demo/test examples for OpenMP variants of asphere
This commit is contained in:
Axel Kohlmeyer
56
examples/USER/openmp/in.ellipse.gayberne
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56
examples/USER/openmp/in.ellipse.gayberne
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# GayBerne ellipsoids in LJ background fluid
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units lj
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atom_style ellipsoid
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dimension 2
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lattice sq 0.02
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region box block 0 20 0 20 -0.5 0.5
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create_box 2 box
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create_atoms 1 box
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replicate 3 3 1
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set group all type/fraction 2 0.1 95392
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set group all quat/random 18238
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mass 1 1.0
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mass 2 1.5
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shape 1 1 1 1
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shape 2 3 1 1
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compute rot all temp/asphere
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group spheroid type 1
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variable dof equal count(spheroid)+2
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compute_modify rot extra ${dof}
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velocity all create 2.4 87287 loop geom
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pair_style gayberne 1.0 3.0 1.0 4.0
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pair_coeff 1 1 3.0 1.0 1 1 1 1 1 1 2.5
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pair_coeff 1 2 3.0 1.0 1 1 1 0 0 0
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pair_coeff 2 2 1.0 1.0 1 1 0.2 0 0 0
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neighbor 0.8 bin
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thermo_style custom step c_rot epair etotal press vol
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thermo 100
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timestep 0.002
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fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 &
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mtk no pchain 0 tchain 1
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fix 2 all enforce2d
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compute_modify 1_temp extra ${dof}
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# equilibrate to shrink box around dilute system
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run 2000
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# run dynamics on dense system
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unfix 1
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fix 1 all nve/asphere
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run 2000
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56
examples/USER/openmp/in.ellipse.gayberne-omp
Normal file
56
examples/USER/openmp/in.ellipse.gayberne-omp
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@ -0,0 +1,56 @@
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# GayBerne ellipsoids in LJ background fluid
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||||
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units lj
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atom_style ellipsoid
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dimension 2
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||||
|
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lattice sq 0.02
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region box block 0 20 0 20 -0.5 0.5
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create_box 2 box
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create_atoms 1 box
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replicate 3 3 1
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set group all type/fraction 2 0.1 95392
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set group all quat/random 18238
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mass 1 1.0
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mass 2 1.5
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shape 1 1 1 1
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shape 2 3 1 1
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compute rot all temp/asphere
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group spheroid type 1
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variable dof equal count(spheroid)+2
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compute_modify rot extra ${dof}
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velocity all create 2.4 87287 loop geom
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pair_style gayberne/omp 1.0 3.0 1.0 4.0
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pair_coeff 1 1 3.0 1.0 1 1 1 1 1 1 2.5
