forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12598 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
06836dc54e
commit
c5ad12114d
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@ -1,27 +0,0 @@
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These example scripts can be run with the USER-CUDA package, assuming
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you built LAMMPS with the package and the precision you want.
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Note that these benchmark problems are identical to those in the
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examples/cuda directory which use the USER-CUDA package.
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You can run any of the scripts as follows. You can also reset the
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x,y,z variables in the command line to change the size of the problem.
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With the USER-CUDA package on 1 GPU:
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lmp_machine -c on -sf cuda < in.cuda.melt.2.5
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lmp_machine -c on -sf cuda -v x 6 -v y 6 -v z 6 < in.cuda.phosphate
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With the USER-CUDA package on 2 GPUs:
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mpirun -np 2 lmp_machine -c on -sf cuda -pk cuda 2 < in.cuda.melt.2.5
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mpirun -np 2 lmp_machine -c on -sf cuda -pk cuda 2 < in.cuda.rhodo
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CPU-only:
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lmp_machine in.cuda.melt.2.5
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mpirun -np 4 lmp_machine < in.cuda.melt.5.0
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mpirun -np 8 lmp_machine -v x 1 -v y 1 -v z 2 < in.cuda.rhodo
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Note that with the USER-CUDA package you must insure the number of MPI
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tasks equals the number of GPUs (both per node).
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File diff suppressed because it is too large
Load Diff
191072
examples/cuda/data.rhodo
191072
examples/cuda/data.rhodo
File diff suppressed because it is too large
Load Diff
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@ -1,31 +0,0 @@
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# 3d Lennard-Jones melt
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variable x index 2
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variable y index 2
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variable z index 2
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variable xx equal 20*$x
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variable yy equal 20*$y
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variable zz equal 20*$z
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units lj
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atom_style atomic
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lattice fcc 0.8442
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region box block 0 ${xx} 0 ${yy} 0 ${zz}
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create_box 1 box
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create_atoms 1 box
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mass 1 1.0
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velocity all create 1.44 87287 loop geom
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pair_style lj/cut 2.5
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pair_coeff 1 1 1.0 1.0 2.5
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neighbor 0.3 bin
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neigh_modify delay 0 every 20 check no
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fix 1 all nve
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thermo 100
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run 1000
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@ -1,31 +0,0 @@
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# 3d Lennard-Jones melt
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variable x index 2
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variable y index 2
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variable z index 2
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variable xx equal 20*$x
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variable yy equal 20*$y
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variable zz equal 20*$z
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units lj
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atom_style atomic
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lattice fcc 0.8442
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region box block 0 ${xx} 0 ${yy} 0 ${zz}
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create_box 1 box
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create_atoms 1 box
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mass 1 1.0
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velocity all create 1.44 87287 loop geom
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pair_style lj/cut 5.0
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pair_coeff 1 1 1.0 1.0 5.0
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neighbor 0.3 bin
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neigh_modify delay 0 every 20 check no
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fix 1 all nve
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thermo 100
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run 1000
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@ -1,31 +0,0 @@
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# GI-System
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variable x index 3
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variable y index 3
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variable z index 3
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units metal
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atom_style charge
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read_data data.phosphate
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replicate $x $y $z
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pair_style lj/cut/coul/long 15.0
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pair_coeff 1 1 0.0 0.29
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pair_coeff 1 2 0.0 0.29
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pair_coeff 1 3 0.000668 2.5738064
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pair_coeff 2 2 0.0 0.29
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pair_coeff 2 3 0.004251 1.91988674
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pair_coeff 3 3 0.012185 2.91706967
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kspace_style pppm 1e-5
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neighbor 2.0 bin
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thermo 100
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timestep 0.001
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fix 1 all npt temp 400 400 0.01 iso 1000.0 1000.0 1.0
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run 200
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@ -1,33 +0,0 @@
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# Rhodopsin model
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variable x index 2
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variable y index 2
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variable z index 2
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units real
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neigh_modify delay 5 every 1
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atom_style full
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bond_style harmonic
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angle_style charmm
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dihedral_style charmm
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improper_style harmonic
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pair_style lj/charmm/coul/long 8.0 10.0
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pair_modify mix arithmetic
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kspace_style pppm 1e-4
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read_data data.rhodo
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replicate $x $y $z
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fix 1 all shake 0.0001 5 0 m 1.0 a 232
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fix 2 all npt temp 300.0 300.0 100.0 &
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z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
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special_bonds charmm
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thermo 100
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thermo_style multi
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timestep 2.0
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run 200
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@ -1,31 +0,0 @@
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These example scripts can be run with the USER-CUDA package, assuming
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you built LAMMPS with the package and the precision you want.
