on a single sphere. #
# #
# Here, gamma (used in the calculation of the particle-fluid interaction #
# force) is calculated by default. The resulting equilibrium drag force #
# should correspond to the Stokes drag force on a sphere with a slightly #
# larger "hydrodynamic" radius, than that given by the placement of the #
# particle nodes. #
# #
# Sample output from this run can be found in the file: #
# 'defaultgamma_drag.out' #
#===========================================================================#
units micro
dimension 3
boundary p p f
atom_style atomic
#----------------------------------------------------------------------------
# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing
# to ensure that the particles belonging to a given processor remain inside
# that processors lattice-Boltzmann grid.
# The arguments for neigh_modify have been set to "delay 0 every 1", again
# to ensure that the particles belonging to a given processor remain inside
# that processors lattice-Boltzmann grid. However, these values can likely
# be somewhat increased without issue. If a problem does arise (a particle
# is outside of its processors LB grid) an error message is printed and
# the simulation is terminated.
#----------------------------------------------------------------------------
neighbor 1.0 bin
neigh_modify delay 0 every 1
read_data data.one_radius16d2
#----------------------------------------------------------------------------
# None of the particles comprising the spherical colloidal object should
# interact with one another.
#----------------------------------------------------------------------------
pair_style lj/cut 2.45
pair_coeff * * 0.0 0.0 2.45
neigh_modify exclude type 1 1
#----------------------------------------------------------------------------
# Need to use a large particle mass in order to approximate an infintely
# massive particle, moving at constant velocity through the fluid.
#----------------------------------------------------------------------------
mass * 10000.0
timestep 3.0
velocity all set 0.0 0.0001 0.0 units box
#---------------------------------------------------------------------------
# Create a lattice-Boltzmann fluid covering the simulation domain.
# All of the particles in the simulation apply a force to the fluid.
# Use the standard LB integration scheme, a fluid density = 1.0,
# fluid viscosity = 1.0, lattice spacing dx=4.0, and mass unit, dm=10.0.
# Use the default method to calculate the interaction force between the
# particles and the fluid. This calculation requires the surface area
# of the composite object represented by each particle node. By default
# this area is assumed equal to dx*dx; however, since this is not the case
# here, it is input through the setArea keyword (i.e. particles of type 1
# correspond to a surface area of 10.3059947).
# Use the trilinear interpolation stencil to distribute the force from
# a given particle onto the fluid mesh (results in a smaller hydrodynamic
# radius than if the Peskin stencil is used).
# Print the force and torque acting on the particle to the screen at each
# timestep.
#----------------------------------------------------------------------------
fix 1 all lb/fluid 1 1 1.0 1.0 setArea 1 10.3059947 dx 4.0 dm 10.0 trilinear calcforce 10 all
#---------------------------------------------------------------------------
# For this simulation the colloidal particle moves at a constant velocity
# through the fluid. As such, we do not wish to apply the force from
# the fluid back onto the object. Therefore, we do not use any of the
# viscous_lb, rigid_pc_sphere, or pc fixes, and simply integrate the
# particle motion using one of the built-in LAMMPS integrators.
#---------------------------------------------------------------------------
fix 2 all nve
run 100000

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#===========================================================================#
# single particle drag tests #
# #
# Run consists of a colloidal particle being dragged with a constant force #
# through an LB-fluid. The colloidal particle could be single atom or #
# be a composite particle. Composite particles could be bonded or just #
# rigidly constrained to stay together. You can set flags in the script to #
# change these. #
# #
# Sample output from this run can be found in the files with "log." #
# located in the same directory. #
#===========================================================================#
units nano
dimension 3
boundary p p f
atom_style molecular
region mydomain block -24.0 24.0 -24.0 24.0 -24.0 24.0
#----------------------------------------------------------------------------
# Set up particles with n_nodes and decide if bonded or rigid
#----------------------------------------------------------------------------
variable n_nodes equal 4 # 1, 4, 6 are options with definitions below
variable is_bonded equal 0 # 0 or 1 (1 only if n_nodes > 1,
# bond parameters set for n_node = 4 case)
variable stpts equal 3 # 2, 3, 4 number of stencil points in any direction.
variable tstep equal 0.00025
if "${is_bonded} == 1" then &
"create_box 1 mydomain bond/types 1 extra/bond/per/atom 6" &
else &
"create_box 1 mydomain"
if "${n_nodes} == 1" then &
"create_atoms 1 single 0.0 0.0 0.0" &
elif "${n_nodes} == 4" &
"create_atoms 1 single 0.0 0.0 0.204124" &
"create_atoms 1 single -0.096225 -0.166667 -0.0680414" &
"create_atoms 1 single -0.096225 0.166667 -0.0680414" &
"create_atoms 1 single 0.19245 0. -0.0680414" &
elif "${n_nodes} == 6" &
"create_atoms 1 single 0.204124 0.0000000 0.0000000" &
"create_atoms 1 single -0.204124 0.0000000 0.0000000" &
"create_atoms 1 single 0.0000000 0.204124 0.0000000" &
"create_atoms 1 single 0.0000000 -0.204124 0.0000000" &
"create_atoms 1 single 0.0000000 0.0000000 0.204124" &
"create_atoms 1 single 0.0000000 0.0000000 -0.204124"
#----------------------------------------------------------------------------
# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing
# to ensure that the particles belonging to a given processor remain inside
# that processors lattice-Boltzmann grid.
# The arguments for neigh_modify have been set to "delay 0 every 1", again
# to ensure that the particles belonging to a given processor remain inside
# that processors lattice-Boltzmann grid. However, these values can likely
# be somewhat increased without issue. If a problem does arise (a particle
# is outside of its processors LB grid) an error message is printed and
# the simulation is terminated.
#----------------------------------------------------------------------------
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
comm_modify cutoff 2.5 # cutoff for communcation shoud be at least 2 dx
#----------------------------------------------------------------------------
# Implement a hard-sphere interactions between particles & create bonds
#----------------------------------------------------------------------------
pair_style lj/cut 5.88
pair_coeff * * 0.0 0.0 5.88
variable total_mass equal 0.002398 # particle mass
variable node_mass equal "v_total_mass / v_n_nodes"
mass * ${node_mass}
if "${is_bonded} == 1" then &
"bond_style harmonic" &
"bond_coeff 1 1.0 0.333333333" &
"create_bonds many all all 1 0.3 0.35"
#velocity all set 0.02 0.0 0.0
#----------------------------------------------------------------------------
# Define external forces (SHOULD COME BEFORE lb/fluid and lb/viscous FIXes)
# to drag particles through the fluid.
#----------------------------------------------------------------------------
variable total_force equal 1.0 # total external force on the particle
variable node_force equal "v_total_force / v_n_nodes"
variable oscillateY equal cos(step*0.0005)/(-0.03+400*v_tstep)/v_n_nodes
variable oscillateZ equal cos(step*0.0003)/(-0.03+400*v_tstep)/v_n_nodes
fix drag all addforce ${node_force} v_oscillateY v_oscillateZ
#---------------------------------------------------------------------------
# Create a lattice-Boltzmann fluid covering the simulation domain.
# This fluid feels a force due to the particle (group all here)
# (however, this fix does not explicity apply a force back on to these
# particles...this is accomplished through the use of the lb/viscous fix).
# Use a fluid viscosity = 1.0, fluid density= 0.0009982071,(i.e. water) and
# lattice spacing dx=1.2.
# Different ".log" files in this directory show the output with the stencil
# option being stencil 2, stencil 3, and stencil 4 (triliner, IBM, Key's).
#----------------------------------------------------------------------------
timestep ${tstep}
fix FL all lb/fluid 1 1.0 0.0009982071 stencil ${stpts} dx 1.2
#dumpxdmf 1000 fflow
#----------------------------------------------------------------------------
# Apply the force from the fluid to the particles, and integrate their
# motion, constraining them to move and rotate together as a single rigid
# spherical object or an elastically bonded object
#----------------------------------------------------------------------------
fix 2 all lb/viscous
if "${n_nodes} == 1 || ${is_bonded} == 1" then &
"fix 3 all nve" &
else &
"fix 3 all rigid group 1 all"
#----------------------------------------------------------------------------
# Create variables containing the positions/velocity of the colloids center
# of mass.
#----------------------------------------------------------------------------
variable cmx equal xcm(all,x)
variable cmy equal xcm(all,y)
variable cmz equal xcm(all,z)
variable vcmx equal vcm(all,x)
variable vcmy equal vcm(all,y)
variable vcmz equal vcm(all,z)
if "${is_bonded} == 1" then &
"variable comdatafile string drag_nb${n_nodes}_st${stpts}_dt${tstep}.out" &
else &
"variable comdatafile string drag_n${n_nodes}_st${stpts}_dt${tstep}.out"
#fix printCM all print 100 "$(step) ${cmx} ${cmy} ${cmz} ${vcmx} ${vcmy} ${vcmz}" file ${comdatafile} screen no
run 10000
#run 100000

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examples/PACKAGES/latboltz/dragforce/in.setgamma_drag
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#===========================================================================#
# Drag force on a single sphere. #
# #
# Here, gamma (used in the calculation of the particle-fluid interaction #
# force) is set by the user (gamma = 13.0 for this simulation.) This #
# type of simulation is used to calibrate the value for gamma which will #
# give the desired Stokes drag force. #
# #
# Sample output from this run can be found in the file: #
# 'setgamma13d0_drag.out' #
#===========================================================================#
units micro
dimension 3
boundary p p f
atom_style atomic
#----------------------------------------------------------------------------
# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing
# to ensure that the particles belonging to a given processor remain inside
# that processors lattice-Boltzmann grid.
# The arguments for neigh_modify have been set to "delay 0 every 1", again
# to ensure that the particles belonging to a given processor remain inside
# that processors lattice-Boltzmann grid. However, these values can likely
# be somewhat increased without issue. If a problem does arise (a particle
# is outside of its processors LB grid) an error message is printed and
# the simulation is terminated.
#----------------------------------------------------------------------------
neighbor 1.0 bin
neigh_modify delay 0 every 1
read_data data.one_radius16d2
#----------------------------------------------------------------------------
# None of the particles comprising the spherical colloidal object should
# interact with one another.
#----------------------------------------------------------------------------
pair_style lj/cut 2.45
pair_coeff * * 0.0 0.0 2.45
neigh_modify exclude type 1 1
mass * 1.0
timestep 4.0
velocity all set 0.0 0.0001 0.0 units box
#---------------------------------------------------------------------------
# Create a lattice-Boltzmann fluid covering the simulation domain.
# All of the particles in the simulation apply a force to the fluid.
# Use the LB integration scheme of Ollila et. al. (for stability reasons,
# this integration scheme should be used when a large user set value for
# gamma is specified), a fluid density = 1.0, fluid viscosity = 1.0, value
# for gamma=13.0, lattice spacing dx=4.0, and mass unit, dm=10.0.
# Print the force and torque acting on the particle to the screen at each
# timestep.
#----------------------------------------------------------------------------
fix 1 all lb/fluid 1 2 1.0 1.0 setGamma 13.0 dx 4.0 dm 10.0 calcforce 10 all
#---------------------------------------------------------------------------
# For this simulation the colloidal particle moves at a constant velocity
# through the fluid. As such, we do not wish to apply the force from
# the fluid back onto the object. Therefore, we do not use any of the
# viscous_lb, rigid_pc_sphere, or pc fixes, and simply integrate the
# particle motion using one of the built-in LAMMPS integrators.
#---------------------------------------------------------------------------
fix 2 all nve
run 100000

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LAMMPS (17 Feb 2022)
#===========================================================================#
# single particle drag tests #
# #
# Run consists of a colloidal particle being dragged with a constant force #
# through an LB-fluid. The colloidal particle could be single atom or #
# be a composite particle. Composite particles could be bonded or just #
# rigidly constrained to stay together. You can set flags in the script to #
# change these. #
# #
# Sample output from this run can be found in the files with "log." #
# located in the same directory. #
#===========================================================================#
units nano
dimension 3
boundary p p f
atom_style molecular
region mydomain block -24.0 24.0 -24.0 24.0 -24.0 24.0
#----------------------------------------------------------------------------
# Set up particles with n_nodes and decide if bonded or rigid
#----------------------------------------------------------------------------
variable n_nodes equal 4 # 1, 4, 6 are options with definitions below
variable is_bonded equal 0 # 0 or 1 (1 only if n_nodes > 1,
# bond parameters set for n_node = 4 case)
variable stpts equal 3 # 2, 3, 4 number of stencil points in any direction.
variable tstep equal 0.00025
if "${is_bonded} == 1" then "create_box 1 mydomain bond/types 1 extra/bond/per/atom 6" else "create_box 1 mydomain"
create_box 1 mydomain
Created orthogonal box = (-24 -24 -24) to (24 24 24)
1 by 1 by 1 MPI processor grid
if "${n_nodes} == 1" then "create_atoms 1 single 0.0 0.0 0.0" elif "${n_nodes} == 4" "create_atoms 1 single 0.0 0.0 0.204124" "create_atoms 1 single -0.096225 -0.166667 -0.0680414" "create_atoms 1 single -0.096225 0.166667 -0.0680414" "create_atoms 1 single 0.19245 0. -0.0680414" elif "${n_nodes} == 6" "create_atoms 1 single 0.204124 0.0000000 0.0000000" "create_atoms 1 single -0.204124 0.0000000 0.0000000" "create_atoms 1 single 0.0000000 0.204124 0.0000000" "create_atoms 1 single 0.0000000 -0.204124 0.0000000" "create_atoms 1 single 0.0000000 0.0000000 0.204124" "create_atoms 1 single 0.0000000 0.0000000 -0.204124"
create_atoms 1 single 0.0 0.0 0.204124
Created 1 atoms
using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24)
create_atoms CPU = 0.001 seconds
create_atoms 1 single -0.096225 -0.166667 -0.0680414
Created 1 atoms
using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24)
create_atoms CPU = 0.001 seconds
create_atoms 1 single -0.096225 0.166667 -0.0680414
Created 1 atoms
using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24)
create_atoms CPU = 0.000 seconds
create_atoms 1 single 0.19245 0. -0.0680414
Created 1 atoms
using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24)
create_atoms CPU = 0.000 seconds
#----------------------------------------------------------------------------
# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing
# to ensure that the particles belonging to a given processor remain inside
# that processors lattice-Boltzmann grid.
# The arguments for neigh_modify have been set to "delay 0 every 1", again
# to ensure that the particles belonging to a given processor remain inside
# that processors lattice-Boltzmann grid. However, these values can likely
# be somewhat increased without issue. If a problem does arise (a particle
# is outside of its processors LB grid) an error message is printed and
# the simulation is terminated.
#----------------------------------------------------------------------------
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
comm_modify cutoff 2.5 # cutoff for communcation shoud be at least 2 dx
#----------------------------------------------------------------------------
# Implement a hard-sphere interactions between particles & create bonds
#----------------------------------------------------------------------------
pair_style lj/cut 5.88
pair_coeff * * 0.0 0.0 5.88
variable total_mass equal 0.002398 # particle mass
variable node_mass equal "v_total_mass / v_n_nodes"
mass * ${node_mass}
mass * 0.0005995
if "${is_bonded} == 1" then "bond_style harmonic" "bond_coeff 1 1.0 0.333333333" "create_bonds many all all 1 0.3 0.35"
#velocity all set 0.02 0.0 0.0
#----------------------------------------------------------------------------
# Define external forces (SHOULD COME BEFORE lb/fluid and lb/viscous FIXes)
# to drag particles through the fluid.
#----------------------------------------------------------------------------
variable total_force equal 1.0 # total external force on the particle
variable node_force equal "v_total_force / v_n_nodes"
variable oscillateY equal cos(step*0.0005)/(-0.03+400*v_tstep)/v_n_nodes
variable oscillateZ equal cos(step*0.0003)/(-0.03+400*v_tstep)/v_n_nodes
fix drag all addforce ${node_force} v_oscillateY v_oscillateZ
fix drag all addforce 0.25 v_oscillateY v_oscillateZ
#---------------------------------------------------------------------------
# Create a lattice-Boltzmann fluid covering the simulation domain.
# This fluid feels a force due to the particle (group all here)
# (however, this fix does not explicity apply a force back on to these
# particles...this is accomplished through the use of the lb/viscous fix).
# Use a fluid viscosity = 1.0, fluid density= 0.0009982071,(i.e. water) and
# lattice spacing dx=1.2.
# Different ".log" files in this directory show the output with the stencil
# option being stencil 2, stencil 3, and stencil 4 (triliner, IBM, Key's).
#----------------------------------------------------------------------------
timestep ${tstep}
timestep 0.00025
fix FL all lb/fluid 1 1.0 0.0009982071 stencil ${stpts} dx 1.2
fix FL all lb/fluid 1 1.0 0.0009982071 stencil 3 dx 1.2
Using a lattice-Boltzmann grid of 40 by 40 by 41 total grid points. (../fix_lb_fluid.cpp:486)
Local Grid Geometry created. (../fix_lb_fluid.cpp:1018)
#dumpxdmf 1000 fflow
#----------------------------------------------------------------------------
# Apply the force from the fluid to the particles, and integrate their
# motion, constraining them to move and rotate together as a single rigid
# spherical object or an elastically bonded object
#----------------------------------------------------------------------------
fix 2 all lb/viscous
if "${n_nodes} == 1 || ${is_bonded} == 1" then "fix 3 all nve" else "fix 3 all rigid group 1 all"
fix 3 all rigid group 1 all
1 rigid bodies with 4 atoms
#----------------------------------------------------------------------------
# Create variables containing the positions/velocity of the colloids center
# of mass.
#----------------------------------------------------------------------------
variable cmx equal xcm(all,x)
variable cmy equal xcm(all,y)
variable cmz equal xcm(all,z)
variable vcmx equal vcm(all,x)
variable vcmy equal vcm(all,y)
variable vcmz equal vcm(all,z)
if "${is_bonded} == 1" then "variable comdatafile string drag_nb${n_nodes}_st${stpts}_dt${tstep}.out" else "variable comdatafile string drag_n${n_nodes}_st${stpts}_dt${tstep}.out"
variable comdatafile string drag_n${n_nodes}_st${stpts}_dt${tstep}.out
variable comdatafile string drag_n4_st${stpts}_dt${tstep}.out
variable comdatafile string drag_n4_st3_dt${tstep}.out
variable comdatafile string drag_n4_st3_dt0.00025.out
#fix printCM all print 100 "$(step) ${cmx} ${cmy} ${cmz} ${vcmx} ${vcmy} ${vcmz}" file ${comdatafile} screen no
run 10000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- fix lb/fluid command:
@Article{Denniston et al.,
author = {C. Denniston, N. Afrasiabian, M.G. Cole-Andre,F.E. Mackay, S.T.T. Ollila, T. Whitehead},
title = {LAMMPS lb/fluid fix version 2: Improved Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid}, journal = {Comp.~Phys.~Comm.},
year = 2022,
volume = 275,
pages = {108318}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.18
ghost atom cutoff = 6.18
binsize = 3.09, bins = 16 16 16
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
WARNING: Communication cutoff adjusted to 6.18 (../comm.cpp:732)
Per MPI rank memory allocation (min/avg/max) = 7.15 | 7.15 | 7.15 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 0 0 0 2.1529156e-12
10000 0.021008983 0 0 0.00043509092 1.4149298e-08
Loop time of 185.434 on 1 procs for 10000 steps with 4 atoms
Performance: 1164.837 ns/day, 0.021 hours/ns, 53.928 timesteps/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.02024 | 0.02024 | 0.02024 | 0.0 | 0.01
Bond | 0.0011585 | 0.0011585 | 0.0011585 | 0.0 | 0.00
Neigh | 8.88e-05 | 8.88e-05 | 8.88e-05 | 0.0 | 0.00
Comm | 0.011615 | 0.011615 | 0.011615 | 0.0 | 0.01
Output | 8.32e-05 | 8.32e-05 | 8.32e-05 | 0.0 | 0.00
Modify | 185.36 | 185.36 | 185.36 | 0.0 | 99.96
Other | | 0.04469 | | | 0.02
Nlocal: 4 ave 4 max 4 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 6 ave 6 max 6 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 6
Ave neighs/atom = 1.5
Ave special neighs/atom = 0
Neighbor list builds = 9
Dangerous builds = 0
#run 100000
Total wall time: 0:03:05

212
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LAMMPS (17 Feb 2022)
#===========================================================================#
# single particle drag tests #
# #
# Run consists of a colloidal particle being dragged with a constant force #
# through an LB-fluid. The colloidal particle could be single atom or #
# be a composite particle. Composite particles could be bonded or just #
# rigidly constrained to stay together. You can set flags in the script to #
# change these. #
# #
# Sample output from this run can be found in the files with "log." #
# located in the same directory. #
#===========================================================================#
units nano
dimension 3
boundary p p f
atom_style molecular
region mydomain block -24.0 24.0 -24.0 24.0 -24.0 24.0
#----------------------------------------------------------------------------
# Set up particles with n_nodes and decide if bonded or rigid
#----------------------------------------------------------------------------
variable n_nodes equal 4 # 1, 4, 6 are options with definitions below
variable is_bonded equal 0 # 0 or 1 (1 only if n_nodes > 1,
# bond parameters set for n_node = 4 case)
variable stpts equal 3 # 2, 3, 4 number of stencil points in any direction.
variable tstep equal 0.00025
if "${is_bonded} == 1" then "create_box 1 mydomain bond/types 1 extra/bond/per/atom 6" else "create_box 1 mydomain"
create_box 1 mydomain
Created orthogonal box = (-24 -24 -24) to (24 24 24)
1 by 2 by 2 MPI processor grid
if "${n_nodes} == 1" then "create_atoms 1 single 0.0 0.0 0.0" elif "${n_nodes} == 4" "create_atoms 1 single 0.0 0.0 0.204124" "create_atoms 1 single -0.096225 -0.166667 -0.0680414" "create_atoms 1 single -0.096225 0.166667 -0.0680414" "create_atoms 1 single 0.19245 0. -0.0680414" elif "${n_nodes} == 6" "create_atoms 1 single 0.204124 0.0000000 0.0000000" "create_atoms 1 single -0.204124 0.0000000 0.0000000" "create_atoms 1 single 0.0000000 0.204124 0.0000000" "create_atoms 1 single 0.0000000 -0.204124 0.0000000" "create_atoms 1 single 0.0000000 0.0000000 0.204124" "create_atoms 1 single 0.0000000 0.0000000 -0.204124"
create_atoms 1 single 0.0 0.0 0.204124
Created 1 atoms
using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24)
create_atoms CPU = 0.001 seconds
create_atoms 1 single -0.096225 -0.166667 -0.0680414
Created 1 atoms
using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24)
create_atoms CPU = 0.000 seconds
create_atoms 1 single -0.096225 0.166667 -0.0680414
Created 1 atoms
using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24)
create_atoms CPU = 0.000 seconds
create_atoms 1 single 0.19245 0. -0.0680414
Created 1 atoms
using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24)
create_atoms CPU = 0.001 seconds
#----------------------------------------------------------------------------
# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing
# to ensure that the particles belonging to a given processor remain inside
# that processors lattice-Boltzmann grid.
# The arguments for neigh_modify have been set to "delay 0 every 1", again
# to ensure that the particles belonging to a given processor remain inside
# that processors lattice-Boltzmann grid. However, these values can likely
# be somewhat increased without issue. If a problem does arise (a particle
# is outside of its processors LB grid) an error message is printed and
# the simulation is terminated.
#----------------------------------------------------------------------------
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
comm_modify cutoff 2.5 # cutoff for communcation shoud be at least 2 dx
#----------------------------------------------------------------------------
# Implement a hard-sphere interactions between particles & create bonds
#----------------------------------------------------------------------------
pair_style lj/cut 5.88
pair_coeff * * 0.0 0.0 5.88
variable total_mass equal 0.002398 # particle mass
variable node_mass equal "v_total_mass / v_n_nodes"
mass * ${node_mass}
mass * 0.0005995
if "${is_bonded} == 1" then "bond_style harmonic" "bond_coeff 1 1.0 0.333333333" "create_bonds many all all 1 0.3 0.35"
#velocity all set 0.02 0.0 0.0
#----------------------------------------------------------------------------
# Define external forces (SHOULD COME BEFORE lb/fluid and lb/viscous FIXes)
# to drag particles through the fluid.
#----------------------------------------------------------------------------
variable total_force equal 1.0 # total external force on the particle
variable node_force equal "v_total_force / v_n_nodes"
variable oscillateY equal cos(step*0.0005)/(-0.03+400*v_tstep)/v_n_nodes
variable oscillateZ equal cos(step*0.0003)/(-0.03+400*v_tstep)/v_n_nodes
fix drag all addforce ${node_force} v_oscillateY v_oscillateZ
fix drag all addforce 0.25 v_oscillateY v_oscillateZ
#---------------------------------------------------------------------------
# Create a lattice-Boltzmann fluid covering the simulation domain.
# This fluid feels a force due to the particle (group all here)
# (however, this fix does not explicity apply a force back on to these
# particles...this is accomplished through the use of the lb/viscous fix).
# Use a fluid viscosity = 1.0, fluid density= 0.0009982071,(i.e. water) and
# lattice spacing dx=1.2.
# Different ".log" files in this directory show the output with the stencil
# option being stencil 2, stencil 3, and stencil 4 (triliner, IBM, Key's).
#----------------------------------------------------------------------------
timestep ${tstep}
timestep 0.00025
fix FL all lb/fluid 1 1.0 0.0009982071 stencil ${stpts} dx 1.2
fix FL all lb/fluid 1 1.0 0.0009982071 stencil 3 dx 1.2
Using a lattice-Boltzmann grid of 40 by 40 by 41 total grid points. (../fix_lb_fluid.cpp:486)
Local Grid Geometry created. (../fix_lb_fluid.cpp:1018)
#dumpxdmf 1000 fflow
#----------------------------------------------------------------------------
# Apply the force from the fluid to the particles, and integrate their
# motion, constraining them to move and rotate together as a single rigid
# spherical object or an elastically bonded object
#----------------------------------------------------------------------------
fix 2 all lb/viscous
if "${n_nodes} == 1 || ${is_bonded} == 1" then "fix 3 all nve" else "fix 3 all rigid group 1 all"
fix 3 all rigid group 1 all
1 rigid bodies with 4 atoms
#----------------------------------------------------------------------------
# Create variables containing the positions/velocity of the colloids center
# of mass.
#----------------------------------------------------------------------------
variable cmx equal xcm(all,x)
variable cmy equal xcm(all,y)
variable cmz equal xcm(all,z)
variable vcmx equal vcm(all,x)
variable vcmy equal vcm(all,y)
variable vcmz equal vcm(all,z)
if "${is_bonded} == 1" then "variable comdatafile string drag_nb${n_nodes}_st${stpts}_dt${tstep}.out" else "variable comdatafile string drag_n${n_nodes}_st${stpts}_dt${tstep}.out"
variable comdatafile string drag_n${n_nodes}_st${stpts}_dt${tstep}.out
variable comdatafile string drag_n4_st${stpts}_dt${tstep}.out
variable comdatafile string drag_n4_st3_dt${tstep}.out
variable comdatafile string drag_n4_st3_dt0.00025.out
#fix printCM all print 100 "$(step) ${cmx} ${cmy} ${cmz} ${vcmx} ${vcmy} ${vcmz}" file ${comdatafile} screen no
run 10000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- fix lb/fluid command:
@Article{Denniston et al.,
author = {C. Denniston, N. Afrasiabian, M.G. Cole-Andre,F.E. Mackay, S.T.T. Ollila, T. Whitehead},
title = {LAMMPS lb/fluid fix version 2: Improved Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid}, journal = {Comp.~Phys.~Comm.},
year = 2022,
volume = 275,
pages = {108318}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.18
ghost atom cutoff = 6.18
binsize = 3.09, bins = 16 16 16
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
WARNING: Communication cutoff adjusted to 6.18 (../comm.cpp:732)
Per MPI rank memory allocation (min/avg/max) = 6.763 | 6.857 | 7.138 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 0 0 0 2.1529156e-12
10000 0.021008983 0 0 0.00043509092 1.4149298e-08
Loop time of 154.466 on 4 procs for 10000 steps with 4 atoms
Performance: 1398.367 ns/day, 0.017 hours/ns, 64.739 timesteps/s
99.9% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.013169 | 0.01792 | 0.021577 | 2.3 | 0.01
Bond | 0.0019565 | 0.0021447 | 0.0023408 | 0.4 | 0.00
Neigh | 7.55e-05 | 9.69e-05 | 0.0001173 | 0.0 | 0.00
Comm | 0.07056 | 0.076818 | 0.084499 | 2.1 | 0.05
Output | 2.85e-05 | 4.4925e-05 | 9.24e-05 | 0.0 | 0.00
Modify | 154.16 | 154.17 | 154.18 | 0.1 | 99.81
Other | | 0.1998 | | | 0.13
Nlocal: 1 ave 4 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Nghost: 3 ave 4 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 1.5 ave 6 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Total # of neighbors = 6
Ave neighs/atom = 1.5
Ave special neighs/atom = 0
Neighbor list builds = 9
Dangerous builds = 0
#run 100000
Total wall time: 0:02:34

10035
examples/PACKAGES/latboltz/dragforce/setgamma13d0_drag.out
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1290
examples/PACKAGES/latboltz/fourspheres/data.four
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15039
examples/PACKAGES/latboltz/fourspheres/fourspheres_velocity0d0001_defaultgamma.out
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15039
examples/PACKAGES/latboltz/fourspheres/fourspheres_velocity0d0001_setgamma.out
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84
examples/PACKAGES/latboltz/fourspheres/in.fourspheres_default_gamma
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@ -1,84 +0,0 @@
#===========================================================================#
# System of 2 pairs of rigid particles moving towards one another. #
# At each timestep, the hydrodynamic force acting on one of these four #
# rigid particles is printed to the screen. #
# #
# Here, gamma (used in the calculation of the particle-fluid interaction #
# force) is calculated by default. Thus, the colloidal objects will have #
# slightly larger "hydrodynamic" radii than given by the placement of the #
# particle nodes. #
# #
# Sample output from this run can be found in the file: #
# 'fourspheres_velocity0d0001_defaultgamma.out' #
#===========================================================================#
units micro
dimension 3
boundary p p p
atom_style atomic
#----------------------------------------------------------------------------
# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing
# to ensure that the particles belonging to a given processor remain inside
# that processors lattice-Boltzmann grid.
# The arguments for neigh_modify have been set to "delay 0 every 1", again
# to ensure that the particles belonging to a given processor remain inside
# that processors lattice-Boltzmann grid. However, these values can likely
# be somewhat increased without issue. If a problem does arise (a particle
# is outside of its processors LB grid) an error message is printed and
# the simulation is terminated.
#----------------------------------------------------------------------------
neighbor 1.0 bin
neigh_modify delay 0 every 1 exclude type 1 1
read_data data.four
#----------------------------------------------------------------------------
# None of the particles interact with one another.
#----------------------------------------------------------------------------
pair_style lj/cut 2.45
pair_coeff * * 0.0 0.0 2.45
#----------------------------------------------------------------------------
# Need to use a large particle mass in order to approximate an infintely
# massive particle, moving at constant velocity through the fluid.
#----------------------------------------------------------------------------
mass * 10000.0
timestep 3.0
group sphere1 id <> 1 320
group sphere2 id <> 321 640
group sphere3 id <> 641 960
group sphere4 id <> 961 1280
velocity sphere1 set 0.0 0.0001 0.0 units box
velocity sphere2 set 0.0 -0.0001 0.0 units box
velocity sphere3 set 0.0 0.0001 0.0 units box
velocity sphere4 set 0.0 -0.0001 0.0 units box
#---------------------------------------------------------------------------
# Create a lattice-Boltzmann fluid covering the simulation domain.
# All of the particles in the simulation apply a force to the fluid.
# Use the standard LB integration scheme, a fluid density = 1.0,
# fluid viscosity = 1.0, lattice spacing dx=4.0, and mass unit, dm=10.0.
# Use the default method to calculate the interaction force between the
# particles and the fluid. This calculation requires the surface area
# of the composite object represented by each particle node. By default
# this area is assumed equal to dx*dx; however, since this is not the case
# here, it is input through the setArea keyword (i.e. particles of type 1
# correspond to a surface area of 2.640508625).
# Print the force and torque acting on one of the spherical colloidal objects
# to the screen at each timestep.
#----------------------------------------------------------------------------
fix 1 all lb/fluid 1 1 1.0 1.0 setArea 1 2.640508625 dx 4.0 dm 10.0 calcforce 20 sphere1
#---------------------------------------------------------------------------
# For this simulation the colloidal particles move at a constant velocity
# through the fluid. As such, we do not wish to apply the force from
# the fluid back onto these objects. Therefore, we do not use any of the
# viscous_lb, rigid_pc_sphere, or pc fixes, and simply integrate the
# particle motions using one of the built-in LAMMPS integrators.
#---------------------------------------------------------------------------
fix 2 all nve
run 300000

76
examples/PACKAGES/latboltz/fourspheres/in.fourspheres_set_gamma
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@ -1,76 +0,0 @@
#===========================================================================#
# System of 2 pairs of rigid particles moving towards one another. #
# At each timestep, the hydrodynamic force acting on one of these four #
# rigid particles is printed to the screen. #
# #
# Here, gamma (used in the calculation of the particle-fluid interaction #
# force) is set by the user (gamma = 3.303 for this simulation...this #
# value has been calibrated a priori through simulations of the drag #
# force acting on a single particle of the same radius). #
# #
# Sample output from this run can be found in the file: #
# 'fourspheres_velocity0d0001_setgamma.out' #
#===========================================================================#
units micro
dimension 3
boundary p p p
atom_style atomic
#----------------------------------------------------------------------------
# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing
# to ensure that the particles belonging to a given processor remain inside
# that processors lattice-Boltzmann grid.
# The arguments for neigh_modify have been set to "delay 0 every 1", again
# to ensure that the particles belonging to a given processor remain inside
# that processors lattice-Boltzmann grid. However, these values can likely
# be somewhat increased without issue. If a problem does arise (a particle
# is outside of its processors LB grid) an error message is printed and
# the simulation is terminated.
#----------------------------------------------------------------------------
neighbor 1.0 bin
neigh_modify delay 0 every 1 exclude type 1 1
read_data data.four
#----------------------------------------------------------------------------
# None of the particles interact with one another.
#----------------------------------------------------------------------------
pair_style lj/cut 2.45
pair_coeff * * 0.0 0.0 2.45
mass * 1.0
timestep 4.0
group sphere1 id <> 1 320
group sphere2 id <> 321 640
group sphere3 id <> 641 960
group sphere4 id <> 961 1280
velocity sphere1 set 0.0 0.0001 0.0 units box
velocity sphere2 set 0.0 -0.0001 0.0 units box
velocity sphere3 set 0.0 0.0001 0.0 units box
velocity sphere4 set 0.0 -0.0001 0.0 units box
#---------------------------------------------------------------------------
# Create a lattice-Boltzmann fluid covering the simulation domain.
# All of the particles in the simulation apply a force to the fluid.
# Use the LB integration scheme of Ollila et. al. (for stability reasons,
# this integration scheme should be used when a large user set value for
# gamma is specified), a fluid density = 1.0, fluid viscosity = 1.0, value
# for gamma=3.303, lattice spacing dx=4.0, and mass unit, dm=10.0.
# Print the force and torque acting on one of the spherical colloidal objects
# to the screen at each timestep.
#----------------------------------------------------------------------------
fix 1 all lb/fluid 1 2 1.0 1.0 setGamma 3.303 dx 4.0 dm 10.0 calcforce 20 sphere1
#---------------------------------------------------------------------------
# For this simulation the colloidal particles move at a constant velocity
# through the fluid. As such, we do not wish to apply the force from
# the fluid back onto these objects. Therefore, we do not use any of the
# viscous_lb, rigid_pc_sphere, or pc fixes, and simply integrate the
# particle motions using one of the built-in LAMMPS integrators.
#---------------------------------------------------------------------------
fix 2 all nve
run 300000