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pair_coeff 1 2 3.0 1.0 1 1 1 0 0 0
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pair_coeff 2 2 1.0 1.0 1 1 0.2 0 0 0
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neighbor 0.8 bin
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thermo_style custom step c_rot epair etotal press vol
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thermo 100
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timestep 0.002
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|
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fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 &
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mtk no pchain 0 tchain 1
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fix 2 all enforce2d
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compute_modify 1_temp extra ${dof}
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# equilibrate to shrink box around dilute system
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run 2000
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# run dynamics on dense system
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unfix 1
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fix 1 all nve/asphere
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run 2000
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56
examples/USER/openmp/in.ellipse.resquared
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56
examples/USER/openmp/in.ellipse.resquared
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@ -0,0 +1,56 @@
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# RESquared ellipsoids in LJ background fluid
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units lj
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atom_style ellipsoid
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dimension 2
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lattice sq 0.02
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region box block 0 20 0 20 -0.5 0.5
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create_box 2 box
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create_atoms 1 box
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replicate 3 3 1
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|
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set group all type/fraction 2 0.1 95392
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set group all quat/random 18238
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|
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mass 1 1.0
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mass 2 1.5
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shape 1 1 1 1
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shape 2 3 1 1
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compute rot all temp/asphere
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group spheroid type 1
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variable dof equal count(spheroid)+2
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compute_modify rot extra ${dof}
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velocity all create 2.4 87287 loop geom
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pair_style resquared 4.0
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pair_coeff 1 1 3.0 1 1 1 1 1 1 1 2.5
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pair_coeff 1 2 3.0 1 1 1 1 0 0 0
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pair_coeff 2 2 1.0 1 1 1 0.2 0 0 0
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neighbor 0.8 bin
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|
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thermo_style custom step c_rot epair etotal press vol
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thermo 100
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|
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timestep 0.002
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|
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fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 &
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mtk no pchain 0 tchain 1
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fix 2 all enforce2d
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||||
|
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compute_modify 1_temp extra ${dof}
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# equilibrate to shrink box around dilute system
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run 2000
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# run dynamics on dense system
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unfix 1
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fix 1 all nve/asphere
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run 2000
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56
examples/USER/openmp/in.ellipse.resquared-omp
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56
examples/USER/openmp/in.ellipse.resquared-omp
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@ -0,0 +1,56 @@