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Note that these benchmark problems are identical to those in the
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examples/gpu directory which use the GPU package.
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You can run any of the scripts as follows. You can also reset the
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x,y,z variables in the command line to change the size of the problem.
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With the GPU package on 1 GPU:
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lmp_machine -sf gpu < in.gpu.melt.2.5
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mpirun -np 8 lmp_machine -sf gpu -v x 6 -v y 6 -v z 6 < in.gpu.phosphate
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With the GPU package on 2 GPUs:
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mpirun -np 4 lmp_machine -sf gpu -pk gpu 2 tpa 8 < in.gpu.melt.5.0
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mpirun -np 12 lmp_machine -sf gpu -pk gpu 2 < in.gpu.rhodo
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CPU-only:
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lmp_machine < in.gpu.melt.2.5
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mpirun -np 4 lmp_machine < in.gpu.melt.5.0
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mpirun -np 8 lmp_machine -v x 1 -v y 1 -v z 2 < in.gpu.rhodo
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Note that with the GPU package you can have more MPI tasks
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than the number of GPUs (both per node).
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Also note that when running the in.gpu.melt.5.0 problem on the GPU,
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which has a long cutoff, the package gpu "tpa" setting should be > 1
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(e.g. 8) for best performance.
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File diff suppressed because it is too large
Load Diff
191072
examples/gpu/data.rhodo
191072
examples/gpu/data.rhodo
File diff suppressed because it is too large
Load Diff
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@ -1,31 +0,0 @@
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# 3d Lennard-Jones melt
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variable x index 2
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variable y index 2
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variable z index 2
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variable xx equal 20*$x
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variable yy equal 20*$y
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variable zz equal 20*$z
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units lj
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atom_style atomic
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lattice fcc 0.8442
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region box block 0 ${xx} 0 ${yy} 0 ${zz}
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create_box 1 box
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create_atoms 1 box
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mass 1 1.0
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velocity all create 1.44 87287 loop geom
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pair_style lj/cut 2.5
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pair_coeff 1 1 1.0 1.0 2.5
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neighbor 0.3 bin
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neigh_modify delay 0 every 20 check no
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fix 1 all nve
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thermo 100
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run 1000
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@ -1,31 +0,0 @@
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# 3d Lennard-Jones melt
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variable x index 2
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variable y index 2
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variable z index 2
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variable xx equal 20*$x
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variable yy equal 20*$y
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variable zz equal 20*$z
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units lj
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atom_style atomic
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lattice fcc 0.8442
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region box block 0 ${xx} 0 ${yy} 0 ${zz}
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create_box 1 box
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create_atoms 1 box
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mass 1 1.0
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velocity all create 1.44 87287 loop geom
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pair_style lj/cut 5.0
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pair_coeff 1 1 1.0 1.0 5.0
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neighbor 0.3 bin
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neigh_modify delay 0 every 20 check no
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fix 1 all nve
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thermo 100
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run 1000
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@ -1,31 +0,0 @@
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# GI-System
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variable x index 3
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variable y index 3
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variable z index 3
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units metal
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atom_style charge
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read_data data.phosphate
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replicate $x $y $z
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pair_style lj/cut/coul/long 15.0