38
examples/PACKAGES/latboltz/microrheology/in.microrheology_default_gamma → examples/PACKAGES/latboltz/microrheology/in.microrheology
View File

@ -4,13 +4,9 @@
# Run consists of 2 colloidal particles undergoing Brownian motion in a #
# thermal lattice-Boltzmann fluid. #
# #
# Here, gamma (used in the calculation of the particle-fluid interaction #
# force) is calculated by default. Thus, the colloidal objects will have #
# a slightly larger "hydrodynamic" radii than given by the placement of #
# the particle nodes. #
# #
# Sample output from this run can be found in the file: #
# 'microrheology_setgamma.out' #
# If you uncomment the "fix printCM..." line, sample output from this run #
# can be found in the file: #
# 'twocolloid.out' #
#===========================================================================#
units nano
@ -35,6 +31,8 @@ neigh_modify delay 0 every 1
neigh_modify exclude type 2 2
neigh_modify exclude type 2 1
comm_modify cutoff 2.5 # cutoff for communcation shoud be at least 2 dx
#----------------------------------------------------------------------------
# Implement a hard-sphere interaction between the particles at the center of
# each colloidal object (use a truncated and shifted Lennard-Jones
@ -62,22 +60,16 @@ group FluidAtoms type 2
# Create a lattice-Boltzmann fluid covering the simulation domain.
# This fluid feels a force due to the particles specified through FluidAtoms
# (however, this fix does not explicitly apply a force back on to these
# particles...this is accomplished through the use of the viscous_lb fix).
# Use the standard LB integration scheme, a fluid viscosity = 1.0, fluid
# density= 0.0009982071, lattice spacing dx=1.2, and mass unit, dm=0.003.
# Use the default method to calculate the interaction force between the
# particles and the fluid. This calculation requires the surface area
# of the composite object represented by each particle node. By default
# this area is assumed equal to dx*dx; however, since this is not the case
# here, it is input through the setArea keyword (i.e. particles of type 2
# correspond to a surface area of 0.3015928947).
# particles...this is accomplished through the use of the lb/viscous fix).
# Use a fluid viscosity = 1.0, fluid density= 0.0009982071 (water), and a
# lattice spacing dx=1.2.
# Use the trilinear interpolation stencil to distribute the force from
# a given particle onto the fluid mesh.
# Use a thermal lattice-Boltzmann fluid (temperature 300K, random number
# seed=2762). This enables the particles to undergo Brownian motion in
# the fluid.
#----------------------------------------------------------------------------
fix 1 FluidAtoms lb/fluid 1 1 1.0 0.0009982071 setArea 2 0.3015928947 dx 1.2 dm 0.003 trilinear noise 300.0 2762
fix 1 FluidAtoms lb/fluid 1 1.0 0.0009982071 dx 1.2 stencil 2 noise 300.0 2762
#----------------------------------------------------------------------------
# Apply the force due to the fluid onto the FluidAtoms particles (again,
@ -96,10 +88,10 @@ fix 3 all rigid molecule
#----------------------------------------------------------------------------
# To ensure that numerical errors do not lead to a buildup of momentum in the
# system, the momentum_lb fix is used every 10000 timesteps to zero out the
# system, the momentum_lb fix is used every 50000 timesteps to zero out the
# total (particle plus fluid) momentum in the system.
#----------------------------------------------------------------------------
fix 4 all lb/momentum 10000 linear 1 1 1
fix 4 all lb/momentum 50000 linear 1 1 1
#----------------------------------------------------------------------------
# Create variables containing the positions of the central atoms (these
@ -113,7 +105,9 @@ variable x2 equal x[242]
variable y2 equal y[242]
variable z2 equal z[242]
thermo_style custom v_x1 v_y1 v_z1 v_x2 v_y2 v_z2
thermo 1
#fix printCM all print 100 "$(step) ${x1} ${y1} ${z1} ${x2} ${y2} ${z2}" file twocolloid.out screen no
thermo_style custom step v_x1 v_y1 v_z1 v_x2 v_y2 v_z2
thermo 100
run 2000000000
run 2000
#run 2000000000

113
examples/PACKAGES/latboltz/microrheology/in.microrheology_set_gamma
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@ -1,113 +0,0 @@
#===========================================================================#
# 2 particle microrheology test #
# #
# Run consists of 2 colloidal particles undergoing Brownian motion in a #
# thermal lattice-Boltzmann fluid. #
# #
# Here, gamma (used in the calculation of the particle-fluid interaction #
# force) is set by the user (gamma = 1.4692 for this simulation...this #
# value has been calibrated a priori through simulations of the drag #
# force acting on a single particle of the same radius). #
# #
# Sample output from this run can be found in the file: #
# 'microrheology_setgamma.out' #
#===========================================================================#
units nano
dimension 3
boundary p p p
atom_style molecular
read_data data.two
#----------------------------------------------------------------------------
# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing
# to ensure that the particles belonging to a given processor remain inside
# that processors lattice-Boltzmann grid.
# The arguments for neigh_modify have been set to "delay 0 every 1", again
# to ensure that the particles belonging to a given processor remain inside
# that processors lattice-Boltzmann grid. However, these values can likely
# be somewhat increased without issue. If a problem does arise (a particle
# is outside of its processors LB grid) an error message is printed and
# the simulation is terminated.
#----------------------------------------------------------------------------
neighbor 0.3 bin
neigh_modify delay 0 every 1
neigh_modify exclude type 2 2
neigh_modify exclude type 2 1
#----------------------------------------------------------------------------
# Implement a hard-sphere interaction between the particles at the center of
# each colloidal object (use a truncated and shifted Lennard-Jones
# potential).
#----------------------------------------------------------------------------
pair_style lj/cut 5.88
pair_coeff * * 0.0 0.0 5.88
pair_coeff 1 1 100.0 5.238484463 5.88
pair_modify shift yes
mass * 0.0002398
timestep 0.00045
#----------------------------------------------------------------------------
# ForceAtoms are the particles at the center of each colloidal object which
# do not interact with the fluid, but are used to implement the hard-sphere
# interactions.
# FluidAtoms are the particles representing the surface of the colloidal
# object which do interact with the fluid.
#----------------------------------------------------------------------------
group ForceAtoms type 1
group FluidAtoms type 2
#---------------------------------------------------------------------------
# Create a lattice-Boltzmann fluid covering the simulation domain.
# This fluid feels a force due to the particles specified through FluidAtoms
# (however, this fix does not explicitly apply a force back on to these
# particles...this is accomplished through the use of the rigid_pc_sphere
# fix).
# Use the LB integration scheme of Ollila et. al. (for stability reasons,
# this integration scheme should be used when a large user set value for
# gamma is specified), a fluid viscosity = 1.0, fluid density= 0.0009982071,
# value for gamma=1.4692, lattice spacing dx=1.2, and mass unit, dm=0.003.
# Use a thermal lattice-Boltzmann fluid (temperature 300K, random number
# seed=2762). This enables the particles to undergo Brownian motion in
# the fluid.
#----------------------------------------------------------------------------
fix 1 FluidAtoms lb/fluid 1 2 1.0 0.0009982071 setGamma 1.4692 dx 1.2 dm 0.003 noise 300.0 2762
#----------------------------------------------------------------------------
# Apply the force from the fluid to the particles, and integrate their
# motion, constraining them to move and rotate together as a single rigid
# spherical object.
# Since both the ForceAtoms (central atoms), and the FluidAtoms (spherical
# shell) should move and rotate together, this fix is applied to all of
# the atoms in the system. However, since the central atoms should not
# feel a force due to the fluid, they are excluded from the fluid force
# calculation through the use of the 'innerNodes' keyword.
# NOTE: This fix should only be used when the user specifies a value for
# gamma (through the setGamma keyword) in the lb_fluid fix.
#----------------------------------------------------------------------------
fix 2 all lb/rigid/pc/sphere molecule innerNodes ForceAtoms
#----------------------------------------------------------------------------
# To ensure that numerical errors do not lead to a buildup of momentum in the
# system, the momentum_lb fix is used every 10000 timesteps to zero out the
# total (particle plus fluid) momentum in the system.
#----------------------------------------------------------------------------
fix 3 all lb/momentum 10000 linear 1 1 1
#----------------------------------------------------------------------------
# Create variables containing the positions of the central atoms (these
# values should correspond to the center of mass of each composite
# colloidal particle), and output these quantities to the screen.
#----------------------------------------------------------------------------
variable x1 equal x[1]
variable y1 equal y[1]
variable z1 equal z[1]
variable x2 equal x[242]
variable y2 equal y[242]
variable z2 equal z[242]
thermo_style custom v_x1 v_y1 v_z1 v_x2 v_y2 v_z2
thermo 1
run 2000000000

216
examples/PACKAGES/latboltz/microrheology/log.09Mar22.microrheology.g++.4 Normal file
View File

@ -0,0 +1,216 @@
LAMMPS (17 Feb 2022)
#===========================================================================#
# 2 particle microrheology test #
# #
# Run consists of 2 colloidal particles undergoing Brownian motion in a #
# thermal lattice-Boltzmann fluid. #
# #
# If you uncomment the "fix printCM..." line, sample output from this run #
# can be found in the file: #
# 'twocolloid.out' #
#===========================================================================#
units nano
dimension 3
boundary p p p
atom_style molecular
read_data data.two
Reading data file ...
orthogonal box = (-48 -48 -48) to (48 48 48)
1 by 2 by 2 MPI processor grid
reading atoms ...
482 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.033 seconds
#----------------------------------------------------------------------------
# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing
# to ensure that the particles belonging to a given processor remain inside
# that processors lattice-Boltzmann grid.
# The arguments for neigh_modify have been set to "delay 0 every 1", again
# to ensure that the particles belonging to a given processor remain inside
# that processors lattice-Boltzmann grid. However, these values can likely
# be somewhat increased without issue. If a problem does arise (a particle
# is outside of its processors LB grid) an error message is printed and
# the simulation is terminated.
#----------------------------------------------------------------------------
neighbor 0.3 bin
neigh_modify delay 0 every 1
neigh_modify exclude type 2 2
neigh_modify exclude type 2 1
comm_modify cutoff 2.5 # cutoff for communcation shoud be at least 2 dx
#----------------------------------------------------------------------------
# Implement a hard-sphere interaction between the particles at the center of
# each colloidal object (use a truncated and shifted Lennard-Jones
# potential).
#----------------------------------------------------------------------------
pair_style lj/cut 5.88
pair_coeff * * 0.0 0.0 5.88
pair_coeff 1 1 100.0 5.238484463 5.88
pair_modify shift yes
mass * 0.0002398
timestep 0.00025
#----------------------------------------------------------------------------
# ForceAtoms are the particles at the center of each colloidal object which
# do not interact with the fluid, but are used to implement the hard-sphere
# interactions.
# FluidAtoms are the particles representing the surface of the colloidal
# object which do interact with the fluid.
#----------------------------------------------------------------------------
group ForceAtoms type 1
2 atoms in group ForceAtoms
group FluidAtoms type 2
480 atoms in group FluidAtoms
#---------------------------------------------------------------------------
# Create a lattice-Boltzmann fluid covering the simulation domain.
# This fluid feels a force due to the particles specified through FluidAtoms
# (however, this fix does not explicitly apply a force back on to these
# particles...this is accomplished through the use of the lb/viscous fix).
# Use a fluid viscosity = 1.0, fluid density= 0.0009982071 (water), and a
# lattice spacing dx=1.2.
# Use the trilinear interpolation stencil to distribute the force from
# a given particle onto the fluid mesh.
# Use a thermal lattice-Boltzmann fluid (temperature 300K, random number
# seed=2762). This enables the particles to undergo Brownian motion in
# the fluid.
#----------------------------------------------------------------------------
fix 1 FluidAtoms lb/fluid 1 1.0 0.0009982071 dx 1.2 stencil 2 noise 300.0 2762
Using a lattice-Boltzmann grid of 80 by 80 by 80 total grid points. (../fix_lb_fluid.cpp:486)
Local Grid Geometry created. (../fix_lb_fluid.cpp:1018)
#----------------------------------------------------------------------------
# Apply the force due to the fluid onto the FluidAtoms particles (again,
# these atoms represent the surface of the colloidal object, which should
# interact with the fluid).
#----------------------------------------------------------------------------
fix 2 FluidAtoms lb/viscous
#----------------------------------------------------------------------------
# Each colloidal object (spherical shell of particles and central particle)
# is specified as a separate molecule in the confinedcolloids.dat data
# file. Integrate the motion of these sets of particles as rigid objects
# which each move and rotate together.
#----------------------------------------------------------------------------
fix 3 all rigid molecule
2 rigid bodies with 482 atoms
#----------------------------------------------------------------------------
# To ensure that numerical errors do not lead to a buildup of momentum in the
# system, the momentum_lb fix is used every 50000 timesteps to zero out the
# total (particle plus fluid) momentum in the system.
#----------------------------------------------------------------------------
fix 4 all lb/momentum 50000 linear 1 1 1
#----------------------------------------------------------------------------
# Create variables containing the positions of the central atoms (these
# values should correspond to the center of mass of each composite
# colloidal particle), and output these quantities to the screen.
#----------------------------------------------------------------------------
variable x1 equal x[1]
variable y1 equal y[1]
variable z1 equal z[1]
variable x2 equal x[242]
variable y2 equal y[242]
variable z2 equal z[242]
#fix printCM all print 100 "$(step) ${x1} ${y1} ${z1} ${x2} ${y2} ${z2}" file twocolloid.out screen no
thermo_style custom step v_x1 v_y1 v_z1 v_x2 v_y2 v_z2
thermo 100
run 2000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- fix lb/fluid command:
@Article{Denniston et al.,
author = {C. Denniston, N. Afrasiabian, M.G. Cole-Andre,F.E. Mackay, S.T.T. Ollila, T. Whitehead},
title = {LAMMPS lb/fluid fix version 2: Improved Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid}, journal = {Comp.~Phys.~Comm.},
year = 2022,
volume = 275,
pages = {108318}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.18
ghost atom cutoff = 6.18
binsize = 3.09, bins = 32 32 32
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
WARNING: Communication cutoff adjusted to 6.18 (../comm.cpp:732)
Per MPI rank memory allocation (min/avg/max) = 7.071 | 7.133 | 7.196 Mbytes
Step v_x1 v_y1 v_z1 v_x2 v_y2 v_z2
0 -6 -6 -6 6 6 6
100 -5.9728258 -6.0005827 -5.9442685 5.9742978 6.0301171 5.9331116
200 -5.9160265 -5.9832234 -5.9485519 6.0258914 6.0954103 5.8748455
300 -5.859605 -5.9503512 -5.9827305 6.0472442 6.0610438 5.8531801
400 -5.8495832 -5.923183 -6.0205706 6.1502952 5.9975714 5.8964144
500 -5.8229958 -5.9256007 -5.963852 6.1738854 5.8961268 5.8723276
600 -5.7813718 -5.9423848 -5.9309537 6.2083705 5.866578 5.9308017
700 -5.7652512 -5.8737534 -5.9083059 6.2502919 5.757157 5.9690204
800 -5.7586139 -5.8559089 -5.8863028 6.2708214 5.7307727 5.9443721
900 -5.7200104 -5.8603762 -5.8944329 6.28719 5.7723113 5.9660136
1000 -5.7224239 -5.8487095 -5.9013071 6.3156272 5.8026721 5.9558441
1100 -5.576187 -5.8604571 -5.9254376 6.3778561 5.7655467 5.9702619
1200 -5.5348377 -5.8086817 -5.9982829 6.3979309 5.8028207 5.930579
1300 -5.5937473 -5.7733457 -6.0596682 6.3630776 5.937045 5.9662317
1400 -5.6207137 -5.7027974 -6.0641922 6.3079248 5.9631009 5.9707377
1500 -5.6648138 -5.6229854 -6.0989624 6.2784552 5.9448163 5.9254903
1600 -5.6905161 -5.5479418 -6.0704567 6.3133179 5.941372 5.8933924
1700 -5.6878847 -5.5415566 -6.0222328 6.3633902 5.9957476 5.7994115
1800 -5.6500526 -5.5204331 -5.9767389 6.4081067 5.9651289 5.7297962
1900 -5.7221835 -5.4972898 -5.9670446 6.4470403 5.9161644 5.6902098
2000 -5.7427378 -5.4637388 -6.0196569 6.3668465 5.9127502 5.6931183
Loop time of 358.9 on 4 procs for 2000 steps with 482 atoms
Performance: 120.368 ns/day, 0.199 hours/ns, 5.573 timesteps/s
100.0% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0026566 | 0.0054654 | 0.0084461 | 3.6 | 0.00
Bond | 0.0003946 | 0.000476 | 0.0005288 | 0.0 | 0.00
Neigh | 0.0011268 | 0.0045933 | 0.0080717 | 5.0 | 0.00
Comm | 0.053156 | 0.057764 | 0.062919 | 1.9 | 0.02
Output | 0.0009824 | 0.0018621 | 0.0043906 | 3.4 | 0.00
Modify | 358.62 | 358.63 | 358.64 | 0.0 | 99.93
Other | | 0.1963 | | | 0.05
Nlocal: 120.5 ave 241 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 181 ave 297 max 80 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 0
Neighbor list builds = 20
Dangerous builds = 0
#run 2000000000
Total wall time: 0:05:59

50000
examples/PACKAGES/latboltz/microrheology/microrheology_defaultgamma.out
View File

File diff suppressed because it is too large Load Diff

50000
examples/PACKAGES/latboltz/microrheology/microrheology_setgamma.out
View File

File diff suppressed because it is too large Load Diff

6
examples/PACKAGES/latboltz/dragforce/data.one_radius16d2 → examples/PACKAGES/latboltz/pit_geometry/data.one_radius16d2
View File

@ -2,9 +2,9 @@
320 atoms
1 atom types
-160.0 160.0 xlo xhi
-160.0 160.0 ylo yhi
-160.0 160.0 zlo zhi
-120.0 120.0 xlo xhi
-100.0 100.0 ylo yhi
-120.0 120.0 zlo zhi
Atoms

82
examples/PACKAGES/latboltz/planewall/in.planewall_set_gamma → examples/PACKAGES/latboltz/pit_geometry/in.pits
View File

@ -1,16 +1,16 @@
#===========================================================================#
# Rigid sphere freely moving near a stationary plane wall in a system #
# undergoing shear flow. #
# Every 10 time steps the center of mass velocity and angular velocity of #
# the sphere are printed to the screen. #
# #
# Here, gamma (used in the calculation of the particle-fluid interaction #
# force) is set by the user (gamma = 13.655 for this simulation...this #
# value has been calibrated a priori through simulations of the drag #
# force acting on a single particle of the same radius). #
# Rigid sphere freely moving in a system with pressure driven flow through #
# a pit geometry. #
# #
# Sample output from this run can be found in the file: #
# 'wall_setgamma.out' #
# If uncommented, the example produces several output files: #
# 'flow.xdmf', 'flow.raw' ... xdmf and accompanying binary file for the #
# fluid density and velocity which can be read#
# and plotted using Paraview. #
# 'dumpatomsXX.vtp', 'dumpatomsXX_boundingBox.vtr' ... produces by the #
# dumpvtk routine (requires that lammps be #
# compiled with the vtk package). These filed#
# can also be read and plotted using Paraview.#
# XX is the timestep of the dump output. #
#===========================================================================#
units micro
@ -42,7 +42,7 @@ pair_coeff * * 0.0 0.0 2.45
neigh_modify exclude type 1 1
mass * 100.0
timestep 4.0
timestep 2.0
group sphere1 id <> 1 320
@ -54,26 +54,48 @@ velocity all set 0.0 0.0 0.0 units box
#----------------------------------------------------------------------------
# Create a lattice-Boltzmann fluid covering the simulation domain.
# All of the particles in the simulation apply a force to the fluid.
# (however, this fix does not explicitly apply a force back on to these
# particles...this is accomplished through the use of the rigid_pc_sphere
# fix).
# Use the LB integration scheme of Ollila et. al. (for stability reasons,
# this integration scheme should be used when a large user set value for
# gamma is specified), a fluid density = 1.0, fluid viscosity = 1.0, value
# for gamma=13.655, lattice spacing dx=4.0, and mass unit, dm=10.0.
# Create shear in the system, by giving the upper z-wall a velocity of 0.0001
# along the y-direction, while keeping the lower z-wall stationary.
# (however, this fix does not explicity apply a force back on to these
# particles...this is accomplished through the use of the lb/viscous fix).
# Set the fluid density = 1.0, fluid viscosity = 1.0 (water), and lattice
# spacing dx=4.0.
# dumpxdmf is set to output to the xdmf file (fflow.xdmf and fflow.raw) every
# 2500 steps, indexed by the frame number (rather than timestep).
# The flow is generated via a pressure jump at the otherwise periodic x-
# boundary using the pressurebcx option.
# The initial conditions are set as linear interpolation between boundary
# values using the linearInit option.
#-----------------------------------------------------------------------------
fix 1 all lb/fluid 1 2 1.0 1.0 setGamma 13.655 dx 4.0 dm 10.0 zwall_velocity 0.0 0.0001
fix 1 all lb/fluid 1 1.0 1.0 dx 4.0 linearInit pressurebcx 0.01 npits 2 20 40 5 0 wp 30 # dumpxdmf 2500 fflow 0
#-----------------------------------------------------------------------------
# You can get some other interesting geometries by replacing the npits options
# at the end of the above lb/fluid fix with one of the following:
#-----------------------------------------------------------------------------
# Channel with 2 pits placed symmetrically about center in x:
#npits 2 20 20 10 5 sw
# Channel with 1 pit placed at center:
#npits 1 20 20 20 sw
# Full channel with 1 "speedbump" placed in right end of the channel:
#npits 2 20 40 5 0 sw
# Channel with 2 "potholes" placed symmetrically about center in x:
#npits 2 20 15 10 10 wp 30
# Channel with T-shaped cross-section with a "speedbump" in right end:
#npits 2 20 40 5 0 wp 30
# Long rectangular channel (all pit, no slit):
#npits 1 20 65 5 0 sw
#----------------------------------------------------------------------------
# Apply the force from the fluid to the particles, and integrate their
# motion, constraining them to move and rotate together as a single rigid
# spherical object.
# NOTE: This fix should only be used when the user specifies a value for
# gamma (through the setGamma keyword) in the lb_fluid fix.
#----------------------------------------------------------------------------
fix 2 all lb/rigid/pc/sphere group 1 sphere1
#----------------------------------------------------------------------------
fix 2 all lb/viscous
fix 3 all rigid group 1 sphere1
#----------------------------------------------------------------------------
# Create variables for the center-of-mass and angular velocities, and output
@ -86,7 +108,9 @@ variable omegax equal omega(all,x)
variable omegay equal omega(all,y)
variable omegaz equal omega(all,z)
thermo_style custom v_vx v_vy v_vz v_omegax v_omegay v_omegaz
thermo 10
thermo_style custom step f_1[2] v_vx v_vy v_vz v_omegax v_omegay v_omegaz
thermo 500
run 200000
#dump dumpvtk all vtk 2500 dumpatoms*.vtp vx vy vz
run 2500

193
examples/PACKAGES/latboltz/pit_geometry/log.09Mar22.pits.g++.1 Normal file
View File

@ -0,0 +1,193 @@
LAMMPS (17 Feb 2022)
#===========================================================================#
# Rigid sphere freely moving in a system with pressure driven flow through #
# a pit geometry. #
# #
# If uncommented, the example produces several output files: #
# 'flow.xdmf', 'flow.raw' ... xdmf and accompanying binary file for the #
# fluid density and velocity which can be read#
# and plotted using Paraview. #
# 'dumpatomsXX.vtp', 'dumpatomsXX_boundingBox.vtr' ... produces by the #
# dumpvtk routine (requires that lammps be #
# compiled with the vtk package). These filed#
# can also be read and plotted using Paraview.#
# XX is the timestep of the dump output. #
#===========================================================================#
units micro
dimension 3
boundary p p f
atom_style atomic
#----------------------------------------------------------------------------
# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing
# to ensure that the particles belonging to a given processor remain inside
# that processors lattice-Boltzmann grid.
# The arguments for neigh_modify have been set to "delay 0 every 1", again
# to ensure that the particles belonging to a given processor remain inside
# that processors lattice-Boltzmann grid. However, these values can likely
# be somewhat increased without issue. If a problem does arise (a particle
# is outside of its processors LB grid) an error message is printed and
# the simulation is terminated.
#----------------------------------------------------------------------------
neighbor 1.0 bin
neigh_modify delay 0 every 1
read_data data.one_radius16d2
Reading data file ...
orthogonal box = (-120 -100 -120) to (120 100 120)
1 by 1 by 1 MPI processor grid
reading atoms ...
320 atoms
read_data CPU = 0.010 seconds
#----------------------------------------------------------------------------
# None of the particles interact with one another.
#----------------------------------------------------------------------------
pair_style lj/cut 2.45
pair_coeff * * 0.0 0.0 2.45
neigh_modify exclude type 1 1
mass * 100.0
timestep 2.0
group sphere1 id <> 1 320
320 atoms in group sphere1
#----------------------------------------------------------------------------
# Colloidal particle is initially stationary.
#----------------------------------------------------------------------------
velocity all set 0.0 0.0 0.0 units box
#----------------------------------------------------------------------------
# Create a lattice-Boltzmann fluid covering the simulation domain.
# All of the particles in the simulation apply a force to the fluid.
# (however, this fix does not explicity apply a force back on to these
# particles...this is accomplished through the use of the lb/viscous fix).
# Set the fluid density = 1.0, fluid viscosity = 1.0 (water), and lattice
# spacing dx=4.0.
# dumpxdmf is set to output to the xdmf file (fflow.xdmf and fflow.raw) every
# 2500 steps, indexed by the frame number (rather than timestep).
# The flow is generated via a pressure jump at the otherwise periodic x-
# boundary using the pressurebcx option.
# The initial conditions are set as linear interpolation between boundary
# values using the linearInit option.
#-----------------------------------------------------------------------------
fix 1 all lb/fluid 1 1.0 1.0 dx 4.0 linearInit pressurebcx 0.01 npits 2 20 40 5 0 wp 30 # dumpxdmf 2500 fflow 0
Using a lattice-Boltzmann grid of 60 by 50 by 61 total grid points. (../fix_lb_fluid.cpp:486)
length of pits and end segments larger than system size in x-direction: truncation will occur (../fix_lb_fluid.cpp:505)
Local Grid Geometry created. (../fix_lb_fluid.cpp:1018)
#-----------------------------------------------------------------------------
# You can get some other interesting geometries by replacing the npits options
# at the end of the above lb/fluid fix with one of the following:
#-----------------------------------------------------------------------------
# Channel with 2 pits placed symmetrically about center in x:
#npits 2 20 20 10 5 sw
# Channel with 1 pit placed at center:
#npits 1 20 20 20 sw
# Full channel with 1 "speedbump" placed in right end of the channel:
#npits 2 20 40 5 0 sw
# Channel with 2 "potholes" placed symmetrically about center in x:
#npits 2 20 15 10 10 wp 30
# Channel with T-shaped cross-section with a "speedbump" in right end:
#npits 2 20 40 5 0 wp 30
# Long rectangular channel (all pit, no slit):
#npits 1 20 65 5 0 sw
#----------------------------------------------------------------------------
# Apply the force from the fluid to the particles, and integrate their
# motion, constraining them to move and rotate together as a single rigid
# spherical object.
#----------------------------------------------------------------------------
fix 2 all lb/viscous
fix 3 all rigid group 1 sphere1
1 rigid bodies with 320 atoms
#----------------------------------------------------------------------------
# Create variables for the center-of-mass and angular velocities, and output
# these quantities to the screen.
#----------------------------------------------------------------------------
variable vx equal vcm(all,x)
variable vy equal vcm(all,y)
variable vz equal vcm(all,z)
variable omegax equal omega(all,x)
variable omegay equal omega(all,y)
variable omegaz equal omega(all,z)
thermo_style custom step f_1[2] v_vx v_vy v_vz v_omegax v_omegay v_omegaz
thermo 500
#dump dumpvtk all vtk 2500 dumpatoms*.vtp vx vy vz
run 2500
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- fix lb/fluid command:
@Article{Denniston et al.,
author = {C. Denniston, N. Afrasiabian, M.G. Cole-Andre,F.E. Mackay, S.T.T. Ollila, T. Whitehead},
title = {LAMMPS lb/fluid fix version 2: Improved Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid}, journal = {Comp.~Phys.~Comm.},
year = 2022,
volume = 275,
pages = {108318}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3.45
ghost atom cutoff = 3.45
binsize = 1.725, bins = 140 116 140
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 14.01 | 14.01 | 14.01 Mbytes
Step f_1[2] v_vx v_vy v_vz v_omegax v_omegay v_omegaz
0 10054461 0 0 0 0 0 0
500 10055203 0.008268321 2.9442616e-05 0.0019660229 -5.0307394e-07 2.1873981e-05 2.2701522e-07
1000 10055487 0.015301314 4.219514e-05 0.0029217734 -6.9936017e-07 6.8198965e-05 5.2031048e-07
1500 10055663 0.02117119 2.9194379e-05 0.002365636 -7.5401298e-07 0.00011557032 4.0311183e-07
2000 10055781 0.02523262 -9.149834e-06 -0.0001724854 -2.5872732e-07 0.00014864932 3.7644295e-07
2500 10055866 0.02651785 -5.2469712e-05 -0.0030476651 2.9151609e-07 0.00014663544 7.8650891e-07
Loop time of 111.461 on 1 procs for 2500 steps with 320 atoms
Performance: 3875808849.457 ns/day, 0.000 hours/ns, 22.429 timesteps/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0072314 | 0.0072314 | 0.0072314 | 0.0 | 0.01
Neigh | 0.26791 | 0.26791 | 0.26791 | 0.0 | 0.24
Comm | 0.0092553 | 0.0092553 | 0.0092553 | 0.0 | 0.01
Output | 0.0054858 | 0.0054858 | 0.0054858 | 0.0 | 0.00
Modify | 111.15 | 111.15 | 111.15 | 0.0 | 99.72
Other | | 0.01779 | | | 0.02
Nlocal: 320 ave 320 max 320 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 176
Dangerous builds = 0
Total wall time: 0:01:51

193
examples/PACKAGES/latboltz/pit_geometry/log.09Mar22.pits.g++.4 Normal file
View File

