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This commit is contained in:
Axel Kohlmeyer
2023-05-04 02:21:55 -04:00
parent 62858115b2
commit 42e090d945
8 changed files with 151 additions and 151 deletions
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26
bench/in.chain
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# FENE beadspring benchmark
units lj
atom_style bond
units lj
atom_style bond
special_bonds fene
read_data data.chain
read_data data.chain
neighbor 0.4 bin
neigh_modify every 1 delay 1
neighbor 0.4 bin
neigh_modify every 1 delay 1
bond_style fene
bond_coeff 1 30.0 1.5 1.0 1.0
bond_coeff 1 30.0 1.5 1.0 1.0
pair_style lj/cut 1.12
pair_modify shift yes
pair_coeff 1 1 1.0 1.0 1.12
pair_style lj/cut 1.12
pair_modify shift yes
pair_coeff 1 1 1.0 1.0 1.12
fix 1 all nve
fix 2 all langevin 1.0 1.0 10.0 904297
fix 1 all nve
fix 2 all langevin 1.0 1.0 10.0 904297
thermo 100
timestep 0.012
timestep 0.012
run 100
run 100

36
bench/in.chain.scaled
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@ -1,32 +1,32 @@
# FENE beadspring benchmark
variable x index 1
variable y index 1
variable z index 1
variable x index 1
variable y index 1
variable z index 1
units lj
atom_style bond
atom_modify map hash
units lj
atom_style bond
atom_modify map hash
special_bonds fene
read_data data.chain
read_data data.chain
replicate $x $y $z
replicate $x $y $z
neighbor 0.4 bin
neigh_modify every 1 delay 1
neighbor 0.4 bin
neigh_modify every 1 delay 1
bond_style fene
bond_coeff 1 30.0 1.5 1.0 1.0
bond_coeff 1 30.0 1.5 1.0 1.0
pair_style lj/cut 1.12
pair_modify shift yes
pair_coeff 1 1 1.0 1.0 1.12
pair_style lj/cut 1.12
pair_modify shift yes
pair_coeff 1 1 1.0 1.0 1.12
fix 1 all nve
fix 2 all langevin 1.0 1.0 10.0 904297
fix 1 all nve
fix 2 all langevin 1.0 1.0 10.0 904297
thermo 100
timestep 0.012
timestep 0.012
run 100
run 100

44
bench/in.chute
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@ -1,33 +1,33 @@
# LAMMPS benchmark of granular flow
# chute flow of 32000 atoms with frozen base at 26 degrees
units lj
atom_style sphere
boundary p p fs
newton off
comm_modify vel yes
units lj
atom_style sphere
boundary p p fs
newton off
comm_modify vel yes
read_data data.chute
read_data data.chute
pair_style gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0
pair_coeff * *
pair_style gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0
pair_coeff * *
neighbor 0.1 bin
neigh_modify every 1 delay 0
neighbor 0.1 bin
neigh_modify every 1 delay 0
timestep 0.0001
timestep 0.0001
group bottom type 2
group active subtract all bottom
neigh_modify exclude group bottom bottom
group bottom type 2
group active subtract all bottom
neigh_modify exclude group bottom bottom
fix 1 all gravity 1.0 chute 26.0
fix 2 bottom freeze
fix 3 active nve/sphere
fix 1 all gravity 1.0 chute 26.0
fix 2 bottom freeze
fix 3 active nve/sphere
compute 1 all erotate/sphere
thermo_style custom step atoms ke c_1 vol
thermo_modify norm no
thermo 100
compute 1 all erotate/sphere
thermo_style custom step atoms ke c_1 vol
thermo_modify norm no
thermo 100
run 100
run 100

50
bench/in.chute.scaled
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@ -1,38 +1,38 @@
# LAMMPS benchmark of granular flow
# chute flow of 32000 atoms with frozen base at 26 degrees
variable x index 1
variable y index 1
variable x index 1
variable y index 1
units lj
atom_style sphere
boundary p p fs
newton off
comm_modify vel yes
units lj
atom_style sphere
boundary p p fs
newton off
comm_modify vel yes
read_data data.chute
read_data data.chute
replicate $x $y 1
replicate $x $y 1
pair_style gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0
pair_coeff * *
pair_style gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0
pair_coeff * *
neighbor 0.1 bin
neigh_modify every 1 delay 0
neighbor 0.1 bin
neigh_modify every 1 delay 0
timestep 0.0001
timestep 0.0001
group bottom type 2
group active subtract all bottom
neigh_modify exclude group bottom bottom
group bottom type 2
group active subtract all bottom
neigh_modify exclude group bottom bottom
fix 1 all gravity 1.0 chute 26.0
fix 2 bottom freeze
fix 3 active nve/sphere
fix 1 all gravity 1.0 chute 26.0
fix 2 bottom freeze
fix 3 active nve/sphere
compute 1 all erotate/sphere
thermo_style custom step atoms ke c_1 vol
thermo_modify norm no
thermo 100
compute 1 all erotate/sphere
thermo_style custom step atoms ke c_1 vol
thermo_modify norm no
thermo 100
run 100
run 100