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# RESquared ellipsoids in LJ background fluid
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||||
|
||||
units lj
|
||||
atom_style ellipsoid
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dimension 2
|
||||
|
||||
lattice sq 0.02
|
||||
region box block 0 20 0 20 -0.5 0.5
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create_box 2 box
|
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create_atoms 1 box
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||||
|
||||
replicate 3 3 1
|
||||
|
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set group all type/fraction 2 0.1 95392
|
||||
set group all quat/random 18238
|
||||
|
||||
mass 1 1.0
|
||||
mass 2 1.5
|
||||
shape 1 1 1 1
|
||||
shape 2 3 1 1
|
||||
|
||||
compute rot all temp/asphere
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||||
group spheroid type 1
|
||||
variable dof equal count(spheroid)+2
|
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compute_modify rot extra ${dof}
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||||
|
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velocity all create 2.4 87287 loop geom
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||||
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pair_style resquared/omp 4.0
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||||
pair_coeff 1 1 3.0 1 1 1 1 1 1 1 2.5
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||||
pair_coeff 1 2 3.0 1 1 1 1 0 0 0
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||||
pair_coeff 2 2 1.0 1 1 1 0.2 0 0 0
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||||
|
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neighbor 0.8 bin
|
||||
|
||||
thermo_style custom step c_rot epair etotal press vol
|
||||
thermo 100
|
||||
|
||||
timestep 0.002
|
||||
|
||||
fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 &
|
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mtk no pchain 0 tchain 1
|
||||
fix 2 all enforce2d
|
||||
|
||||
compute_modify 1_temp extra ${dof}
|
||||
|
||||
# equilibrate to shrink box around dilute system
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||||
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||||
run 2000
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||||
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# run dynamics on dense system
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unfix 1
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fix 1 all nve/asphere
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run 2000
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154
examples/USER/openmp/log.gayberne
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154
examples/USER/openmp/log.gayberne
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@ -0,0 +1,154 @@
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LAMMPS (5 Jun 2010-ICMS)
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# GayBerne ellipsoids in LJ background fluid
|
||||
|
||||
units lj
|
||||
atom_style ellipsoid
|
||||
dimension 2
|
||||
|
||||
lattice sq 0.02
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||||
Lattice spacing in x,y,z = 7.07107 7.07107 7.07107
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region box block 0 20 0 20 -0.5 0.5
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create_box 2 box
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Created orthogonal box = (0 0 -3.53553) to (141.421 141.421 3.53553)
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2 by 2 by 1 processor grid
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using 1 OpenMP thread(s) per MPI task
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create_atoms 1 box
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Created 400 atoms
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replicate 3 3 1
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orthogonal box = (0 0 -3.53553) to (424.264 424.264 3.53553)
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2 by 2 by 1 processor grid
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using 1 OpenMP thread(s) per MPI task
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3600 atoms
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set group all type/fraction 2 0.1 95392
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382 settings made for type/fraction
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set group all quat/random 18238
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3600 settings made for quat/random
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mass 1 1.0
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mass 2 1.5
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shape 1 1 1 1
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shape 2 3 1 1
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compute rot all temp/asphere
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group spheroid type 1
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3218 atoms in group spheroid
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variable dof equal count(spheroid)+2
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compute_modify rot extra ${dof}