@ -0,0 +1,193 @@
LAMMPS (17 Feb 2022)
#===========================================================================#
# Rigid sphere freely moving in a system with pressure driven flow through #
# a pit geometry. #
# #
# If uncommented, the example produces several output files: #
# 'flow.xdmf', 'flow.raw' ... xdmf and accompanying binary file for the #
# fluid density and velocity which can be read#
# and plotted using Paraview. #
# 'dumpatomsXX.vtp', 'dumpatomsXX_boundingBox.vtr' ... produces by the #
# dumpvtk routine (requires that lammps be #
# compiled with the vtk package). These filed#
# can also be read and plotted using Paraview.#
# XX is the timestep of the dump output. #
#===========================================================================#
units micro
dimension 3
boundary p p f
atom_style atomic
#----------------------------------------------------------------------------
# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing
# to ensure that the particles belonging to a given processor remain inside
# that processors lattice-Boltzmann grid.
# The arguments for neigh_modify have been set to "delay 0 every 1", again
# to ensure that the particles belonging to a given processor remain inside
# that processors lattice-Boltzmann grid. However, these values can likely
# be somewhat increased without issue. If a problem does arise (a particle
# is outside of its processors LB grid) an error message is printed and
# the simulation is terminated.
#----------------------------------------------------------------------------
neighbor 1.0 bin
neigh_modify delay 0 every 1
read_data data.one_radius16d2
Reading data file ...
orthogonal box = (-120 -100 -120) to (120 100 120)
2 by 1 by 2 MPI processor grid
reading atoms ...
320 atoms
read_data CPU = 0.012 seconds
#----------------------------------------------------------------------------
# None of the particles interact with one another.
#----------------------------------------------------------------------------
pair_style lj/cut 2.45
pair_coeff * * 0.0 0.0 2.45
neigh_modify exclude type 1 1
mass * 100.0
timestep 2.0
group sphere1 id <> 1 320
320 atoms in group sphere1
#----------------------------------------------------------------------------
# Colloidal particle is initially stationary.
#----------------------------------------------------------------------------
velocity all set 0.0 0.0 0.0 units box
#----------------------------------------------------------------------------
# Create a lattice-Boltzmann fluid covering the simulation domain.
# All of the particles in the simulation apply a force to the fluid.
# (however, this fix does not explicity apply a force back on to these
# particles...this is accomplished through the use of the lb/viscous fix).
# Set the fluid density = 1.0, fluid viscosity = 1.0 (water), and lattice
# spacing dx=4.0.
# dumpxdmf is set to output to the xdmf file (fflow.xdmf and fflow.raw) every
# 2500 steps, indexed by the frame number (rather than timestep).
# The flow is generated via a pressure jump at the otherwise periodic x-
# boundary using the pressurebcx option.
# The initial conditions are set as linear interpolation between boundary
# values using the linearInit option.
#-----------------------------------------------------------------------------
fix 1 all lb/fluid 1 1.0 1.0 dx 4.0 linearInit pressurebcx 0.01 npits 2 20 40 5 0 wp 30 # dumpxdmf 2500 fflow 0
Using a lattice-Boltzmann grid of 60 by 50 by 61 total grid points. (../fix_lb_fluid.cpp:486)
length of pits and end segments larger than system size in x-direction: truncation will occur (../fix_lb_fluid.cpp:505)
Local Grid Geometry created. (../fix_lb_fluid.cpp:1018)
#-----------------------------------------------------------------------------
# You can get some other interesting geometries by replacing the npits options
# at the end of the above lb/fluid fix with one of the following:
#-----------------------------------------------------------------------------
# Channel with 2 pits placed symmetrically about center in x:
#npits 2 20 20 10 5 sw
# Channel with 1 pit placed at center:
#npits 1 20 20 20 sw
# Full channel with 1 "speedbump" placed in right end of the channel:
#npits 2 20 40 5 0 sw
# Channel with 2 "potholes" placed symmetrically about center in x:
#npits 2 20 15 10 10 wp 30
# Channel with T-shaped cross-section with a "speedbump" in right end:
#npits 2 20 40 5 0 wp 30
# Long rectangular channel (all pit, no slit):
#npits 1 20 65 5 0 sw
#----------------------------------------------------------------------------
# Apply the force from the fluid to the particles, and integrate their
# motion, constraining them to move and rotate together as a single rigid
# spherical object.
#----------------------------------------------------------------------------
fix 2 all lb/viscous
fix 3 all rigid group 1 sphere1
1 rigid bodies with 320 atoms
#----------------------------------------------------------------------------
# Create variables for the center-of-mass and angular velocities, and output
# these quantities to the screen.
#----------------------------------------------------------------------------
variable vx equal vcm(all,x)
variable vy equal vcm(all,y)
variable vz equal vcm(all,z)
variable omegax equal omega(all,x)
variable omegay equal omega(all,y)
variable omegaz equal omega(all,z)
thermo_style custom step f_1[2] v_vx v_vy v_vz v_omegax v_omegay v_omegaz
thermo 500
#dump dumpvtk all vtk 2500 dumpatoms*.vtp vx vy vz
run 2500
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- fix lb/fluid command:
@Article{Denniston et al.,
author = {C. Denniston, N. Afrasiabian, M.G. Cole-Andre,F.E. Mackay, S.T.T. Ollila, T. Whitehead},
title = {LAMMPS lb/fluid fix version 2: Improved Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid}, journal = {Comp.~Phys.~Comm.},
year = 2022,
volume = 275,
pages = {108318}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3.45
ghost atom cutoff = 3.45
binsize = 1.725, bins = 140 116 140
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.973 | 6.973 | 6.973 Mbytes
Step f_1[2] v_vx v_vy v_vz v_omegax v_omegay v_omegaz
0 10054461 0 0 0 0 0 0
500 10055203 0.008268321 2.9442616e-05 0.0019660229 -5.0307394e-07 2.1873981e-05 2.2701522e-07
1000 10055487 0.015301314 4.219514e-05 0.0029217734 -6.9936017e-07 6.8198965e-05 5.2031048e-07
1500 10055663 0.02117119 2.9194379e-05 0.002365636 -7.5401298e-07 0.00011557032 4.0311183e-07
2000 10055781 0.02523262 -9.149834e-06 -0.0001724854 -2.5872732e-07 0.00014864932 3.7644295e-07
2500 10055866 0.02651785 -5.2469712e-05 -0.0030476651 2.9151609e-07 0.00014663544 7.8650891e-07
Loop time of 86.7379 on 4 procs for 2500 steps with 320 atoms
Performance: 4980523049.256 ns/day, 0.000 hours/ns, 28.822 timesteps/s
99.1% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.005625 | 0.0081021 | 0.011663 | 2.9 | 0.01
Neigh | 0.25946 | 0.26966 | 0.28604 | 2.0 | 0.31
Comm | 0.032947 | 0.047576 | 0.069872 | 7.0 | 0.05
Output | 0.0038996 | 0.0041104 | 0.0047328 | 0.6 | 0.00
Modify | 86.297 | 86.325 | 86.351 | 0.3 | 99.52
Other | | 0.08361 | | | 0.10
Nlocal: 80 ave 219 max 0 min
Histogram: 2 0 0 0 1 0 0 0 0 1
Nghost: 17.75 ave 36 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 176
Dangerous builds = 0
Total wall time: 0:01:26

6
examples/PACKAGES/latboltz/planewall/data.one_radius16d2
View File

@ -2,9 +2,9 @@
320 atoms
1 atom types
-160.0 160.0 xlo xhi
-160.0 160.0 ylo yhi
-40.0 280.0 zlo zhi
-120.0 120.0 xlo xhi
-120.0 120.0 ylo yhi
-120.0 120.0 zlo zhi
Atoms

64
examples/PACKAGES/latboltz/planewall/in.planewall_default_gamma → examples/PACKAGES/latboltz/planewall/in.planewall
View File

@ -1,16 +1,11 @@
#===========================================================================#
# Rigid sphere freely moving near a stationary plane wall in a system #
# undergoing shear flow. #
# undergoing shear flow. #
# Every 10 time steps the center of mass velocity and angular velocity of #
# the sphere are printed to the screen. #
# #
# Here, gamma (used in the calculation of the particle-fluid interaction #
# force) is calculated by default. Thus, the colloidal objects will have #
# a slightly larger "hydrodynamic" radii than given by the placement of #
# the particle nodes. #
# the sphere are printed to the screen. #
# To run this example, LAMMPS needs to be compiled with a the following #
# packages: RIGID, LATBOLTZ #
# #
# Sample output from this run can be found in the file: #
# 'wall_defaultgamma.out' #
#===========================================================================#
units micro
@ -28,9 +23,12 @@ atom_style atomic
# be somewhat increased without issue. If a problem does arise (a particle
# is outside of its processors LB grid) an error message is printed and
# the simulation is terminated.
# The communcation cutoff is set to 2.5 dx to ensure that all particles in the
# processor ghost fluid region (of width 2dx) are known to local processor.
#----------------------------------------------------------------------------
neighbor 1.0 bin
neigh_modify delay 0 every 1
comm_modify cutoff 10.0
read_data data.one_radius16d2
@ -41,8 +39,9 @@ pair_style lj/cut 2.45
pair_coeff * * 0.0 0.0 2.45
neigh_modify exclude type 1 1
mass * 100.0
timestep 3.0
mass * 1.0
timestep 4.0
group sphere1 id <> 1 320
@ -55,21 +54,15 @@ velocity all set 0.0 0.0 0.0 units box
# Create a lattice-Boltzmann fluid covering the simulation domain.
# All of the particles in the simulation apply a force to the fluid.
# (however, this fix does not explicitly apply a force back on to these
# particles...this is accomplished through the use of the viscous_lb fix.
# Use the standard LB integration scheme, a fluid density = 1.0,
# fluid viscosity = 1.0, lattice spacing dx=4.0, and mass unit, dm=10.0.
# Use the default method to calculate the interaction force between the
# particles and the fluid. This calculation requires the surface area
# of the composite object represented by each particle node. By default
# this area is assumed equal to dx*dx; however, since this is not the case
# here, it is input through the setArea keyword (i.e. particles of type 1
# correspond to a surface area of 10.3059947).
# Use the trilinear interpolation stencil to distribute the force from
# a given particle onto the fluid mesh.
# particles...this is accomplished through the use of the lb/viscous fix.
# Use a fluid density = 1.0, fluid viscosity = 1.0 (water), and a lattice
# spacing dx=4.0.
# Use the trilinear interpolation stencil (default) to distribute the force
# from a given particle onto the fluid mesh.
# Create shear in the system, by giving the upper z-wall a velocity of 0.0001
# along the y-direction, while keeping the lower z-wall stationary.
#-----------------------------------------------------------------------------
fix 1 all lb/fluid 1 1 1.0 1.0 setArea 1 10.3059947 dx 4.0 dm 10.0 trilinear zwall_velocity 0.0 0.0001
fix 1 all lb/fluid 1 1.0 1.0 dx 4.0 zwall_velocity 0.0 0.0001
#----------------------------------------------------------------------------
# Apply the force due to the fluid onto the particles.
@ -78,13 +71,18 @@ fix 2 all lb/viscous
#----------------------------------------------------------------------------
# Integrate the motion of the particles, constraining them to move and
# rotate together as a single rigid spherical object.
# rotate together as a single rigid spherical object. Use the first
# version to allow the sphere to freely rotate and move with the fluid
# and the 2nd version to measure the force and torque on a fixed sphere
# in the shear flow which will allow you to measure the Stokes drag and
# torque on the sphere.
#----------------------------------------------------------------------------
fix 3 all rigid group 1 sphere1
fix 3 all rigid group 1 sphere1
#fix 3 all rigid group 1 sphere1 force * off off off torque * off off off
#----------------------------------------------------------------------------
# Create variables for the center-of-mass and angular velocities, and output
# these quantities to the screen.
# Create variables for the center-of-mass velocities, angular velocities, and
# force and torque on the CM. Then output these quantities to the screen.
#----------------------------------------------------------------------------
variable vx equal vcm(all,x)
variable vy equal vcm(all,y)
@ -92,8 +90,14 @@ variable vz equal vcm(all,z)
variable omegax equal omega(all,x)
variable omegay equal omega(all,y)
variable omegaz equal omega(all,z)
variable fx equal fcm(all,x)
variable fy equal fcm(all,y)
variable fz equal fcm(all,z)
variable tx equal torque(all,x)
variable ty equal torque(all,y)
variable tz equal torque(all,z)
thermo_style custom v_vx v_vy v_vz v_omegax v_omegay v_omegaz
thermo 10
thermo_style custom v_vx v_vy v_vz v_omegax v_omegay v_omegaz v_fx v_fy v_fz v_tx v_ty v_tz
thermo 100
run 200000
run 7500

249
examples/PACKAGES/latboltz/planewall/log.09Mar22.planewall.g++.4 Normal file
View File

@ -0,0 +1,249 @@
LAMMPS (17 Feb 2022)
#===========================================================================#
# Rigid sphere freely moving near a stationary plane wall in a system #
# undergoing shear flow. #
# Every 10 time steps the center of mass velocity and angular velocity of #
# the sphere are printed to the screen. #
# To run this example, LAMMPS needs to be compiled with a the following #
# packages: RIGID, LATBOLTZ #
# #
#===========================================================================#
units micro
dimension 3
boundary p p f
atom_style atomic
#----------------------------------------------------------------------------
# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing
# to ensure that the particles belonging to a given processor remain inside
# that processors lattice-Boltzmann grid.
# The arguments for neigh_modify have been set to "delay 0 every 1", again
# to ensure that the particles belonging to a given processor remain inside
# that processors lattice-Boltzmann grid. However, these values can likely
# be somewhat increased without issue. If a problem does arise (a particle
# is outside of its processors LB grid) an error message is printed and
# the simulation is terminated.
# The communcation cutoff is set to 2.5 dx to ensure that all particles in the
# processor ghost fluid region (of width 2dx) are known to local processor.
#----------------------------------------------------------------------------
neighbor 1.0 bin
neigh_modify delay 0 every 1
comm_modify cutoff 10.0
read_data data.one_radius16d2
Reading data file ...
orthogonal box = (-120 -120 -120) to (120 120 120)
1 by 2 by 2 MPI processor grid
reading atoms ...
320 atoms
read_data CPU = 0.015 seconds
#----------------------------------------------------------------------------
# None of the particles interact with one another.
#----------------------------------------------------------------------------
pair_style lj/cut 2.45
pair_coeff * * 0.0 0.0 2.45
neigh_modify exclude type 1 1
mass * 1.0
timestep 4.0
group sphere1 id <> 1 320
320 atoms in group sphere1
#----------------------------------------------------------------------------
# Colloidal particle is initially stationary.
#----------------------------------------------------------------------------
velocity all set 0.0 0.0 0.0 units box
#----------------------------------------------------------------------------
# Create a lattice-Boltzmann fluid covering the simulation domain.
# All of the particles in the simulation apply a force to the fluid.
# (however, this fix does not explicitly apply a force back on to these
# particles...this is accomplished through the use of the lb/viscous fix.
# Use a fluid density = 1.0, fluid viscosity = 1.0 (water), and a lattice
# spacing dx=4.0.
# Use the trilinear interpolation stencil (default) to distribute the force
# from a given particle onto the fluid mesh.
# Create shear in the system, by giving the upper z-wall a velocity of 0.0001
# along the y-direction, while keeping the lower z-wall stationary.
#-----------------------------------------------------------------------------
fix 1 all lb/fluid 1 1.0 1.0 dx 4.0 zwall_velocity 0.0 0.0001
Using a lattice-Boltzmann grid of 60 by 60 by 61 total grid points. (../fix_lb_fluid.cpp:486)
Local Grid Geometry created. (../fix_lb_fluid.cpp:1018)
#----------------------------------------------------------------------------
# Apply the force due to the fluid onto the particles.
#----------------------------------------------------------------------------
fix 2 all lb/viscous
#----------------------------------------------------------------------------
# Integrate the motion of the particles, constraining them to move and
# rotate together as a single rigid spherical object. Use the first
# version to allow the sphere to freely rotate and move with the fluid
# and the 2nd version to measure the force and torque on a fixed sphere
# in the shear flow which will allow you to measure the Stokes drag and
# torque on the sphere.
#----------------------------------------------------------------------------
fix 3 all rigid group 1 sphere1
1 rigid bodies with 320 atoms
#fix 3 all rigid group 1 sphere1 force * off off off torque * off off off
#----------------------------------------------------------------------------
# Create variables for the center-of-mass velocities, angular velocities, and
# force and torque on the CM. Then output these quantities to the screen.
#----------------------------------------------------------------------------
variable vx equal vcm(all,x)
variable vy equal vcm(all,y)
variable vz equal vcm(all,z)
variable omegax equal omega(all,x)
variable omegay equal omega(all,y)
variable omegaz equal omega(all,z)
variable fx equal fcm(all,x)
variable fy equal fcm(all,y)
variable fz equal fcm(all,z)
variable tx equal torque(all,x)
variable ty equal torque(all,y)
variable tz equal torque(all,z)
thermo_style custom v_vx v_vy v_vz v_omegax v_omegay v_omegaz v_fx v_fy v_fz v_tx v_ty v_tz
thermo 100
run 7500
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- fix lb/fluid command:
@Article{Denniston et al.,
author = {C. Denniston, N. Afrasiabian, M.G. Cole-Andre,F.E. Mackay, S.T.T. Ollila, T. Whitehead},
title = {LAMMPS lb/fluid fix version 2: Improved Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid}, journal = {Comp.~Phys.~Comm.},
year = 2022,
volume = 275,
pages = {108318}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3.45
ghost atom cutoff = 10
binsize = 1.725, bins = 140 140 140
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 8.426 | 8.426 | 8.426 Mbytes
v_vx v_vy v_vz v_omegax v_omegay v_omegaz v_fx v_fy v_fz v_tx v_ty v_tz
0 0 0 0 0 0 0 0 0 0 0 0
-2.3202888e-15 6.0709101e-09 -2.4412623e-13 -3.320168e-10 -1.1339769e-14 3.4045799e-14 -4.5990491e-16 3.6944668e-08 -1.4797148e-12 -3.3087894e-07 -3.2319943e-12 4.0825356e-11
2.2614166e-13 3.5465948e-07 -9.9990351e-12 -1.2716738e-08 -5.1515303e-13 1.1802563e-12 4.4099503e-13 6.2398067e-07 -1.4010079e-11 -3.2779726e-06 -5.5610241e-11 3.8420418e-10
9.9446526e-13 1.6203654e-06 -2.9965809e-11 -4.2770461e-08 -1.8551769e-12 3.935908e-12 7.0873308e-13 1.3654678e-06 -1.6036096e-11 -4.7351845e-06 -9.5164548e-11 5.5370816e-10
1.8577304e-12 3.6408926e-06 -4.7867194e-11 -7.6340276e-08 -3.4227185e-12 7.0027746e-12 6.4525598e-13 1.8162442e-06 -1.2450308e-11 -4.49885e-06 -9.721214e-11 5.2404154e-10
2.5784818e-12 6.0541618e-06 -6.1511675e-11 -1.0586215e-07 -4.8340636e-12 9.6842864e-12 5.0954806e-13 2.0115015e-06 -9.6836459e-12 -3.7358552e-06 -8.3756951e-11 4.3294805e-10
3.1388911e-12 8.606157e-06 -7.2849939e-11 -1.2968814e-07 -5.9880947e-12 1.18341e-11 3.9602348e-13 2.0531243e-06 -8.7301633e-12 -2.9477e-06 -6.7497759e-11 3.3979481e-10
3.5088487e-12 1.1153105e-05 -8.4778552e-11 -1.4827121e-07 -6.9042127e-12 1.3490413e-11 1.4926704e-13 2.012457e-06 -1.1121284e-11 -2.2774279e-06 -5.6689366e-11 2.5766138e-10
3.6203369e-12 1.3620493e-05 -1.0074918e-10 -1.6255823e-07 -7.6327828e-12 1.4733197e-11 2.8190134e-14 1.9308502e-06 -1.3951766e-11 -1.743828e-06 -4.5410719e-11 1.9387811e-10
3.5893239e-12 1.5972746e-05 -1.1992769e-10 -1.7347444e-07 -8.2060683e-12 1.5658564e-11 -7.5902354e-14 1.8309433e-06 -1.6655785e-11 -1.3300214e-06 -3.6956327e-11 1.4453207e-10
3.4369216e-12 1.8195336e-05 -1.4242882e-10 -1.8179239e-07 -8.6609693e-12 1.6339062e-11 -1.5582523e-13 1.7248165e-06 -1.9125572e-11 -1.0126439e-06 -3.0479042e-11 1.0521684e-10
3.1272907e-12 2.0284863e-05 -1.6693014e-10 -1.8812271e-07 -9.0539095e-12 1.6840547e-11 -3.2806998e-13 1.6187734e-06 -1.7338933e-11 -7.7034531e-07 -4.18956e-11 7.893297e-11
2.6336268e-12 2.2243653e-05 -1.8945116e-10 -1.9293745e-07 -9.4581385e-12 1.720649e-11 -4.4473581e-13 1.5159979e-06 -1.8187251e-11 -5.858335e-07 -3.9427386e-11 5.7483932e-11
2.0046303e-12 2.4076859e-05 -2.0991971e-10 -1.9659836e-07 -9.7540611e-12 1.7464607e-11 -5.3232938e-13 1.417998e-06 -1.33357e-11 -4.4535934e-07 -2.2183067e-11 4.087927e-11
1.8043659e-12 2.57909e-05 -2.251392e-10 -1.9938137e-07 -9.9135163e-12 1.7702226e-11 -8.1829532e-14 1.3253893e-06 -1.1758285e-11 -3.3855787e-07 -1.1111144e-11 3.6790045e-11
1.6716765e-12 2.7392642e-05 -2.3970723e-10 -2.0149677e-07 -1.0039419e-11 1.7837499e-11 -9.9475985e-14 1.2383189e-06 -1.1662512e-11 -2.5732441e-07 -9.4988118e-12 2.1805637e-11
1.4587868e-12 2.8888967e-05 -2.5363201e-10 -2.0310437e-07 -1.0169348e-11 1.7892616e-11 -5.6898373e-14 1.1566938e-06 -9.8557007e-12 -1.9551474e-07 -1.9984471e-11 4.8846772e-12
1.4100591e-12 3.0286556e-05 -2.6363101e-10 -2.0432561e-07 -1.0375492e-11 1.7885827e-11 -2.116508e-13 1.0803004e-06 -7.2760242e-12 -1.484988e-07 -1.9669998e-11 -3.7541543e-12
5.0115337e-13 3.1591785e-05 -2.7207072e-10 -2.0525299e-07 -1.040677e-11 1.7783826e-11 -8.2321665e-13 1.0088701e-06 -4.5772437e-12 -1.1272217e-07 4.4307683e-12 -3.0620406e-12
-5.8233e-13 3.2810682e-05 -2.7706702e-10 -2.0595685e-07 -1.0331077e-11 1.7711421e-11 -9.0024161e-13 9.4212051e-07 -1.7450813e-12 -8.552747e-08 1.6465807e-11 -1.1919394e-11
-1.2278986e-12 3.3948917e-05 -2.7737567e-10 -2.0649056e-07 -1.0269686e-11 1.7690544e-11 -2.7606089e-13 8.7976413e-07 1.1137199e-12 -6.4828506e-08 5.969611e-12 6.1895863e-12
-1.5406065e-12 3.5011807e-05 -2.7530664e-10 -2.0689506e-07 -1.0230405e-11 1.7713982e-11 -2.4182843e-13 8.2152268e-07 2.0572801e-12 -4.9118994e-08 6.9332841e-12 4.3109123e-12
-1.8436988e-12 3.6004328e-05 -2.7268697e-10 -2.0720139e-07 -1.0182673e-11 1.7730423e-11 -2.4623511e-13 7.6712961e-07 2.060507e-12 -3.7177338e-08 8.304141e-12 2.8568851e-12
-2.1592812e-12 3.693113e-05 -2.7044735e-10 -2.074331e-07 -1.0124124e-11 1.7740913e-11 -2.6133386e-13 7.1633405e-07 1.4428527e-12 -2.8098731e-08 9.7066289e-12 1.8079946e-12
-2.1007619e-12 3.7796564e-05 -2.6680968e-10 -2.0760821e-07 -9.9957059e-12 1.7730904e-11 3.5315241e-13 6.689009e-07 3.8443622e-12 -2.1224576e-08 2.4710992e-11 -1.7986278e-12
-1.9557805e-12 3.860469e-05 -2.5957119e-10 -2.0774047e-07 -9.8753834e-12 1.7718848e-11 -2.9478921e-14 6.2460647e-07 6.106131e-12 -1.6021507e-08 1.1023998e-11 4.1076291e-12
-2.032736e-12 3.9359303e-05 -2.5158305e-10 -2.0784005e-07 -9.7873438e-12 1.7712473e-11 -5.9512464e-14 5.8324585e-07 6.1916716e-12 -1.2039909e-08 1.2585113e-11 -1.3834171e-12
-2.1127776e-12 4.0063946e-05 -2.440354e-10 -2.0791478e-07 -9.6912281e-12 1.7690577e-11 -6.3724538e-14 5.4462318e-07 5.7542824e-12 -9.0191552e-09 1.4276089e-11 -2.3574292e-12
-2.3902344e-12 4.0721927e-05 -2.3654619e-10 -2.0797067e-07 -9.6167465e-12 1.7704683e-11 -4.4176097e-13 5.0855857e-07 6.2479839e-12 -6.7282157e-09 6.7015199e-12 9.6977453e-12
-2.9449998e-12 4.1336337e-05 -2.2904024e-10 -2.0801226e-07 -9.5792815e-12 1.7759253e-11 -4.1120238e-13 4.7488125e-07 5.6719561e-12 -4.9923338e-09 5.5881453e-12 9.0637113e-12
-3.4106994e-12 4.191006e-05 -2.2244742e-10 -2.0804302e-07 -9.5439345e-12 1.7819348e-11 -3.2449553e-13 4.4343429e-07 4.8497242e-12 -3.6777395e-09 5.1150823e-12 9.0947463e-12
-3.5852249e-12 4.2445791e-05 -2.1618947e-10 -2.080656e-07 -9.4749377e-12 1.7845812e-11 1.0655839e-13 4.1407045e-07 5.2707815e-12 -2.6881271e-09 1.5541392e-11 -1.5116726e-12
-3.4019698e-12 4.2946045e-05 -2.1010849e-10 -2.0808201e-07 -9.3573737e-12 1.7835452e-11 1.6858729e-13 3.8665059e-07 4.4152799e-12 -1.938804e-09 1.7265863e-11 -1.6678153e-12
-3.1820565e-12 4.3413174e-05 -2.0519131e-10 -2.0809376e-07 -9.2323294e-12 1.782123e-11 2.7307342e-13 3.6104485e-07 4.5405606e-12 -1.381731e-09 7.844705e-12 -2.1593177e-11
-1.9265518e-12 4.3849368e-05 -1.9974093e-10 -2.081021e-07 -9.2365556e-12 1.7734315e-11 9.3143689e-13 3.3713551e-07 4.5961813e-12 -9.3911384e-10 -1.0492532e-11 -3.4710604e-11
-7.5558483e-13 4.4256676e-05 -1.9451038e-10 -2.0810757e-07 -9.2981772e-12 1.7593311e-11 8.8290403e-13 3.1481065e-07 3.7293121e-12 -5.9201041e-10 -1.920229e-12 -4.5261347e-12
-6.8078423e-14 4.4637011e-05 -1.9017e-10 -2.0811091e-07 -9.2985302e-12 1.7560504e-11 2.3613824e-13 2.9396314e-07 2.8306791e-12 -3.6072498e-10 1.919591e-12 5.7324777e-14
-2.6872645e-13 4.4992159e-05 -1.8489448e-10 -2.081129e-07 -9.1988109e-12 1.7585096e-11 -3.7386314e-13 2.7449607e-07 4.3641203e-12 -2.0179873e-10 1.7903185e-11 9.4883417e-12
-7.6146932e-13 4.5323788e-05 -1.7973612e-10 -2.0811387e-07 -9.067395e-12 1.7625673e-11 -4.0029726e-13 2.5631874e-07 3.8153502e-12 -7.7154264e-11 1.864561e-11 7.0852862e-12
-1.0073144e-12 4.5633459e-05 -1.7567167e-10 -2.0811405e-07 -8.9461618e-12 1.7602722e-11 -8.8146729e-14 2.3934617e-07 2.900483e-12 1.3609831e-11 1.8144897e-11 -1.0950951e-12
-1.1183452e-12 4.5922622e-05 -1.7267861e-10 -2.0811371e-07 -8.8220108e-12 1.7567954e-11 -8.7131925e-14 2.2349647e-07 1.9871901e-12 7.3396979e-11 1.8201205e-11 -3.3808282e-12
-1.2336249e-12 4.6192637e-05 -1.7082009e-10 -2.0811304e-07 -8.6931853e-12 1.7534253e-11 -1.0358975e-13 2.0869604e-07 9.8971584e-13 1.1034572e-10 1.8570854e-11 -4.1945968e-12
-1.395039e-12 4.644477e-05 -1.7090836e-10 -2.0811204e-07 -8.5394724e-12 1.7470422e-11 -2.2192138e-13 1.9487513e-07 -1.0653437e-12 1.5048013e-10 2.2960595e-11 -7.9254026e-12
-1.5887239e-12 4.6680205e-05 -1.726235e-10 -2.0811078e-07 -8.3735722e-12 1.7394789e-11 5.3191009e-14 1.8196634e-07 -1.4136613e-12 2.2963534e-10 2.654505e-11 -1.8261053e-12
-1.4689452e-12 4.6900047e-05 -1.7480066e-10 -2.081091e-07 -8.2058094e-12 1.7351678e-11 1.2094829e-13 1.6991911e-07 -2.6013388e-12 2.4677201e-10 1.76692e-11 -7.1825235e-12
-1.3595687e-12 4.7105333e-05 -1.7899795e-10 -2.081074e-07 -8.0435813e-12 1.7311436e-11 -2.3058185e-13 1.586669e-07 -5.9352116e-12 2.143538e-10 3.2425344e-11 -1.0330713e-11
-1.6431943e-12 4.7297025e-05 -1.8929524e-10 -2.0810597e-07 -7.7996954e-12 1.7199148e-11 -2.3195078e-13 1.4815965e-07 -9.1089087e-12 2.0069043e-10 2.7268474e-11 -1.5424889e-11
-1.9503819e-12 4.7476021e-05 -2.0221518e-10 -2.0810468e-07 -7.655314e-12 1.7080428e-11 -2.618849e-13 1.383469e-07 -1.0767028e-11 1.6168876e-10 1.2892606e-11 -1.6616695e-11
-2.293052e-12 4.7643164e-05 -2.1485895e-10 -2.0810355e-07 -7.6010878e-12 1.6957401e-11 -2.8846319e-13 1.2918561e-07 -9.5229628e-12 1.583733e-10 4.7988904e-12 -1.7439504e-11
-2.5677362e-12 4.7799238e-05 -2.3224794e-10 -2.0810274e-07 -7.733652e-12 1.6817843e-11 4.7024153e-15 1.2062891e-07 -1.6977112e-11 1.0067875e-10 -5.9706483e-12 -6.6309632e-12
-2.5737947e-12 4.7944975e-05 -2.542538e-10 -2.0810213e-07 -7.6510888e-12 1.676216e-11 -3.154599e-14 1.1264034e-07 -1.7155189e-11 8.6731774e-11 1.320634e-11 -5.9239428e-12
-3.3012431e-12 4.808106e-05 -2.7606974e-10 -2.0810154e-07 -7.5285751e-12 1.6730121e-11 -5.5195274e-13 1.051819e-07 -1.8102675e-11 7.9086408e-11 2.549833e-11 3.8248179e-12
-4.0407963e-12 4.8208133e-05 -2.9913872e-10 -2.0810087e-07 -7.3675841e-12 1.6729661e-11 -1.056947e-13 9.8215693e-08 -2.0564122e-11 8.9889186e-11 9.0969559e-12 -5.0411456e-12
-4.0017866e-12 4.8326792e-05 -3.2578824e-10 -2.0810019e-07 -7.3309734e-12 1.6685377e-11 3.9903591e-14 9.1714102e-08 -2.2544733e-11 9.4144708e-11 -9.2931714e-12 5.3254879e-12
-3.7606866e-12 4.8437596e-05 -3.5569049e-10 -2.080996e-07 -7.4780802e-12 1.6680934e-11 2.7466593e-13 8.5641003e-08 -2.425075e-11 7.7669196e-11 -2.2631547e-11 5.8077979e-13
-3.4574887e-12 4.8541063e-05 -3.8545474e-10 -2.0809901e-07 -7.6093713e-12 1.6646067e-11 2.5876746e-14 7.997313e-08 -2.317586e-11 1.0544046e-10 -1.5314944e-11 6.8357155e-12
-2.9114149e-12 4.8637681e-05 -4.1425452e-10 -2.0809838e-07 -7.7070087e-12 1.6659672e-11 6.2786281e-13 7.4677646e-08 -2.2436087e-11 8.9235324e-11 -1.3645085e-11 1.4694507e-11
-2.2825362e-12 4.8727902e-05 -4.4462584e-10 -2.0809808e-07 -7.7463431e-12 1.6727387e-11 4.986996e-13 6.973271e-08 -2.3823592e-11 4.8349103e-11 -4.917953e-12 1.0180248e-11
-1.6721448e-12 4.881215e-05 -4.7395477e-10 -2.080978e-07 -7.798864e-12 1.6781065e-11 5.8461703e-13 6.5116697e-08 -2.2923269e-11 3.3917578e-11 -1.4512356e-11 3.0753823e-12
-1.0108835e-12 4.889082e-05 -5.0054848e-10 -2.0809742e-07 -7.8734886e-12 1.6821117e-11 5.5262937e-13 6.0804995e-08 -2.0048603e-11 6.7540691e-11 -9.5748309e-12 5.1419531e-12
-5.2913704e-13 4.8964281e-05 -5.2361079e-10 -2.0809688e-07 -7.9342525e-12 1.6809498e-11 1.7857863e-13 5.6779412e-08 -1.7008275e-11 8.4873628e-11 -8.0821684e-12 -1.3432203e-11
-6.0869323e-13 4.9032877e-05 -5.4391464e-10 -2.0809612e-07 -7.9700834e-12 1.6669189e-11 -2.2181063e-13 5.3018043e-08 -1.6188875e-11 1.2254388e-10 -3.4719243e-12 -2.5582696e-11
5.3160987e-14 4.909693e-05 -5.685844e-10 -2.0809534e-07 -7.8445232e-12 1.6543112e-11 3.7931128e-13 4.9508006e-08 -2.3478774e-11 1.0539577e-10 3.8278786e-11 -1.7435743e-11
6.9879599e-13 4.9156741e-05 -6.0029127e-10 -2.0809434e-07 -7.4710339e-12 1.6485438e-11 5.2135936e-13 4.6228138e-08 -2.7953013e-11 1.1306415e-10 3.9827585e-11 -4.0676347e-12
1.3291032e-12 4.921259e-05 -6.3478917e-10 -2.0809343e-07 -7.1919325e-12 1.6475734e-11 8.0744289e-13 4.3164468e-08 -2.9352787e-11 1.9393928e-10 2.1395748e-11 -1.3540015e-11
1.9099631e-12 4.9264739e-05 -6.713946e-10 -2.0809198e-07 -7.14109e-12 1.6362552e-11 5.0399245e-13 4.0306735e-08 -3.0085714e-11 2.4238628e-10 -1.2562062e-11 -3.1127285e-11
2.5888559e-12 4.9313435e-05 -7.0699965e-10 -2.0809031e-07 -7.149238e-12 1.6227991e-11 5.2667785e-13 3.7637786e-08 -2.8432993e-11 2.6235217e-10 -2.232043e-12 -2.2764185e-11
3.2694582e-12 4.9358908e-05 -7.414765e-10 -2.0808825e-07 -7.1300019e-12 1.6100817e-11 5.4583215e-13 3.5147252e-08 -2.5050106e-11 3.5891383e-10 3.6724193e-12 -1.8864321e-11
3.3319364e-12 4.9401369e-05 -7.717209e-10 -2.0808576e-07 -7.1044853e-12 1.6070581e-11 -1.2307553e-12 3.2817485e-08 -1.9476032e-11 3.1425065e-10 2.5407039e-13 2.4318892e-12
1.3098859e-12 4.9441018e-05 -7.9443484e-10 -2.0808358e-07 -7.0912957e-12 1.6079833e-11 -1.9382883e-12 3.0644803e-08 -1.7818422e-11 3.1668434e-10 -1.5502234e-12 -3.3879027e-12
-9.4132416e-13 4.9478041e-05 -8.1438431e-10 -2.0808148e-07 -7.0899773e-12 1.6074809e-11 -1.1537277e-12 2.8614527e-08 -1.2295571e-11 2.623115e-10 -1.1222739e-12 6.3245613e-12
-1.6613373e-12 4.9512612e-05 -8.2794953e-10 -2.0807969e-07 -7.0886692e-12 1.6035491e-11 -3.2150631e-13 2.6719935e-08 -1.0632544e-11 2.5483461e-10 -7.889241e-13 -4.5931115e-12
-2.0923849e-12 4.9544894e-05 -8.4103126e-10 -2.080779e-07 -7.0787296e-12 1.598084e-11 -3.6458701e-13 2.4950759e-08 -1.0668225e-11 2.5363261e-10 2.557409e-12 -7.4330019e-12
-2.6074079e-12 4.9575038e-05 -8.5484831e-10 -2.0807608e-07 -7.0458889e-12 1.5917995e-11 -4.6370161e-13 2.3298683e-08 -1.1706817e-11 2.5798545e-10 6.4493257e-12 -9.0570787e-12
-3.1912867e-12 4.9603187e-05 -8.7103016e-10 -2.0807419e-07 -6.9729658e-12 1.5869196e-11 -5.4662034e-13 2.1756065e-08 -1.4183469e-11 2.6950321e-10 1.2401403e-11 -9.1121813e-12
-2.6896504e-12 4.9629471e-05 -8.8354072e-10 -2.0807269e-07 -6.9518789e-12 1.5862597e-11 7.7697632e-13 2.0315473e-08 -9.1356461e-12 1.9455164e-10 -5.2929772e-13 -4.0871645e-12
Loop time of 348.592 on 4 procs for 7500 steps with 320 atoms
Performance: 7435633235.428 ns/day, 0.000 hours/ns, 21.515 timesteps/s
99.9% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.024506 | 0.025477 | 0.026424 | 0.6 | 0.01
Neigh | 0.030494 | 0.03257 | 0.034614 | 1.0 | 0.01
Comm | 0.2132 | 0.21532 | 0.22048 | 0.6 | 0.06
Output | 0.011234 | 0.016341 | 0.031613 | 6.9 | 0.00
Modify | 347.96 | 347.98 | 348 | 0.1 | 99.83
Other | | 0.3181 | | | 0.09
Nlocal: 80 ave 86 max 74 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Nghost: 122.75 ave 126 max 120 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:05:48