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pair_coeff 1 1 0.0 0.29
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pair_coeff 1 2 0.0 0.29
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pair_coeff 1 3 0.000668 2.5738064
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pair_coeff 2 2 0.0 0.29
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pair_coeff 2 3 0.004251 1.91988674
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pair_coeff 3 3 0.012185 2.91706967
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kspace_style pppm 1e-5
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neighbor 2.0 bin
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thermo 100
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timestep 0.001
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fix 1 all npt temp 400 400 0.01 iso 1000.0 1000.0 1.0
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run 200
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@ -1,33 +0,0 @@
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# Rhodopsin model
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variable x index 2
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variable y index 2
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variable z index 2
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units real
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neigh_modify delay 5 every 1
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atom_style full
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bond_style harmonic
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angle_style charmm
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dihedral_style charmm
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improper_style harmonic
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pair_style lj/charmm/coul/long 8.0 10.0
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pair_modify mix arithmetic
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kspace_style pppm 1e-4
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read_data data.rhodo
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replicate $x $y $z
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fix 1 all shake 0.0001 5 0 m 1.0 a 232
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fix 2 all npt temp 300.0 300.0 100.0 &
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z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
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special_bonds charmm
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thermo 100
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thermo_style multi
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timestep 2.0
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run 200
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@ -1,80 +0,0 @@
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LAMMPS (1 Feb 2014)
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# 3d Lennard-Jones melt
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newton off
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package gpu force/neigh 0 1 1
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variable x index 2
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variable y index 2
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||||
variable z index 2
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variable xx equal 20*$x
|
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variable xx equal 20*2
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variable yy equal 20*$y
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variable yy equal 20*2
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variable zz equal 20*$z
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variable zz equal 20*2
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units lj
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atom_style atomic
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lattice fcc 0.8442
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Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
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region box block 0 ${xx} 0 ${yy} 0 ${zz}
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region box block 0 40 0 ${yy} 0 ${zz}
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region box block 0 40 0 40 0 ${zz}
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region box block 0 40 0 40 0 40
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create_box 1 box
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Created orthogonal box = (0 0 0) to (67.1838 67.1838 67.1838)
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1 by 1 by 1 MPI processor grid
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create_atoms 1 box
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Created 256000 atoms
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mass 1 1.0
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velocity all create 1.44 87287 loop geom
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pair_style lj/cut/gpu 2.5
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pair_coeff 1 1 1.0 1.0 2.5
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|
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neighbor 0.3 bin
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neigh_modify delay 0 every 20 check no
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fix 1 all nve
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|
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thermo 100
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run 1000
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Memory usage per processor = 46.8462 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 1.44 -6.7733683 0 -4.6133768 -5.0196737
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100 0.75865617 -5.760326 0 -4.6223462 0.19586079
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200 0.75643086 -5.7572859 0 -4.6226441 0.22641241
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300 0.74927423 -5.7463997 0 -4.6224927 0.29737707