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compute_modify rot extra 3220
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||||
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velocity all create 2.4 87287 loop geom
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||||
|
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pair_style gayberne 1.0 3.0 1.0 4.0
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pair_coeff 1 1 3.0 1.0 1 1 1 1 1 1 2.5
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||||
pair_coeff 1 2 3.0 1.0 1 1 1 0 0 0
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||||
pair_coeff 2 2 1.0 1.0 1 1 0.2 0 0 0
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||||
|
||||
neighbor 0.8 bin
|
||||
|
||||
thermo_style custom step c_rot epair etotal press vol
|
||||
thermo 100
|
||||
|
||||
timestep 0.002
|
||||
|
||||
fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 mtk no pchain 0 tchain 1
|
||||
fix 2 all enforce2d
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||||
|
||||
compute_modify 1_temp extra ${dof}
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||||
compute_modify 1_temp extra 3220
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||||
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# equilibrate to shrink box around dilute system
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||||
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run 2000
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Memory usage per processor = 0.645947 Mbytes
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||||
Step rot E_pair TotEng Press Volume
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||||
0 2.2790501 0 2.3993333 0.047986667 180000
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100 1.7385816 0 1.83034 0.035611105 185032.85
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200 2.282733 0 2.4032106 0.046625191 185555.45
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300 1.8530281 0 1.9508268 0.042280727 166103.5
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400 2.1732473 -0.00039663481 2.2875495 0.066836437 123148.21
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500 1.9768227 -0.032523061 2.0387898 0.098113886 76256.729
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600 2.1295025 -0.20970907 1.9711811 0.26995376 41865.236
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700 2.0538209 -0.71396939 1.3711589 0.58459861 22568.342
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800 1.9960346 -1.6438808 0.37999866 1.3595401 12919.483
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900 2.0615393 -2.9928048 -0.90393609 2.9751647 8488.1474
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1000 1.5260175 -4.3514083 -2.7937553 2.2262084 6889.8439
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1100 1.9669016 -4.7207436 -2.7002325 2.4253829 6517.7113
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1200 1.9844463 -4.4715412 -2.4359932 0.68793504 6953.1224
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1300 1.9926594 -4.0559518 -2.0101616 0.67339163 7621.2282
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1400 2.0892935 -3.7235706 -1.5789518 0.54011064 8381.9253
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1500 1.9477693 -3.4961143 -1.4922301 0.3669007 9155.7605
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1600 2.0991247 -3.3712141 -1.2168762 0.68465091 9724.9864
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1700 1.9285388 -3.3323179 -1.3568356 0.47737448 10180.027
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1800 2.0531208 -3.2756545 -1.1725408 0.88219585 10337.444
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1900 1.9581701 -3.3531003 -1.3442822 0.65801447 10354.677
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2000 2.0448928 -3.4462555 -1.3500274 0.84823357 10094.487
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Loop time of 3.14099 on 4 procs / 1 threads for 2000 steps with 3600 atoms
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||||
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Pair time (%) = 2.06926 (65.8795)
|
||||
Neigh time (%) = 0.0390816 (1.24425)
|
||||
Comm time (%) = 0.374444 (11.9212)
|
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Outpt time (%) = 0.00085634 (0.0272634)
|
||||
Other time (%) = 0.65734 (20.9278)
|
||||
|
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Nlocal: 900 ave 916 max 888 min
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Histogram: 2 0 0 0 0 0 1 0 0 1
|
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Nghost: 364.5 ave 392 max 329 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 0 2
|
||||
Neighs: 6851.25 ave 7026 max 6596 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 0 2
|
||||
|
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Total # of neighbors = 27405
|
||||
Ave neighs/atom = 7.6125
|
||||
Neighbor list builds = 155
|
||||
Dangerous builds = 91
|
||||
|
||||
# run dynamics on dense system
|
||||
|
||||
unfix 1
|
||||
fix 1 all nve/asphere
|
||||
|
||||
run 2000
|
||||
Memory usage per processor = 2.297 Mbytes
|
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Step rot E_pair TotEng Press Volume