20031
examples/PACKAGES/latboltz/planewall/wall_defaultgamma.out
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20031
examples/PACKAGES/latboltz/planewall/wall_setgamma.out
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File diff suppressed because it is too large Load Diff

104
examples/PACKAGES/latboltz/polymer/in.polymer_default_gamma → examples/PACKAGES/latboltz/polymer/in.polymer
View File

@ -4,11 +4,10 @@
# Run consists of a lone 32-bead coarse-grained polymer #
# undergoing Brownian motion in thermal lattice-Boltzmann fluid. #
# #
# Here, gamma (used in the calculation of the monomer-fluid interaction #
# force) is set by the user (gamma = 0.03 for this simulation...this #
# value has been calibrated a priori through simulations of the drag #
# force acting on a single particle of the same radius). #
# Sample output from this run can be found in the file: #
# To run this example, LAMMPS needs to be compiled with a the following #
# packages: MOLECULE, RIGID, LATBOTLZ #
# #
# If uncommented, sample output from this run can be found in the file: #
# 'dump.polymer.lammpstrj' #
# and viewed using, e.g., the VMD software. #
# #
@ -16,23 +15,26 @@
units nano
dimension 3
boundary p p p
boundary p p f
atom_style hybrid molecular
special_bonds fene
read_data data.polymer
#----------------------------------------------------------------------------
# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing
# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing
# to ensure that the particles belonging to a given processor remain inside
# that processors lattice-Boltzmann grid.
#----------------------------------------------------------------------------
# that processors lattice-Boltzmann grid.
# The communcation cutoff is set to 2.5 dx to ensure that all particles in the
# processor ghost fluid region (of width 2dx) are known to local processor.
#----------------------------------------------------------------------------
neighbor 0.5 bin
neigh_modify delay 0 every 1 check yes
neigh_modify exclude type 2 2
neigh_modify exclude type 2 1
comm_modify cutoff 2.5
#----------------------------------------------------------------------------
# Implement a hard-sphere interaction between the particles at the center of
# Implement a hard-sphere interaction between the particles at the center of
# each monomer (use a truncated and shifted Lennard-Jones potential).
#----------------------------------------------------------------------------
bond_style fene
@ -42,66 +44,68 @@ pair_coeff 1 1 4.14195 1.5 1.68369
pair_coeff 1 2 4.14195 1.5 1.68369
pair_coeff 2 2 0 1.0
mass * 0.000000771064
timestep 0.00003
# The mass is set 4/3 PI r^3 fluid_density/31 , where r=0.617, 31 is number of
# nodes in a single monomer
mass * 0.00000318
timestep 0.0001
#----------------------------------------------------------------------------
# ForceAtoms are the particles at the center of each monomer which
# ForceAtoms are the particles at the center of each monomer which
# do not interact with the fluid, but are used to implement the hard-sphere
# interactions.
# interactions.
# FluidAtoms are the particles representing the surface of the monomer
# which do interact with the fluid. Monomer surface is shell of radius 0.7
# which do interact with the fluid.
#----------------------------------------------------------------------------
group ForceAtoms type 1
group FluidAtoms type 2
#----------------------------------------------------------------------------
# Placement of a trap (similar to an 1D optical trap) for the polymer
# Note that the addforce fix needs to go before the lb/fluid and lb/viscous
# fix as these fixes rescale the forces to account for the added mass of the
# fluid that gets dragged around with the particle so need prior knowledge of
# all forces applied to the particles involved in these fixes before they are
# called.
#----------------------------------------------------------------------------
variable fx atom -(x-20.0)*20.0/31.0
fix trap all addforce v_fx 0.0 0.0 # call before fix lb/fluid and lb/viscous
#---------------------------------------------------------------------------
# Create a lattice-Boltzmann fluid covering the simulation domain.
# This fluid feels a force due to the particles specified through FluidAtoms
# (however, this fix does not explicitly apply a force back on to these
# particles. This is accomplished through the use of the lb/viscous
# fix).
# Uses the standard LB integration scheme, fluid viscosity = 0.023333333,
# fluid density= 0.0000166368, lattice spacing dx=1.0, and mass unit,
# dm=0.0000166368.
# Use the default method to calculate the interaction force between the
# particles and the fluid. This calculation requires the surface area
# of the composite object represented by each particle node. By default
# this area is assumed equal to dx*dx; however, since this is not the case
# here, it is input through the setArea keyword (i.e. particles of type 2
# correspond to a surface area of 0.2025=4 Pi R^2/N ).
# Use the trilinear interpolation stencil to distribute the force from
# a given particle onto the fluid mesh (results in a smaller hydrodynamic
# radius than if the Peskin stencil is used).
# Use a thermal lattice-Boltzmann fluid (temperature 300K, random number
# seed=15003). This enables the particles to undergo Brownian motion in
# This fluid feels a force due to the particles specified through FluidAtoms
# (however, this fix does not explicity apply a force back on to these
# particles. This is accomplished through the use of the lb/viscous fix).
# We set fluid viscosity = 0.1 and fluid density = 0.00009982071 which
# means the kinematic viscosity is idential to that of water but the
# dynamic viscosity is a factor of 10 less than that of water which
# increases the diffusive dynamics by a corresponding factor of 10.
# lattice spacing dx=1.0.
# Use a thermal lattice-Boltzmann fluid (temperature 300K, random number
# seed=15003). This enables the particles to undergo Brownian motion in
# the fluid.
#----------------------------------------------------------------------------
fix 1 FluidAtoms lb/fluid 3 1 0.023333333 0.0000166368 setArea 2 0.20525 dx 1.0 dm 0.0000166368 noise 300.0 15003
fix 1 all lb/fluid 1 0.1 0.00009982071 dx 1.0 noise 300.0 15003
#----------------------------------------------------------------------------
# Apply the force from the fluid to the particles, and integrate their
# motion, constraining them to move and rotate together as a single rigid
# spherical object.
# Apply the force from the fluid to the particles, and integrate their
# motion, constraining each monomerto move and rotate as a single rigid
# spherical object.
# Since both the ForceAtoms (central atoms), and the FluidAtoms (spherical
# shell) should move and rotate together, this fix is applied to all of
# the atoms in the system. However, since the central atoms should not
# feel a force due to the fluid, they are excluded from the fluid force
# calculation.
# shell) should move and rotate together, this fix is applied to all of
# the atoms in the system.
#----------------------------------------------------------------------------
fix 2 FluidAtoms lb/viscous
fix 3 all rigid molecule
fix 2 all lb/viscous
fix 3 all rigid/small molecule
#----------------------------------------------------------------------------
# To ensure that numerical errors do not lead to a buildup of momentum in the
# system, the momentum_lb fix is used every 10000 timesteps to zero out the
# system, the momentum_lb fix is used every 100000 timesteps to zero out the
# total (particle plus fluid) momentum in the system.
#----------------------------------------------------------------------------
fix 4 all lb/momentum 10000 linear 1 1 1
fix 4 all lb/momentum 100000 linear 1 1 1
#----------------------------------------------------------------------------
# Write position and velocity coordinates into a file every 2000 time steps.
#----------------------------------------------------------------------------
dump 1 ForceAtoms custom 2000 dump.polymer_default_gamma.lammpstrj id x y z vx vy vz
run 2000001
#dump 1 ForceAtoms custom 10 trapped_polymer.lammpstrj id x y z vx vy vz
#run 2000001
run 10000

105
examples/PACKAGES/latboltz/polymer/in.polymer_setgamma
View File

@ -1,105 +0,0 @@
#===========================================================================#
# polymer test #
# #
# Run consists of a lone 32-bead coarse-grained polymer #
# undergoing Brownian motion in thermal lattice-Boltzmann fluid. #
# #
# Here, gamma (used in the calculation of the monomer-fluid interaction #
# force) is set by the user (gamma = 0.03 for this simulation...this #
# value has been calibrated a priori through simulations of the drag #
# force acting on a single particle of the same radius). #
# Sample output from this run can be found in the file: #
# 'dump.polymer.lammpstrj' #
# and viewed using, e.g., the VMD software. #
# #
# Santtu Ollila #
# santtu.ollila@aalto.fi #
# Aalto University #
# August 14, 2013 #
#===========================================================================#
units nano
dimension 3
boundary p p p
atom_style hybrid molecular
special_bonds fene
read_data data.polymer
#----------------------------------------------------------------------------
# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing
# to ensure that the particles belonging to a given processor remain inside
# that processors lattice-Boltzmann grid.
#----------------------------------------------------------------------------
neighbor 0.5 bin
neigh_modify delay 0 every 1 check yes
neigh_modify exclude type 2 2
neigh_modify exclude type 2 1
#----------------------------------------------------------------------------
# Implement a hard-sphere interaction between the particles at the center of
# each monomer (use a truncated and shifted Lennard-Jones potential).
#----------------------------------------------------------------------------
bond_style fene
bond_coeff 1 60.0 2.25 4.14195 1.5
pair_style lj/cut 1.68369
pair_coeff 1 1 4.14195 1.5 1.68369
pair_coeff 1 2 4.14195 1.5 1.68369
pair_coeff 2 2 0 1.0
mass * 0.000000771064
timestep 0.00003
#----------------------------------------------------------------------------
# ForceAtoms are the particles at the center of each monomer which
# do not interact with the fluid, but are used to implement the hard-sphere
# interactions.
# FluidAtoms are the particles representing the surface of the monomer
# which do interact with the fluid.
#----------------------------------------------------------------------------
group ForceAtoms type 1
group FluidAtoms type 2
#---------------------------------------------------------------------------
# Create a lattice-Boltzmann fluid covering the simulation domain.
# This fluid feels a force due to the particles specified through FluidAtoms
# (however, this fix does not explicitly apply a force back on to these
# particles. This is accomplished through the use of the rigid_pc_sphere
# fix).
# Use the LB integration scheme of Ollila et. al. (for stability reasons,
# this integration scheme should be used when a large user set value for
# gamma is specified), a fluid viscosity = 0.023333333,
# fluid density= 0.0000166368,
# value for gamma=0.03, lattice spacing dx=1.0, and mass unit, dm=0.0000166368.
# Use a thermal lattice-Boltzmann fluid (temperature 300K, random number
# seed=15003). This enables the particles to undergo Brownian motion in
# the fluid.
#----------------------------------------------------------------------------
fix 1 FluidAtoms lb/fluid 5 1 0.023333333 0.0000166368 setGamma 0.03 dx 1.0 dm 0.0000166368 noise 300.0 15003
#----------------------------------------------------------------------------
# Apply the force from the fluid to the particles, and integrate their
# motion, constraining them to move and rotate together as a single rigid
# spherical object.
# Since both the ForceAtoms (central atoms), and the FluidAtoms (spherical
# shell) should move and rotate together, this fix is applied to all of
# the atoms in the system. However, since the central atoms should not
# feel a force due to the fluid, they are excluded from the force
# calculation through the use of the 'innerNodes' keyword.
# NOTE: This fix should only be used when the user specifies a value for
# gamma (through the setGamma keyword) in the lb_fluid fix.
#----------------------------------------------------------------------------
fix 2 all lb/rigid/pc/sphere molecule innerNodes ForceAtoms
#----------------------------------------------------------------------------
# To ensure that numerical errors do not lead to a buildup of momentum in the
# system, the momentum_lb fix is used every 10000 timesteps to zero out the
# total (particle plus fluid) momentum in the system.
#----------------------------------------------------------------------------
fix 3 all lb/momentum 10000 linear 1 1 1
#----------------------------------------------------------------------------
# Write position and velocity coordinates into a file every 2000 time steps.
#----------------------------------------------------------------------------
dump 1 ForceAtoms custom 2000 dump.polymer_setgamma.lammpstrj id x y z vx vy vz
run 2000001

199
examples/PACKAGES/latboltz/polymer/log.09Mar22.polymer.g++.4 Normal file
View File

@ -0,0 +1,199 @@
LAMMPS (17 Feb 2022)
#===========================================================================#
# polymer test #
# #
# Run consists of a lone 32-bead coarse-grained polymer #
# undergoing Brownian motion in thermal lattice-Boltzmann fluid. #
# #
# To run this example, LAMMPS needs to be compiled with a the following #
# packages: MOLECULE, RIGID, LATBOTLZ #
# #
# If uncommented, sample output from this run can be found in the file: #
# 'dump.polymer.lammpstrj' #
# and viewed using, e.g., the VMD software. #
# #
#===========================================================================#
units nano
dimension 3
boundary p p f
atom_style hybrid molecular
special_bonds fene
read_data data.polymer
Reading data file ...
orthogonal box = (0 0 0) to (40 40 40)
1 by 2 by 2 MPI processor grid
reading atoms ...
992 atoms
scanning bonds ...
1 = max bonds/atom
reading bonds ...
31 bonds
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 1 1
special bond factors coul: 0 1 1
2 = max # of 1-2 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.037 seconds
#----------------------------------------------------------------------------
# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing
# to ensure that the particles belonging to a given processor remain inside
# that processors lattice-Boltzmann grid.
# The communcation cutoff is set to 2.5 dx to ensure that all particles in the
# processor ghost fluid region (of width 2dx) are known to local processor.
#----------------------------------------------------------------------------
neighbor 0.5 bin
neigh_modify delay 0 every 1 check yes
neigh_modify exclude type 2 2
neigh_modify exclude type 2 1
comm_modify cutoff 2.5
#----------------------------------------------------------------------------
# Implement a hard-sphere interaction between the particles at the center of
# each monomer (use a truncated and shifted Lennard-Jones potential).
#----------------------------------------------------------------------------
bond_style fene
bond_coeff 1 60.0 2.25 4.14195 1.5
pair_style lj/cut 1.68369
pair_coeff 1 1 4.14195 1.5 1.68369
pair_coeff 1 2 4.14195 1.5 1.68369
pair_coeff 2 2 0 1.0
# The mass is set 4/3 PI r^3 fluid_density/31 , where r=0.617, 31 is number of
# nodes in a single monomer
mass * 0.00000318
timestep 0.0001
#----------------------------------------------------------------------------
# ForceAtoms are the particles at the center of each monomer which
# do not interact with the fluid, but are used to implement the hard-sphere
# interactions.
# FluidAtoms are the particles representing the surface of the monomer
# which do interact with the fluid.
#----------------------------------------------------------------------------
group ForceAtoms type 1
32 atoms in group ForceAtoms
group FluidAtoms type 2
960 atoms in group FluidAtoms
#----------------------------------------------------------------------------
# Placement of a trap (similar to an 1D optical trap) for the polymer
# Note that the addforce fix needs to go before the lb/fluid and lb/viscous
# fix as these fixes rescale the forces to account for the added mass of the
# fluid that gets dragged around with the particle so need prior knowledge of
# all forces applied to the particles involved in these fixes before they are
# called.
#----------------------------------------------------------------------------
variable fx atom -(x-20.0)*20.0/31.0
fix trap all addforce v_fx 0.0 0.0 # call before fix lb/fluid and lb/viscous
#---------------------------------------------------------------------------
# Create a lattice-Boltzmann fluid covering the simulation domain.
# This fluid feels a force due to the particles specified through FluidAtoms
# (however, this fix does not explicity apply a force back on to these
# particles. This is accomplished through the use of the lb/viscous fix).
# We set fluid viscosity = 0.1 and fluid density = 0.00009982071 which
# means the kinematic viscosity is idential to that of water but the
# dynamic viscosity is a factor of 10 less than that of water which
# increases the diffusive dynamics by a corresponding factor of 10.
# lattice spacing dx=1.0.
# Use a thermal lattice-Boltzmann fluid (temperature 300K, random number
# seed=15003). This enables the particles to undergo Brownian motion in
# the fluid.
#----------------------------------------------------------------------------
fix 1 all lb/fluid 1 0.1 0.00009982071 dx 1.0 noise 300.0 15003
Using a lattice-Boltzmann grid of 40 by 40 by 41 total grid points. (../fix_lb_fluid.cpp:486)
Local Grid Geometry created. (../fix_lb_fluid.cpp:1018)
#----------------------------------------------------------------------------
# Apply the force from the fluid to the particles, and integrate their
# motion, constraining each monomerto move and rotate as a single rigid
# spherical object.
# Since both the ForceAtoms (central atoms), and the FluidAtoms (spherical
# shell) should move and rotate together, this fix is applied to all of
# the atoms in the system.
#----------------------------------------------------------------------------
fix 2 all lb/viscous
fix 3 all rigid/small molecule
create bodies CPU = 0.000 seconds
32 rigid bodies with 992 atoms
0.70010803 = max distance from body owner to body atom
#----------------------------------------------------------------------------
# To ensure that numerical errors do not lead to a buildup of momentum in the
# system, the momentum_lb fix is used every 100000 timesteps to zero out the
# total (particle plus fluid) momentum in the system.
#----------------------------------------------------------------------------
fix 4 all lb/momentum 100000 linear 1 1 1
#dump 1 ForceAtoms custom 10 trapped_polymer.lammpstrj id x y z vx vy vz
#run 2000001
run 10000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- fix lb/fluid command:
@Article{Denniston et al.,
author = {C. Denniston, N. Afrasiabian, M.G. Cole-Andre,F.E. Mackay, S.T.T. Ollila, T. Whitehead},
title = {LAMMPS lb/fluid fix version 2: Improved Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid}, journal = {Comp.~Phys.~Comm.},
year = 2022,
volume = 275,
pages = {108318}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.18369
ghost atom cutoff = 2.5
binsize = 1.091845, bins = 37 37 37
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
WARNING: Communication cutoff 2.5 is shorter than a bond length based estimate of 2.6825. This may lead to errors. (../comm.cpp:723)
Per MPI rank memory allocation (min/avg/max) = 7.861 | 9.842 | 11.95 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -8.2758489 2790.7741 2782.4982 0.85835765
10000 15.559756 -10.240592 2817.6714 2827.7319 -0.0015697449
Loop time of 269.705 on 4 procs for 10000 steps with 992 atoms
Performance: 320.351 ns/day, 0.075 hours/ns, 37.078 timesteps/s
99.9% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.01457 | 0.047368 | 0.1221 | 20.3 | 0.02
Bond | 0.010081 | 0.022047 | 0.043793 | 9.3 | 0.01
Neigh | 0.61943 | 0.62713 | 0.63223 | 0.7 | 0.23
Comm | 0.10937 | 0.33658 | 0.61517 | 39.3 | 0.12
Output | 3.44e-05 | 7.7575e-05 | 0.0001653 | 0.0 | 0.00
Modify | 268.04 | 268.34 | 268.53 | 1.2 | 99.49
Other | | 0.3359 | | | 0.12
Nlocal: 248 ave 802 max 0 min
Histogram: 2 0 1 0 0 0 0 0 0 1
Nghost: 113.25 ave 190 max 42 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 4.25 ave 15 max 0 min
Histogram: 2 1 0 0 0 0 0 0 0 1
Total # of neighbors = 17
Ave neighs/atom = 0.017137097
Ave special neighs/atom = 0.0625
Neighbor list builds = 495
Dangerous builds = 0
Total wall time: 0:04:29

83
examples/PACKAGES/latboltz/polymer/out.polymer_default_gamma
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@ -1,83 +0,0 @@
LAMMPS (10 Aug 2015)
Reading data file ...
orthogonal box = (0 0 0) to (40 40 40)
2 by 2 by 4 MPI processor grid
reading atoms ...
992 atoms
scanning bonds ...
1 = max bonds/atom
reading bonds ...
31 bonds
Finding 1-2 1-3 1-4 neighbors ...
Special bond factors lj: 0 1 1
Special bond factors coul: 0 1 1
2 = max # of 1-2 neighbors
2 = max # of special neighbors
32 atoms in group ForceAtoms
960 atoms in group FluidAtoms
Using a lattice-Boltzmann grid of 40 by 40 by 40 total grid points. (../fix_lb_fluid.cpp:385)
32 rigid bodies with 992 atoms
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
master list distance cutoff = 2.18369
ghost atom cutoff = 2.18369
Setting up Verlet run ...
Unit style : nano
Current step: 0
Time step : 3e-05
Memory usage per processor = 0.111926 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -8.2758489 2790.7741 2782.4982 1.9081958e-20
2000001 4.3017148 0 2792.6037 2798.2163 -0.00077006865
Loop time of 51900 on 16 procs for 2000001 steps with 992 atoms
Pair time (%) = 4.33729 (0.00835701)
Bond time (%) = 3.33134 (0.00641876)
Neigh time (%) = 35.1247 (0.0676777)
Comm time (%) = 61.528 (0.118551)
Outpt time (%) = 0.361813 (0.000697135)
Other time (%) = 51795.3 (99.7983)
Nlocal: 62 ave 465 max 0 min
Histogram: 11 0 3 1 0 0 0 0 0 1
Nghost: 94.8125 ave 340 max 0 min
Histogram: 9 0 0 0 4 0 0 1 0 2
Neighs: 0.25 ave 2 max 0 min
Histogram: 13 0 0 0 0 2 0 0 0 1
Total # of neighbors = 4
Ave neighs/atom = 0.00403226
Ave special neighs/atom = 0.0625
Neighbor list builds = 23853
Dangerous builds = 0
------------------------------------------------------------
Sender: LSF System <lsfadmin@lsfhost.localdomain>
Subject: Job 883849: </opt/hpmpi/bin/mpirun -srun ./lmp_mpi -in in.polymer_default_gamma> Done
Job </opt/hpmpi/bin/mpirun -srun ./lmp_mpi -in in.polymer_default_gamma> was submitted from host <req770> by user <colin>.
Job was executed on host(s) <16*lsfhost.localdomain>, in queue <mpi>, as user <colin>.
</home/colin> was used as the home directory.
</home/colin/lammps-10Aug15/examples/USER/lb/tested/polymer_default> was used as the working directory.
Started at Mon Aug 24 11:13:12 2015
Results reported at Tue Aug 25 01:38:50 2015
Your job looked like:
------------------------------------------------------------
# LSBATCH: User input
/opt/hpmpi/bin/mpirun -srun ./lmp_mpi -in in.polymer_default_gamma
------------------------------------------------------------
Successfully completed.
Resource usage summary:
CPU time : 829343.88 sec.
Max Memory : 43 MB
Max Swap : 805 MB
The output (if any) is above this job summary.

83
examples/PACKAGES/latboltz/polymer/out.polymer_setgamma
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@ -1,83 +0,0 @@
LAMMPS (10 Aug 2015)
Reading data file ...
orthogonal box = (0 0 0) to (40 40 40)
2 by 2 by 4 MPI processor grid
reading atoms ...
992 atoms
scanning bonds ...
1 = max bonds/atom
reading bonds ...
31 bonds
Finding 1-2 1-3 1-4 neighbors ...
Special bond factors lj: 0 1 1
Special bond factors coul: 0 1 1
2 = max # of 1-2 neighbors
2 = max # of special neighbors
32 atoms in group ForceAtoms
960 atoms in group FluidAtoms
Using a lattice-Boltzmann grid of 40 by 40 by 40 total grid points. (../fix_lb_fluid.cpp:385)
32 rigid bodies with 992 atoms
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
master list distance cutoff = 2.18369
ghost atom cutoff = 2.18369
Setting up Verlet run ...
Unit style : nano
Current step: 0
Time step : 3e-05
Memory usage per processor = 0.108554 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -8.2758489 2790.7741 2782.4982 -0.00085093693
2000001 0.5548925 0 2792.3403 2803.7286 -0.0037777326
Loop time of 50862.3 on 16 procs for 2000001 steps with 992 atoms
Pair time (%) = 4.10128 (0.0080635)
Bond time (%) = 3.29621 (0.00648066)
Neigh time (%) = 40.0195 (0.0786822)
Comm time (%) = 89.3201 (0.175612)
Outpt time (%) = 1.05399 (0.00207224)
Other time (%) = 50724.5 (99.7291)
Nlocal: 62 ave 501 max 0 min
Histogram: 14 0 0 0 0 0 0 0 0 2
Nghost: 29 ave 259 max 0 min
Histogram: 14 0 0 0 0 0 0 1 0 1
Neighs: 0.375 ave 3 max 0 min
Histogram: 14 0 0 0 0 0 0 0 0 2
Total # of neighbors = 6
Ave neighs/atom = 0.00604839
Ave special neighs/atom = 0.0625
Neighbor list builds = 30671
Dangerous builds = 0
------------------------------------------------------------
Sender: LSF System <lsfadmin@lsfhost.localdomain>
Subject: Job 883848: </opt/hpmpi/bin/mpirun -srun ./lmp_mpi -in in.polymer> Done
Job </opt/hpmpi/bin/mpirun -srun ./lmp_mpi -in in.polymer> was submitted from host <req770> by user <colin>.
Job was executed on host(s) <16*lsfhost.localdomain>, in queue <mpi>, as user <colin>.
</home/colin> was used as the home directory.
</home/colin/lammps-10Aug15/examples/USER/lb/tested/polymer> was used as the working directory.
Started at Mon Aug 24 11:12:37 2015
Results reported at Tue Aug 25 01:20:46 2015
Your job looked like:
------------------------------------------------------------
# LSBATCH: User input
/opt/hpmpi/bin/mpirun -srun ./lmp_mpi -in in.polymer
------------------------------------------------------------
Successfully completed.
Resource usage summary:
CPU time : 812767.44 sec.
Max Memory : 44 MB
Max Swap : 812 MB
The output (if any) is above this job summary.