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400 0.74049393 -5.7329259 0 -4.6221893 0.3776681
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500 0.73092107 -5.7182622 0 -4.6218849 0.46900655
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600 0.72320925 -5.7064076 0 -4.6215979 0.53444495
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700 0.71560947 -5.6946702 0 -4.6212602 0.59905402
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800 0.71306623 -5.6906095 0 -4.6210143 0.62859381
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900 0.70675364 -5.6807352 0 -4.6206089 0.68471945
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1000 0.7044073 -5.6771664 0 -4.6205596 0.70033364
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Loop time of 21.016 on 1 procs for 1000 steps with 256000 atoms
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Pair time (%) = 13.4638 (64.0646)
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Neigh time (%) = 6.74725e-05 (0.000321052)
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Comm time (%) = 1.09447 (5.20779)
|
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Outpt time (%) = 0.0103211 (0.0491108)
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Other time (%) = 6.44732 (30.6781)
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Nlocal: 256000 ave 256000 max 256000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 69917 ave 69917 max 69917 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
|
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Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
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Total # of neighbors = 0
|
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Ave neighs/atom = 0
|
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Neighbor list builds = 50
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Dangerous builds = 0
|
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|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
|
|
@ -1,80 +0,0 @@
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|||
LAMMPS (1 Feb 2014)
|
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# 3d Lennard-Jones melt
|
||||
|
||||
newton off
|
||||
package gpu force/neigh 0 1 1
|
||||
|
||||
variable x index 2
|
||||
variable y index 2
|
||||
variable z index 2
|
||||
|
||||
variable xx equal 20*$x
|
||||
variable xx equal 20*2
|
||||
variable yy equal 20*$y
|
||||
variable yy equal 20*2
|
||||
variable zz equal 20*$z
|
||||
variable zz equal 20*2
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
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lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
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||||
region box block 0 ${xx} 0 ${yy} 0 ${zz}
|
||||
region box block 0 40 0 ${yy} 0 ${zz}
|
||||
region box block 0 40 0 40 0 ${zz}
|
||||
region box block 0 40 0 40 0 40
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (67.1838 67.1838 67.1838)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 256000 atoms
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
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||||
|
||||
pair_style lj/cut/gpu 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 20 check no
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 100
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||||
run 1000
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||||
Memory usage per processor = 14.5208 Mbytes
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Step Temp E_pair E_mol TotEng Press
|
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0 1.44 -6.7733683 0 -4.6133768 -5.0196737
|
||||
100 0.75865617 -5.760326 0 -4.6223462 0.19586079
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||||
200 0.75643087 -5.7572859 0 -4.6226441 0.2264124
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||||
300 0.74927423 -5.7463997 0 -4.6224927 0.29737713
|
||||
400 0.7404939 -5.7329258 0 -4.6221893 0.37766836
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||||
500 0.73092104 -5.7182626 0 -4.6218853 0.46900587
|
||||
600 0.72320865 -5.7064076 0 -4.6215989 0.53444677
|
||||
700 0.71560468 -5.6946635 0 -4.6212607 0.59907258
|
||||
800 0.7130474 -5.6905859 0 -4.621019 0.62875333
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||||
900 0.70683795 -5.680864 0 -4.6206112 0.6839564
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1000 0.70454326 -5.6773491 0 -4.6205384 0.69975744
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||||
Loop time of 8.72938 on 4 procs for 1000 steps with 256000 atoms
|
||||
|
||||
Pair time (%) = 5.30046 (60.7198)
|
||||
Neigh time (%) = 5.78761e-05 (0.000663004)
|
||||
Comm time (%) = 1.62433 (18.6076)
|
||||
Outpt time (%) = 0.0129588 (0.14845)
|
||||
Other time (%) = 1.79157 (20.5235)
|
||||
|
||||
Nlocal: 64000 ave 64066 max 63924 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 0 2
|
||||
Nghost: 30535 ave 30559 max 30518 min
|
||||
Histogram: 1 0 1 0 1 0 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 = 50
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
|
|
@ -1,80 +0,0 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
newton off
|
||||
package gpu force/neigh 0 1 1 threads_per_atom 8
|
||||
|
||||
variable x index 2
|
||||
variable y index 2
|
||||
variable z index 2
|
||||
|
||||
variable xx equal 20*$x
|
||||
variable xx equal 20*2
|
||||
variable yy equal 20*$y
|
||||
variable yy equal 20*2
|
||||
variable zz equal 20*$z
|
||||
variable zz equal 20*2
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 ${xx} 0 ${yy} 0 ${zz}
|
||||
region box block 0 40 0 ${yy} 0 ${zz}
|
||||
region box block 0 40 0 40 0 ${zz}
|
||||
region box block 0 40 0 40 0 40
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (67.1838 67.1838 67.1838)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 256000 atoms
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
pair_style lj/cut/gpu 5.0
|
||||
pair_coeff 1 1 1.0 1.0 5.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 20 check no
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 100
|
||||
run 1000
|
||||
Memory usage per processor = 58.5717 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -7.1616931 0 -5.0017016 -5.6743465