40
bench/in.eam
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@ -1,32 +1,32 @@
# bulk Cu lattice
variable x index 1
variable y index 1
variable z index 1
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable yy equal 20*$y
variable zz equal 20*$z
variable xx equal 20*$x
variable yy equal 20*$y
variable zz equal 20*$z
units metal
atom_style atomic
units metal
atom_style atomic
lattice fcc 3.615
region box block 0 ${xx} 0 ${yy} 0 ${zz}
create_box 1 box
create_atoms 1 box
lattice fcc 3.615
region box block 0 ${xx} 0 ${yy} 0 ${zz}
create_box 1 box
create_atoms 1 box
pair_style eam
pair_coeff 1 1 Cu_u3.eam
pair_style eam
pair_coeff 1 1 Cu_u3.eam
velocity all create 1600.0 376847 loop geom
velocity all create 1600.0 376847 loop geom
neighbor 1.0 bin
neighbor 1.0 bin
neigh_modify every 1 delay 5 check yes
fix 1 all nve
fix 1 all nve
timestep 0.005
thermo 50
timestep 0.005
thermo 50
run 100
run 100

40
bench/in.lj
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@ -1,30 +1,30 @@
# 3d Lennard-Jones melt
variable x index 1
variable y index 1
variable z index 1
variable x index 1
variable y index 1
variable z index 1
variable xx equal 20*$x
variable yy equal 20*$y
variable zz equal 20*$z
variable xx equal 20*$x
variable yy equal 20*$y
variable zz equal 20*$z
units lj
atom_style atomic
units lj
atom_style atomic
lattice fcc 0.8442
region box block 0 ${xx} 0 ${yy} 0 ${zz}
create_box 1 box
create_atoms 1 box
mass 1 1.0
lattice fcc 0.8442
region box block 0 ${xx} 0 ${yy} 0 ${zz}
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 20 check no
neighbor 0.3 bin
neigh_modify delay 0 every 20 check no
fix 1 all nve
fix 1 all nve
run 100
run 100

28
bench/in.rhodo
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@ -1,27 +1,27 @@
# Rhodopsin model
units real
neigh_modify delay 5 every 1
units real
neigh_modify delay 5 every 1
atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
pair_style lj/charmm/coul/long 8.0 10.0
pair_modify mix arithmetic
kspace_style pppm 1e-4
atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
pair_style lj/charmm/coul/long 8.0 10.0
pair_modify mix arithmetic
kspace_style pppm 1e-4
read_data data.rhodo
fix 1 all shake 0.0001 5 0 m 1.0 a 232
fix 2 all npt temp 300.0 300.0 100.0 &
z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
special_bonds charmm
thermo 50
thermo_style multi
thermo_style multi
timestep 2.0
run 100
run 100

38
bench/in.rhodo.scaled
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@ -1,34 +1,34 @@
# Rhodopsin model
variable x index 1
variable y index 1
variable z index 1
variable x index 1
variable y index 1
variable z index 1
units real
neigh_modify delay 5 every 1
units real
neigh_modify delay 5 every 1
atom_style full
atom_modify map hash
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
pair_style lj/charmm/coul/long 8.0 10.0
pair_modify mix arithmetic
kspace_style pppm 1e-4
atom_style full
atom_modify map hash
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
pair_style lj/charmm/coul/long 8.0 10.0
pair_modify mix arithmetic
kspace_style pppm 1e-4
read_data data.rhodo
replicate $x $y $z
replicate $x $y $z
fix 1 all shake 0.0001 5 0 m 1.0 a 232
fix 2 all npt temp 300.0 300.0 100.0 &
z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
special_bonds charmm
thermo 50
thermo_style multi
thermo_style multi
timestep 2.0
run 100
run 100