503
examples/PACKAGES/latboltz/toycar/in.toycar Normal file
View File

@ -0,0 +1,503 @@
#===========================================================================#
# Toy car driving down a system with a floor and ceiling. #
# #
# The car is first constructed by condensing particles onto various regions#
# that make up the car's parts. Then the car moves in a lattice Boltzmann #
# fluid. This requires compilation with the RIGID and LATBOLTZ packages #
# You will need to uncomment the dump options to get useful output. #
#===========================================================================#
units cgs
dimension 3
boundary p p f
atom_style atomic
processors * 1 *
#-------------------------------------------------------------------------#
# Set up the simulation box
#-------------------------------------------------------------------------#
variable dx equal 1.5
variable more equal 6.5
variable xl equal "-32*v_dx"
variable xh equal "32*v_dx"
variable yl equal "-60*v_dx"
variable yh equal "420*v_dx"
variable zl equal "-6*v_dx"
variable zh equal "58*v_dx"
region mybox block ${xl} ${xh} ${yl} ${yh} ${zl} ${zh}
create_box 14 mybox
#-------------------------------------------------------------------------#
# Creating the regions and filling them with atoms assigned to surge_group
#-------------------------------------------------------------------------#
variable density equal 0.001184
variable sigma equal "1.2*v_dx" #"1.2*v_dx"
variable rcutlj equal "v_sigma*2^(1/6)"
variable rcutlj93 equal "v_sigma*(2/5)^(1/6)"
#-------------------------------------------------------------------------#
# Creating the cylinder
#-------------------------------------------------------------------------#
variable c1 equal 12.5
variable c2 equal -1.5
variable radius equal 6.0
variable lo equal 9.5
variable hi equal 12.5
region mycylinderinside1 cylinder x ${c1} ${c2} ${radius} ${lo} ${hi}
variable n_nodes_Cy_1 equal "round(v_more*0.28*((2*PI*v_radius*(v_hi-v_lo))+(2*PI*(v_radius)^2)))"
create_atoms 1 random ${n_nodes_Cy_1} 1234 mycylinderinside1 units box
variable radius_2 equal "v_radius + v_rcutlj93"
variable hi_2 equal "v_hi + 2*v_rcutlj93"
variable lo_2 equal "v_lo - v_rcutlj93"
region mycylinder1 cylinder x ${c1} ${c2} ${radius_2} ${lo_2} ${hi_2}
group gcylinder1 region mycylinder1
#-------------------------------------------------------------------------#
# Creating the cylinder
#-------------------------------------------------------------------------#
variable c1 equal -9.0
variable c2 equal -1.5
variable radius equal 6.0
variable lo equal 9.5
variable hi equal 12.5
region mycylinderinside2 cylinder x ${c1} ${c2} ${radius} ${lo} ${hi}
variable n_nodes_Cy_2 equal "round(v_more*0.28*((2*PI*v_radius*(v_hi-v_lo))+(2*PI*(v_radius)^2)))"
create_atoms 2 random ${n_nodes_Cy_2} 1234 mycylinderinside2 units box
variable radius_2 equal "v_radius + v_rcutlj93"
variable hi_2 equal "v_hi + 2*v_rcutlj93"
variable lo_2 equal "v_lo - v_rcutlj93"
region mycylinder2 cylinder x ${c1} ${c2} ${radius_2} ${lo_2} ${hi_2}
group gcylinder2 region mycylinder2
#-------------------------------------------------------------------------#
# Creating the cylinder
#-------------------------------------------------------------------------#
variable c1 equal -9.0
variable c2 equal -1.5
variable radius equal 6.0
variable lo equal -12.5
variable hi equal -9.5
region mycylinderinside3 cylinder x ${c1} ${c2} ${radius} ${lo} ${hi}
variable n_nodes_Cy_3 equal "round(v_more*0.28*((2*PI*v_radius*(v_hi-v_lo))+(2*PI*(v_radius)^2)))"
create_atoms 3 random ${n_nodes_Cy_3} 1234 mycylinderinside3 units box
variable radius_2 equal "v_radius + v_rcutlj93"
variable hi_2 equal "v_hi + v_rcutlj93"
variable lo_2 equal "v_lo - 2*v_rcutlj93"
region mycylinder3 cylinder x ${c1} ${c2} ${radius_2} ${lo_2} ${hi_2}
group gcylinder3 region mycylinder3
#-------------------------------------------------------------------------#
# Creating the cylinder
#-------------------------------------------------------------------------#
variable c1 equal 12.0
variable c2 equal -1.5
variable radius equal 6.0
variable lo equal -12.5
variable hi equal -9.5
region mycylinderinside4 cylinder x ${c1} ${c2} ${radius} ${lo} ${hi}
variable n_nodes_Cy_4 equal "round(v_more*0.28*((2*PI*v_radius*(v_hi-v_lo))+(2*PI*(v_radius)^2)))"
create_atoms 4 random ${n_nodes_Cy_4} 1234 mycylinderinside4 units box
variable radius_2 equal "v_radius + v_rcutlj93"
variable hi_2 equal "v_hi + v_rcutlj93"
variable lo_2 equal "v_lo - 2*v_rcutlj93"
region mycylinder4 cylinder x ${c1} ${c2} ${radius_2} ${lo_2} ${hi_2}
group gcylinder4 region mycylinder4
#-------------------------------------------------------------------------#
# Creating the prism
#-------------------------------------------------------------------------#
variable xlo1 equal -5.0
variable xhi1 equal 5.0
variable ylo1 equal -15.0
variable yhi1 equal 15.0
variable zlo1 equal -6.0
variable zhi1 equal 6.0
region myprisminside1 block ${xlo1} ${xhi1} ${ylo1} ${yhi1} ${zlo1} ${zhi1}
variable n_nodes_P_1 equal "(round(v_more*3.4*(6*(10.0)^2)/(PI*v_dx^2)))"
create_atoms 5 random ${n_nodes_P_1} 1234 myprisminside1 units box
variable xlo1_2 equal "v_xlo1 - v_rcutlj93/2"
variable xhi1_2 equal "v_xhi1 + v_rcutlj93/2"
variable ylo1_2 equal "v_ylo1 - v_rcutlj93/2"
variable yhi1_2 equal "v_yhi1 + v_rcutlj93/2"
variable zlo1_2 equal "v_zlo1 - v_rcutlj93/2"
variable zhi1_2 equal "v_zhi1 + v_rcutlj93/2"
region myprism1 block ${xlo1_2} ${xhi1_2} ${ylo1_2} ${yhi1_2} ${zlo1_2} ${zhi1_2}
group gprism1 region myprism1
#-------------------------------------------------------------------------#
# Creating the rear wing
#-------------------------------------------------------------------------#
variable xlo2 equal -10.0
variable xhi2 equal 10.0
variable ylo2 equal 14.0
variable yhi2 equal 22.0
variable zlo2 equal 10.0
variable zhi2 equal 12.0
region myprisminside2 block ${xlo2} ${xhi2} ${ylo2} ${yhi2} ${zlo2} ${zhi2}
variable n_nodes_P_2 equal "(round(v_more*0.93*(6*(7.0)^2)/(PI*v_dx^2)))"
create_atoms 6 random ${n_nodes_P_2} 1234 myprisminside2 units box
variable xlo2_2 equal "v_xlo2 - v_rcutlj93/2"
variable xhi2_2 equal "v_xhi2 + v_rcutlj93/2"
variable ylo2_2 equal "v_ylo2 - v_rcutlj93/2"
variable yhi2_2 equal "v_yhi2 + v_rcutlj93/2"
variable zlo2_2 equal "v_zlo2 - v_rcutlj93/2"
variable zhi2_2 equal "v_zhi2 + v_rcutlj93/2"
region myprism2 block ${xlo2_2} ${xhi2_2} ${ylo2_2} ${yhi2_2} ${zlo2_2} ${zhi2_2}
group gprism2 region myprism2
#-------------------------------------------------------------------------#
# Creating the rear wing stand
#-------------------------------------------------------------------------#
variable xlo3 equal -2.0
variable xhi3 equal 2.0
variable ylo3 equal 17.0
variable yhi3 equal 19.0
variable zlo3 equal -2.0
variable zhi3 equal 7.0
region myprisminside3 block ${xlo3} ${xhi3} ${ylo3} ${yhi3} ${zlo3} ${zhi3}
variable n_nodes_P_3 equal "(round(v_more*0.32*(6*(6.0)^2)/(PI*v_dx^2)))"
create_atoms 7 random ${n_nodes_P_3} 1234 myprisminside3 units box
variable xlo3_2 equal "v_xlo3 - v_rcutlj93/2"
variable xhi3_2 equal "v_xhi3 + v_rcutlj93/2"
variable ylo3_2 equal "v_ylo3 - v_rcutlj93/2"
variable yhi3_2 equal "v_yhi3 + v_rcutlj93/2"
variable zlo3_2 equal "v_zlo3 - v_rcutlj93/2"
variable zhi3_2 equal "v_zhi3 + v_rcutlj93/2"
region myprism3 block ${xlo3_2} ${xhi3_2} ${ylo3_2} ${yhi3_2} ${zlo3_2} ${zhi3_2}
group gprism3 region myprism3
#-------------------------------------------------------------------------#
# Creating the front wing
#-------------------------------------------------------------------------#
variable xlo4 equal -10.0
variable xhi4 equal 10.0
variable ylo4 equal -26.5
variable yhi4 equal -22.0
variable zlo4 equal -5.0
variable zhi4 equal -3.0
region myprisminside4 block ${xlo4} ${xhi4} ${ylo4} ${yhi4} ${zlo4} ${zhi4}
variable n_nodes_P_4 equal "(round(v_more*1.47*(6*(4.0)^2)/(PI*v_dx^2)))"
create_atoms 8 random ${n_nodes_P_4} 1234 myprisminside4 units box
variable xlo4_2 equal "v_xlo4 - v_rcutlj93/2"
variable xhi4_2 equal "v_xhi4 + v_rcutlj93/2"
variable ylo4_2 equal "v_ylo4 - v_rcutlj93/2"
variable yhi4_2 equal "v_yhi4 + v_rcutlj93/2"
variable zlo4_2 equal "v_zlo4 - v_rcutlj93/2"
variable zhi4_2 equal "v_zhi4 + v_rcutlj93/2"
region myprism4 block ${xlo4_2} ${xhi4_2} ${ylo4_2} ${yhi4_2} ${zlo4_2} ${zhi4_2}
group gprism4 region myprism4
#-------------------------------------------------------------------------#
# Creating the front wing stand
#-------------------------------------------------------------------------#
variable xlo5 equal -4.0
variable xhi5 equal 4.0
variable ylo5 equal -20.0
variable yhi5 equal -18.0
variable zlo5 equal -5.0
variable zhi5 equal 3.0
region myprisminside5 block ${xlo5} ${xhi5} ${ylo5} ${yhi5} ${zlo5} ${zhi5}
variable n_nodes_P_5 equal "(round(v_more*2.15*(6*(3.0)^2)/(PI*v_dx^2)))"
create_atoms 9 random ${n_nodes_P_5} 1234 myprisminside5 units box
variable xlo5_2 equal "v_xlo5 - v_rcutlj93/2"
variable xhi5_2 equal "v_xhi5 + v_rcutlj93/2"
variable ylo5_2 equal "v_ylo5 - v_rcutlj93/2"
variable yhi5_2 equal "v_yhi5 + v_rcutlj93/2"
variable zlo5_2 equal "v_zlo5 - v_rcutlj93/2"
variable zhi5_2 equal "v_zhi5 + v_rcutlj93/2"
region myprism5 block ${xlo5_2} ${xhi5_2} ${ylo5_2} ${yhi5_2} ${zlo5_2} ${zhi5_2}
group gprism5 region myprism5
#-------------------------------------------------------------------------#
# Creating the driver
#-------------------------------------------------------------------------#
variable radius2 equal 1.0
variable xloc equal 0.0
variable yloc equal 3.0
variable zloc equal 9.5
region mysphereinside2 sphere ${xloc} ${yloc} ${zloc} ${radius2}
variable n_nodes_S_2 equal "(round(v_more*2.0*(2*v_radius2^2/v_dx^2)))"
create_atoms 10 random ${n_nodes_S_2} 1234 mysphereinside2 units box
variable radius2_2 equal "v_radius2 + v_rcutlj93"
region mysphere2 sphere ${xloc} ${yloc} ${zloc} ${radius2_2}
group gball2 region mysphere2
#-------------------------------------------------------------------------#
# Creating the rear wing side
#-------------------------------------------------------------------------#
variable xlo5 equal 12.0
variable xhi5 equal 14.25
variable ylo5 equal 14.0
variable yhi5 equal 22.0
variable zlo5 equal 10.0
variable zhi5 equal 14.0
region myprisminside6 block ${xlo5} ${xhi5} ${ylo5} ${yhi5} ${zlo5} ${zhi5}
variable n_nodes_P_6 equal "(round(v_more*1.0*(6*(3.0)^2)/(PI*v_dx^2)))"
create_atoms 11 random ${n_nodes_P_6} 1234 myprisminside6 units box
variable xlo5_2 equal "v_xlo5 - v_rcutlj93/2"
variable xhi5_2 equal "v_xhi5 + v_rcutlj93/2"
variable ylo5_2 equal "v_ylo5 - v_rcutlj93/2"
variable yhi5_2 equal "v_yhi5 + v_rcutlj93/2"
variable zlo5_2 equal "v_zlo5 - v_rcutlj93/2"
variable zhi5_2 equal "v_zhi5 + v_rcutlj93/2"
region myprism6 block ${xlo5_2} ${xhi5_2} ${ylo5_2} ${yhi5_2} ${zlo5_2} ${zhi5_2}
group gprism6 region myprism6
#-------------------------------------------------------------------------#
# Creating the rear wing side
#-------------------------------------------------------------------------#
variable xlo5 equal -14.25
variable xhi5 equal -12.0
variable ylo5 equal 14.0
variable yhi5 equal 22.0
variable zlo5 equal 10.0
variable zhi5 equal 14.0
region myprisminside7 block ${xlo5} ${xhi5} ${ylo5} ${yhi5} ${zlo5} ${zhi5}
variable n_nodes_P_7 equal "(round(v_more*1.0*(6*(3.0)^2)/(PI*v_dx^2)))"
create_atoms 12 random ${n_nodes_P_7} 1234 myprisminside7 units box
variable xlo5_2 equal "v_xlo5 - v_rcutlj93/2"
variable xhi5_2 equal "v_xhi5 + v_rcutlj93/2"
variable ylo5_2 equal "v_ylo5 - v_rcutlj93/2"
variable yhi5_2 equal "v_yhi5 + v_rcutlj93/2"
variable zlo5_2 equal "v_zlo5 - v_rcutlj93/2"
variable zhi5_2 equal "v_zhi5 + v_rcutlj93/2"
region myprism7 block ${xlo5_2} ${xhi5_2} ${ylo5_2} ${yhi5_2} ${zlo5_2} ${zhi5_2}
group gprism7 region myprism7
#-------------------------------------------------------------------------#
# Creating the front wing side
#-------------------------------------------------------------------------#
variable xlo5 equal 12.0
variable xhi5 equal 14.25
variable ylo5 equal -26.0
variable yhi5 equal -20.0
variable zlo5 equal -5.0
variable zhi5 equal -1.0
region myprisminside8 block ${xlo5} ${xhi5} ${ylo5} ${yhi5} ${zlo5} ${zhi5}
variable n_nodes_P_8 equal "(round(v_more*1.8*(6*(2.0)^2)/(PI*v_dx^2)))"
create_atoms 11 random ${n_nodes_P_8} 1234 myprisminside8 units box
variable xlo5_2 equal "v_xlo5 - v_rcutlj93/2"
variable xhi5_2 equal "v_xhi5 + v_rcutlj93/2"
variable ylo5_2 equal "v_ylo5 - v_rcutlj93/2"
variable yhi5_2 equal "v_yhi5 + v_rcutlj93/2"
variable zlo5_2 equal "v_zlo5 - v_rcutlj93/2"
variable zhi5_2 equal "v_zhi5 + v_rcutlj93/2"
region myprism8 block ${xlo5_2} ${xhi5_2} ${ylo5_2} ${yhi5_2} ${zlo5_2} ${zhi5_2}
group gprism8 region myprism8
#-------------------------------------------------------------------------#
# Creating the front wing side
#-------------------------------------------------------------------------#
variable xlo5 equal -14.25
variable xhi5 equal -12.0
variable ylo5 equal -26.0
variable yhi5 equal -20.0
variable zlo5 equal -5.0
variable zhi5 equal -1.0
region myprisminside9 block ${xlo5} ${xhi5} ${ylo5} ${yhi5} ${zlo5} ${zhi5}
variable n_nodes_P_9 equal "(round(v_more*1.8*(6*(2.0)^2)/(PI*v_dx^2)))"
create_atoms 12 random ${n_nodes_P_9} 1234 myprisminside9 units box
variable xlo5_2 equal "v_xlo5 - v_rcutlj93/2"
variable xhi5_2 equal "v_xhi5 + v_rcutlj93/2"
variable ylo5_2 equal "v_ylo5 - v_rcutlj93/2"
variable yhi5_2 equal "v_yhi5 + v_rcutlj93/2"
variable zlo5_2 equal "v_zlo5 - v_rcutlj93/2"
variable zhi5_2 equal "v_zhi5 + v_rcutlj93/2"
region myprism9 block ${xlo5_2} ${xhi5_2} ${ylo5_2} ${yhi5_2} ${zlo5_2} ${zhi5_2}
group gprism9 region myprism9
#------------------------------------------------------------------------#
# creating the union between the regions
#------------------------------------------------------------------------#
group wheels union gcylinder1 gcylinder2 gcylinder3 gcylinder4
group not_wheels union gprism1 gprism2 gprism3 gprism4 gprism5 gball2 gprism6 gprism7 gprism8 gprism9
group aero_group union gprism2 gprism3 gprism4 gprism5 gball2 gprism6 gprism7 gprism8 gprism9
region aero union 9 myprism2 myprism3 myprism4 myprism5 mysphere2 myprism6 myprism7 myprism8 myprism9
group chassis_group union gcylinder1 gcylinder2 gcylinder3 gcylinder4 gprism1
region chassis union 5 mycylinder1 mycylinder2 mycylinder3 mycylinder4 myprism1
group surge_group union aero_group chassis_group
region surge union 2 aero chassis
#------------------------------------------------------------------------#
# Soft Potential
#------------------------------------------------------------------------#
variable softlength equal "0.5*v_rcutlj"
pair_style soft ${softlength}
pair_coeff * * 0.0
variable prefactor equal ramp(0,4.14e-8)
fix 1 all adapt 1 pair soft a * * v_prefactor
#------------------------------------------------------------------------#
# Run parameters and set up dump
#------------------------------------------------------------------------#
timestep 0.2
mass * 1.0e-6
variable nbin equal "v_rcutlj / (4/3)"
neighbor ${nbin} bin
neigh_modify delay 0 every 1 check yes
#variable commcutoff equal "v_dx*2"
#comm_modify cutoff ${commcutoff}
#dump mydump all atom 10000 out.lammpstrj
thermo 5000
#------------------------------------------------------------------------#
# Computes initial interaction
#------------------------------------------------------------------------#
variable epsilon equal 10.0e-10
variable cutofflj93 equal 7.0
fix wall surge_group wall/region surge lj93 ${epsilon} ${sigma} ${cutofflj93}
fix 3 all langevin 31000000.0 50000.0 100.0 5678
fix 2 all nve
#restart 100000 ParticleRestart
run 100000
unfix 1
unfix 2
unfix 3
unfix wall
#------------------------------------------------------------------------#
# Phase 2 : annealing
#------------------------------------------------------------------------#
#------------------------------------------------------------------------#
# Soft Potential
#------------------------------------------------------------------------#
variable softlength equal "0.475*v_rcutlj"
pair_style soft ${softlength}
pair_coeff * * 4.14e-8
#------------------------------------------------------------------------#
# Computes initial interaction
#------------------------------------------------------------------------#
variable epsilon equal 20.0e-10
variable cutofflj93 equal 7.0
fix wall surge_group wall/region surge lj93 ${epsilon} ${sigma} ${cutofflj93}
fix 3 all langevin 100000.0 5000.0 100.0 5678
fix 2 all nve
run 200000
minimize 0.0 1.0e-8 1000 100000
unfix wall
unfix 2
unfix 3
#-------------------------------------------------------------------------#
# The lb/fluid simulation
#
# The sphere travels through the simulation, being pushed by the fluid
#-------------------------------------------------------------------------#
variable number_all equal count(all)
variable node_mass equal "500000 / v_number_all"
mass 5* ${node_mass}
variable wheel_mass equal "v_node_mass/1000"
mass *4 ${wheel_mass}
variable dx equal 1.0
variable density equal 0.001184
neighbor 0.5 bin
neigh_modify delay 0 every 1 check yes
comm_modify cutoff 3.0
pair_style lj/cut 1.2
pair_coeff * * 0.0 0.0
timestep 0.025
if "$(is_defined(dump,mydump))" then "undump mydump"
reset_timestep 0
#dump mydump all atom 10000 run.lammpstrj
#variable total_force equal 0.2
#variable node_force equal "v_total_force / 178"
#fix drag all addforce 0.0 0.0 0.0
velocity all set 0.0 -7.5.0 0.0 units box
# viscosity of air is 0.0001847
fix FL all lb/fluid 1 0.0002 ${density} stencil 2 dx ${dx} zwall_velocity 0 0 # dumpxdmf 1000 sflow 0
variable vx equal vcm(all,x)
variable vy equal vcm(all,y)
variable vz equal vcm(all,z)
#dump mydumpvtk all vtk 1000 out*.vtp vx vy vz
fix 2 all lb/viscous
fix 4 not_wheels nve
fix 3 wheels rigid group 4 gcylinder1 gcylinder2 gcylinder3 gcylinder4 force * off off off torque * on off off
fix 5 not_wheels setforce 0.0 0.0 0.0
thermo_style custom step v_number_all v_node_mass f_FL[2] f_5[1] f_5[2] f_5[3]
thermo 100
run 5000
#-------------------------------------------------------------------------#

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#===========================================================================#
# Immersed Boundary Wall #
# #
# Run consists of a 32-bead coarse-grained polymer #
# translocating through a solid-state atomistic wall #
# under pressure-driven lattice-Boltzmann fluid flow #
# #
# To run this example, LAMMPS needs to be compiled with a the following #
# packages: MOLECULE, RIGID, LATBOLTZ, USER-VTK #
# #
#To run this example on N cores, use command: #
# mpirun -n N /LAMMPS/EXE/FILE -in in.polymer > output.out #
# #
# If uncommented: #
# Sample output for polymer from this run can be found in the file: #
# 'translocationdump.lammpstrj' #
# and viewed using, the VMD software. #
# OR #
# 'dump.translocation.vtk' #
# and viewed using the Paraview software. #
# #
# Sample output for the wall from this run can be found in the file: #
# 'walldump.xyz' #
# and can be viewed using the VMD or Paraview Software. #
#===========================================================================#
units nano
dimension 3
boundary p p p
atom_style hybrid molecular
special_bonds fene
read_data data.translocation
#---------------------------------------------------------------------------
#Creating a atomistic wall on an FCC lattice and removing the block from the
#middle to create the nanopore
#---------------------------------------------------------------------------
lattice fcc 1.0
region wall block 28 38 0 32 0 32
create_atoms 3 region wall
region hole block 28 38 14 18 14 18
delete_atoms region hole compress no
#----------------------------------------------------------------------------
# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing
# to ensure that the particles belonging to a given processor remain inside
# that processors lattice-Boltzmann grid.
# The communcation cutoff is set to 2.5 dx to ensure that all particles in the
# processor ghost fluid region (of width 2dx) are known to local processor.
#----------------------------------------------------------------------------
neighbor 0.5 bin
neigh_modify delay 0 every 1 check yes
neigh_modify exclude type 2 2
neigh_modify exclude type 2 1
neigh_modify exclude type 2 3
neigh_modify exclude type 3 3
comm_modify cutoff 2.5
#----------------------------------------------------------------------------
# Implement a hard-sphere interaction between the particles at the center of
# each monomer with each other and the wall atoms
# (use a truncated and shifted Lennard-Jones potential).
#----------------------------------------------------------------------------
bond_style fene
bond_coeff 1 60.0 2.25 4.14195 1.5
pair_style lj/cut 1.68369
pair_coeff * * 0 1.5
pair_coeff 1 1 4.14195 1.5 1.68369
pair_coeff 1 3 4.14195 1.5 1.68369
#-----------------------------------------------------------------------------
# The mass is set 4/3 PI r^3 fluid_density/31 , where r=0.617, 31 is number of
# nodes in a single monomer. The mass of wall atoms is chosen heavy as they
# are fixed.
# ----------------------------------------------------------------------------
mass * 0.00000318
#-----------------------------------------------------------------------------
timestep 0.00005
#----------------------------------------------------------------------------
# ForceAtoms are the particles at the center of each monomer which
# do not interact with the fluid, but are used to implement the hard-sphere
# interactions.
# FluidAtoms are the particles representing the surface of the monomer
# which do interact with the fluid. The nanopore particles are also included
# in this group as they interact with the fluid.
# Polymer is the entire set of monomers of the composite polymer chain.
# WallAtoms are the particles of the nanopore.
#----------------------------------------------------------------------------
group ForceAtoms type 1
group FluidAtoms type 2 3
group Polymer type 1 2
group WallAtoms type 3
#---------------------------------------------------------------------------
# Create a lattice-Boltzmann fluid covering the simulation domain.
# This fluid feels a force due to the particles specified through FluidAtoms
# (however, this fix does not explicity apply a force back on to these
# particles. This is accomplished through the use of the lb/viscous fix).
# We set fluid viscosity = 0.1 and fluid density = 0.00009982071 which
# means the kinematic viscosity is idential to that of water but the
# dynamic viscosity is a factor of 10 less than that of water which
# increases the diffusive dynamics by a corresponding factor of 10.
# lattice spacing dx=1.0, and mass unit, dm=0.00009982071 (makes density 1)
# Use a thermal lattice-Boltzmann fluid (temperature 300K, random number
# seed=5252). This enables the particles to undergo Brownian motion in
# the fluid.
# In this case we use the scaleGamma argument to set the mass of the WallAtoms
# to infinity.
# The commented out line can be substituted to look at the flow without noise
# which should be similar to the average flow field in the case with noise.
#----------------------------------------------------------------------------
fix 1 FluidAtoms lb/fluid 1 0.1 0.00009982071 dx 1.0 scaleGamma 3 -1 stencil 2 pressurebcx 1200 noise 300.0 5252
#fix 1 FluidAtoms lb/fluid 1 0.1 0.00009982071 dx 1.0 scaleGamma 3 -1 stencil 2 pressurebcx 1200 dumpxdmf 1000 flow 0
#----------------------------------------------------------------------------
# Apply the force from the fluid to the particles, and integrate their
# motion, constraining each monomer to move and rotate as a single rigid
# spherical object.
# Since both the ForceAtoms (central atoms), and the FluidAtoms (spherical
# shell) should move and rotate together, this fix is applied to all Polymer
# of atoms in the system.
# The wall atoms are frozen in space and all the calculated forces on the atoms
# are set to zero at each timestep.
#----------------------------------------------------------------------------#
fix 2 FluidAtoms lb/viscous
fix 3 Polymer rigid/small molecule
fix freeze WallAtoms setforce 0 0 0
#----------------------------------------------------------------------------
# Write position and velocity coordinates into a file every 2000 time steps.
#----------------------------------------------------------------------------
#variable x1 equal x[1]
#variable y1 equal y[1]
#variable z1 equal z[1]
#variable vx1 equal vx[1]
#variable vy1 equal vy[1]
#variable vz1 equal vz[1]
#variable x2 equal x[249]
#variable y2 equal y[249]
#variable z2 equal z[249]
#variable vx2 equal vx[249]
#variable vy2 equal vy[249]
#variable vz2 equal vz[249]
#variable x3 equal x[497]
#variable y3 equal y[497]
#variable z3 equal z[497]
#variable vx3 equal vx[497]
#variable vy3 equal vy[497]
#variable vz3 equal vz[497]
#variable x4 equal x[745]
#variable y4 equal y[745]
#variable z4 equal z[745]
#variable vx4 equal vx[745]
#variable vy4 equal vy[745]
#variable vz4 equal vz[745]
#thermo_style custom v_x1 v_y1 v_z1 v_vx1 v_vy1 v_vz1 v_x2 v_y2 v_z2 v_vx2 v_vy2 v_vz2 v_x3 v_y3 v_z3 v_vx3 v_vy3 v_vz3 v_x4 v_y4 v_z4 v_x4 v_y4 v_z4
#thermo 10
#---------------------------------------------------------------------------------
# Write coordinates of the centre of mass and radius of gyration tensor components
#---------------------------------------------------------------------------------
compute centre ForceAtoms com
compute rg ForceAtoms gyration
thermo_style custom c_rg c_rg[1] c_rg[2] c_rg[3] c_rg[4] c_rg[5] c_rg[6] c_centre[1] c_centre[2] c_centre[3]
thermo 1000
#--------------------------------------------------------------------------------
# Define number of steps variable. Write dump files for the polymer in both LAMMPS
# trajectory and vtk format (commented out here). Write xyz dump file
#--------------------------------------------------------------------------------
variable numofsteps equal 400001
#dump 1 ForceAtoms custom 500 translocationdump.lammpstrj id xu yu zu vx vy vz
#dump 2 ForceAtoms vtk 1000 dump*.translocation.vtk id xu yu zu vx vy vz
#dump 4 WallAtoms xyz $(v_numofsteps-1) walldump.xyz
#restart 50000 4nmrestart.*
run ${numofsteps} # For 250001 steps without noise, 16 minutes on AMD Ryzen Threadripper 1950X 16-Core, 41 mintues on Intel(R) Core(TM) i7-10510U CPU @ 1.80GHz 4-core