|
||||
2000 2.0448928 -3.4467193 -1.3504912 0.84576603 10094.487
|
||||
2100 2.0269949 -3.4285418 -1.3822491 0.58217253 10094.487
|
||||
2200 2.0209023 -3.4219829 -1.4016426 0.72366811 10094.487
|
||||
2300 2.0290537 -3.4306413 -1.3899401 0.6265438 10094.487
|
||||
2400 2.0152334 -3.4171724 -1.3914066 0.73314698 10094.487
|
||||
2500 2.0118114 -3.4129003 -1.4027286 0.62689434 10094.487
|
||||
2600 2.0248855 -3.4265748 -1.3895509 0.58922076 10094.487
|
||||
2700 2.0298282 -3.4324996 -1.4080333 0.71521499 10094.487
|
||||
2800 2.0110595 -3.4130201 -1.3965702 0.65787113 10094.487
|
||||
2900 1.9914452 -3.3927878 -1.396802 0.6664554 10094.487
|
||||
3000 2.0128138 -3.4138611 -1.3959652 0.67956906 10094.487
|
||||
3100 2.0061095 -3.4061749 -1.4009568 0.45495721 10094.487
|
||||
3200 1.9906076 -3.3903279 -1.3962199 0.65893294 10094.487
|
||||
3300 1.9936044 -3.3934453 -1.3995117 0.56558118 10094.487
|
||||
3400 2.0089532 -3.4103078 -1.4006373 0.70959466 10094.487
|
||||
3500 1.9906165 -3.3912022 -1.3932537 0.60679869 10094.487
|
||||
3600 2.0068678 -3.4081008 -1.3933192 0.61998429 10094.487
|
||||
3700 1.9892563 -3.3903191 -1.3908299 0.72995459 10094.487
|
||||
3800 2.01358 -3.4146248 -1.3998168 0.52853215 10094.487
|
||||
3900 1.9969024 -3.3967408 -1.4012839 0.60586751 10094.487
|
||||
4000 1.9856104 -3.3838355 -1.3961061 0.57959919 10094.487
|
||||
Loop time of 3.19271 on 4 procs / 1 threads for 2000 steps with 3600 atoms
|
||||
|
||||
Pair time (%) = 2.63354 (82.486)
|
||||
Neigh time (%) = 0.0189828 (0.594566)
|
||||
Comm time (%) = 0.24251 (7.59574)
|
||||
Outpt time (%) = 0.000913978 (0.028627)
|
||||
Other time (%) = 0.296766 (9.2951)
|
||||
|
||||
Nlocal: 900 ave 917 max 855 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 3
|
||||
Nghost: 373 ave 411 max 347 min
|
||||
Histogram: 2 0 0 0 0 1 0 0 0 1
|
||||
Neighs: 6869.75 ave 7145 max 6299 min
|
||||
Histogram: 1 0 0 0 0 0 0 1 0 2
|
||||
|
||||
Total # of neighbors = 27479
|
||||
Ave neighs/atom = 7.63306
|
||||
Neighbor list builds = 56
|
||||
Dangerous builds = 0
|
||||
154
examples/USER/openmp/log.gayberne-omp
Normal file
154
examples/USER/openmp/log.gayberne-omp
Normal file
@ -0,0 +1,154 @@
|
||||
LAMMPS (5 Jun 2010-ICMS)
|
||||
# GayBerne ellipsoids in LJ background fluid
|
||||
|
||||
units lj
|
||||
atom_style ellipsoid
|
||||
dimension 2
|
||||
|
||||
lattice sq 0.02
|
||||
Lattice spacing in x,y,z = 7.07107 7.07107 7.07107
|
||||
region box block 0 20 0 20 -0.5 0.5
|
||||
create_box 2 box
|
||||
Created orthogonal box = (0 0 -3.53553) to (141.421 141.421 3.53553)
|
||||
2 by 2 by 1 processor grid
|
||||
using 2 OpenMP thread(s) per MPI task
|
||||
create_atoms 1 box
|
||||
Created 400 atoms
|
||||
|
||||
replicate 3 3 1
|
||||
orthogonal box = (0 0 -3.53553) to (424.264 424.264 3.53553)
|
||||
2 by 2 by 1 processor grid
|
||||
using 2 OpenMP thread(s) per MPI task
|
||||
3600 atoms
|
||||
|
||||
set group all type/fraction 2 0.1 95392
|
||||
382 settings made for type/fraction
|
||||
set group all quat/random 18238
|
||||
3600 settings made for quat/random
|
||||
|
||||
mass 1 1.0
|
||||
mass 2 1.5
|
||||
shape 1 1 1 1
|
||||
shape 2 3 1 1
|
||||
|
||||
compute rot all temp/asphere
|
||||
group spheroid type 1
|
||||
3218 atoms in group spheroid
|
||||
variable dof equal count(spheroid)+2
|
||||
compute_modify rot extra ${dof}
|
||||
compute_modify rot extra 3220
|
||||
|
||||
velocity all create 2.4 87287 loop geom
|
||||
|
||||
pair_style gayberne/omp 1.0 3.0 1.0 4.0
|
||||
pair_coeff 1 1 3.0 1.0 1 1 1 1 1 1 2.5
|
||||
pair_coeff 1 2 3.0 1.0 1 1 1 0 0 0
|
||||
pair_coeff 2 2 1.0 1.0 1 1 0.2 0 0 0
|
||||
|
||||
neighbor 0.8 bin
|
||||
|
||||
thermo_style custom step c_rot epair etotal press vol
|
||||
thermo 100
|
||||
|
||||
timestep 0.002
|
||||
|
||||
fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 mtk no pchain 0 tchain 1
|
||||
fix 2 all enforce2d
|
||||
|
||||
compute_modify 1_temp extra ${dof}
|
||||
compute_modify 1_temp extra 3220
|
||||
|
||||
# equilibrate to shrink box around dilute system
|
||||
|
||||
run 2000
|
||||
Memory usage per processor = 0.646084 Mbytes
|
||||
Step rot E_pair TotEng Press Volume
|
||||
0 2.2790501 0 2.3993333 0.047986667 180000
|
||||
100 1.7385816 0 1.83034 0.035611105 185032.85
|
||||
200 2.282733 0 2.4032106 0.046625191 185555.45
|
||||
300 1.8530281 0 1.9508268 0.042280727 166103.5
|
||||
400 2.1732473 -0.00039663481 2.2875495 0.066836437 123148.21
|
||||
500 1.9768227 -0.032523061 2.0387898 0.098113886 76256.729
|
||||
600 2.1295025 -0.20970907 1.9711811 0.26995376 41865.236
|
||||
700 2.0538209 -0.71396939 1.3711589 0.58459861 22568.342
|
||||
800 1.9960346 -1.6438808 0.37999866 1.3595401 12919.483
|
||||
900 2.0615393 -2.9928048 -0.90393609 2.9751647 8488.1474
|
||||
1000 1.5260175 -4.3514083 -2.7937553 2.2262084 6889.8439
|
||||
1100 1.9669016 -4.7207436 -2.7002325 2.4253829 6517.7113
|
||||
1200 1.9844463 -4.4715412 -2.4359932 0.68793504 6953.1224
|
||||
1300 1.9926594 -4.0559518 -2.0101616 0.67339163 7621.2282
|
||||
1400 2.0892935 -3.7235706 -1.5789518 0.54011064 8381.9253
|
||||
1500 1.9477693 -3.4961143 -1.4922301 0.3669007 9155.7605
|
||||
1600 2.0991247 -3.3712141 -1.2168762 0.68465091 9724.9864
|
||||