|
||||
100 0.75998441 -6.1430228 0 -5.0030506 -0.43702263
|
||||
200 0.75772859 -6.1397321 0 -5.0031437 -0.40563811
|
||||
300 0.75030002 -6.1286578 0 -5.0032122 -0.33104717
|
||||
400 0.73999054 -6.1132463 0 -5.0032649 -0.24001424
|
||||
500 0.73224838 -6.1016938 0 -5.0033255 -0.16524979
|
||||
600 0.72455889 -6.0902001 0 -5.003366 -0.099949772
|
||||
700 0.71911385 -6.0820798 0 -5.0034133 -0.046759186
|
||||
800 0.71253787 -6.0722342 0 -5.0034316 0.0019671065
|
||||
900 0.70835425 -6.0659819 0 -5.0034546 0.037482543
|
||||
1000 0.70648171 -6.0631852 0 -5.0034668 0.057159495
|
||||
Loop time of 53.1575 on 1 procs for 1000 steps with 256000 atoms
|
||||
|
||||
Pair time (%) = 45.4859 (85.5682)
|
||||
Neigh time (%) = 7.9155e-05 (0.000148907)
|
||||
Comm time (%) = 1.40304 (2.63941)
|
||||
Outpt time (%) = 0.00999498 (0.0188026)
|
||||
Other time (%) = 6.25847 (11.7734)
|
||||
|
||||
Nlocal: 256000 ave 256000 max 256000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 141542 ave 141542 max 141542 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 = 50
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
|
|
@ -1,80 +0,0 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
newton off
|
||||
package gpu force/neigh 0 1 1 threads_per_atom 8
|
||||
|
||||
variable x index 2
|
||||
variable y index 2
|
||||
variable z index 2
|
||||
|
||||
variable xx equal 20*$x
|
||||
variable xx equal 20*2
|
||||
variable yy equal 20*$y
|
||||
variable yy equal 20*2
|
||||
variable zz equal 20*$z
|
||||
variable zz equal 20*2
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 ${xx} 0 ${yy} 0 ${zz}
|
||||
region box block 0 40 0 ${yy} 0 ${zz}
|
||||
region box block 0 40 0 40 0 ${zz}
|
||||
region box block 0 40 0 40 0 40
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (67.1838 67.1838 67.1838)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 256000 atoms
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
pair_style lj/cut/gpu 5.0
|
||||
pair_coeff 1 1 1.0 1.0 5.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 20 check no
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 100
|
||||
run 1000
|
||||
Memory usage per processor = 20.382 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -7.1616931 0 -5.0017016 -5.6743465
|
||||
100 0.75998441 -6.1430228 0 -5.0030506 -0.43702263
|
||||
200 0.75772859 -6.1397321 0 -5.0031437 -0.40563811
|
||||
300 0.75030002 -6.1286578 0 -5.0032122 -0.33104718
|
||||
400 0.73999055 -6.1132463 0 -5.0032649 -0.24001425
|
||||
500 0.73224835 -6.1016938 0 -5.0033256 -0.16524973
|
||||
600 0.72455878 -6.0902 0 -5.0033661 -0.099949172
|
||||
700 0.71911606 -6.0820833 0 -5.0034134 -0.046771469
|
||||
800 0.71253754 -6.0722337 0 -5.0034316 0.0019725827
|
||||
900 0.70832904 -6.0659437 0 -5.0034543 0.03758241
|
||||
1000 0.70634002 -6.062973 0 -5.0034671 0.057951142
|
||||
Loop time of 26.0448 on 4 procs for 1000 steps with 256000 atoms
|
||||
|
||||
Pair time (%) = 18.6673 (71.674)
|
||||
Neigh time (%) = 6.55651e-05 (0.00025174)
|
||||
Comm time (%) = 5.797 (22.2578)
|
||||
Outpt time (%) = 0.0719919 (0.276416)
|
||||
Other time (%) = 1.50839 (5.79152)
|
||||
|
||||
Nlocal: 64000 ave 64092 max 63823 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||
Nghost: 64384.2 ave 64490 max 64211 min
|
||||
Histogram: 1 0 0 0 0 0 1 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
|
||||
Neighbor list builds = 50
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
|
|
@ -1,80 +0,0 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# GI-System
|
||||
|
||||
units metal
|
||||
newton off
|
||||
package gpu force/neigh 0 1 1
|
||||
|
||||
atom_style charge
|
||||
read_data data.phosphate
|
||||
orthogonal box = (33.0201 33.0201 33.0201) to (86.9799 86.9799 86.9799)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
10950 atoms
|
||||
reading velocities ...
|
||||
10950 velocities
|
||||
|
||||
replicate 3 3 3
|
||||
orthogonal box = (33.0201 33.0201 33.0201) to (194.899 194.899 194.899)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
295650 atoms
|
||||
|
||||
pair_style lj/cut/coul/long/gpu 15.0
|
||||
|
||||
pair_coeff 1 1 0.0 0.29
|
||||
pair_coeff 1 2 0.0 0.29
|
||||
pair_coeff 1 3 0.000668 2.5738064
|
||||
pair_coeff 2 2 0.0 0.29
|
||||
pair_coeff 2 3 0.004251 1.91988674
|
||||
pair_coeff 3 3 0.012185 2.91706967
|
||||
|
||||
kspace_style pppm/gpu 1e-5
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
thermo 100
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 all npt temp 400 400 0.01 iso 1000.0 1000.0 1.0
|
||||
run 200
|
||||
PPPM initialization ...
|
||||
G vector (1/distance) = 0.210051
|
||||
grid = 108 108 108
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.000178801
|
||||
estimated relative force accuracy = 1.24171e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 1520875 1259712
|
||||
Memory usage per processor = 266.927 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 400.30257 -2381941.6 0 -2366643.8 -449.96842 4242016.4
|
||||
100 411.69681 -2392428.5 0 -2376695.3 7046.698 4308883.5
|
||||
200 401.28392 -2394152.5 0 -2378817.2 3243.2685 4334284.4
|
||||
Loop time of 154.943 on 1 procs for 200 steps with 295650 atoms
|
||||
|
||||
Pair time (%) = 12.0178 (7.75625)
|
||||
Kspce time (%) = 80.3771 (51.8753)
|
||||
Neigh time (%) = 0.0138304 (0.00892614)
|
||||
Comm time (%) = 0.348981 (0.225232)
|
||||
Outpt time (%) = 0.00180006 (0.00116176)
|
||||
Other time (%) = 62.1834 (40.1331)
|
||||
|
||||
FFT time (% of Kspce) = 56.9885 (70.9013)
|
||||
FFT Gflps 3d (1d only) = 1.24196 3.00739
|
||||
|
||||
Nlocal: 295650 ave 295650 max 295650 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 226982 ave 226982 max 226982 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 = 6
|
||||
Dangerous builds = 0
|
||||
unfix 1
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
|
|
@ -1,80 +0,0 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# GI-System
|
||||
|
||||
units metal
|
||||
newton off
|
||||
package gpu force/neigh 0 1 1
|
||||
|
||||
atom_style charge
|
||||
read_data data.phosphate
|
||||
orthogonal box = (33.0201 33.0201 33.0201) to (86.9799 86.9799 86.9799)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
10950 atoms
|
||||
reading velocities ...