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LAMMPS (17 Feb 2022)
#===========================================================================#
# Immersed Boundary Wall #
# #
# Run consists of a 32-bead coarse-grained polymer #
# translocating through a solid-state atomistic wall #
# under pressure-driven lattice-Boltzmann fluid flow #
# #
# To run this example, LAMMPS needs to be compiled with a the following #
# packages: MOLECULE, RIGID, LATBOLTZ, USER-VTK #
# #
#To run this example on N cores, use command: #
# mpirun -n N /LAMMPS/EXE/FILE -in in.polymer > output.out #
# #
# If uncommented: #
# Sample output for polymer from this run can be found in the file: #
# 'translocationdump.lammpstrj' #
# and viewed using, the VMD software. #
# OR #
# 'dump.translocation.vtk' #
# and viewed using the Paraview software. #
# #
# Sample output for the wall from this run can be found in the file: #
# 'walldump.xyz' #
# and can be viewed using the VMD or Paraview Software. #
#===========================================================================#
units nano
dimension 3
boundary p p p
atom_style hybrid molecular
special_bonds fene
read_data data.translocation
Reading data file ...
orthogonal box = (0 0 0) to (48 32 32)
2 by 1 by 2 MPI processor grid
reading atoms ...
992 atoms
scanning bonds ...
1 = max bonds/atom
reading bonds ...
31 bonds
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 1 1
special bond factors coul: 0 1 1
2 = max # of 1-2 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.044 seconds
#---------------------------------------------------------------------------
#Creating a atomistic wall on an FCC lattice and removing the block from the
#middle to create the nanopore
#---------------------------------------------------------------------------
lattice fcc 1.0
Lattice spacing in x,y,z = 1 1 1
region wall block 28 38 0 32 0 32
create_atoms 3 region wall
Created 43008 atoms
using lattice units in orthogonal box = (0 0 0) to (48 32 32)
create_atoms CPU = 0.011 seconds
region hole block 28 38 14 18 14 18
delete_atoms region hole compress no
Deleted 851 atoms, new total = 43149
#----------------------------------------------------------------------------
# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing
# to ensure that the particles belonging to a given processor remain inside
# that processors lattice-Boltzmann grid.
# The communcation cutoff is set to 2.5 dx to ensure that all particles in the
# processor ghost fluid region (of width 2dx) are known to local processor.
#----------------------------------------------------------------------------
neighbor 0.5 bin
neigh_modify delay 0 every 1 check yes
neigh_modify exclude type 2 2
neigh_modify exclude type 2 1
neigh_modify exclude type 2 3
neigh_modify exclude type 3 3
comm_modify cutoff 2.5
#----------------------------------------------------------------------------
# Implement a hard-sphere interaction between the particles at the center of
# each monomer with each other and the wall atoms
# (use a truncated and shifted Lennard-Jones potential).
#----------------------------------------------------------------------------
bond_style fene
bond_coeff 1 60.0 2.25 4.14195 1.5
pair_style lj/cut 1.68369
pair_coeff * * 0 1.5
pair_coeff 1 1 4.14195 1.5 1.68369
pair_coeff 1 3 4.14195 1.5 1.68369
#-----------------------------------------------------------------------------
# The mass is set 4/3 PI r^3 fluid_density/31 , where r=0.617, 31 is number of
# nodes in a single monomer. The mass of wall atoms is chosen heavy as they
# are fixed.
# ----------------------------------------------------------------------------
mass * 0.00000318
#-----------------------------------------------------------------------------
timestep 0.00005
#----------------------------------------------------------------------------
# ForceAtoms are the particles at the center of each monomer which
# do not interact with the fluid, but are used to implement the hard-sphere
# interactions.
# FluidAtoms are the particles representing the surface of the monomer
# which do interact with the fluid. The nanopore particles are also included
# in this group as they interact with the fluid.
# Polymer is the entire set of monomers of the composite polymer chain.
# WallAtoms are the particles of the nanopore.
#----------------------------------------------------------------------------
group ForceAtoms type 1
32 atoms in group ForceAtoms
group FluidAtoms type 2 3
43117 atoms in group FluidAtoms
group Polymer type 1 2
992 atoms in group Polymer
group WallAtoms type 3
42157 atoms in group WallAtoms
#---------------------------------------------------------------------------
# Create a lattice-Boltzmann fluid covering the simulation domain.
# This fluid feels a force due to the particles specified through FluidAtoms
# (however, this fix does not explicity apply a force back on to these
# particles. This is accomplished through the use of the lb/viscous fix).
# We set fluid viscosity = 0.1 and fluid density = 0.00009982071 which
# means the kinematic viscosity is idential to that of water but the
# dynamic viscosity is a factor of 10 less than that of water which
# increases the diffusive dynamics by a corresponding factor of 10.
# lattice spacing dx=1.0, and mass unit, dm=0.00009982071 (makes density 1)
# Use a thermal lattice-Boltzmann fluid (temperature 300K, random number
# seed=5252). This enables the particles to undergo Brownian motion in
# the fluid.
# In this case we use the scaleGamma argument to set the mass of the WallAtoms
# to infinity.
# The commented out line can be substituted to look at the flow without noise
# which should be similar to the average flow field in the case with noise.
#----------------------------------------------------------------------------
fix 1 FluidAtoms lb/fluid 1 0.1 0.00009982071 dx 1.0 scaleGamma 3 -1 stencil 2 pressurebcx 1200 noise 300.0 5252
Using a lattice-Boltzmann grid of 48 by 32 by 32 total grid points. (../fix_lb_fluid.cpp:486)
Local Grid Geometry created. (../fix_lb_fluid.cpp:1018)
#fix 1 FluidAtoms lb/fluid 1 0.1 0.00009982071 dx 1.0 scaleGamma 3 -1 stencil 2 pressurebcx 1200 dumpxdmf 1000 flow 0
#----------------------------------------------------------------------------
# Apply the force from the fluid to the particles, and integrate their
# motion, constraining each monomer to move and rotate as a single rigid
# spherical object.
# Since both the ForceAtoms (central atoms), and the FluidAtoms (spherical
# shell) should move and rotate together, this fix is applied to all Polymer
# of atoms in the system.
# The wall atoms are frozen in space and all the calculated forces on the atoms
# are set to zero at each timestep.
#----------------------------------------------------------------------------#
fix 2 FluidAtoms lb/viscous
fix 3 Polymer rigid/small molecule
create bodies CPU = 0.001 seconds
32 rigid bodies with 992 atoms
0.70019686 = max distance from body owner to body atom
fix freeze WallAtoms setforce 0 0 0
#----------------------------------------------------------------------------
# Write position and velocity coordinates into a file every 2000 time steps.
#----------------------------------------------------------------------------
#variable x1 equal x[1]
#variable y1 equal y[1]
#variable z1 equal z[1]
#variable vx1 equal vx[1]
#variable vy1 equal vy[1]
#variable vz1 equal vz[1]
#variable x2 equal x[249]
#variable y2 equal y[249]
#variable z2 equal z[249]
#variable vx2 equal vx[249]
#variable vy2 equal vy[249]
#variable vz2 equal vz[249]
#variable x3 equal x[497]
#variable y3 equal y[497]
#variable z3 equal z[497]
#variable vx3 equal vx[497]
#variable vy3 equal vy[497]
#variable vz3 equal vz[497]
#variable x4 equal x[745]
#variable y4 equal y[745]
#variable z4 equal z[745]
#variable vx4 equal vx[745]
#variable vy4 equal vy[745]
#variable vz4 equal vz[745]
#thermo_style custom v_x1 v_y1 v_z1 v_vx1 v_vy1 v_vz1 v_x2 v_y2 v_z2 v_vx2 v_vy2 v_vz2 v_x3 v_y3 v_z3 v_vx3 v_vy3 v_vz3 v_x4 v_y4 v_z4 v_x4 v_y4 v_z4
#thermo 10
#---------------------------------------------------------------------------------
# Write coordinates of the centre of mass and radius of gyration tensor components
#---------------------------------------------------------------------------------
compute centre ForceAtoms com
compute rg ForceAtoms gyration
thermo_style custom c_rg c_rg[1] c_rg[2] c_rg[3] c_rg[4] c_rg[5] c_rg[6] c_centre[1] c_centre[2] c_centre[3]
thermo 1000
#--------------------------------------------------------------------------------
# Define number of steps variable. Write dump files for the polymer in both LAMMPS
# trajectory and vtk format (commented out here). Write xyz dump file
#--------------------------------------------------------------------------------
variable numofsteps equal 400001
#dump 1 ForceAtoms custom 500 translocationdump.lammpstrj id xu yu zu vx vy vz
#dump 2 ForceAtoms vtk 1000 dump*.translocation.vtk id xu yu zu vx vy vz
#dump 4 WallAtoms xyz $(v_numofsteps-1) walldump.xyz
#restart 50000 4nmrestart.*
run ${numofsteps} # For 250001 steps without noise, 16 minutes on AMD Ryzen Threadripper 1950X 16-Core, 41 mintues on Intel(R) Core(TM) i7-10510U CPU @ 1.80GHz 4-core
run 400001
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- fix lb/fluid command:
@Article{Denniston et al.,
author = {C. Denniston, N. Afrasiabian, M.G. Cole-Andre,F.E. Mackay, S.T.T. Ollila, T. Whitehead},
title = {LAMMPS lb/fluid fix version 2: Improved Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid}, journal = {Comp.~Phys.~Comm.},
year = 2022,
volume = 275,
pages = {108318}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.18369
ghost atom cutoff = 2.5
binsize = 1.091845, bins = 44 30 30
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
WARNING: Communication cutoff 2.5 is shorter than a bond length based estimate of 2.6825. This may lead to errors. (../comm.cpp:723)
Per MPI rank memory allocation (min/avg/max) = 11.44 | 20.02 | 30.41 Mbytes
c_rg c_rg[1] c_rg[2] c_rg[3] c_rg[4] c_rg[5] c_rg[6] c_centre[1] c_centre[2] c_centre[3]
5.6791248 22.61273 5.110682 4.5290465 6.700106 3.8164024 3.4765595 12.000543 11.573384 10.635513
5.5867637 21.257084 5.1321825 4.822662 5.634175 3.7281301 3.6276614 11.962266 11.452708 10.387815
5.668832 21.596665 5.6165458 4.9224455 5.647044 4.0344015 4.0048875 11.821122 11.451665 10.569963
5.6598062 20.600614 6.0567785 5.3760133 6.6053545 4.0554069 4.415185 11.9427 11.557594 10.571476
5.8889045 23.387471 6.0242487 5.2674768 7.6894041 4.652066 4.2066414 11.8858 11.664507 10.642731
6.1002855 26.57562 5.2572121 5.3806503 7.2669892 5.4963641 3.9022322 12.020013 11.658221 10.555459
6.3802913 30.250297 4.3928513 6.0649685 7.4030928 6.8471704 3.7581107 11.942494 11.656142 10.62799
6.4211512 30.052916 4.0869264 7.0913409 6.4493764 7.3015592 4.274762 11.983282 11.552276 10.499697
6.4029294 29.889365 4.0196733 7.0884671 6.5903461 6.8110154 4.0382413 11.9905 11.501962 10.425593
6.3161388 28.57849 3.8057293 7.5093902 5.7575295 6.6646378 4.1567522 12.113646 11.531039 10.529351
6.4338248 29.706116 3.4974686 8.1905167 5.5124312 7.9019084 4.5042964 12.426431 11.340065 10.399931
6.5364361 30.677501 3.6562753 8.3912202 5.1990078 7.3140488 4.8107991 12.472307 11.438123 10.425278
6.6943364 31.785713 3.6152177 9.4132091 5.6058833 7.7153622 5.1164739 12.583773 11.540381 10.504743
6.7208928 32.711587 3.7061318 8.7526817 6.8070192 6.7581599 4.5471865 12.517937 11.50458 10.470699
6.6375209 30.970999 3.6881577 9.3975267 7.3010233 5.4926275 4.1912585 12.684547 11.592933 10.675434
6.8324705 33.049694 4.0146629 9.6182957 8.7999601 7.2978407 4.3307267 12.660956 11.750078 10.71392
6.779281 33.083238 3.9016444 8.9737675 8.7458049 7.7168786 4.3419836 12.501914 11.814334 10.76077
6.6792036 32.828561 3.2387228 8.5444765 7.7842222 8.5969674 3.4661156 12.790705 11.968511 10.642253
6.5389782 31.772538 3.0722036 7.9134935 6.9299213 8.9153301 3.3680216 12.861509 11.85712 10.51657
6.4748361 31.540469 3.0212413 7.3617912 6.3057097 8.4191336 3.2625709 12.657649 11.704529 10.392716
6.3985321 29.710818 2.6283214 8.6020734 5.8853082 9.3362301 3.397929 12.688643 11.780723 10.424565
6.5059208 31.090823 2.6100712 8.6261116 6.5141681 10.225958 3.6286489 12.725294 12.0647 10.108992
6.4892221 30.985335 2.4997331 8.6249351 6.4886837 10.018904 3.3600422 12.855965 12.036702 9.9287436
6.4795231 30.758266 2.8637784 8.3621758 7.1748369 10.562754 3.5302178 12.896069 12.260403 10.11639
6.4439652 28.968436 2.3431114 10.21314 6.6140604 10.553576 3.2945616 12.721326 12.375786 10.216421
6.4585206 28.635315 2.1556643 10.921509 6.5660708 11.04493 3.0441915 12.688395 12.432736 10.446406
6.4828021 29.600008 2.0553059 10.371409 6.1193108 11.704064 2.6435946 12.670355 12.450579 10.754392
6.562285 30.709961 1.9685065 10.385117 5.9437889 12.632018 2.3117868 12.914159 12.707126 10.756693
6.6264405 31.273462 2.410996 10.225256 7.2739788 12.4541 2.9699821 12.81881 12.66146 10.672797
6.7415185 32.457723 2.3242798 10.666069 7.2496003 13.12296 2.9964595 12.784276 12.647643 10.60663
6.9008565 33.656929 2.7042837 11.260607 8.5449163 14.476583 3.8202075 12.710092 12.579311 10.58884
7.061302 35.296351 3.5107103 11.054924 10.064083 15.035769 4.4216887 13.175009 12.627831 10.482424
7.1032842 36.482445 3.6799052 10.294296 10.673901 14.749052 4.3151465 13.200713 12.621232 10.584217
7.1414828 36.185373 4.297132 10.518271 11.586979 15.307501 5.1527843 13.234596 12.688071 10.498004
6.9448583 33.990665 2.8733935 11.366998 8.6757703 15.425795 3.8675398 13.552629 12.904762 10.360584
7.0012016 32.933829 3.6133714 12.469623 9.9078147 16.084749 4.8325968 13.711685 12.775596 10.565942
7.0165074 33.824117 3.4135972 11.993662 9.4449537 15.727888 4.3550075 13.648024 12.818681 10.403745
7.0456647 33.8123 3.8273095 12.001781 9.9901691 15.354572 4.7262984 13.704142 12.865313 10.379126
7.0704851 35.593578 4.4753601 9.922821 10.815193 14.191266 4.3671704 13.568897 12.968225 10.27463
7.2622103 36.997176 5.0189577 10.723566 11.931013 15.173822 5.1502453 13.704027 12.992135 10.023658
7.3237142 36.361814 5.4045676 11.870409 12.36988 16.523084 5.9090879 13.732808 12.986696 9.6059086
7.4085072 37.338445 4.6635913 12.883943 11.559431 18.221441 5.9749906 13.822776 13.056276 9.4491435
7.5435451 38.642986 4.8108253 13.451262 11.762286 19.25048 6.2716652 13.76389 13.028638 9.3396345
7.5041212 37.242572 4.2407367 14.828527 10.397401 20.55556 6.0212974 13.656341 13.093764 9.1329939
7.4871925 37.814264 4.2622814 13.981507 10.161983 20.447606 5.7021938 13.637928 13.132284 8.9440227
7.3541675 36.518431 4.6241377 12.941211 10.094391 18.64877 5.616799 13.607907 13.208134 8.8058927
7.3886114 36.915543 4.9408074 12.735228 10.630813 18.896827 5.7094032 13.752166 13.333961 8.6671299
7.2634179 32.71655 5.167184 14.873507 10.523039 19.079411 6.3878762 13.935234 13.303392 8.6048102
7.3106746 33.990367 5.5659367 13.88966 11.693262 18.632011 6.5331934 13.883039 13.479355 8.6248803
7.2557189 35.200297 4.4884764 12.956683 10.303503 17.915053 5.6282044 13.728328 13.609539 8.6112695
7.3353193 37.845973 3.3837009 12.577235 8.6243964 18.581563 3.7985161 13.536049 13.443702 8.4039237
7.6187173 41.73183 4.4262573 11.886765 10.443613 18.59631 3.7033134 13.201011 13.445133 8.1443418
7.6874247 44.184475 4.0611444 10.850879 10.846122 17.980387 3.5984272 12.76067 13.517519 8.0974318
7.5889076 42.515998 3.8244222 11.251099 9.9966093 17.458176 3.1726154 12.592342 13.578402 8.0274103
7.7744651 44.148982 4.2129835 12.080342 11.586008 18.953803 4.6881973 12.781052 13.744522 8.1609444
7.8762095 46.571962 4.2336595 11.229055 11.956938 18.998552 4.4303527 12.78768 13.885168 8.5476521
7.5991537 41.910661 4.1811631 11.655312 11.231672 18.166889 4.3773455 12.90303 13.93913 8.622434
7.5180184 41.555253 4.1818325 10.783516 11.789934 16.439025 4.5300192 12.834806 13.889747 8.7422201
7.3943137 38.451129 3.5281391 12.696607 10.233182 17.033555 4.7102974 13.063809 13.856187 8.8178674
7.4384703 37.718734 2.9933066 14.6188 8.9987509 18.607817 4.5600437 13.330138 13.653329 8.830152
7.3814288 36.318864 2.9682884 15.198339 8.1447589 18.551238 4.1590099 13.403412 13.460209 8.9327916
7.5394784 38.362656 3.0647462 15.416333 8.1640602 19.326608 4.2298797 13.537652 13.374601 8.977215
7.7262621 40.829884 2.5614313 16.30381 7.5956765 20.560929 3.8808909 13.585574 13.235011 8.8738183
7.7634714 41.306228 2.512465 16.452796 7.6669614 20.470645 3.057384 13.7604 13.0761 8.9920836
7.7392158 41.493078 2.8531936 15.54919 8.0431313 20.099662 3.1955265 13.9152 13.113045 9.058674
7.5985272 40.439807 2.7690182 14.528791 7.9171761 19.019929 2.8658568 13.989693 13.357516 9.1564434
7.4219615 37.367221 2.4948211 15.22347 6.0308738 18.93324 1.504212 14.267885 13.404543 9.4027912
7.4337577 38.2949 2.2630142 14.702839 5.9811355 19.032103 2.0157301 14.111907 13.14959 9.3652
7.576974 39.734563 2.1660892 15.509883 5.9136162 19.743031 2.2197614 13.948861 13.028721 9.3094866
7.613064 39.552571 2.2430107 16.163162 5.2452948 20.628821 1.761766 13.91542 13.11386 9.2609839
7.4304964 37.395035 2.0924773 15.724764 3.8024501 19.174766 1.0800892 13.818389 13.282354 9.3579447
7.402555 37.586705 1.8744432 15.336672 3.8833298 19.105844 1.3149418 14.039309 13.154403 9.4725339
7.5729264 39.147513 1.8465945 16.355106 4.0187048 19.517631 0.85864085 13.933538 13.221032 9.7537823
7.4623367 38.270725 2.1423167 15.273427 3.5813645 19.406363 0.65838543 13.993137 13.355732 9.8478173
7.4989252 39.056297 2.6612859 14.516296 5.6581214 18.561801 1.7589597 13.944902 13.213684 9.7703358
7.7287706 43.107187 2.2708932 14.355815 4.6914188 18.398569 1.0662384 14.078863 13.122087 9.9631384
7.5071044 40.795006 1.9069526 13.654657 4.4827488 17.290511 1.4705619 14.047894 13.114412 10.182659
7.4914737 40.312354 1.6018488 14.207975 3.9314181 17.263651 1.5478043 13.954595 13.077267 10.41147
7.4199565 41.391456 1.6731137 11.991185 4.1824224 15.97579 1.5685213 13.871744 12.989602 10.275845
7.416902 41.912411 1.4033732 11.694651 3.3726716 15.637815 1.0273218 13.976518 13.128562 10.295669
7.2867427 39.805835 1.4707718 11.820012 3.6671966 14.765029 0.94291607 13.805058 12.923892 10.395765
7.2100193 38.434131 1.6766904 11.873557 4.0495584 14.141072 0.97411651 13.926 12.986124 10.072457
7.239882 39.960159 1.5194968 10.936236 3.655041 13.912396 0.69783599 14.044768 13.266022 10.243697
7.1116791 38.675014 1.5083442 10.392622 2.9874908 13.979515 0.16801424 14.044827 13.246321 10.276334
7.0609051 38.430038 1.6243388 9.8020035 4.0093371 13.867168 0.64290222 14.023211 13.135387 10.277262
7.0792993 39.369331 1.5654066 9.1817415 3.771563 13.117196 0.85780388 13.911868 12.999595 10.224534
7.2965527 41.010706 1.846273 10.382702 4.7894996 13.831259 1.6966178 14.099587 13.097114 9.9952306
7.5967021 45.678132 2.2037669 9.827984 5.7691461 15.144652 1.8629728 14.056023 13.048002 9.9193112
7.7387204 47.023532 2.6300635 10.234199 7.4223621 16.142687 2.6995584 14.008434 13.160588 9.6458891
7.7861056 48.298371 2.434936 9.8901328 6.9942023 15.25314 2.233011 14.156387 12.920426 9.52413
7.8750729 50.116698 2.4912142 9.4088616 7.2648067 15.153074 2.1075436 14.241748 12.83115 9.536023
8.0561165 52.922219 2.3358083 9.6429863 7.5204461 16.248453 2.5969094 14.368041 12.813963 9.6838946
7.8601155 50.667202 2.5823911 8.5318218 8.9387409 15.288841 2.637965 14.575368 12.790655 9.512189
7.9519001 53.153145 2.8035923 7.275977 9.3280485 14.607831 2.5512231 14.593888 12.59324 9.529756
8.1215546 56.268574 2.6955302 6.9955446 9.9637943 14.68746 2.7194749 14.562912 12.33595 9.6964953
8.0814716 56.147365 2.5708169 6.5920012 9.6516918 14.956238 2.6988067 14.619295 12.31588 9.5657035
8.0391672 55.40859 2.6706226 6.5489961 9.9815392 14.849532 2.8236448 14.69406 12.413215 9.4677972
7.954281 54.664753 2.2430897 6.3627438 9.1919581 14.531337 2.6262796 14.618053 12.50302 9.5639771
7.9220365 52.728419 3.302899 6.7273453 11.667906 15.582432 3.5889199 14.647553 12.624881 9.7498354
7.9190175 52.316868 3.3224972 7.0714731 11.652483 16.20396 3.6776506 14.63116 12.666085 9.7865207
8.1861926 56.449341 2.8594222 7.704986 11.547243 17.95085 3.7347565 14.571249 12.591979 9.9582757
8.235899 56.694016 2.9928433 8.1431725 11.757348 18.761684 3.703153 14.538856 12.883352 9.6600736
8.2040264 54.969892 3.2151096 9.1210464 12.126997 19.689953 4.0892792 14.49866 12.971747 9.6995321
8.4703361 57.01259 3.326592 11.407412 12.544071 22.70592 4.6661337 14.206986 13.007482 9.7586369
8.3333572 54.140021 3.6896475 11.615174 13.092043 22.055729 5.040511 14.117051 13.204378 9.3697137
8.3796917 54.911236 3.9620237 11.345974 14.024061 21.699122 5.4642459 14.161918 13.223347 9.289839
8.5274099 55.046071 5.2649951 12.405654 16.3991 22.539097 6.7267852 14.235824 13.267759 9.4445772
8.65292 54.358364 6.2485939 14.266066 17.832367 24.641453 8.1490606 14.365197 13.254637 9.4257221
8.406672 51.102236 5.9722191 13.59768 16.81161 23.489353 7.7106841 14.511228 13.048101 9.5571201
8.497874 51.425254 7.2045406 13.584068 18.685944 23.179709 8.6806038 14.444355 12.957985 9.9555803
8.2530171 48.193496 6.2020179 13.716778 16.510431 22.887262 8.0573488 14.546862 13.181599 10.115182
8.5769734 53.146725 7.0307589 13.386989 18.590549 24.076393 8.4487937 14.337882 13.531309 10.238789
8.7349734 56.048538 6.7991794 13.452043 18.790811 25.452642 8.5714374 14.497072 13.477217 10.167778
8.8229687 55.758952 7.5702425 14.515583 19.992558 26.012857 9.5321547 14.47072 13.342111 10.034618
8.9610843 59.19793 7.0951607 14.00794 19.809197 25.778019 8.6862122 14.205504 13.292836 9.9369183
8.8651356 58.274774 7.9490777 12.366778 20.806012 23.389167 8.4413757 14.552846 13.404983 9.7934121
8.840204 57.726476 8.6137658 11.808964 21.541871 23.090188 8.9235658 14.607078 13.507897 9.8225028
8.9027501 58.704007 8.9712417 11.583711 22.000137 23.216096 8.801928 14.887846 13.604962 9.8413585
9.1106818 61.907467 9.9118505 11.185206 23.650567 23.315968 8.6502934 14.809455 13.515307 9.9278773
9.2953169 64.881336 11.225659 10.295921 25.877991 22.909757 8.7180531 15.05584 13.602844 10.030766
9.112855 62.24612 10.300246 10.49776 24.357801 22.730586 8.6773679 15.392899 13.664771 10.210303
9.1613574 64.084769 9.2183066 10.627393 23.685295 23.43904 8.6964146 15.602023 13.550211 10.317227
9.364004 70.040734 7.8720897 9.7717468 22.803607 23.243647 7.6992269 15.633623 13.501114 10.288972
9.6117123 73.839199 8.4993505 10.046464 24.089826 24.453729 8.28423 15.757243 13.614362 10.491274
9.6088911 74.64098 8.3839188 9.3058903 23.835952 23.83324 7.8115082 15.939103 13.697601 10.468357
9.5499408 73.710692 7.9641757 9.5265009 22.796676 24.356785 7.7627539 16.255989 13.522966 10.598448
9.7603599 77.414208 8.1078856 9.7425316 23.451155 25.174127 7.8052431 16.504506 13.52755 10.515104
9.9292472 81.730209 7.0835751 9.7761673 22.620637 25.8336 7.3736019 16.781396 13.708308 10.657181
10.192593 85.934429 7.3870649 10.56746 23.446329 28.103023 7.9755157 17.016784 13.675975 10.64552
10.331132 89.530187 6.2069617 10.995145 21.548171 29.48513 7.7085803 17.214236 13.776577 10.864792
10.689564 96.387474 5.8761902 12.003123 21.778969 31.996275 7.8703615 17.382617 13.809472 10.852016
10.981417 101.04867 6.774335 12.768511 24.191039 34.360184 8.8031364 17.474652 13.70242 10.917676
11.231157 106.64521 6.938227 12.555452 25.060127 34.981471 8.7636491 17.698073 13.78739 11.044
11.484032 111.87421 6.8621336 13.146654 25.168546 37.03647 8.7658063 17.98786 13.904238 11.121442
11.838947 119.6339 7.1586245 13.368149 27.029666 38.8442 8.8328013 18.402276 13.862771 11.111164
12.014911 124.06467 7.0986951 13.194712 27.395345 39.251378 8.7398688 19.069209 13.890573 11.197392
12.236161 129.68558 6.4713826 13.566678 27.009763 40.869816 8.5636631 19.415507 13.879153 11.303454
12.578499 138.52623 5.5654176 14.126975 26.582002 42.792685 8.1170979 19.783952 13.972292 11.278972
12.656684 140.67809 5.466318 14.047226 26.364908 42.734682 7.9352326 20.266129 14.101967 11.422896
12.752092 142.96749 5.02464 14.623712 25.719841 43.781275 7.636268 20.672222 14.17167 11.485268
12.611155 141.59429 4.8234995 12.623442 24.948494 40.530937 7.0767823 21.184353 14.289871 11.727502
12.683493 145.08077 4.3368659 11.453361 24.0622 38.833151 6.3988595 21.60257 14.413808 11.850319
12.512817 141.67117 3.689281 11.210137 21.235542 37.597965 5.6125332 22.143814 14.721444 11.990917
12.704453 146.43903 3.4774081 11.486701 20.597768 39.234772 5.5359685 22.331494 14.81428 12.15573
12.815748 149.86579 3.1401554 11.237454 19.076249 39.326212 4.8900888 22.767125 15.060961 12.246987
12.521903 143.8947 2.8556577 10.047707 16.062093 36.463196 3.9921116 23.438929 15.26232 12.464667
12.613831 147.19107 2.682535 9.2351194 14.851406 35.622125 3.5000243 23.80227 15.402101 12.603147
12.482231 145.47155 2.4422563 7.8922776 13.212049 32.29911 2.9125789 24.324959 15.340398 12.82213
12.447731 145.55257 2.2483828 7.1450659 12.085221 30.905315 2.5006962 24.813595 15.253097 13.02677
12.349556 143.73867 1.8600156 6.9128495 10.367745 30.499356 2.1590445 25.259756 15.16605 13.294286
12.289733 142.27701 1.6864662 7.0740564 10.371615 30.693661 2.1892249 25.770131 15.126038 13.365296
12.233296 143.13767 1.5342447 4.981619 9.66231 25.278909 1.7780183 26.269715 15.093825 13.456342
12.144896 142.12134 1.1700884 4.2070784 6.3134975 22.970694 1.0775416 26.662779 15.034491 13.6381
12.128171 141.65813 1.1500513 4.2843476 6.0320681 23.119673 1.0560618 27.16529 15.091221 13.656038
11.905649 137.19034 1.0214698 3.532676 6.308578 20.166583 1.0702176 27.575125 15.084415 13.823778
11.941392 137.93049 0.97803476 3.688319 5.4908192 20.385825 0.8404333 28.14823 15.301132 13.816009
11.823384 135.90594 0.88231549 3.0041477 6.63445 17.746732 0.84827604 28.59174 15.392449 13.935096
11.736173 133.82936 0.90518628 3.0032057 6.0140779 17.802498 0.8743252 28.985566 15.285766 14.139273
11.600228 131.35983 0.95197593 2.2534848 5.2039166 15.384852 0.77267503 29.334688 15.089752 14.416467
11.536021 130.72093 0.82865117 1.5302055 3.7620337 12.126608 0.49685567 29.895513 15.024208 14.486482
11.478085 129.78662 0.91499731 1.0448077 5.3415729 8.598068 0.5645909 30.482392 15.060175 14.420855
11.551755 131.69353 0.93437291 0.81514768 4.8624628 8.1786544 0.45258372 30.977203 14.871154 14.586073
11.507361 130.37964 1.2980456 0.74167715 3.6758434 7.9904883 0.32692917 31.520994 14.780583 14.669823
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5.589667 7.841533 17.840603 5.5622416 -10.419549 -2.8064807 4.1639596 49.698999 11.001171 14.174651
5.6850452 8.5171271 18.307472 5.4951393 -11.119565 -2.7254304 3.6038449 49.892709 11.08694 13.993214
5.7151529 9.3437619 17.85509 5.4641212 -11.501407 -2.9513946 4.1202551 49.966637 11.187887 13.89124
5.7928615 11.523836 16.078628 5.954781 -12.13624 -3.6479227 4.0957847 49.82478 11.236984 13.931047
5.6366145 11.35929 14.562029 5.8501049 -11.614836 -3.7178687 3.6361083 49.791833 11.006793 13.981714
5.400482 11.135341 12.504864 5.5250011 -10.387605 -3.6011704 2.8322929 49.84837 10.916611 14.03206
5.6306067 14.617081 12.00229 5.0843613 -11.901231 -3.5946713 2.5497592 49.762242 11.033612 14.076177
5.6496381 13.930884 12.527231 5.4602952 -11.996037 -3.7910037 2.9880041 49.942748 10.891029 13.908555
5.7491194 15.537621 11.815971 5.6987816 -12.343997 -3.9020828 2.9992533 50.001245 11.017732 13.651003
5.8822575 15.332473 13.514564 5.7539156 -13.120536 -4.2016184 4.0823636 50.024463 10.683174 13.490053
5.9004414 16.675607 12.688568 5.4510337 -13.057612 -4.4044529 4.0658867 49.718625 10.530073 13.579294
5.8822436 17.818915 11.576515 5.20536 -13.102577 -3.6903119 3.3343492 49.725182 10.235 13.623812
5.9198631 17.784191 11.855425 5.4051634 -13.36147 -3.4480186 2.8926961 49.970879 10.290723 13.899078
6.0563912 18.987194 12.594474 5.0982054 -14.024394 -3.7450006 2.9019224 50.043188 10.489077 14.001096
5.9199326 18.182297 10.793037 6.0702689 -12.397294 -4.3011167 2.3298232 50.166771 10.020193 14.179405
6.1098236 18.758885 11.311768 7.2592908 -12.651175 -5.5446433 3.2699991 50.096632 9.8920853 14.179255
6.057545 17.686764 10.812244 8.1948428 -12.103304 -7.3511096 4.7757228 50.346112 9.9146259 14.21011
5.883733 14.994472 10.500829 9.1230133 -10.947978 -7.242834 4.5879819 50.676948 9.7362112 14.221819
5.8069312 14.201059 10.118952 9.4004391 -10.466011 -7.2530884 4.0800716 50.553819 9.6846589 13.968674
5.7375945 12.593074 11.145339 9.1815776 -10.226911 -5.7533575 3.5143309 50.578267 9.7066159 14.079792
5.7083577 12.04293 11.232739 9.3096788 -10.215849 -5.5956652 3.8189316 50.415963 9.7479403 14.225723
5.7748329 12.637318 10.745286 9.9660917 -10.251909 -5.7186114 3.4741449 50.440551 9.4304799 14.29028
5.7563569 13.612632 10.406434 9.1165793 -10.650474 -5.9744553 3.2244103 50.397118 9.1040767 14.259411
5.8434702 14.698344 10.507691 8.9401094 -10.826606 -5.8919676 2.9823519 50.549914 9.1847107 14.205456
5.8436512 14.807353 10.943627 8.3972796 -10.845671 -5.0332368 1.8886558 50.710018 8.9398774 13.985354
5.8755258 14.721121 10.818262 8.9824196 -10.13763 -5.2749013 1.1991439 50.912448 8.7967624 13.790997
5.7088832 13.402399 10.808647 8.3803012 -8.6778137 -5.135244 0.50162529 51.10606 8.6566422 13.735342
5.6255541 12.164987 11.206002 8.2758691 -8.025322 -5.3792409 1.1986695 51.611135 8.5875627 13.566069
5.5133857 11.606727 10.723956 8.0667388 -7.7006341 -5.2202906 1.9875435 51.388763 8.7848101 13.507427
5.4265893 10.157731 10.818492 8.4716483 -7.2474454 -5.5265731 2.3854803 51.641035 9.0938068 13.599211
5.3182965 8.9651318 10.943437 8.3757082 -6.2007545 -5.056881 1.1368514 51.610352 8.8929902 13.581376
5.3652496 8.7911989 10.665272 9.3294322 -6.021771 -5.8424869 1.5414913 51.493178 8.8854513 13.589163
5.3805842 9.6022799 10.412131 8.9362757 -6.4477204 -6.2779449 1.5157437 51.327589 9.1502737 13.533597
5.2813743 9.1701671 10.023078 8.6996694 -6.0616833 -6.4098214 1.8031144 51.511357 9.2882162 13.650399
5.3364358 9.231983 11.525441 7.7201223 -6.9372423 -6.0456921 2.1560811 51.415333 9.3789596 13.489693
5.2216315 9.0360698 10.74146 7.4879054 -6.7659877 -5.938263 2.4099896 51.579168 9.3391723 13.574691
5.2693755 8.8173745 11.502891 7.4460527 -6.5889143 -5.7866818 2.2888995 52.060607 9.3152636 13.482747
5.4527243 8.5751661 11.995218 9.1618189 -6.9426365 -5.9167953 2.7288445 52.217794 9.3216261 13.5881
5.5407737 9.0460762 12.020147 9.6339496 -7.3040599 -6.139166 2.6263873 52.032689 8.9970713 13.417335
5.4925322 8.3617555 12.50312 9.3030345 -6.6442559 -6.1599685 2.4847009 51.93956 9.095662 13.106108
5.4926197 8.7073708 11.787574 9.6739262 -6.5363865 -6.1921413 2.0929306 51.793926 9.2630432 13.163065
5.4150044 9.0159527 11.803322 8.5029979 -6.7351289 -5.7640713 1.6928394 51.827107 9.4306778 13.249457
5.548641 8.5050176 13.749623 8.5327765 -7.6118043 -5.0191659 2.2519682 52.060941 9.5239621 13.306295
5.5564204 9.1514243 14.595798 7.1265851 -8.5613345 -4.1757282 2.0741589 52.01808 9.6698309 13.145877
5.5699457 9.7851734 14.35299 6.8861324 -9.1237528 -4.9959942 2.8960143 52.052156 9.5620341 13.337446
5.5749693 10.703974 13.128121 7.2481879 -8.9798879 -5.7134968 2.3496775 51.721725 9.7689869 13.356096
5.638834 11.099617 12.820822 7.8760101 -9.506886 -6.1070228 2.6709612 51.794599 9.6156719 13.48407
5.6598728 10.885534 12.78006 8.368566 -9.4902335 -5.5729542 2.3342113 52.174765 9.8576644 13.478152
5.5904285 10.369004 11.992327 8.8915605 -8.76821 -6.5618387 3.193141 52.02322 9.81365 13.359337
5.3741317 9.2405221 11.282499 8.3582708 -8.3727501 -5.8355484 3.3370204 51.866988 9.6388128 13.149419
5.2958639 7.1886261 12.977706 7.8798428 -8.1460083 -4.3881982 3.1812473 51.731285 9.4481046 13.141767
5.402274 7.7470987 12.805009 8.6324567 -8.2179556 -5.2078319 3.1582169 51.804468 9.3848268 13.29982
5.6483697 9.1018115 13.787511 9.0147582 -9.5567762 -5.2509413 3.01344 51.996155 9.1895779 13.300818
5.601747 9.3576298 13.664124 8.3578152 -9.1305397 -5.6217469 3.1180397 52.111675 9.0877198 13.152291
5.5124655 8.9590865 13.684809 7.7433812 -8.7096272 -4.9754549 2.3270945 52.254841 8.8351679 13.21258
5.3988525 8.3910773 12.905567 7.8509638 -7.5245856 -5.0395065 2.3481322 52.263451 8.6620437 13.36041
5.3040294 7.1552401 13.671387 7.3061011 -6.4221018 -4.6709838 2.4084256 52.472518 8.5802722 13.163192
5.3191867 8.2855513 13.241158 6.7670382 -6.7383913 -5.0033962 2.180615 52.183195 8.4360708 13.155001
5.3566829 9.1699753 12.113433 7.410643 -6.9922004 -5.2635118 2.1340211 52.182193 8.6892458 12.963203
5.2008701 8.5170789 12.263922 6.2680487 -6.167442 -4.7136418 1.8542571 52.273008 8.793237 12.860908
4.9919839 7.5835928 11.100441 6.2358693 -5.5481586 -4.3678074 2.2821251 52.335558 8.6666578 12.845611
5.1501062 7.7815697 13.038317 5.7037072 -6.8790721 -3.6697847 2.040492 52.205555 8.4930645 12.655618
5.1693291 8.0359508 12.95638 5.7296317 -7.0564916 -3.8355504 1.9139954 51.959464 8.6423307 12.53081
5.2077361 8.8897921 12.530741 5.6999822 -7.3764196 -3.4364468 0.90215052 51.838638 8.8383661 12.569833
5.1502621 9.0122487 11.77156 5.741391 -7.5423335 -3.5938885 0.88296798 51.822123 8.8415423 12.937326
5.1896461 9.2854716 11.585603 6.0613521 -7.9119183 -3.6359858 0.5268641 51.860261 8.8721682 12.909944
5.2091113 9.6776461 11.157445 6.2997493 -8.1731907 -3.4404707 0.52470693 51.955093 9.1847066 12.772563
5.1487426 9.9171868 11.039362 5.5530018 -8.1346651 -2.7100655 -0.081164579 51.895699 8.999741 12.652846
5.1505237 9.8208447 11.636584 5.0704661 -8.0048156 -2.9229925 -0.38313937 51.846388 9.0258296 12.575848
5.0498117 9.2192048 11.698429 4.582964 -8.0200334 -2.3752653 -0.36708212 51.782671 9.3279563 12.544301
5.0573261 9.5294354 11.88401 4.1631027 -7.5144401 -2.4806001 -0.65999869 51.913647 9.3854399 12.401641
5.0811302 9.3959886 11.808889 4.6130067 -7.0405242 -2.5037582 -1.2769295 52.005268 9.6317929 12.370306
5.1166203 9.3288823 12.45974 4.3911809 -7.2243887 -2.5156447 -1.0041202 52.088074 9.6003874 12.346141
5.2045026 10.450174 12.394069 4.2426047 -7.9173751 -2.3028313 -1.1127183 52.287028 9.4892589 12.53898
4.9696787 9.062347 11.35845 4.2769086 -5.9385609 -2.12694 -1.6437193 52.757473 9.3837415 12.690198
4.9877386 9.1392669 11.48237 4.2558994 -5.5388281 -2.4000297 -1.4755205 52.764043 9.6175641 12.662539
4.8284868 7.8848934 11.225247 4.2041439 -5.3018102 -1.8375233 -1.5376081 53.041399 9.451146 12.688581
4.8237993 7.3389077 11.55467 4.3754617 -5.6106066 -1.4157198 -1.5132442 53.279168 9.5338443 12.633672
4.8314395 7.3896489 11.215416 4.7377428 -6.0145077 -1.7225945 -0.69655935 53.818846 9.5420479 12.368433
4.8765154 8.0784101 10.572769 5.1292237 -6.3322936 -1.8164643 -0.64830774 53.966255 9.5234973 12.344916
4.9186704 8.6712371 10.378472 5.1436092 -6.5208107 -2.2558782 -0.71144157 53.70529 9.6007242 12.232148
4.9251997 7.5655071 11.081228 5.610857 -6.3320091 -2.1481047 -1.5093486 53.793445 9.7713313 12.221771
4.8304168 7.0698238 10.038672 6.2244307 -5.0756276 -2.9001352 -1.4313228 53.859149 9.7696343 12.172882
4.7501946 7.6420634 8.8240346 6.0982512 -4.983994 -2.7043286 -1.3804654 53.836157 10.006061 12.283256
4.7494587 8.0630304 8.6152981 5.879029 -5.1608283 -2.6103501 -1.0780193 53.72011 10.254128 12.239037
4.7488472 8.0743919 8.6038151 5.8733427 -5.1682417 -2.6109895 -1.0859021 53.721404 10.254774 12.239811
Loop time of 13125.6 on 4 procs for 400001 steps with 43149 atoms
Performance: 131.651 ns/day, 0.182 hours/ns, 30.475 timesteps/s
99.2% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.1325 | 53.155 | 102.87 | 679.4 | 0.40
Bond | 1.1958 | 1.5762 | 2.4077 | 38.6 | 0.01
Neigh | 546.84 | 548 | 549.18 | 4.6 | 4.18
Comm | 186.71 | 228.91 | 309.92 | 321.6 | 1.74
Output | 0.13475 | 0.18939 | 0.30625 | 16.1 | 0.00
Modify | 12088 | 12129 | 12174 | 27.8 | 92.41
Other | | 164.7 | | | 1.25
Nlocal: 10787.2 ave 21162 max 24 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 6082.25 ave 11981 max 60 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 3 ave 12 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Total # of neighbors = 12
Ave neighs/atom = 0.0002781061
Ave special neighs/atom = 0.0014368815
Neighbor list builds = 7486
Dangerous builds = 0
Total wall time: 3:38:45