1700 1.9285388 -3.3323179 -1.3568356 0.47737448 10180.027
|
||||
1800 2.0531208 -3.2756545 -1.1725408 0.88219585 10337.444
|
||||
1900 1.9581701 -3.3531003 -1.3442822 0.65801447 10354.677
|
||||
2000 2.0448928 -3.4462555 -1.3500274 0.84823357 10094.487
|
||||
Loop time of 2.14434 on 4 procs / 2 threads for 2000 steps with 3600 atoms
|
||||
|
||||
Pair time (%) = 1.19013 (55.5009)
|
||||
Neigh time (%) = 0.0395239 (1.84317)
|
||||
Comm time (%) = 0.248689 (11.5974)
|
||||
Outpt time (%) = 0.000895441 (0.0417583)
|
||||
Other time (%) = 0.665105 (31.0167)
|
||||
|
||||
Nlocal: 900 ave 916 max 888 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
Nghost: 364.5 ave 392 max 329 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 0 2
|
||||
Neighs: 6851.25 ave 7026 max 6596 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 27405
|
||||
Ave neighs/atom = 7.6125
|
||||
Neighbor list builds = 155
|
||||
Dangerous builds = 91
|
||||
|
||||
# run dynamics on dense system
|
||||
|
||||
unfix 1
|
||||
fix 1 all nve/asphere
|
||||
|
||||
run 2000
|
||||
Memory usage per processor = 2.29713 Mbytes
|
||||
Step rot E_pair TotEng Press Volume
|
||||
2000 2.0448928 -3.4467193 -1.3504912 0.84576603 10094.487
|
||||
2100 2.0269949 -3.4285418 -1.3822491 0.58217252 10094.487
|
||||
2200 2.0209023 -3.4219829 -1.4016426 0.72366805 10094.487
|
||||
2300 2.0290537 -3.4306413 -1.3899401 0.62654389 10094.487
|
||||
2400 2.0152334 -3.4171724 -1.3914066 0.73314716 10094.487
|
||||
2500 2.0118114 -3.4129003 -1.4027285 0.62689477 10094.487
|
||||
2600 2.0248859 -3.4265752 -1.3895508 0.58922087 10094.487
|
||||
2700 2.029828 -3.4324996 -1.4080332 0.71521598 10094.487
|
||||
2800 2.0110575 -3.4130179 -1.3965713 0.65787521 10094.487
|
||||
2900 1.9914532 -3.3927964 -1.3968001 0.66640154 10094.487
|
||||
3000 2.0128412 -3.4138772 -1.3959446 0.67947124 10094.487
|
||||
3100 2.0061521 -3.4062053 -1.4009724 0.45478297 10094.487
|
||||
3200 1.9904607 -3.3901444 -1.3962319 0.65899335 10094.487
|
||||
3300 1.9938033 -3.3936534 -1.3995527 0.56503802 10094.487
|
||||
3400 2.0082738 -3.4095729 -1.4008529 0.71165832 10094.487
|
||||
3500 1.9908568 -3.3913902 -1.3928551 0.61048382 10094.487
|
||||
3600 2.0005367 -3.4014022 -1.3926899 0.6428418 10094.487
|
||||
3700 1.9921455 -3.393381 -1.391821 0.73565343 10094.487
|
||||
3800 2.0091321 -3.4097256 -1.4050665 0.56540391 10094.487
|
||||
3900 1.988273 -3.387924 -1.4005785 0.60607058 10094.487
|
||||
4000 1.985544 -3.3831624 -1.3924124 0.63365444 10094.487
|
||||
Loop time of 1.99651 on 4 procs / 2 threads for 2000 steps with 3600 atoms
|
||||
|
||||
Pair time (%) = 1.4547 (72.8619)
|
||||
Neigh time (%) = 0.0191329 (0.958317)
|
||||
Comm time (%) = 0.219553 (10.9968)
|
||||
Outpt time (%) = 0.000929117 (0.046537)
|
||||
Other time (%) = 0.302201 (15.1364)
|
||||
|
||||
Nlocal: 900 ave 917 max 853 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 3
|
||||
Nghost: 370 ave 409 max 347 min
|
||||
Histogram: 2 0 0 0 1 0 0 0 0 1
|
||||
Neighs: 6859 ave 7122 max 6267 min
|
||||
Histogram: 1 0 0 0 0 0 0 1 0 2
|
||||
|
||||
Total # of neighbors = 27436
|
||||
Ave neighs/atom = 7.62111
|
||||
Neighbor list builds = 56
|
||||
Dangerous builds = 0
|
||||
154
examples/USER/openmp/log.resquared
Normal file
154
examples/USER/openmp/log.resquared
Normal file
@ -0,0 +1,154 @@
|
||||
LAMMPS (5 Jun 2010-ICMS)
|
||||
# RESquared ellipsoids in LJ background fluid
|
||||
|
||||
units lj
|
||||
atom_style ellipsoid
|
||||
dimension 2
|
||||
|
||||
lattice sq 0.02
|
||||
Lattice spacing in x,y,z = 7.07107 7.07107 7.07107
|
||||
region box block 0 20 0 20 -0.5 0.5
|
||||
create_box 2 box
|
||||
Created orthogonal box = (0 0 -3.53553) to (141.421 141.421 3.53553)
|
||||
2 by 2 by 1 processor grid
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
create_atoms 1 box
|
||||
Created 400 atoms
|
||||
|
||||
replicate 3 3 1
|
||||
orthogonal box = (0 0 -3.53553) to (424.264 424.264 3.53553)
|
||||
2 by 2 by 1 processor grid
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
3600 atoms
|
||||
|
||||
set group all type/fraction 2 0.1 95392
|
||||
382 settings made for type/fraction
|
||||
set group all quat/random 18238
|
||||
3600 settings made for quat/random
|
||||
|
||||
mass 1 1.0
|
||||
mass 2 1.5
|
||||
shape 1 1 1 1
|
||||
shape 2 3 1 1
|
||||
|
||||
compute rot all temp/asphere
|
||||
group spheroid type 1
|
||||
3218 atoms in group spheroid
|
||||
variable dof equal count(spheroid)+2
|
||||
compute_modify rot extra ${dof}
|
||||
compute_modify rot extra 3220
|
||||
|
||||
velocity all create 2.4 87287 loop geom
|
||||
|
||||
pair_style resquared 4.0
|
||||
pair_coeff 1 1 3.0 1 1 1 1 1 1 1 2.5
|
||||
pair_coeff 1 2 3.0 1 1 1 1 0 0 0
|
||||
pair_coeff 2 2 1.0 1 1 1 0.2 0 0 0
|
||||
|
||||
neighbor 0.8 bin
|
||||
|
||||
thermo_style custom step c_rot epair etotal press vol
|
||||
thermo 100
|
||||
|
||||
timestep 0.002
|
||||
|
||||
fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 mtk no pchain 0 tchain 1
|
||||
fix 2 all enforce2d
|
||||
|
||||
compute_modify 1_temp extra ${dof}
|
||||
compute_modify 1_temp extra 3220
|
||||
|
||||
# equilibrate to shrink box around dilute system
|
||||
|
||||
run 2000
|
||||
Memory usage per processor = 0.645947 Mbytes
|
||||
Step rot E_pair TotEng Press Volume