|
||||
10950 velocities
|
||||
|
||||
replicate 3 3 3
|
||||
orthogonal box = (33.0201 33.0201 33.0201) to (194.899 194.899 194.899)
|
||||
2 by 1 by 2 MPI processor grid
|
||||
295650 atoms
|
||||
|
||||
pair_style lj/cut/coul/long/gpu 15.0
|
||||
|
||||
pair_coeff 1 1 0.0 0.29
|
||||
pair_coeff 1 2 0.0 0.29
|
||||
pair_coeff 1 3 0.000668 2.5738064
|
||||
pair_coeff 2 2 0.0 0.29
|
||||
pair_coeff 2 3 0.004251 1.91988674
|
||||
pair_coeff 3 3 0.012185 2.91706967
|
||||
|
||||
kspace_style pppm/gpu 1e-5
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
thermo 100
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 all npt temp 400 400 0.01 iso 1000.0 1000.0 1.0
|
||||
run 200
|
||||
PPPM initialization ...
|
||||
G vector (1/distance) = 0.210051
|
||||
grid = 108 108 108
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.000178801
|
||||
estimated relative force accuracy = 1.24171e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 427915 314928
|
||||
Memory usage per processor = 80.0769 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 400.30257 -2381941.6 0 -2366643.8 -449.96842 4242016.4
|
||||
100 411.69681 -2392428.5 0 -2376695.3 7046.698 4308883.5
|
||||
200 401.28392 -2394152.5 0 -2378817.2 3243.2685 4334284.4
|
||||
Loop time of 56.1151 on 4 procs for 200 steps with 295650 atoms
|
||||
|
||||
Pair time (%) = 4.55937 (8.12503)
|
||||
Kspce time (%) = 34.5442 (61.5596)
|
||||
Neigh time (%) = 0.00624901 (0.0111361)
|
||||
Comm time (%) = 0.470437 (0.838343)
|
||||
Outpt time (%) = 0.000446558 (0.000795789)
|
||||
Other time (%) = 16.5344 (29.4651)
|
||||
|
||||
FFT time (% of Kspce) = 22.6526 (65.5758)
|
||||
FFT Gflps 3d (1d only) = 3.12448 11.5533
|
||||
|
||||
Nlocal: 73912.5 ave 74223 max 73638 min
|
||||
Histogram: 1 1 0 0 0 0 0 1 0 1
|
||||
Nghost: 105257 ave 105797 max 104698 min
|
||||
Histogram: 1 0 0 1 0 0 1 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 = 6
|
||||
Dangerous builds = 0
|
||||
unfix 1
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
|
|
@ -1,135 +0,0 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# Rhodopsin model
|
||||
|
||||
newton off
|
||||
package gpu force/neigh 0 1 1
|
||||
|
||||
variable x index 2
|
||||
variable y index 2
|
||||
variable z index 2
|
||||
|
||||
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/gpu 8.0 10.0
|
||||
pair_modify mix arithmetic
|
||||
kspace_style pppm/gpu 1e-4
|
||||
|
||||
read_data data.rhodo
|
||||
orthogonal box = (-27.5 -38.5 -36.2676) to (27.5 38.5 36.2645)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
32000 atoms
|
||||
reading velocities ...
|
||||
32000 velocities
|
||||
scanning bonds ...
|
||||
4 = max bonds/atom
|
||||
scanning angles ...
|
||||
18 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
40 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
4 = max impropers/atom
|
||||
reading bonds ...
|
||||
27723 bonds
|
||||
reading angles ...
|
||||
40467 angles
|
||||
reading dihedrals ...
|
||||
56829 dihedrals
|
||||
reading impropers ...