132612
examples/PACKAGES/machdyn/funnel_flow/boundary.stl
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examples/PACKAGES/meam_spline/TiO.meam.spline
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@ -1,130 +1,130 @@
# Ti-O cubic spline potential where O is in the dilute limit. DATE: 2016-06-05 CONTRIBUTOR: Pinchao Zhang, Dallas R. Trinkle
meam/spline 2 Ti O
spline3eq
13
-20 0
1.742692837 3.744277175966 99.4865081627958
2.05580176725 0.910839730906 10.8702523265355
2.3689106975 0.388045896634 -1.55322418749562
2.68201962775 -0.018840906533 2.43630041329215
2.995128558 -0.248098929639 2.67912713976835
3.30823748825 -0.264489550297 -0.125056384603077
3.6213464185 -0.227196189283 1.10662555360438
3.93445534875 -0.129293090176 -0.592053676745914
4.247564279 -0.059685366933 -0.470123414607672
4.56067320925 -0.031100025561 -0.0380739973059663
4.8737821395 -0.013847363202 -0.0711547960695406
5.18689106975 -0.003203412728 -0.081768292420175
5.5 0 -0.0571422964883619
spline3eq
5
0.155001355787331 0
1.9 0.533321679606674 0
2.8 0.456402081843862 -1.60311717015859
3.7 -0.324281383502201 1.19940299483249
4.6 -0.474029826906675 1.47909794595154
5.5 0 -2.49521499855605
spline3eq
13
0 0
1.742692837 0 0
2.05580176725 0 0
2.3689106975 0 0
2.68201962775 0 0
2.995128558 0 0
3.30823748825 0 0
3.6213464185 0 0
3.93445534875 0 0
4.247564279 0 0
4.56067320925 0 0
4.8737821395 0 0
5.18689106975 0 0
5.5 0 0
spline3eq
11
-1 0
2.055801767 1.7475279661 -525.869786904802
2.2912215903 -5.8677963945 252.796316927755
2.5266414136 -8.3376288737 71.7318388721015
2.7620612369 -5.8398712842 -1.93587742753693
2.9974810602 -3.1140648231 -39.2999192667503
3.2329008835 -1.7257245065 14.3424136002004
3.4683207068 -0.4428977017 -29.4925534559498
3.7037405301 -0.1466643003 -3.18010534572236
3.9391603534 -0.2095507945 3.33490838803603
4.1745801767 -0.1442384563 3.71918691359508
4.41 0 -9.66717019857564
spline3eq
5
-61.9827585211652 0
1.9 11.2293641315584 0
2.8 -27.9976343076148 122.648031332411
3.7 -8.32979773113248 -54.3340881766381
4.6 -1.00863195297399 3.23150064581724
5.5 0 -5.3514242228123
spline3eq
4
0.00776934946045395 0.105197706160344
-55.14233165 -0.29745568008 0.00152870603877451
-44.7409899033333 -0.15449458722 0.00038933722543571
-34.3396481566667 0.05098657168 0.00038124926922248
-23.93830641 0.57342694704 0.0156639264890892
spline3eq
5
-0.00676745157022662 -0.0159520381982146
-23.9928 0.297607384684645 0
-15.9241175 0.216691597077105 -0.0024248755353942
-7.855435 0.0637598673719069 0.00306245895013358
0.213247499999998 -0.00183450621970427 -0.00177588407633909
8.28193 -0.111277018874367 0
spline3eq
10
2.77327511656661 0
2.055801767 -0.1485215264 72.2010867146919
2.31737934844444 1.6845304918 -47.2744689053404
2.57895692988889 2.0113365977 -15.1859578405326
2.84053451133333 1.1444092747 3.33978204841873
3.10211209277778 0.2861606803 2.587867603808
3.36368967422222 -0.3459281126 6.14070694084556
3.62526725566667 -0.6257480601 3.7397696717154
3.88684483711111 -0.6119510826 4.64749084871402
4.14842241855556 -0.3112059651 2.83275746415936
4.41 0 -15.0612086827734
spline3eq
5
12.3315547862781 0
1.9 2.62105440156724 0
2.8 10.2850803058354 -25.439802988016
3.7 3.23933763743897 -7.20203673434025
4.6 -5.79049355858613 39.5509978688682
5.5 0 -41.221771373642
spline3eq
8
8.33642274810572 -60.4024574736564
-1 0.07651409193 -110.652321293778
-0.724509054371429 0.14155824541 44.8853405500508
-0.449018108742857 0.75788697341 -25.3065115342002
-0.173527163114286 0.63011570378 -2.48510144915082
0.101963782514286 0.09049597305 2.68769386908235
0.377454728142857 -0.35741586657 -1.01558570129633
0.652945673771428 -0.65293217647 13.4224786001212
0.9284366194 -6.00912190653 -452.752542694929
spline3eq
5
0.137191606537625 -1.55094230968985
-1 0.0513843442016519 0
-0.5 0.0179024412245673 -2.44986494990154
0 -0.260650876879273 3.91774583656401
0.5 -0.190163791764901 -4.84414871911743
1 -0.763795416646599 0
spline3eq
8
0 0
-1 0 0
-0.724509054371429 0 0
-0.449018108742857 0 0
-0.173527163114286 0 0
0.101963782514286 0 0
0.377454728142857 0 0
0.652945673771428 0 0
0.9284366194 0 0
# Ti-O cubic spline potential where O is in the dilute limit. DATE: 2016-06-05 CONTRIBUTOR: Pinchao Zhang, Dallas R. Trinkle
meam/spline 2 Ti O
spline3eq
13
-20 0
1.742692837 3.744277175966 99.4865081627958
2.05580176725 0.910839730906 10.8702523265355
2.3689106975 0.388045896634 -1.55322418749562
2.68201962775 -0.018840906533 2.43630041329215
2.995128558 -0.248098929639 2.67912713976835
3.30823748825 -0.264489550297 -0.125056384603077
3.6213464185 -0.227196189283 1.10662555360438
3.93445534875 -0.129293090176 -0.592053676745914
4.247564279 -0.059685366933 -0.470123414607672
4.56067320925 -0.031100025561 -0.0380739973059663
4.8737821395 -0.013847363202 -0.0711547960695406
5.18689106975 -0.003203412728 -0.081768292420175
5.5 0 -0.0571422964883619
spline3eq
5
0.155001355787331 0
1.9 0.533321679606674 0
2.8 0.456402081843862 -1.60311717015859
3.7 -0.324281383502201 1.19940299483249
4.6 -0.474029826906675 1.47909794595154
5.5 0 -2.49521499855605
spline3eq
13
0 0
1.742692837 0 0
2.05580176725 0 0
2.3689106975 0 0
2.68201962775 0 0
2.995128558 0 0
3.30823748825 0 0
3.6213464185 0 0
3.93445534875 0 0
4.247564279 0 0
4.56067320925 0 0
4.8737821395 0 0
5.18689106975 0 0
5.5 0 0
spline3eq
11
-1 0
2.055801767 1.7475279661 -525.869786904802
2.2912215903 -5.8677963945 252.796316927755
2.5266414136 -8.3376288737 71.7318388721015
2.7620612369 -5.8398712842 -1.93587742753693
2.9974810602 -3.1140648231 -39.2999192667503
3.2329008835 -1.7257245065 14.3424136002004
3.4683207068 -0.4428977017 -29.4925534559498
3.7037405301 -0.1466643003 -3.18010534572236
3.9391603534 -0.2095507945 3.33490838803603
4.1745801767 -0.1442384563 3.71918691359508
4.41 0 -9.66717019857564
spline3eq
5
-61.9827585211652 0
1.9 11.2293641315584 0
2.8 -27.9976343076148 122.648031332411
3.7 -8.32979773113248 -54.3340881766381
4.6 -1.00863195297399 3.23150064581724
5.5 0 -5.3514242228123
spline3eq
4
0.00776934946045395 0.105197706160344
-55.14233165 -0.29745568008 0.00152870603877451
-44.7409899033333 -0.15449458722 0.00038933722543571
-34.3396481566667 0.05098657168 0.00038124926922248
-23.93830641 0.57342694704 0.0156639264890892
spline3eq
5
-0.00676745157022662 -0.0159520381982146
-23.9928 0.297607384684645 0
-15.9241175 0.216691597077105 -0.0024248755353942
-7.855435 0.0637598673719069 0.00306245895013358
0.213247499999998 -0.00183450621970427 -0.00177588407633909
8.28193 -0.111277018874367 0
spline3eq
10
2.77327511656661 0
2.055801767 -0.1485215264 72.2010867146919
2.31737934844444 1.6845304918 -47.2744689053404
2.57895692988889 2.0113365977 -15.1859578405326
2.84053451133333 1.1444092747 3.33978204841873
3.10211209277778 0.2861606803 2.587867603808
3.36368967422222 -0.3459281126 6.14070694084556
3.62526725566667 -0.6257480601 3.7397696717154
3.88684483711111 -0.6119510826 4.64749084871402
4.14842241855556 -0.3112059651 2.83275746415936
4.41 0 -15.0612086827734
spline3eq
5
12.3315547862781 0
1.9 2.62105440156724 0
2.8 10.2850803058354 -25.439802988016
3.7 3.23933763743897 -7.20203673434025
4.6 -5.79049355858613 39.5509978688682
5.5 0 -41.221771373642
spline3eq
8
8.33642274810572 -60.4024574736564
-1 0.07651409193 -110.652321293778
-0.724509054371429 0.14155824541 44.8853405500508
-0.449018108742857 0.75788697341 -25.3065115342002
-0.173527163114286 0.63011570378 -2.48510144915082
0.101963782514286 0.09049597305 2.68769386908235
0.377454728142857 -0.35741586657 -1.01558570129633
0.652945673771428 -0.65293217647 13.4224786001212
0.9284366194 -6.00912190653 -452.752542694929
spline3eq
5
0.137191606537625 -1.55094230968985
-1 0.0513843442016519 0
-0.5 0.0179024412245673 -2.44986494990154
0 -0.260650876879273 3.91774583656401
0.5 -0.190163791764901 -4.84414871911743
1 -0.763795416646599 0
spline3eq
8
0 0
-1 0 0
-0.724509054371429 0 0
-0.449018108742857 0 0
-0.173527163114286 0 0
0.101963782514286 0 0
0.377454728142857 0 0
0.652945673771428 0 0
0.9284366194 0 0

80
examples/PACKAGES/mop/in.compute_stress_mop
View File

@ -1,40 +1,40 @@
variable T equal 0.8
variable p_solid equal 0.05
read_data data.mop
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0
pair_coeff 1 2 0.5 1.0
pair_coeff 2 2 0.0 0.0
neigh_modify delay 0
group liquid type 1
group solid type 2
region bottom block INF INF INF INF INF 7.0
group bottom region bottom
group solid_bottom intersect solid bottom
group solid_up subtract solid solid_bottom
variable faSolid equal ${p_solid}*lx*ly/count(solid_up)
fix piston_up solid_up aveforce NULL NULL -${faSolid}
fix freeze_up solid_up setforce 0.0 0.0 NULL
fix freeze_bottom solid_bottom setforce 0.0 0.0 0.0
fix nvesol solid nve
compute Tliq liquid temp
fix nvtliq liquid nvt temp $T $T 0.5
fix_modify nvtliq temp Tliq
thermo 1000
thermo_modify flush yes temp Tliq
fix fxbal all balance 1000 1.05 shift z 10 1.05
compute mopz0 all stress/mop z center kin conf
fix mopz0t all ave/time 1 1 1 c_mopz0[*] file mopz0.time
compute moppz liquid stress/mop/profile z 0.0 0.1 kin conf
fix moppzt all ave/time 1 1 1 c_moppz[*] ave running overwrite file moppz.time mode vector
run 0
variable T equal 0.8
variable p_solid equal 0.05
read_data data.mop
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0
pair_coeff 1 2 0.5 1.0
pair_coeff 2 2 0.0 0.0
neigh_modify delay 0
group liquid type 1
group solid type 2
region bottom block INF INF INF INF INF 7.0
group bottom region bottom
group solid_bottom intersect solid bottom
group solid_up subtract solid solid_bottom
variable faSolid equal ${p_solid}*lx*ly/count(solid_up)
fix piston_up solid_up aveforce NULL NULL -${faSolid}
fix freeze_up solid_up setforce 0.0 0.0 NULL
fix freeze_bottom solid_bottom setforce 0.0 0.0 0.0
fix nvesol solid nve
compute Tliq liquid temp
fix nvtliq liquid nvt temp $T $T 0.5
fix_modify nvtliq temp Tliq
thermo 1000
thermo_modify flush yes temp Tliq
fix fxbal all balance 1000 1.05 shift z 10 1.05
compute mopz0 all stress/mop z center kin conf
fix mopz0t all ave/time 1 1 1 c_mopz0[*] file mopz0.time
compute moppz liquid stress/mop/profile z 0.0 0.1 kin conf
fix moppzt all ave/time 1 1 1 c_moppz[*] ave running overwrite file moppz.time mode vector
run 0

132
examples/PACKAGES/reaction/create_atoms_polystyrene/grow_styrene.map
View File

@ -1,66 +1,66 @@
map file: styrene growth
1 edgeIDs
30 equivalences
16 createIDs
InitiatorIDs
4
13
EdgeIDs
30
CreateIDs
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
Equivalences
1 45
2 46
3 44
4 43
5 42
6 41
7 40
8 39
9 38
10 37
11 36
12 35
13 34
14 33
15 32
16 31
17 17
18 18
19 19
20 20
21 21
22 22
23 23
24 24
25 25
26 26
27 27
28 28
29 29
30 30
map file: styrene growth
1 edgeIDs
30 equivalences
16 createIDs
InitiatorIDs
4
13
EdgeIDs
30
CreateIDs
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
Equivalences
1 45
2 46
3 44
4 43
5 42
6 41
7 40
8 39
9 38
10 37
11 36
12 35
13 34
14 33
15 32
16 31
17 17
18 18
19 19
20 20
21 21
22 22
23 23
24 24
25 25
26 26
27 27
28 28
29 29
30 30

912
examples/PACKAGES/reaction/create_atoms_polystyrene/grow_styrene_post.data_template
View File

@ -1,456 +1,456 @@
molecule template: end of chain plus polymerized styrene
46 atoms
48 bonds
81 angles
121 dihedrals
35 impropers
1 fragments
Fragments
create_fit 34 44
Types
1 1
2 2
3 1
4 5
5 1
6 2
7 1
8 2
9 1
10 2
11 1
12 2
13 2
14 6
15 2
16 2
17 1
18 2
19 1
20 5
21 1
22 2
23 1
24 2
25 1
26 2
27 1
28 2
29 2
30 6
31 1
32 2
33 1
34 5
35 1
36 2
37 1
38 2
39 1
40 2
41 1
42 2
43 2
44 6
45 2
46 2
Charges
1 -0.129000
2 0.123700
3 0.026600
4 -0.018200
5 -0.129000
6 0.123700
7 -0.173400
8 0.140300
9 -0.113400
10 0.128800
11 -0.173400
12 0.140300
13 0.051600
14 -0.069600
15 0.035400
16 0.035400
17 -0.129000
18 0.123700
19 0.026600
20 -0.018200
21 -0.129000
22 0.123700
23 -0.173400
24 0.140300
25 -0.113400
26 0.128800
27 -0.173400
28 0.140300
29 0.051600
30 -0.069600
31 -0.129000
32 0.123700
33 0.026600
34 -0.018200
35 -0.129000
36 0.123700
37 -0.173400
38 0.140300
39 -0.113400
40 0.128800
41 -0.173400
42 0.140300
43 0.051600
44 -0.069600
45 0.035400
46 0.035400
Coords
1 24.130699 1.043900 -1.309300
2 25.062700 1.582900 -1.309300
3 22.900700 1.753900 -1.309300
4 22.900700 3.253900 -1.309300
5 21.670700 1.043900 -1.309300
6 20.738701 1.582900 -1.309300
7 21.670700 -0.376100 -1.309300
8 20.738701 -0.915100 -1.309300
9 22.900700 -1.086100 -1.309300
10 22.900700 -2.163100 -1.309300
11 24.130699 -0.376100 -1.309300
12 25.062700 -0.915100 -1.309300
13 23.766701 3.658900 -0.952300
14 21.622700 3.802900 -1.871300
15 21.672701 4.544900 -1.970300
16 20.979700 2.979900 -2.165300
17 13.465800 0.682500 -1.658900
18 14.397800 1.221500 -1.658900
19 12.235800 1.392500 -1.658900
20 12.235800 2.892500 -1.658900
21 11.005800 0.682500 -1.658900
22 10.073800 1.221500 -1.658900
23 11.005800 -0.737500 -1.658900
24 10.073800 -1.276500 -1.658900
25 12.235800 -1.447500 -1.658900
26 12.235800 -2.524500 -1.658900
27 13.465800 -0.737500 -1.658900
28 14.397800 -1.276500 -1.658900
29 13.101800 3.297500 -1.301900
30 10.957800 3.441500 -2.220900
31 18.663500 0.855500 -1.372100
32 19.595501 1.394500 -1.372100
33 17.433500 1.565500 -1.372100
34 17.433500 3.065500 -1.372100
35 16.203501 0.855500 -1.372100
36 15.271500 1.394500 -1.372100
37 16.203501 -0.564500 -1.372100
38 15.271500 -1.103500 -1.372100
39 17.433500 -1.274500 -1.372100
40 17.433500 -2.351500 -1.372100
41 18.663500 -0.564500 -1.372100
42 19.595501 -1.103500 -1.372100
43 18.299500 3.470500 -1.015100
44 16.155500 3.614500 -1.934100
45 16.205500 4.356500 -2.033100
46 15.512500 2.791500 -2.228100
Bonds
1 1 1 2
2 2 1 3
3 2 1 11
4 11 3 4
5 2 3 5
6 12 13 4
7 13 4 14
8 1 5 6
9 2 5 7
10 1 7 8
11 2 7 9
12 1 9 10
13 2 9 11
14 1 11 12
15 10 15 14
16 10 16 14
17 9 14 34
18 1 17 18
19 2 17 19
20 2 17 27
21 7 19 20
22 2 19 21
23 8 29 20
24 9 30 20
25 9 44 20
26 1 21 22
27 2 21 23
28 1 23 24
29 2 23 25
30 1 25 26
31 2 25 27
32 1 27 28
33 1 31 32
34 2 31 33
35 2 31 41
36 7 33 34
37 2 33 35
38 8 43 34
39 9 44 34
40 1 35 36
41 2 35 37
42 1 37 38
43 2 37 39
44 1 39 40
45 2 39 41
46 1 41 42
47 10 45 44
48 10 46 44
Angles
1 1 3 1 2
2 1 11 1 2
3 2 3 1 11
4 17 1 3 4
5 2 1 3 5
6 17 5 3 4
7 18 3 4 13
8 19 3 4 14
9 20 13 4 14
10 1 3 5 6
11 2 3 5 7
12 1 7 5 6
13 1 5 7 8
14 2 5 7 9
15 1 9 7 8
16 1 7 9 10
17 2 7 9 11
18 1 11 9 10
19 2 1 11 9
20 1 1 11 12
21 1 9 11 12
22 21 15 14 4
23 21 16 14 4
24 22 4 14 34
25 15 15 14 16
26 14 15 14 34
27 14 16 14 34
28 1 19 17 18
29 1 27 17 18
30 2 19 17 27
31 9 17 19 20
32 2 17 19 21
33 9 21 19 20
34 10 19 20 29
35 11 19 20 30
36 11 19 20 44
37 12 29 20 30
38 12 29 20 44
39 13 30 20 44
40 1 19 21 22
41 2 19 21 23
42 1 23 21 22
43 1 21 23 24
44 2 21 23 25
45 1 25 23 24
46 1 23 25 26
47 2 23 25 27
48 1 27 25 26
49 2 17 27 25
50 1 17 27 28
51 1 25 27 28
52 1 33 31 32
53 1 41 31 32
54 2 33 31 41
55 9 31 33 34
56 2 31 33 35
57 9 35 33 34
58 11 33 34 14
59 12 43 34 14
60 13 14 34 44
61 10 33 34 43
62 11 33 34 44
63 12 43 34 44
64 1 33 35 36
65 2 33 35 37
66 1 37 35 36
67 1 35 37 38
68 2 35 37 39
69 1 39 37 38
70 1 37 39 40
71 2 37 39 41
72 1 41 39 40
73 2 31 41 39
74 1 31 41 42
75 1 39 41 42
76 16 20 44 34
77 14 45 44 20
78 14 46 44 20
79 14 45 44 34
80 14 46 44 34
81 15 45 44 46
Dihedrals
1 20 2 1 3 4
2 2 5 3 1 2
3 21 11 1 3 4
4 4 11 1 3 5
5 2 9 11 1 2
6 5 2 1 11 12
7 4 3 1 11 9
8 2 3 1 11 12
9 22 1 3 4 13
10 23 1 3 4 14
11 22 5 3 4 13
12 23 5 3 4 14
13 2 1 3 5 6
14 4 1 3 5 7
15 20 6 5 3 4
16 21 7 5 3 4
17 24 3 4 14 15
18 24 3 4 14 16
19 25 3 4 14 34
20 26 13 4 14 15
21 26 13 4 14 16
22 27 13 4 14 34
23 2 3 5 7 8
24 4 3 5 7 9
25 5 6 5 7 8
26 2 9 7 5 6
27 2 5 7 9 10
28 4 5 7 9 11
29 5 8 7 9 10
30 2 11 9 7 8
31 4 7 9 11 1
32 2 7 9 11 12
33 2 1 11 9 10
34 5 10 9 11 12
35 28 4 14 34 33
36 29 4 14 34 43
37 30 4 14 34 44
38 31 15 14 34 33
39 32 15 14 34 43
40 33 15 14 34 44
41 31 16 14 34 33
42 32 16 14 34 43
43 33 16 14 34 44
44 10 18 17 19 20
45 2 21 19 17 18
46 11 27 17 19 20
47 4 27 17 19 21
48 2 25 27 17 18
49 5 18 17 27 28
50 4 19 17 27 25
51 2 19 17 27 28
52 12 17 19 20 29
53 13 17 19 20 30
54 13 17 19 20 44
55 12 21 19 20 29
56 13 21 19 20 30
57 13 21 19 20 44
58 2 17 19 21 22
59 4 17 19 21 23
60 10 22 21 19 20
61 11 23 21 19 20
62 34 34 44 20 19
63 31 45 44 20 19
64 31 46 44 20 19
65 35 34 44 20 29
66 32 45 44 20 29
67 32 46 44 20 29
68 36 34 44 20 30
69 33 45 44 20 30
70 33 46 44 20 30
71 2 19 21 23 24
72 4 19 21 23 25
73 5 22 21 23 24
74 2 25 23 21 22
75 2 21 23 25 26
76 4 21 23 25 27
77 5 24 23 25 26
78 2 27 25 23 24
79 4 23 25 27 17
80 2 23 25 27 28
81 2 17 27 25 26
82 5 26 25 27 28
83 10 32 31 33 34
84 2 35 33 31 32
85 11 41 31 33 34
86 4 41 31 33 35
87 2 39 41 31 32
88 5 32 31 41 42
89 4 33 31 41 39
90 2 33 31 41 42
91 13 31 33 34 14
92 12 31 33 34 43
93 13 31 33 34 44
94 13 35 33 34 14
95 12 35 33 34 43
96 13 35 33 34 44
97 2 31 33 35 36
98 4 31 33 35 37
99 10 36 35 33 34
100 11 37 35 33 34
101 36 20 44 34 14
102 33 45 44 34 14
103 33 46 44 34 14
104 34 20 44 34 33
105 31 45 44 34 33
106 31 46 44 34 33
107 35 20 44 34 43
108 32 45 44 34 43
109 32 46 44 34 43
110 2 33 35 37 38
111 4 33 35 37 39
112 5 36 35 37 38
113 2 39 37 35 36
114 2 35 37 39 40
115 4 35 37 39 41
116 5 38 37 39 40
117 2 41 39 37 38
118 4 37 39 41 31
119 2 37 39 41 42
120 2 31 41 39 40
121 5 40 39 41 42
Impropers
1 1 3 1 11 2
2 8 1 3 5 4
3 9 3 4 13 14
4 1 3 5 7 6
5 1 5 7 9 8
6 1 7 9 11 10
7 1 1 11 9 12
8 1 19 17 27 18
9 5 17 19 21 20
10 1 19 21 23 22
11 1 21 23 25 24
12 1 23 25 27 26
13 1 17 27 25 28
14 1 33 31 41 32
15 5 31 33 35 34
16 1 33 35 37 36
17 1 35 37 39 38
18 1 37 39 41 40
19 1 31 41 39 42
20 1 15 14 16 4
21 1 15 14 4 34
22 1 16 14 4 34
23 1 15 14 16 34
24 1 19 20 29 30
25 1 19 20 29 44
26 1 19 20 30 44
27 1 29 20 30 44
28 1 33 34 43 14
29 1 33 34 14 44
30 1 43 34 14 44
31 1 33 34 43 44
32 1 45 44 34 20
33 1 46 44 34 20
34 1 45 44 46 20
35 1 45 44 46 34
molecule template: end of chain plus polymerized styrene
46 atoms
48 bonds
81 angles
121 dihedrals
35 impropers
1 fragments
Fragments
create_fit 34 44
Types
1 1
2 2
3 1
4 5
5 1
6 2
7 1
8 2
9 1
10 2
11 1
12 2
13 2
14 6
15 2
16 2
17 1
18 2
19 1
20 5
21 1
22 2
23 1
24 2
25 1
26 2
27 1
28 2
29 2
30 6
31 1
32 2
33 1
34 5
35 1
36 2
37 1
38 2
39 1
40 2
41 1
42 2
43 2
44 6
45 2
46 2
Charges
1 -0.129000
2 0.123700
3 0.026600
4 -0.018200
5 -0.129000
6 0.123700
7 -0.173400
8 0.140300
9 -0.113400
10 0.128800
11 -0.173400
12 0.140300
13 0.051600
14 -0.069600
15 0.035400
16 0.035400
17 -0.129000
18 0.123700
19 0.026600
20 -0.018200
21 -0.129000
22 0.123700
23 -0.173400
24 0.140300
25 -0.113400
26 0.128800
27 -0.173400
28 0.140300
29 0.051600
30 -0.069600
31 -0.129000
32 0.123700
33 0.026600
34 -0.018200
35 -0.129000
36 0.123700
37 -0.173400
38 0.140300
39 -0.113400
40 0.128800
41 -0.173400
42 0.140300
43 0.051600
44 -0.069600
45 0.035400
46 0.035400
Coords
1 24.130699 1.043900 -1.309300
2 25.062700 1.582900 -1.309300
3 22.900700 1.753900 -1.309300
4 22.900700 3.253900 -1.309300
5 21.670700 1.043900 -1.309300
6 20.738701 1.582900 -1.309300
7 21.670700 -0.376100 -1.309300
8 20.738701 -0.915100 -1.309300
9 22.900700 -1.086100 -1.309300
10 22.900700 -2.163100 -1.309300
11 24.130699 -0.376100 -1.309300
12 25.062700 -0.915100 -1.309300
13 23.766701 3.658900 -0.952300
14 21.622700 3.802900 -1.871300
15 21.672701 4.544900 -1.970300
16 20.979700 2.979900 -2.165300
17 13.465800 0.682500 -1.658900
18 14.397800 1.221500 -1.658900
19 12.235800 1.392500 -1.658900
20 12.235800 2.892500 -1.658900
21 11.005800 0.682500 -1.658900
22 10.073800 1.221500 -1.658900
23 11.005800 -0.737500 -1.658900
24 10.073800 -1.276500 -1.658900
25 12.235800 -1.447500 -1.658900
26 12.235800 -2.524500 -1.658900
27 13.465800 -0.737500 -1.658900
28 14.397800 -1.276500 -1.658900
29 13.101800 3.297500 -1.301900
30 10.957800 3.441500 -2.220900
31 18.663500 0.855500 -1.372100
32 19.595501 1.394500 -1.372100
33 17.433500 1.565500 -1.372100
34 17.433500 3.065500 -1.372100
35 16.203501 0.855500 -1.372100
36 15.271500 1.394500 -1.372100
37 16.203501 -0.564500 -1.372100
38 15.271500 -1.103500 -1.372100
39 17.433500 -1.274500 -1.372100
40 17.433500 -2.351500 -1.372100
41 18.663500 -0.564500 -1.372100
42 19.595501 -1.103500 -1.372100
43 18.299500 3.470500 -1.015100
44 16.155500 3.614500 -1.934100
45 16.205500 4.356500 -2.033100
46 15.512500 2.791500 -2.228100
Bonds
1 1 1 2
2 2 1 3
3 2 1 11
4 11 3 4
5 2 3 5
6 12 13 4
7 13 4 14
8 1 5 6
9 2 5 7
10 1 7 8
11 2 7 9
12 1 9 10
13 2 9 11
14 1 11 12
15 10 15 14
16 10 16 14
17 9 14 34
18 1 17 18
19 2 17 19
20 2 17 27
21 7 19 20
22 2 19 21
23 8 29 20
24 9 30 20
25 9 44 20
26 1 21 22
27 2 21 23
28 1 23 24
29 2 23 25
30 1 25 26
31 2 25 27
32 1 27 28
33 1 31 32
34 2 31 33
35 2 31 41
36 7 33 34
37 2 33 35
38 8 43 34
39 9 44 34
40 1 35 36
41 2 35 37
42 1 37 38
43 2 37 39
44 1 39 40
45 2 39 41
46 1 41 42
47 10 45 44
48 10 46 44
Angles
1 1 3 1 2
2 1 11 1 2
3 2 3 1 11
4 17 1 3 4
5 2 1 3 5
6 17 5 3 4
7 18 3 4 13
8 19 3 4 14
9 20 13 4 14
10 1 3 5 6
11 2 3 5 7
12 1 7 5 6
13 1 5 7 8
14 2 5 7 9
15 1 9 7 8
16 1 7 9 10
17 2 7 9 11
18 1 11 9 10
19 2 1 11 9
20 1 1 11 12
21 1 9 11 12
22 21 15 14 4
23 21 16 14 4
24 22 4 14 34
25 15 15 14 16
26 14 15 14 34
27 14 16 14 34
28 1 19 17 18
29 1 27 17 18
30 2 19 17 27
31 9 17 19 20
32 2 17 19 21
33 9 21 19 20
34 10 19 20 29
35 11 19 20 30
36 11 19 20 44
37 12 29 20 30
38 12 29 20 44
39 13 30 20 44
40 1 19 21 22
41 2 19 21 23
42 1 23 21 22
43 1 21 23 24
44 2 21 23 25
45 1 25 23 24
46 1 23 25 26
47 2 23 25 27
48 1 27 25 26
49 2 17 27 25
50 1 17 27 28
51 1 25 27 28
52 1 33 31 32
53 1 41 31 32
54 2 33 31 41
55 9 31 33 34
56 2 31 33 35
57 9 35 33 34
58 11 33 34 14
59 12 43 34 14
60 13 14 34 44
61 10 33 34 43
62 11 33 34 44
63 12 43 34 44
64 1 33 35 36
65 2 33 35 37
66 1 37 35 36
67 1 35 37 38
68 2 35 37 39
69 1 39 37 38
70 1 37 39 40
71 2 37 39 41
72 1 41 39 40
73 2 31 41 39
74 1 31 41 42
75 1 39 41 42
76 16 20 44 34
77 14 45 44 20
78 14 46 44 20
79 14 45 44 34
80 14 46 44 34
81 15 45 44 46
Dihedrals
1 20 2 1 3 4
2 2 5 3 1 2
3 21 11 1 3 4
4 4 11 1 3 5
5 2 9 11 1 2
6 5 2 1 11 12
7 4 3 1 11 9
8 2 3 1 11 12
9 22 1 3 4 13
10 23 1 3 4 14
11 22 5 3 4 13
12 23 5 3 4 14
13 2 1 3 5 6
14 4 1 3 5 7
15 20 6 5 3 4
16 21 7 5 3 4
17 24 3 4 14 15
18 24 3 4 14 16
19 25 3 4 14 34
20 26 13 4 14 15
21 26 13 4 14 16
22 27 13 4 14 34
23 2 3 5 7 8
24 4 3 5 7 9
25 5 6 5 7 8
26 2 9 7 5 6
27 2 5 7 9 10
28 4 5 7 9 11
29 5 8 7 9 10
30 2 11 9 7 8
31 4 7 9 11 1
32 2 7 9 11 12
33 2 1 11 9 10
34 5 10 9 11 12
35 28 4 14 34 33
36 29 4 14 34 43
37 30 4 14 34 44
38 31 15 14 34 33
39 32 15 14 34 43
40 33 15 14 34 44
41 31 16 14 34 33
42 32 16 14 34 43
43 33 16 14 34 44
44 10 18 17 19 20
45 2 21 19 17 18
46 11 27 17 19 20
47 4 27 17 19 21
48 2 25 27 17 18
49 5 18 17 27 28
50 4 19 17 27 25
51 2 19 17 27 28
52 12 17 19 20 29
53 13 17 19 20 30
54 13 17 19 20 44
55 12 21 19 20 29
56 13 21 19 20 30
57 13 21 19 20 44
58 2 17 19 21 22
59 4 17 19 21 23
60 10 22 21 19 20
61 11 23 21 19 20
62 34 34 44 20 19
63 31 45 44 20 19
64 31 46 44 20 19
65 35 34 44 20 29
66 32 45 44 20 29
67 32 46 44 20 29
68 36 34 44 20 30
69 33 45 44 20 30
70 33 46 44 20 30
71 2 19 21 23 24
72 4 19 21 23 25
73 5 22 21 23 24
74 2 25 23 21 22
75 2 21 23 25 26
76 4 21 23 25 27
77 5 24 23 25 26
78 2 27 25 23 24
79 4 23 25 27 17
80 2 23 25 27 28
81 2 17 27 25 26
82 5 26 25 27 28
83 10 32 31 33 34
84 2 35 33 31 32
85 11 41 31 33 34
86 4 41 31 33 35
87 2 39 41 31 32
88 5 32 31 41 42
89 4 33 31 41 39
90 2 33 31 41 42
91 13 31 33 34 14
92 12 31 33 34 43
93 13 31 33 34 44
94 13 35 33 34 14
95 12 35 33 34 43
96 13 35 33 34 44
97 2 31 33 35 36
98 4 31 33 35 37
99 10 36 35 33 34
100 11 37 35 33 34
101 36 20 44 34 14
102 33 45 44 34 14
103 33 46 44 34 14
104 34 20 44 34 33
105 31 45 44 34 33
106 31 46 44 34 33
107 35 20 44 34 43
108 32 45 44 34 43
109 32 46 44 34 43
110 2 33 35 37 38
111 4 33 35 37 39
112 5 36 35 37 38
113 2 39 37 35 36
114 2 35 37 39 40
115 4 35 37 39 41
116 5 38 37 39 40
117 2 41 39 37 38
118 4 37 39 41 31
119 2 37 39 41 42
120 2 31 41 39 40
121 5 40 39 41 42
Impropers
1 1 3 1 11 2
2 8 1 3 5 4
3 9 3 4 13 14
4 1 3 5 7 6
5 1 5 7 9 8
6 1 7 9 11 10
7 1 1 11 9 12
8 1 19 17 27 18
9 5 17 19 21 20
10 1 19 21 23 22
11 1 21 23 25 24
12 1 23 25 27 26
13 1 17 27 25 28
14 1 33 31 41 32
15 5 31 33 35 34
16 1 33 35 37 36
17 1 35 37 39 38
18 1 37 39 41 40
19 1 31 41 39 42
20 1 15 14 16 4
21 1 15 14 4 34
22 1 16 14 4 34
23 1 15 14 16 34
24 1 19 20 29 30
25 1 19 20 29 44
26 1 19 20 30 44
27 1 29 20 30 44
28 1 33 34 43 14
29 1 33 34 14 44
30 1 43 34 14 44
31 1 33 34 43 44
32 1 45 44 34 20
33 1 46 44 34 20
34 1 45 44 46 20
35 1 45 44 46 34

96
examples/PACKAGES/reaction/create_atoms_polystyrene/in.grow_styrene
View File

@ -1,48 +1,48 @@
# use bond/react 'create atoms' feature to add 30 new styrene monomers to chain
units real
boundary p p p
atom_style full
kspace_style pppm 1.0e-4
pair_style lj/class2/coul/long 8.5
angle_style class2
bond_style class2
dihedral_style class2
improper_style class2
variable T equal 530
read_data trimer.data &
extra/bond/per/atom 5 &
extra/angle/per/atom 15 &
extra/dihedral/per/atom 15 &
extra/improper/per/atom 25 &
extra/special/per/atom 25
molecule mol1 grow_styrene_pre.data_template
molecule mol2 grow_styrene_post.data_template
fix myrxns all bond/react stabilization yes statted_grp .03 &
react rxn1 all 1 0 3.0 mol1 mol2 grow_styrene.map &
modify_create fit create_fit overlap 2.0 &
stabilize_steps 100 max_rxn 30
fix 1 statted_grp_REACT nvt temp $T $T 100
fix 4 bond_react_MASTER_group temp/rescale 1 $T $T 1 1
thermo_style custom step temp press density f_myrxns[1]
thermo 100
run 8000
# write_data final.data nofix
# use bond/react 'create atoms' feature to add 30 new styrene monomers to chain
units real
boundary p p p
atom_style full
kspace_style pppm 1.0e-4
pair_style lj/class2/coul/long 8.5
angle_style class2
bond_style class2
dihedral_style class2
improper_style class2
variable T equal 530
read_data trimer.data &
extra/bond/per/atom 5 &
extra/angle/per/atom 15 &
extra/dihedral/per/atom 15 &
extra/improper/per/atom 25 &
extra/special/per/atom 25
molecule mol1 grow_styrene_pre.data_template
molecule mol2 grow_styrene_post.data_template
fix myrxns all bond/react stabilization yes statted_grp .03 &
react rxn1 all 1 0 3.0 mol1 mol2 grow_styrene.map &
modify_create fit create_fit overlap 2.0 &
stabilize_steps 100 max_rxn 30
fix 1 statted_grp_REACT nvt temp $T $T 100
fix 4 bond_react_MASTER_group temp/rescale 1 $T $T 1 1
thermo_style custom step temp press density f_myrxns[1]
thermo 100
run 8000
# write_data final.data nofix

12012
examples/SPIN/cobalt_fcc/Co_PurjaPun_2012.eam.alloy
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30018
examples/SPIN/iron/Fe_Mishin2006.eam.alloy
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examples/SPIN/read_restart/Co_PurjaPun_2012.eam.alloy
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examples/SPIN/test_problems/validation_nve/Fe_Mishin2006.eam.alloy
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examples/SPIN/test_problems/validation_nvt/Fe_Mishin2006.eam.alloy
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158
examples/SPIN/vmd/vmd_nano.vmd
View File