|
||||
0 2.2790501 0 2.3993333 0.047986667 180000
|
||||
100 1.7385816 0 1.83034 0.035611105 185032.85
|
||||
200 2.282733 0 2.4032106 0.046625191 185555.45
|
||||
300 1.8530281 0 1.9508268 0.042280727 166103.5
|
||||
400 2.1731335 -2.313851e-05 2.2878035 0.066876969 123148.47
|
||||
500 1.9622908 0.013947038 2.062494 0.11049722 76310.663
|
||||
600 2.2320819 0.096431108 2.3728517 0.36222016 42644.861
|
||||
700 1.9873469 0.20556294 2.223516 0.93855891 24703.93
|
||||
800 1.8165136 0.26220013 2.0990306 1.5827057 16573.618
|
||||
900 1.8299002 0.25806293 2.1237335 1.8655977 13758.691
|
||||
1000 1.8351081 0.13940841 2.0148101 1.2225385 14032.478
|
||||
1100 2.1247317 0.11504899 2.289491 1.0084271 16245.87
|
||||
1200 1.843201 0.058058051 1.943255 0.56182272 20274.947
|
||||
1300 2.1985152 0.060475258 2.308348 0.50255726 25219.732
|
||||
1400 1.8696547 0.043856975 1.9539955 0.3388156 29868.883
|
||||
1500 2.1967858 0.056048939 2.2904517 0.38726579 31654.122
|
||||
1600 1.9327245 0.086322935 2.0502392 0.44956627 29641.878
|
||||
1700 2.1264356 0.14158234 2.3040837 0.72123556 24907.385
|
||||
1800 1.9553394 0.1849335 2.1725647 1.0089405 20087.469
|
||||
1900 1.9424308 0.22364918 2.1986115 1.3999132 16638.707
|
||||
2000 1.9616253 0.20908093 2.2108675 1.5037274 14943.206
|
||||
Loop time of 4.99409 on 4 procs / 1 threads for 2000 steps with 3600 atoms
|
||||
|
||||
Pair time (%) = 4.01195 (80.3338)
|
||||
Neigh time (%) = 0.0353667 (0.708171)
|
||||
Comm time (%) = 0.287946 (5.76573)
|
||||
Outpt time (%) = 0.000863671 (0.0172939)
|
||||
Other time (%) = 0.657971 (13.175)
|
||||
|
||||
Nlocal: 900 ave 911 max 890 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
Nghost: 304.75 ave 313 max 293 min
|
||||
Histogram: 1 0 0 0 0 0 1 1 0 1
|
||||
Neighs: 4285.25 ave 4377 max 4188 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 17141
|
||||
Ave neighs/atom = 4.76139
|
||||
Neighbor list builds = 187
|
||||
Dangerous builds = 169
|
||||
|
||||
# run dynamics on dense system
|
||||
|
||||
unfix 1
|
||||
fix 1 all nve/asphere
|
||||
|
||||
run 2000
|
||||
Memory usage per processor = 2.28845 Mbytes
|
||||
Step rot E_pair TotEng Press Volume
|
||||
2000 1.9616253 0.20914316 2.2109297 1.5047014 14943.206
|
||||
2100 2.0057039 0.16278494 2.1718705 1.2700096 14943.206
|
||||
2200 1.9980397 0.17088577 2.1621616 1.3171912 14943.206
|
||||
2300 1.9979868 0.17090993 2.1688603 1.3107273 14943.206
|
||||
2400 1.9970749 0.17187856 2.150187 1.3104588 14943.206
|
||||
2500 1.9720907 0.19817988 2.1623733 1.4411167 14943.206
|
||||
2600 1.9891373 0.18026155 2.1651177 1.3446035 14943.206
|
||||
2700 1.9839479 0.18573287 2.1690366 1.3812779 14943.206
|
||||
2800 1.9836188 0.1860647 2.1552688 1.377763 14943.206
|
||||
2900 1.9989997 0.16989592 2.1578921 1.3063021 14943.206
|
||||
3000 1.9825521 0.18723398 2.1612448 1.3908774 14943.206
|
||||
3100 1.9836833 0.18600871 2.1540026 1.3615215 14943.206
|
||||
3200 2.0100216 0.15826066 2.1760623 1.2701066 14943.206
|
||||
3300 2.0113989 0.15678981 2.1686164 1.2469743 14943.206
|
||||
3400 1.9843957 0.18523915 2.1762238 1.381068 14943.206
|
||||
3500 1.9948424 0.17423946 2.1645209 1.3220473 14943.206
|
||||
3600 1.9927591 0.1764311 2.1736796 1.3422642 14943.206
|
||||
3700 1.9957932 0.17328119 2.1729736 1.3291819 14943.206
|
||||
3800 2.0015543 0.1671867 2.1792764 1.2993991 14943.206
|
||||
3900 1.9810975 0.18876938 2.170916 1.413982 14943.206
|
||||
4000 2.0035557 0.16509517 2.1744066 1.2905003 14943.206
|
||||
Loop time of 8.39471 on 4 procs / 1 threads for 2000 steps with 3600 atoms
|
||||
|
||||
Pair time (%) = 7.67823 (91.4651)
|
||||
Neigh time (%) = 0.0155922 (0.185739)
|
||||
Comm time (%) = 0.392105 (4.67085)
|
||||
Outpt time (%) = 0.000941575 (0.0112163)
|
||||
Other time (%) = 0.307838 (3.66704)
|
||||
|
||||
Nlocal: 900 ave 912 max 891 min
|
||||
Histogram: 1 0 1 0 1 0 0 0 0 1
|
||||
Nghost: 302.5 ave 317 max 281 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 1 1
|
||||
Neighs: 4200 ave 4317 max 4092 min
|
||||
Histogram: 1 1 0 0 0 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 16800
|
||||
Ave neighs/atom = 4.66667
|
||||
Neighbor list builds = 59
|
||||
Dangerous builds = 0
|
||||
154
examples/USER/openmp/log.resquared-omp
Normal file
154
examples/USER/openmp/log.resquared-omp
Normal file
@ -0,0 +1,154 @@
|
||||
LAMMPS (5 Jun 2010-ICMS)
|
||||
# RESquared ellipsoids in LJ background fluid
|
||||
|
||||
units lj
|
||||
atom_style ellipsoid
|
||||
dimension 2
|
||||
|
||||
lattice sq 0.02
|
||||
Lattice spacing in x,y,z = 7.07107 7.07107 7.07107
|
||||
region box block 0 20 0 20 -0.5 0.5
|
||||
create_box 2 box
|
||||
Created orthogonal box = (0 0 -3.53553) to (141.421 141.421 3.53553)
|
||||
2 by 2 by 1 processor grid
|
||||
using 2 OpenMP thread(s) per MPI task
|
||||
create_atoms 1 box
|
||||
Created 400 atoms
|
||||
|
||||
replicate 3 3 1
|
||||
orthogonal box = (0 0 -3.53553) to (424.264 424.264 3.53553)
|
||||
2 by 2 by 1 processor grid
|
||||
using 2 OpenMP thread(s) per MPI task
|
||||
3600 atoms
|
||||
|
||||
set group all type/fraction 2 0.1 95392
|
||||
382 settings made for type/fraction
|
||||
set group all quat/random 18238
|
||||
3600 settings made for quat/random
|
||||
|
||||
mass 1 1.0
|
||||
mass 2 1.5