|
||||
1034 impropers
|
||||
4 = max # of 1-2 neighbors
|
||||
12 = max # of 1-3 neighbors
|
||||
24 = max # of 1-4 neighbors
|
||||
26 = max # of special neighbors
|
||||
|
||||
replicate $x $y $z
|
||||
replicate 2 $y $z
|
||||
replicate 2 2 $z
|
||||
replicate 2 2 2
|
||||
orthogonal box = (-27.5 -38.5 -36.2676) to (82.5 115.5 108.797)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
256000 atoms
|
||||
221784 bonds
|
||||
323736 angles
|
||||
454632 dihedrals
|
||||
8272 impropers
|
||||
4 = max # of 1-2 neighbors
|
||||
12 = max # of 1-3 neighbors
|
||||
24 = max # of 1-4 neighbors
|
||||
26 = max # of special neighbors
|
||||
|
||||
fix 1 all shake 0.0001 5 0 m 1.0 a 232
|
||||
12936 = # of size 2 clusters
|
||||
29064 = # of size 3 clusters
|
||||
5976 = # of size 4 clusters
|
||||
33864 = # of frozen angles
|
||||
fix 2 all npt temp 300.0 300.0 100.0 z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
|
||||
|
||||
special_bonds charmm
|
||||
|
||||
thermo 100
|
||||
thermo_style multi
|
||||
timestep 2.0
|
||||
|
||||
run 200
|
||||
PPPM initialization ...
|
||||
G vector (1/distance) = 0.245959
|
||||
grid = 48 64 60
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0410392
|
||||
estimated relative force accuracy = 0.000123588
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 237705 184320
|
||||
Memory usage per processor = 760.048 Mbytes
|
||||
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
|
||||
TotEng = 157024.0504 KinEng = 172792.6155 Temp = 301.1796
|
||||
PotEng = -15768.5651 E_bond = 28164.9917 E_angle = 117224.0742
|
||||
E_dihed = 61174.8491 E_impro = 3752.0273 E_vdwl = 10108.6323
|
||||
E_coul = 1894295.6635 E_long = -2130488.8032 Press = 9562.1557
|
||||
Volume = 2457390.7959
|
||||
---------------- Step 100 ----- CPU = 36.3779 (sec) ----------------
|
||||
TotEng = -233301.6813 KinEng = 123222.9259 Temp = 214.7790
|
||||
PotEng = -356524.6072 E_bond = 13098.4672 E_angle = 56766.9111
|
||||
E_dihed = 45556.8240 E_impro = 1313.9378 E_vdwl = -40863.9278
|
||||
E_coul = 1705084.7672 E_long = -2137481.5867 Press = -1634.3912
|
||||
Volume = 2522232.6302
|
||||
---------------- Step 200 ----- CPU = 70.7784 (sec) ----------------
|
||||
TotEng = -308342.0030 KinEng = 108937.4160 Temp = 189.8792
|
||||
PotEng = -417279.4189 E_bond = 9579.0134 E_angle = 47373.6274
|
||||
E_dihed = 39847.4817 E_impro = 967.6755 E_vdwl = -23635.2960
|
||||
E_coul = 1646633.4711 E_long = -2138045.3918 Press = -1185.9327
|
||||
Volume = 2554683.1533
|
||||
Loop time of 70.7784 on 1 procs for 200 steps with 256000 atoms
|
||||
|
||||
Pair time (%) = 10.0374 (14.1815)
|
||||
Bond time (%) = 27.2471 (38.4963)
|
||||
Kspce time (%) = 7.19169 (10.1608)
|
||||
Neigh time (%) = 5.43951 (7.68527)
|
||||
Comm time (%) = 0.681534 (0.962912)
|
||||
Outpt time (%) = 0.00139809 (0.0019753)
|
||||
Other time (%) = 20.1798 (28.5112)
|
||||
|
||||
FFT time (% of Kspce) = 5.17983 (72.0253)
|
||||
FFT Gflps 3d (1d only) = 1.72575 2.95071
|
||||
|
||||
Nlocal: 256000 ave 256000 max 256000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 161662 ave 161662 max 161662 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
|
||||
Ave special neighs/atom = 7.43187
|
||||
Neighbor list builds = 31
|
||||
Dangerous builds = 12
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
|
|
@ -1,135 +0,0 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# Rhodopsin model
|
||||
|
||||
newton off
|
||||
package gpu force/neigh 0 1 1
|
||||
|
||||
variable x index 2
|
||||
variable y index 2
|
||||
variable z index 2
|
||||
|
||||
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/gpu 8.0 10.0
|
||||
pair_modify mix arithmetic
|
||||
kspace_style pppm/gpu 1e-4
|
||||
|
||||
read_data data.rhodo
|
||||
orthogonal box = (-27.5 -38.5 -36.2676) to (27.5 38.5 36.2645)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
32000 atoms
|
||||
reading velocities ...
|
||||
32000 velocities
|
||||
scanning bonds ...
|
||||
4 = max bonds/atom
|
||||
scanning angles ...
|
||||
18 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
40 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
4 = max impropers/atom
|
||||
reading bonds ...