@ -1,79 +1,79 @@
proc vmd_draw_arrow {mol start end} {
set middle [vecadd $start [vecscale 0.9 [vecsub $end $start]]]
graphics $mol cylinder $start $middle radius 0.05
graphics $mol cone $middle $end radius 0.01 color 3
}
proc vmd_draw_vector {args} {
set usage {"draw vector {x1 y1 z1} {x2 y2 z2} [scale <s>] [resolution <res>] [radius <r>] [filled <yes/no>]"}
# defaults
set scale 2.0
set res 50
set radius 0.1
set filled yes
if {[llength $args] < 3} {
error "wrong # args: should be $usage"
}
set mol [lindex $args 0]
set center [lindex $args 1]
set vector [lindex $args 2]
if {[llength $center] != 3 || [llength $vector] != 3} {
error "wrong type of args: should be $usage"
}
foreach {flag value} [lrange $args 3 end] {
switch -glob $flag {
scale {set scale $value}
res* {set res $value}
rad* {set radius $value}
fill* {set filled $value}
default {error "unknown option '$flag': should be $usage" }
}
}
set vechalf [vecscale [expr $scale * 0.5] $vector]
return [list \
[graphics $mol color yellow]\
[graphics $mol cylinder [vecsub $center $vechalf]\
[vecadd $center [vecscale 0.7 $vechalf]] \
radius $radius resolution $res filled $filled] \
[graphics $mol color orange]\
[graphics $mol cone [vecadd $center [vecscale 0.6 $vechalf]] \
[vecadd $center $vechalf] radius [expr $radius * 2.5] \
resolution $res]]
}
proc vmd_draw_spin {args} {
global molid
graphics $molid delete all
set frame [molinfo $molid get frame]
set natoms [molinfo $molid get numatoms]
for {set i 0} {$i < $natoms} {incr i} {
set sel [atomselect top "index $i"]
# set sel [atomselect top "index 1200"]
set coords [lindex [$sel get {x y z}] $molid]
set velocities [lindex [$sel get {vx vy vz}] $molid]
draw vector $coords $velocities
set uvx [lindex [$sel get {vx}] $molid]
set uvy [lindex [$sel get {vy}] $molid]
set uvz [lindex [$sel get {vz}] $molid]
$sel set user [vecadd [vecadd [vecscale $uvy $uvy] [vecscale $uvz $uvz] ] [vecscale $uvx $uvx]]
$sel set user $uvy
#draw vector $coords {0.0 uvy 0.0}
}
#pbc box -color 3
}
proc enable_trace {} {
global vmd_frame
trace variable vmd_frame([molinfo top]) w vmd_draw_spin
}
set molid [mol addfile {/home/jtranch/Documents/lammps/src/dump.lammpstrj} type {lammpstrj} autobonds off first 0 last -1 step 1 waitfor all]
scale by 0.5
animate style Loop
enable_trace
proc vmd_draw_arrow {mol start end} {
set middle [vecadd $start [vecscale 0.9 [vecsub $end $start]]]
graphics $mol cylinder $start $middle radius 0.05
graphics $mol cone $middle $end radius 0.01 color 3
}
proc vmd_draw_vector {args} {
set usage {"draw vector {x1 y1 z1} {x2 y2 z2} [scale <s>] [resolution <res>] [radius <r>] [filled <yes/no>]"}
# defaults
set scale 2.0
set res 50
set radius 0.1
set filled yes
if {[llength $args] < 3} {
error "wrong # args: should be $usage"
}
set mol [lindex $args 0]
set center [lindex $args 1]
set vector [lindex $args 2]
if {[llength $center] != 3 || [llength $vector] != 3} {
error "wrong type of args: should be $usage"
}
foreach {flag value} [lrange $args 3 end] {
switch -glob $flag {
scale {set scale $value}
res* {set res $value}
rad* {set radius $value}
fill* {set filled $value}
default {error "unknown option '$flag': should be $usage" }
}
}
set vechalf [vecscale [expr $scale * 0.5] $vector]
return [list \
[graphics $mol color yellow]\
[graphics $mol cylinder [vecsub $center $vechalf]\
[vecadd $center [vecscale 0.7 $vechalf]] \
radius $radius resolution $res filled $filled] \
[graphics $mol color orange]\
[graphics $mol cone [vecadd $center [vecscale 0.6 $vechalf]] \
[vecadd $center $vechalf] radius [expr $radius * 2.5] \
resolution $res]]
}
proc vmd_draw_spin {args} {
global molid
graphics $molid delete all
set frame [molinfo $molid get frame]
set natoms [molinfo $molid get numatoms]
for {set i 0} {$i < $natoms} {incr i} {
set sel [atomselect top "index $i"]
# set sel [atomselect top "index 1200"]
set coords [lindex [$sel get {x y z}] $molid]
set velocities [lindex [$sel get {vx vy vz}] $molid]
draw vector $coords $velocities
set uvx [lindex [$sel get {vx}] $molid]
set uvy [lindex [$sel get {vy}] $molid]
set uvz [lindex [$sel get {vz}] $molid]
$sel set user [vecadd [vecadd [vecscale $uvy $uvy] [vecscale $uvz $uvz] ] [vecscale $uvx $uvx]]
$sel set user $uvy
#draw vector $coords {0.0 uvy 0.0}
}
#pbc box -color 3
}
proc enable_trace {} {
global vmd_frame
trace variable vmd_frame([molinfo top]) w vmd_draw_spin
}
set molid [mol addfile {/home/jtranch/Documents/lammps/src/dump.lammpstrj} type {lammpstrj} autobonds off first 0 last -1 step 1 waitfor all]
scale by 0.5
animate style Loop
enable_trace

24
examples/mscg/control.in
View File

@ -1,12 +1,12 @@
block_size 1
start_frame 1
n_frames 19
nonbonded_cutoff 10.0
basis_type 0
primary_output_style 0
output_solution_flag 1
output_spline_coeffs_flag 1
pair_nonbonded_bspline_basis_order 6
pair_nonbonded_basis_set_resolution 0.7
pair_nonbonded_output_binwidth 0.1
matrix_type 0
block_size 1
start_frame 1
n_frames 19
nonbonded_cutoff 10.0
basis_type 0
primary_output_style 0
output_solution_flag 1
output_spline_coeffs_flag 1
pair_nonbonded_bspline_basis_order 6
pair_nonbonded_basis_set_resolution 0.7
pair_nonbonded_output_binwidth 0.1
matrix_type 0

44
examples/python/in.fix_python_invoke
View File

@ -1,21 +1,21 @@
# 3d Lennard-Jones melt
units lj
atom_style atomic
units lj
atom_style atomic
lattice fcc 0.8442
region box block 0 10 0 10 0 10
create_box 1 box
create_atoms 1 box
mass 1 1.0
lattice fcc 0.8442
region box block 0 10 0 10 0 10
create_box 1 box
create_atoms 1 box
mass 1 1.0
velocity all create 3.0 87287
velocity all create 3.0 87287
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no
python end_of_step_callback here """
from __future__ import print_function
@ -32,19 +32,19 @@ def post_force_callback(lmp, v):
print("### POST_FORCE ###", t)
"""
fix 1 all nve
fix 1 all nve
fix 2 all python/invoke 50 end_of_step end_of_step_callback
fix 3 all python/invoke 50 post_force post_force_callback
#dump id all atom 50 dump.melt
#dump id all atom 50 dump.melt
#dump 2 all image 25 image.*.jpg type type &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 2 all image 25 image.*.jpg type type &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
#dump 3 all movie 25 movie.mpg type type &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
thermo 50
run 250
thermo 50
run 250

44
examples/python/in.fix_python_invoke_neighlist
View File

@ -1,22 +1,22 @@
# 3d Lennard-Jones melt
units lj
atom_style atomic
units lj
atom_style atomic
lattice fcc 0.8442
region box block 0 2 0 2 0 2
create_box 1 box
create_atoms 1 box
mass 1 1.0
lattice fcc 0.8442
region box block 0 2 0 2 0 2
create_box 1 box
create_atoms 1 box
mass 1 1.0
velocity all create 3.0 87287
velocity all create 3.0 87287
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.1 bin
neighbor 0.1 bin
neigh_modify every 20 delay 0 check no
neigh_modify every 20 delay 0 check no
python post_force_callback here """
from __future__ import print_function
@ -55,18 +55,18 @@ def post_force_callback(lmp, v):
print(e)
"""
fix 1 all nve
fix 1 all nve
fix 3 all python/invoke 50 post_force post_force_callback
#dump id all atom 1 dump.melt
#dump id all atom 1 dump.melt
#dump 2 all image 1 image.*.jpg type type &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 2 all image 1 image.*.jpg type type &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 1 movie.mpg type type &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
#dump 3 all movie 1 movie.mpg type type &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
thermo 1
run 100
thermo 1
run 100

30
examples/python/in.fix_python_move_nve_melt
View File

@ -1,23 +1,23 @@
# 3d Lennard-Jones melt
units lj
atom_style atomic
units lj
atom_style atomic
lattice fcc 0.8442
region box block 0 10 0 10 0 10
create_box 1 box
create_atoms 1 box
mass * 1.0
lattice fcc 0.8442
region box block 0 10 0 10 0 10
create_box 1 box
create_atoms 1 box
mass * 1.0
velocity all create 3.0 87287
velocity all create 3.0 87287
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no
fix 1 all python/move py_nve.NVE
fix 1 all python/move py_nve.NVE
thermo 50
run 250
thermo 50
run 250

30
examples/python/in.fix_python_move_nve_melt_opt
View File

@ -1,23 +1,23 @@
# 3d Lennard-Jones melt
units lj
atom_style atomic
units lj
atom_style atomic
lattice fcc 0.8442
region box block 0 10 0 10 0 10
create_box 1 box
create_atoms 1 box
mass * 1.0
lattice fcc 0.8442
region box block 0 10 0 10 0 10
create_box 1 box
create_atoms 1 box
mass * 1.0
velocity all create 3.0 87287
velocity all create 3.0 87287
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no
fix 1 all python/move py_nve.NVE_Opt
fix 1 all python/move py_nve.NVE_Opt
thermo 50
run 250
thermo 50
run 250

28
examples/python/in.pair_python_coulomb
View File

@ -1,27 +1,27 @@
units real
atom_style full
units real
atom_style full
read_data data.spce
read_data data.spce
pair_style hybrid/overlay coul/cut 12.0 python 12.0
pair_style hybrid/overlay coul/cut 12.0 python 12.0
pair_coeff * * coul/cut
pair_coeff * * python py_pot.LJCutSPCE OW NULL
pair_coeff * * coul/cut
pair_coeff * * python py_pot.LJCutSPCE OW NULL
bond_style harmonic
angle_style harmonic
dihedral_style none
improper_style none
bond_style harmonic
angle_style harmonic
dihedral_style none
improper_style none
bond_coeff 1 1000.00 1.000
angle_coeff 1 100.0 109.47
bond_coeff 1 1000.00 1.000
angle_coeff 1 100.0 109.47
special_bonds lj/coul 0.0 0.0 1.0
neighbor 2.0 bin
fix 1 all shake 0.0001 20 0 b 1 a 1
fix 2 all nvt temp 300.0 300.0 100.0
fix 1 all shake 0.0001 20 0 b 1 a 1
fix 2 all nvt temp 300.0 300.0 100.0
# create combined lj/coul table for all atom types
# generate tabulated potential from python variant

84
examples/python/in.pair_python_harmonic Normal file
View File

@ -0,0 +1,84 @@
# 3d soft repulsive particles
units real
atom_style atomic
lattice fcc 5.0 origin 0.1 0.1 0.1
region box block -5 5 -5 5 -5 5
create_box 2 box
create_atoms 1 box
set type 1 type/ratio 2 0.5 424662346
mass * 1.0
velocity all create 3.0 87287
pair_style python 9.0
pair_coeff * * py_pot.Harmonic A B
neighbor 1.0 bin
neigh_modify every 2 delay 4 check yes
fix 1 all nve
thermo 50
run 250 post no
write_restart repulsive.restart
clear
read_restart repulsive.restart
pair_style python 10.0
pair_coeff * * py_pot.Harmonic A B
shell rm -f python.dat
pair_write 1 1 1000 rsq 0.1 10.0 python.dat PYTH_A_A
pair_write 2 2 1000 rsq 0.1 10.0 python.dat PYTH_B_B
pair_write 1 2 1000 rsq 0.1 10.0 python.dat PYTH_A_B
fix 1 all nve
thermo 50
run 250 post no
clear
read_restart repulsive.restart
pair_style harmonic/cut
pair_coeff 1 1 0.2 9.0
pair_coeff 2 2 0.4 9.0
shell rm -f harmonic.dat
pair_write 1 1 1000 rsq 0.1 10.0 harmonic.dat HARM_1_1
pair_write 2 2 1000 rsq 0.1 10.0 harmonic.dat HARM_2_2
pair_write 1 2 1000 rsq 0.1 10.0 harmonic.dat HARM_1_2
neighbor 1.0 bin
neigh_modify every 2 delay 4 check yes
fix 1 all nve
thermo 50
run 250 post no
clear
read_restart repulsive.restart
pair_style table spline 1000
pair_coeff 1 1 python.dat PYTH_A_A
pair_coeff 1 2 python.dat PYTH_A_B
pair_coeff 2 2 python.dat PYTH_B_B
neighbor 1.0 bin
neigh_modify every 2 delay 4 check yes
fix 1 all nve
thermo 50
run 250 post no
# remove temporary files
shell rm repulsive.restart harmonic.dat python.dat

58
examples/python/in.pair_python_hybrid
View File

@ -1,29 +1,29 @@
# 3d Lennard-Jones hybrid
units lj
atom_style atomic
units lj
atom_style atomic
lattice fcc 0.8442
region box block 0 10 0 10 0 10
create_box 2 box
create_atoms 1 box
mass * 1.0
lattice fcc 0.8442
region box block 0 10 0 10 0 10
create_box 2 box
create_atoms 1 box
mass * 1.0
region half block -0.1 4.9 0 10 0 10
set region half type 2
velocity all create 3.0 87287
velocity all create 3.0 87287
pair_style hybrid lj/cut 2.5 python 2.5
pair_coeff * * python py_pot.LJCutMelt lj NULL
pair_style hybrid lj/cut 2.5 python 2.5
pair_coeff * * python py_pot.LJCutMelt lj NULL
pair_coeff * 2 lj/cut 1.0 1.0
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no
fix 1 all nve
fix 1 all nve
thermo 50
run 250
thermo 50
run 250
write_data hybrid.data
write_restart hybrid.restart
@ -32,32 +32,32 @@ clear
read_restart hybrid.restart
pair_style hybrid lj/cut 2.5 python 2.5
pair_coeff * * python py_pot.LJCutMelt lj NULL
pair_style hybrid lj/cut 2.5 python 2.5
pair_coeff * * python py_pot.LJCutMelt lj NULL
pair_coeff * 2 lj/cut 1.0 1.0
fix 1 all nve
fix 1 all nve
thermo 50
run 250
thermo 50
run 250
clear
units lj
atom_style atomic
units lj
atom_style atomic
read_data hybrid.data
pair_style hybrid lj/cut 2.5 python 2.5
pair_coeff * * python py_pot.LJCutMelt lj NULL
pair_style hybrid lj/cut 2.5 python 2.5
pair_coeff * * python py_pot.LJCutMelt lj NULL
pair_coeff * 2 lj/cut 1.0 1.0
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no
fix 1 all nve
fix 1 all nve
thermo 50
run 250
thermo 50
run 250
shell rm hybrid.data hybrid.restart

28
examples/python/in.pair_python_long
View File

@ -1,25 +1,25 @@
units real
atom_style full
units real
atom_style full
read_data data.spce
read_data data.spce
pair_style python 12.0
pair_coeff * * py_pot.LJCutSPCE OW HW
pair_style python 12.0
pair_coeff * * py_pot.LJCutSPCE OW HW
bond_style harmonic
angle_style harmonic
dihedral_style none
improper_style none
bond_style harmonic
angle_style harmonic
dihedral_style none
improper_style none
bond_coeff 1 1000.00 1.000
angle_coeff 1 100.0 109.47
bond_coeff 1 1000.00 1.000
angle_coeff 1 100.0 109.47
special_bonds lj/coul 0.0 0.0 1.0
neighbor 2.0 bin
fix 1 all shake 0.0001 20 0 b 1 a 1
fix 2 all nvt temp 300.0 300.0 100.0
fix 1 all shake 0.0001 20 0 b 1 a 1
fix 2 all nvt temp 300.0 300.0 100.0
# create only lj/cut table for the oxygen atoms from python
shell rm -f spce.table
@ -27,7 +27,7 @@ pair_write 1 1 2000 rsq 0.1 12 spce.table OW-OW
# switch to tabulated potential with long-range coulomb as overlay
pair_style hybrid/overlay coul/long 12.0 table linear 2000
kspace_style pppm 1.0e-6
kspace_style pppm 1.0e-6
pair_coeff * * coul/long
pair_coeff 1 1 table spce.table OW-OW

58
examples/python/in.pair_python_melt
View File

@ -1,26 +1,26 @@
# 3d Lennard-Jones melt
units lj
atom_style atomic
units lj
atom_style atomic
lattice fcc 0.8442
region box block 0 10 0 10 0 10
create_box 1 box
create_atoms 1 box
mass * 1.0
lattice fcc 0.8442
region box block 0 10 0 10 0 10
create_box 1 box
create_atoms 1 box
mass * 1.0
velocity all create 3.0 87287
velocity all create 3.0 87287
pair_style python 2.5
pair_coeff * * py_pot.LJCutMelt lj
pair_style python 2.5
pair_coeff * * py_pot.LJCutMelt lj
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no
fix 1 all nve
fix 1 all nve
thermo 50
run 250
thermo 50
run 250
write_data melt.data
write_restart melt.restart
@ -29,30 +29,30 @@ clear
read_restart melt.restart
pair_style python 2.5
pair_coeff * * py_pot.LJCutMelt lj
pair_style python 2.5
pair_coeff * * py_pot.LJCutMelt lj
fix 1 all nve
fix 1 all nve
thermo 50
run 250
thermo 50
run 250
clear
units lj
atom_style atomic
units lj
atom_style atomic
read_data melt.data
pair_style python 2.5
pair_coeff * * py_pot.LJCutMelt lj
pair_style python 2.5
pair_coeff * * py_pot.LJCutMelt lj
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no
fix 1 all nve
fix 1 all nve
thermo 50
run 250
thermo 50
run 250
shell rm melt.data melt.restart

30
examples/python/in.pair_python_spce
View File

@ -1,28 +1,28 @@
units real
atom_style full
units real
atom_style full
read_data data.spce
read_data data.spce
pair_style hybrid/overlay coul/long 12.0 python 12.0
kspace_style pppm 1.0e-6
pair_style hybrid/overlay coul/long 12.0 python 12.0
kspace_style pppm 1.0e-6
pair_coeff * * coul/long
pair_coeff * * python py_pot.LJCutSPCE OW NULL
pair_coeff * * coul/long
pair_coeff * * python py_pot.LJCutSPCE OW NULL
bond_style harmonic
angle_style harmonic
dihedral_style none
improper_style none
bond_style harmonic
angle_style harmonic
dihedral_style none
improper_style none
bond_coeff 1 1000.00 1.000
angle_coeff 1 100.0 109.47
bond_coeff 1 1000.00 1.000
angle_coeff 1 100.0 109.47
special_bonds lj/coul 0.0 0.0 1.0
neighbor 2.0 bin
fix 1 all shake 0.0001 20 0 b 1 a 1
fix 2 all nvt temp 300.0 300.0 100.0
fix 1 all shake 0.0001 20 0 b 1 a 1
fix 2 all nvt temp 300.0 300.0 100.0
thermo 10
run 100

30
examples/python/in.pair_python_table
View File

@ -1,18 +1,18 @@
# 3d Lennard-Jones melt
units lj
atom_style atomic
units lj
atom_style atomic
lattice fcc 0.8442
region box block 0 10 0 10 0 10
create_box 1 box
create_atoms 1 box
mass * 1.0
lattice fcc 0.8442
region box block 0 10 0 10 0 10
create_box 1 box
create_atoms 1 box
mass * 1.0
velocity all create 3.0 87287
velocity all create 3.0 87287
pair_style python 2.5
pair_coeff * * py_pot.LJCutMelt lj
pair_style python 2.5
pair_coeff * * py_pot.LJCutMelt lj
# generate tabulated potential from python variant
pair_write 1 1 2000 rsq 0.01 2.5 lj_1_1.table LJ
@ -20,13 +20,13 @@ pair_write 1 1 2000 rsq 0.01 2.5 lj_1_1.table LJ
pair_style table linear 2000
pair_coeff 1 1 lj_1_1.table LJ
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no
fix 1 all nve
fix 1 all nve
thermo 50
run 250
thermo 50
run 250
shell rm lj_1_1.table

28
examples/python/in.python
View File

@ -1,25 +1,25 @@
# 3d Lennard-Jones melt with Python functions added
units lj
atom_style atomic
units lj
atom_style atomic
lattice fcc 0.8442
region box block 0 10 0 10 0 10
create_box 1 box
create_atoms 1 box
mass 1 1.0
lattice fcc 0.8442
region box block 0 10 0 10 0 10
create_box 1 box
create_atoms 1 box
mass 1 1.0
velocity all create 1.44 87287 loop geom
velocity all create 1.44 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
fix 1 all nve
run 10
run 10
# 1st Python function
# example of catching a syntax error

235
examples/python/log.18Mar22.pair_python_harmonic.g++.1 Normal file
View File

@ -0,0 +1,235 @@
LAMMPS (17 Feb 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# 3d soft repulsive particles
units real
atom_style atomic
lattice fcc 5.0 origin 0.1 0.1 0.1
Lattice spacing in x,y,z = 5 5 5
region box block -5 5 -5 5 -5 5
create_box 2 box
Created orthogonal box = (-25 -25 -25) to (25 25 25)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 4000 atoms
using lattice units in orthogonal box = (-25 -25 -25) to (25 25 25)
create_atoms CPU = 0.001 seconds
set type 1 type/ratio 2 0.5 424662346
Setting atom values ...
2000 settings made for type/ratio
mass * 1.0
velocity all create 3.0 87287
pair_style python 9.0
pair_coeff * * py_pot.Harmonic A B
neighbor 1.0 bin
neigh_modify every 2 delay 4 check yes
fix 1 all nve
thermo 50
run 250 post no
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 2 steps, delay 4 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10
ghost atom cutoff = 10
binsize = 5, bins = 10 10 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair python, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.139 | 4.139 | 4.139 Mbytes
Step Temp E_pair E_mol TotEng Press
0 3 423789.56 0 423825.32 249259.3
50 75.889551 422919.46 0 423824.08 248893.24
100 105.20972 422570.47 0 423824.6 250756.6
150 132.08764 422249.71 0 423824.23 251894.29
200 118.14116 422416.43 0 423824.7 252088.96
250 128.40086 422293.71 0 423824.28 252057.16
Loop time of 17.4414 on 1 procs for 250 steps with 4000 atoms
write_restart repulsive.restart
System init for write_restart ...
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
read_restart repulsive.restart
Reading restart file ...
restart file = 17 Feb 2022, LAMMPS = 17 Feb 2022
restoring atom style atomic from restart
orthogonal box = (-25 -25 -25) to (25 25 25)
1 by 1 by 1 MPI processor grid
pair style python stores no restart info
4000 atoms
read_restart CPU = 0.001 seconds
pair_style python 10.0
pair_coeff * * py_pot.Harmonic A B
shell rm -f python.dat
pair_write 1 1 1000 rsq 0.1 10.0 python.dat PYTH_A_A
Creating table file python.dat with DATE: 2022-03-18
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 9 9 9
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair python, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
pair_write 2 2 1000 rsq 0.1 10.0 python.dat PYTH_B_B
Appending to table file python.dat with DATE: 2022-03-18
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
pair_write 1 2 1000 rsq 0.1 10.0 python.dat PYTH_A_B
Appending to table file python.dat with DATE: 2022-03-18
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
fix 1 all nve
thermo 50
run 250 post no
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 4.977 | 4.977 | 4.977 Mbytes
Step Temp E_pair E_mol TotEng Press
250 128.40086 422293.71 0 423824.28 252057.16
300 119.72871 422397.4 0 423824.6 251985.11
350 124.88375 422335.77 0 423824.42 252051.28
400 121.76143 422373.11 0 423824.53 252006.39
450 125.29847 422330.9 0 423824.49 251997.23
500 126.87408 422312.08 0 423824.45 252053.51
Loop time of 23.4715 on 1 procs for 250 steps with 4000 atoms
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
read_restart repulsive.restart
Reading restart file ...
restart file = 17 Feb 2022, LAMMPS = 17 Feb 2022
restoring atom style atomic from restart
orthogonal box = (-25 -25 -25) to (25 25 25)
1 by 1 by 1 MPI processor grid
pair style python stores no restart info
4000 atoms
read_restart CPU = 0.000 seconds
pair_style harmonic/cut
pair_coeff 1 1 0.2 9.0
pair_coeff 2 2 0.4 9.0
shell rm -f harmonic.dat
pair_write 1 1 1000 rsq 0.1 10.0 harmonic.dat HARM_1_1
Creating table file harmonic.dat with DATE: 2022-03-18
generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 11
ghost atom cutoff = 11
binsize = 5.5, bins = 10 10 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair harmonic/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
pair_write 2 2 1000 rsq 0.1 10.0 harmonic.dat HARM_2_2
Appending to table file harmonic.dat with DATE: 2022-03-18
generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
pair_write 1 2 1000 rsq 0.1 10.0 harmonic.dat HARM_1_2
Appending to table file harmonic.dat with DATE: 2022-03-18
generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
neighbor 1.0 bin
neigh_modify every 2 delay 4 check yes
fix 1 all nve
thermo 50
run 250 post no
generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 4.138 | 4.138 | 4.138 Mbytes
Step Temp E_pair E_mol TotEng Press
250 128.40086 422293.71 0 423824.28 252057.16
300 119.72871 422397.4 0 423824.6 251985.11
350 124.88375 422335.77 0 423824.42 252051.28
400 121.76143 422373.11 0 423824.53 252006.39
450 125.29847 422330.9 0 423824.49 251997.23
500 126.87408 422312.08 0 423824.45 252053.51
Loop time of 0.843376 on 1 procs for 250 steps with 4000 atoms
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
read_restart repulsive.restart
Reading restart file ...
restart file = 17 Feb 2022, LAMMPS = 17 Feb 2022
restoring atom style atomic from restart
orthogonal box = (-25 -25 -25) to (25 25 25)
1 by 1 by 1 MPI processor grid
pair style python stores no restart info
4000 atoms
read_restart CPU = 0.000 seconds
pair_style table spline 1000
pair_coeff 1 1 python.dat PYTH_A_A
Reading pair table potential file python.dat with DATE: 2022-03-18
pair_coeff 1 2 python.dat PYTH_A_B
Reading pair table potential file python.dat with DATE: 2022-03-18
pair_coeff 2 2 python.dat PYTH_B_B
Reading pair table potential file python.dat with DATE: 2022-03-18
neighbor 1.0 bin
neigh_modify every 2 delay 4 check yes
fix 1 all nve
thermo 50
run 250 post no
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 2 steps, delay 4 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 11
ghost atom cutoff = 11
binsize = 5.5, bins = 10 10 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair table, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.552 | 4.552 | 4.552 Mbytes
Step Temp E_pair E_mol TotEng Press
250 128.40086 422293.71 0 423824.28 252057.14
300 119.72876 422397.4 0 423824.6 251985.1
350 124.88381 422335.77 0 423824.42 252051.26
400 121.76148 422373.11 0 423824.53 252006.37
450 125.29842 422330.9 0 423824.49 251997.21
500 126.87418 422312.08 0 423824.46 252053.48
Loop time of 1.57415 on 1 procs for 250 steps with 4000 atoms
# remove temporary files
shell rm repulsive.restart harmonic.dat python.dat
Total wall time: 0:00:43

235
examples/python/log.18Mar22.pair_python_harmonic.g++.4 Normal file
View File

@ -0,0 +1,235 @@
LAMMPS (17 Feb 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# 3d soft repulsive particles
units real
atom_style atomic
lattice fcc 5.0 origin 0.1 0.1 0.1
Lattice spacing in x,y,z = 5 5 5
region box block -5 5 -5 5 -5 5
create_box 2 box
Created orthogonal box = (-25 -25 -25) to (25 25 25)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 4000 atoms
using lattice units in orthogonal box = (-25 -25 -25) to (25 25 25)
create_atoms CPU = 0.000 seconds
set type 1 type/ratio 2 0.5 424662346
Setting atom values ...
2000 settings made for type/ratio
mass * 1.0
velocity all create 3.0 87287
pair_style python 9.0
pair_coeff * * py_pot.Harmonic A B
neighbor 1.0 bin
neigh_modify every 2 delay 4 check yes
fix 1 all nve
thermo 50
run 250 post no
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 2 steps, delay 4 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10
ghost atom cutoff = 10
binsize = 5, bins = 10 10 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair python, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.225 | 3.225 | 3.225 Mbytes
Step Temp E_pair E_mol TotEng Press
0 3 423843.22 0 423878.98 249277.9
50 79.665061 422928.03 0 423877.66 248995.64
100 108.5878 422583.81 0 423878.21 250822.76
150 130.90607 422317.45 0 423877.89 251949.08
200 120.05458 422447.24 0 423878.33 252105.09
250 135.76605 422259.47 0 423877.84 252077.41
Loop time of 4.70112 on 4 procs for 250 steps with 4000 atoms
write_restart repulsive.restart
System init for write_restart ...
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
read_restart repulsive.restart
Reading restart file ...
restart file = 17 Feb 2022, LAMMPS = 17 Feb 2022
restoring atom style atomic from restart
orthogonal box = (-25 -25 -25) to (25 25 25)
1 by 2 by 2 MPI processor grid
pair style python stores no restart info
4000 atoms
read_restart CPU = 0.001 seconds
pair_style python 10.0
pair_coeff * * py_pot.Harmonic A B
shell rm -f python.dat
pair_write 1 1 1000 rsq 0.1 10.0 python.dat PYTH_A_A
Creating table file python.dat with DATE: 2022-03-18
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 9 9 9
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair python, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
pair_write 2 2 1000 rsq 0.1 10.0 python.dat PYTH_B_B
Appending to table file python.dat with DATE: 2022-03-18
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
pair_write 1 2 1000 rsq 0.1 10.0 python.dat PYTH_A_B
Appending to table file python.dat with DATE: 2022-03-18
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
fix 1 all nve
thermo 50
run 250 post no
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 3.666 | 3.667 | 3.667 Mbytes
Step Temp E_pair E_mol TotEng Press
250 135.76605 422259.47 0 423877.84 252077.41
300 119.63404 422452.21 0 423878.28 251958.74
350 129.35013 422336.12 0 423878 252069.99
400 123.04377 422411.48 0 423878.19 252024.23
450 126.01375 422375.98 0 423878.1 252019.19
500 126.91094 422365.34 0 423878.15 252012.59
Loop time of 6.20423 on 4 procs for 250 steps with 4000 atoms
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
read_restart repulsive.restart
Reading restart file ...
restart file = 17 Feb 2022, LAMMPS = 17 Feb 2022
restoring atom style atomic from restart
orthogonal box = (-25 -25 -25) to (25 25 25)
1 by 2 by 2 MPI processor grid
pair style python stores no restart info
4000 atoms
read_restart CPU = 0.001 seconds
pair_style harmonic/cut
pair_coeff 1 1 0.2 9.0
pair_coeff 2 2 0.4 9.0
shell rm -f harmonic.dat
pair_write 1 1 1000 rsq 0.1 10.0 harmonic.dat HARM_1_1
Creating table file harmonic.dat with DATE: 2022-03-18
generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 11
ghost atom cutoff = 11
binsize = 5.5, bins = 10 10 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair harmonic/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
pair_write 2 2 1000 rsq 0.1 10.0 harmonic.dat HARM_2_2
Appending to table file harmonic.dat with DATE: 2022-03-18
generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
pair_write 1 2 1000 rsq 0.1 10.0 harmonic.dat HARM_1_2
Appending to table file harmonic.dat with DATE: 2022-03-18
generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
neighbor 1.0 bin
neigh_modify every 2 delay 4 check yes
fix 1 all nve
thermo 50
run 250 post no
generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 3.227 | 3.227 | 3.229 Mbytes
Step Temp E_pair E_mol TotEng Press
250 135.76605 422259.47 0 423877.84 252077.41
300 119.63404 422452.21 0 423878.28 251958.74
350 129.35013 422336.12 0 423878 252069.99
400 123.04377 422411.48 0 423878.19 252024.23
450 126.01375 422375.98 0 423878.1 252019.19
500 126.91094 422365.34 0 423878.15 252012.59
Loop time of 0.257048 on 4 procs for 250 steps with 4000 atoms
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
read_restart repulsive.restart
Reading restart file ...
restart file = 17 Feb 2022, LAMMPS = 17 Feb 2022
restoring atom style atomic from restart
orthogonal box = (-25 -25 -25) to (25 25 25)
1 by 2 by 2 MPI processor grid
pair style python stores no restart info
4000 atoms
read_restart CPU = 0.000 seconds
pair_style table spline 1000
pair_coeff 1 1 python.dat PYTH_A_A
Reading pair table potential file python.dat with DATE: 2022-03-18
pair_coeff 1 2 python.dat PYTH_A_B
Reading pair table potential file python.dat with DATE: 2022-03-18
pair_coeff 2 2 python.dat PYTH_B_B
Reading pair table potential file python.dat with DATE: 2022-03-18
neighbor 1.0 bin
neigh_modify every 2 delay 4 check yes
fix 1 all nve
thermo 50
run 250 post no
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 2 steps, delay 4 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 11
ghost atom cutoff = 11
binsize = 5.5, bins = 10 10 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair table, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.257 | 3.257 | 3.257 Mbytes
Step Temp E_pair E_mol TotEng Press
250 135.76605 422259.47 0 423877.84 252077.38
300 119.63401 422452.21 0 423878.28 251958.73
350 129.35009 422336.11 0 423878 252069.98
400 123.04383 422411.48 0 423878.19 252024.21
450 126.01378 422375.98 0 423878.1 252019.16
500 126.91078 422365.34 0 423878.15 252012.57
Loop time of 0.497624 on 4 procs for 250 steps with 4000 atoms
# remove temporary files
shell rm repulsive.restart harmonic.dat python.dat
Total wall time: 0:00:11

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