git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12494 f3b2605a-c512-4ea7-a41b-209d697bcdaa

examples/README

@@ -63,6 +63,7 @@ body:     body particles, 2d system
 colloid:  big colloid particles in a small particle solvent, 2d system
 comb:	  models using the COMB potential
 crack:	  crack propagation in a 2d solid
+cuda:     use of the USER-CUDA package for GPU acceleration
 deposit:  deposition of atoms and molecules onto a 3d substrate
 dipole:   point dipolar particles, 2d system
 dreiding: methanol via Dreiding FF

examples/USER/cuda/in.melt_2.5.cuda

@@ -1,34 +0,0 @@
-# 3d Lennard-Jones melt
-
-package         cuda gpu/node 2
-newton          off
-
-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/USER/cuda/in.melt_5.0.cuda

@@ -1,34 +0,0 @@
-# 3d Lennard-Jones melt
-
-package 	cuda gpu/node 2
-newton 	        off
-
-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/USER/cuda/in.phosphate.cuda

@@ -1,32 +0,0 @@
-# GI-System
-
-package 	cuda 
-units metal
-newton off
-atom_style      charge 
-
-read_data 	data.phosphate
-
-replicate 	3 3 3
-
-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/cuda 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
-unfix 1
-

examples/USER/cuda/in.rhodo.cuda

@@ -1,34 +0,0 @@
-# Rhodopsin model
-
-package		cuda gpu/node 2 
-
-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/cuda 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

examples/gpu/README

@@ -1,13 +1,16 @@
 These example scripts can be run with the USER-CUDA package, assuming
 you built LAMMPS with the package and the precision you want.
 
+Note that these benchmark problems are identical to those in the
+examples/gpu directory which use the GPU 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 the GPU package on 1 GPU:
 
 lmp_machine -sf gpu < in.gpu.melt.2.5
-mpirun -np 8 lmp_machine -sf gpu < in.gpu.phosphate
+mpirun -np 8 lmp_machine -sf gpu -v x 6 -v y 6 -v z 6 < in.gpu.phosphate
 
 With the GPU package on 2 GPUs:
 
@@ -18,7 +21,7 @@ CPU-only:
 
 lmp_machine < in.gpu.melt.2.5
 mpirun -np 4 lmp_machine < in.gpu.melt.5.0
-mpirun -np 8 lmp_machine < in.gpu.rhodo
+mpirun -np 8 lmp_machine -v x 1 -v y 1 -v z 2 < in.gpu.rhodo
 
 Note that with the GPU package you can have more MPI tasks
 than the number of GPUs (both per node).

examples/gpu/in.gpu.phosphate

@@ -1,11 +1,15 @@
 # GI-System
 
-units metal
+variable	x index 3
+variable	y index 3
+variable	z index 3
 
+units metal
 atom_style      charge 
+
 read_data 	data.phosphate
 
-replicate 	3 3 3
+replicate	$x $y $z
 
 pair_style      lj/cut/coul/long 15.0
 
@@ -20,9 +24,8 @@ kspace_style    pppm 1e-5
 
 neighbor	2.0 bin
 
-thermo 100
-
-timestep 0.001
+thermo          100
+timestep        0.001
 
 fix 		1 all npt temp 400 400 0.01 iso 1000.0 1000.0 1.0
 run 		200