|
||||
shape 1 1 1 1
|
||||
shape 2 3 1 1
|
||||
|
||||
compute rot all temp/asphere
|
||||
group spheroid type 1
|
||||
3218 atoms in group spheroid
|
||||
variable dof equal count(spheroid)+2
|
||||
compute_modify rot extra ${dof}
|
||||
compute_modify rot extra 3220
|
||||
|
||||
velocity all create 2.4 87287 loop geom
|
||||
|
||||
pair_style resquared/omp 4.0
|
||||
pair_coeff 1 1 3.0 1 1 1 1 1 1 1 2.5
|
||||
pair_coeff 1 2 3.0 1 1 1 1 0 0 0
|
||||
pair_coeff 2 2 1.0 1 1 1 0.2 0 0 0
|
||||
|
||||
neighbor 0.8 bin
|
||||
|
||||
thermo_style custom step c_rot epair etotal press vol
|
||||
thermo 100
|
||||
|
||||
timestep 0.002
|
||||
|
||||
fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 mtk no pchain 0 tchain 1
|
||||
fix 2 all enforce2d
|
||||
|
||||
compute_modify 1_temp extra ${dof}
|
||||
compute_modify 1_temp extra 3220
|
||||
|
||||
# equilibrate to shrink box around dilute system
|
||||
|
||||
run 2000
|
||||
Memory usage per processor = 0.646084 Mbytes
|
||||
Step rot E_pair TotEng Press Volume
|
||||
0 2.2790501 0 2.3993333 0.047986667 180000
|
||||
100 1.7385816 0 1.83034 0.035611105 185032.85
|
||||
200 2.282733 0 2.4032106 0.046625191 185555.45
|
||||
300 1.8530281 0 1.9508268 0.042280727 166103.5
|
||||
400 2.1731335 -2.313851e-05 2.2878035 0.066876969 123148.47
|
||||
500 1.9622908 0.013947038 2.062494 0.11049722 76310.663
|
||||
600 2.2320819 0.096431108 2.3728517 0.36222016 42644.861
|
||||
700 1.9873469 0.20556294 2.223516 0.93855891 24703.93
|
||||
800 1.8165136 0.26220013 2.0990306 1.5827057 16573.618
|
||||
900 1.8299002 0.25806293 2.1237335 1.8655977 13758.691
|
||||
1000 1.8351081 0.13940841 2.0148101 1.2225385 14032.478
|
||||
1100 2.1247317 0.11504899 2.289491 1.0084271 16245.87
|
||||
1200 1.8432012 0.058058132 1.9432553 0.56182309 20274.945
|
||||
1300 2.1985149 0.060475478 2.308348 0.50255823 25219.717
|
||||
1400 1.8696547 0.043856976 1.9539955 0.33881588 29868.856
|
||||
1500 2.1967862 0.056048327 2.2904514 0.38726429 31654.09
|
||||
1600 1.9327243 0.086323548 2.0502399 0.44956875 29641.855
|
||||
1700 2.1264363 0.14158078 2.3040831 0.72123089 24907.377
|
||||
1800 1.9553446 0.1849239 2.1725586 1.0088935 20087.467
|
||||
1900 1.9424319 0.22364759 2.1986105 1.3999089 16638.711
|
||||
2000 1.9616416 0.20906176 2.2108609 1.5036049 14943.246
|
||||
Loop time of 3.03838 on 4 procs / 2 threads for 2000 steps with 3600 atoms
|
||||
|
||||
Pair time (%) = 2.10806 (69.3812)
|
||||
Neigh time (%) = 0.0364012 (1.19805)
|
||||
Comm time (%) = 0.214576 (7.0622)
|
||||
Outpt time (%) = 0.000849783 (0.0279683)
|
||||
Other time (%) = 0.678488 (22.3306)
|
||||
|
||||
Nlocal: 900 ave 911 max 890 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
Nghost: 304.75 ave 313 max 293 min
|
||||
Histogram: 1 0 0 0 0 0 1 1 0 1
|
||||
Neighs: 4285.25 ave 4377 max 4188 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 17141
|
||||
Ave neighs/atom = 4.76139
|
||||
Neighbor list builds = 187
|
||||
Dangerous builds = 169
|
||||
|
||||
# run dynamics on dense system
|
||||
|
||||
unfix 1
|
||||
fix 1 all nve/asphere
|
||||
|
||||
run 2000
|
||||
Memory usage per processor = 2.28859 Mbytes
|
||||
Step rot E_pair TotEng Press Volume
|
||||
2000 1.9616416 0.20912322 2.2109223 1.5045763 14943.246
|
||||
2100 2.0056739 0.16281345 2.1718707 1.2701622 14943.246
|
||||
2200 1.9979805 0.17094563 2.1621065 1.3174229 14943.246
|
||||
2300 1.998095 0.17079204 2.1687366 1.3097813 14943.246
|
||||
2400 1.9972859 0.1716557 2.1500123 1.3085885 14943.246
|
||||
2500 1.9717982 0.19848711 2.1626357 1.4428735 14943.246
|
||||
2600 1.9888439 0.1805667 2.1649648 1.3461098 14943.246
|
||||
2700 1.9830471 0.18667663 2.1695456 1.3888198 14943.246
|
||||
2800 1.9844664 0.18516834 2.1550364 1.3766738 14943.246
|
||||
2900 1.9947186 0.17439299 2.1578716 1.3206593 14943.246
|
||||
3000 1.9831748 0.18658368 2.1615438 1.3886075 14943.246
|
||||
3100 1.9808005 0.18904191 2.1618992 1.3833128 14943.246
|
||||
3200 2.0012172 0.16753249 2.1766451 1.3045381 14943.246
|
||||
3300 2.0086839 0.15959692 2.1616468 1.263515 14943.246
|
||||
3400 1.9818926 0.18785047 2.1802166 1.3948393 14943.246
|
||||
3500 1.9777336 0.19220855 2.1668541 1.4315126 14943.246
|
||||
3600 2.0061526 0.16235145 2.1704547 1.2848861 14943.246
|
||||
3700 1.9958569 0.17320418 2.1780734 1.3479256 14943.246
|
||||
3800 1.9961701 0.172877 2.1610706 1.3390578 14943.246
|
||||
3900 2.0072748 0.16116161 2.1710959 1.2708936 14943.246
|
||||
4000 1.9933491 0.17585496 2.1714753 1.3335569 14943.246
|
||||
Loop time of 4.81095 on 4 procs / 2 threads for 2000 steps with 3600 atoms
|
||||
|
||||
Pair time (%) = 4.05847 (84.3591)
|
||||
Neigh time (%) = 0.0158862 (0.330211)
|
||||
Comm time (%) = 0.421506 (8.76141)
|
||||
Outpt time (%) = 0.00101018 (0.0209975)
|
||||
Other time (%) = 0.314075 (6.52833)
|
||||
|
||||
Nlocal: 900 ave 908 max 893 min
|
||||
Histogram: 1 0 0 1 0 1 0 0 0 1
|
||||
Nghost: 303.5 ave 322 max 283 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Neighs: 4192.25 ave 4306 max 4092 min
|
||||
Histogram: 1 1 0 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 16769
|
||||
Ave neighs/atom = 4.65806
|
||||
Neighbor list builds = 59
|
||||
Dangerous builds = 0
|
||||
Reference in New Issue
Block a user