|
||||
27723 bonds
|
||||
reading angles ...
|
||||
40467 angles
|
||||
reading dihedrals ...
|
||||
56829 dihedrals
|
||||
reading impropers ...
|
||||
1034 impropers
|
||||
4 = max # of 1-2 neighbors
|
||||
12 = max # of 1-3 neighbors
|
||||
24 = max # of 1-4 neighbors
|
||||
26 = max # of special neighbors
|
||||
|
||||
replicate $x $y $z
|
||||
replicate 2 $y $z
|
||||
replicate 2 2 $z
|
||||
replicate 2 2 2
|
||||
orthogonal box = (-27.5 -38.5 -36.2676) to (82.5 115.5 108.797)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
256000 atoms
|
||||
221784 bonds
|
||||
323736 angles
|
||||
454632 dihedrals
|
||||
8272 impropers
|
||||
4 = max # of 1-2 neighbors
|
||||
12 = max # of 1-3 neighbors
|
||||
24 = max # of 1-4 neighbors
|
||||
26 = max # of special neighbors
|
||||
|
||||
fix 1 all shake 0.0001 5 0 m 1.0 a 232
|
||||
12936 = # of size 2 clusters
|
||||
29064 = # of size 3 clusters
|
||||
5976 = # of size 4 clusters
|
||||
33864 = # of frozen angles
|
||||
fix 2 all npt temp 300.0 300.0 100.0 z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
|
||||
|
||||
special_bonds charmm
|
||||
|
||||
thermo 100
|
||||
thermo_style multi
|
||||
timestep 2.0
|
||||
|
||||
run 200
|
||||
PPPM initialization ...
|
||||
G vector (1/distance) = 0.245959
|
||||
grid = 48 64 60
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0410392
|
||||
estimated relative force accuracy = 0.000123588
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 68635 46080
|
||||
Memory usage per processor = 250.358 Mbytes
|
||||
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
|
||||
TotEng = 157024.0504 KinEng = 172792.6155 Temp = 301.1796
|
||||
PotEng = -15768.5651 E_bond = 28164.9917 E_angle = 117224.0742
|
||||
E_dihed = 61174.8491 E_impro = 3752.0273 E_vdwl = 10108.6323
|
||||
E_coul = 1894295.6635 E_long = -2130488.8032 Press = 9562.1557
|
||||
Volume = 2457390.7959
|
||||
---------------- Step 100 ----- CPU = 12.3409 (sec) ----------------
|
||||
TotEng = -233301.6797 KinEng = 123222.9259 Temp = 214.7790
|
||||
PotEng = -356524.6057 E_bond = 13098.4672 E_angle = 56766.9111
|
||||
E_dihed = 45556.8240 E_impro = 1313.9378 E_vdwl = -40863.9278
|
||||
E_coul = 1705084.7688 E_long = -2137481.5867 Press = -1634.3910
|
||||
Volume = 2522232.6302
|
||||
---------------- Step 200 ----- CPU = 23.6590 (sec) ----------------
|
||||
TotEng = -308341.9699 KinEng = 108937.4196 Temp = 189.8792
|
||||
PotEng = -417279.3895 E_bond = 9579.0134 E_angle = 47373.6274
|
||||
E_dihed = 39847.4807 E_impro = 967.6755 E_vdwl = -23635.2996
|
||||
E_coul = 1646633.5046 E_long = -2138045.3916 Press = -1185.9299
|
||||
Volume = 2554683.1519
|
||||
Loop time of 23.6591 on 4 procs for 200 steps with 256000 atoms
|
||||
|
||||
Pair time (%) = 4.81669 (20.3587)
|
||||
Bond time (%) = 6.52579 (27.5826)
|
||||
Kspce time (%) = 4.48765 (18.968)
|
||||
Neigh time (%) = 1.3238 (5.5953)
|
||||
Comm time (%) = 0.490551 (2.07342)
|
||||
Outpt time (%) = 0.000454485 (0.00192098)
|
||||
Other time (%) = 6.01414 (25.42)
|
||||
|
||||
FFT time (% of Kspce) = 1.77734 (39.6051)
|
||||
FFT Gflps 3d (1d only) = 5.02949 11.6654
|
||||
|
||||
Nlocal: 64000 ave 64001 max 63999 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Nghost: 70656.5 ave 70660 max 70654 min
|
||||
Histogram: 1 0 0 2 0 0 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
|
||||
Ave special neighs/atom = 7.43187
|
||||
Neighbor list builds = 31
|
||||
Dangerous builds = 12
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Loading…
Reference in New Issue