git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12491 f3b2605a-c512-4ea7-a41b-209d697bcdaa

examples/cuda/README

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+These example scripts can be run with the USER-CUDA
+package, assuming you built LAMMPS with the package.
+
+You can run any of the scripts as follows.  You can also reset the
+x,y,z variables in the command line to change the size of the problem.
+
+With USER-CUDA on 1 GPU:
+
+lmp_machine -c on -sf cuda < in.cuda.melt.2.5
+lmp_machine -c on -sf cuda < in.cuda.phosphate
+
+With USER-CUDA on 2 GPUs:
+
+mpirun -np 2 lmp_machine -c on -sf cuda -pk cuda 2 < in.cuda.melt.2.5
+mpirun -np 2 lmp_machine -c on -sf cuda -pk cuda 2 < in.cuda.rhodo
+
+CPU-only:
+
+lmp_machine in.cuda.melt.2.5
+mpirun -np 4 lmp_machine < in.cuda.melt.5.0
+mpirun -np 8 lmp_machine < in.cuda.rhodo

examples/cuda/in.cuda.melt.2.5

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+# 3d Lennard-Jones melt
+
+variable	x index 2
+variable	y index 2
+variable	z index 2
+
+variable	xx equal 20*$x
+variable	yy equal 20*$y
+variable	zz equal 20*$z
+
+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
+
+velocity	all create 1.44 87287 loop geom
+
+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
+
+fix		1 all nve
+
+thermo 100
+run		5000

examples/cuda/in.cuda.melt.5.0

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+# 3d Lennard-Jones melt
+
+variable	x index 2
+variable	y index 2
+variable	z index 2
+
+variable	xx equal 20*$x
+variable	yy equal 20*$y
+variable	zz equal 20*$z
+
+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
+
+velocity	all create 1.44 87287 loop geom
+
+pair_style	lj/cut 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		5000

examples/cuda/in.cuda.phosphate

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+# GI-System
+
+variable	x index 3
+variable	y index 3
+variable	z index 3
+
+units metal
+atom_style      charge 
+
+read_data 	data.phosphate
+
+replicate	$x $y $z
+
+pair_style      lj/cut/coul/long 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 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 1000
+

examples/cuda/in.cuda.rhodo

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+# Rhodopsin model
+
+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 8.0 10.0 
+pair_modify     mix arithmetic 
+kspace_style    pppm 1e-4 
+
+read_data       data.rhodo
+
+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
+special_bonds   charmm
+ 
+thermo          100
+thermo_style    multi 
+timestep        2.0
+
+run		1000