diff --git a/examples/friction/in.friction b/examples/friction/in.friction
index dcc2247a1..f62e42236 100644
--- a/examples/friction/in.friction
+++ b/examples/friction/in.friction
@@ -1,80 +1,80 @@
 # 2d friction simulation
 
 dimension	2
 boundary	p s p
 
 atom_style	atomic
 neighbor	0.3 bin
 neigh_modify	delay 5
 
 # create geometry
 
 lattice		hex 0.9
 region		box block 0 50 0 22 -0.25 0.25
 create_box	4 box
 
 mass		1 1.0
 mass		2 1.0
 mass		3 1.0
 mass		4 1.0
 
 # atom regions
 
 region          lo-fixed block INF INF INF 1.1 INF INF
 region          lo-slab block INF INF INF 7 INF INF
 region          above-lo block INF INF INF 7 INF INF side out
 region          hi-fixed block INF INF 20.9 INF INF INF
 region          hi-slab block INF INF 15 INF INF INF
 region          below-hi block INF INF 15 INF INF INF side out
 region		lo-asperity sphere 32 7 0 8
 region		hi-asperity sphere 18 15 0 8
 region		lo-half-sphere intersect 2 lo-asperity above-lo
 region		hi-half-sphere intersect 2 hi-asperity below-hi
 
 # create 2 surfaces with asperities
 
-create_atoms	1 lo-slab
-create_atoms	1 hi-slab
-create_atoms	2 lo-half-sphere
-create_atoms	3 hi-half-sphere
+create_atoms	1 region lo-slab
+create_atoms	1 region hi-slab
+create_atoms	2 region lo-half-sphere
+create_atoms	3 region hi-half-sphere
 
 # LJ potentials
 
 pair_style	lj/cut 2.5
 pair_coeff	* * 1.0 1.0 2.5
 
 # define groups
 
 group	        lo region lo-slab
 group		lo type 2
 group		hi region hi-slab
 group		hi type 3
 group		lo-fixed region lo-fixed
 group		hi-fixed region hi-fixed
 group		boundary union lo-fixed hi-fixed
 group		mobile subtract all boundary
 
 set		lo-fixed atom 4
 set		hi-fixed atom 4
 
 # initial velocities
 
 temperature     new mobile partial 0 1 0
 velocity	mobile create 0.1 482748 temp new
 velocity	hi set 1.0 0.0 0.0 sum yes
 
 # fixes
 
 fix		1 all nve
 fix		2 boundary setforce 0.0 0.0 0.0
 fix		3 mobile temp/rescale 200 0.1 0.1 0.02 1.0
 fix_modify	3 temp new
 
 # Run
 
 timestep	0.0025
 thermo		1000
 thermo_modify	temp new
 
 dump		1 all atom 100 dump.friction
 run		20000
diff --git a/examples/shear/in.shear b/examples/shear/in.shear
index 617518a77..21d88148e 100644
--- a/examples/shear/in.shear
+++ b/examples/shear/in.shear
@@ -1,72 +1,70 @@
 # 3d metal shear simulation
 
 units		metal
 boundary	s s p
 
 atom_style	atomic
 lattice		fcc 3.52
 region		box block 0 16.0 0 10.0 0 2.828427
 create_box	3 box
 
-orient		x 1 0 0 
-orient		y 0 1 1
-orient		z 0 -1 1
-origin		0.5 0 0 
+lattice		fcc 3.52 orient	x 1 0 0 orient y 0 1 1 orient z 0 -1 1 &
+		origin 0.5 0 0 
 create_atoms	1
 
 pair_style	eam
 pair_coeff	* * niu3.eam
 
 neighbor	0.3 bin
 neigh_modify	delay 5
 
-region		lower block INF INF INF 1.4 INF INF
-region		upper block INF INF 8.6 INF INF INF
+region		lower block INF INF INF 0.9 INF INF
+region		upper block INF INF 6.1 INF INF INF
 group		lower region lower
 group		upper region upper
 group		boundary union lower upper
 group		mobile subtract all boundary
 
 set		lower atom 2
 set		upper atom 3
 
 # void
 
 #region		void cylinder z 8 5 2.5 INF INF
 #delete_atoms	region void
 
 # temp controllers
 
 temperature	new3d mobile full
 temperature	new2d mobile partial 0 1 1
 
 # equilibrate
 
 velocity	mobile create 300.0 5812775 temp new3d
 fix		1 all nve
 fix		2 boundary setforce 0.0 0.0 0.0
 
 fix		3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
 fix_modify	3 temp new3d
 
 thermo		25
 thermo_modify	temp new3d
 
 timestep	0.001
 run		100
 
 # shear
 
 velocity	upper set 1.0 0 0
 velocity	mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes
 
 unfix		3
 fix		3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
 fix_modify	3 temp new2d
 
 dump		1 all atom 10 dump.shear
 thermo		100
 thermo_modify	temp new2d
 
 reset_timestep	0
 run		3000
diff --git a/examples/shear/in.shear.void b/examples/shear/in.shear.void
index 9900a7809..75e7a231a 100644
--- a/examples/shear/in.shear.void
+++ b/examples/shear/in.shear.void
@@ -1,72 +1,70 @@
 # 3d metal shear simulation
 
 units		metal
 boundary	s s p
 
 atom_style	atomic
 lattice		fcc 3.52
 region		box block 0 16.0 0 10.0 0 2.828427
 create_box	3 box
 
-orient		x 1 0 0 
-orient		y 0 1 1
-orient		z 0 -1 1
-origin		0.5 0 0 
+lattice		fcc 3.52 orient	x 1 0 0 orient y 0 1 1 orient z 0 -1 1 &
+		origin 0.5 0 0 
 create_atoms	1
 
 pair_style	eam
 pair_coeff	* * niu3.eam
 
 neighbor	0.3 bin
 neigh_modify	delay 5
 
-region		lower block INF INF INF 1.4 INF INF
-region		upper block INF INF 8.6 INF INF INF
+region		lower block INF INF INF 0.9 INF INF
+region		upper block INF INF 6.1 INF INF INF
 group		lower region lower
 group		upper region upper
 group		boundary union lower upper
 group		mobile subtract all boundary
 
 set		lower atom 2
 set		upper atom 3
 
 # void
 
-region		void cylinder z 8 5 2.5 INF INF
+region		void cylinder z 8 3.535534 2.5 INF INF
 delete_atoms	region void
 
 # temp controllers
 
 temperature	new3d mobile full
 temperature	new2d mobile partial 0 1 1
 
 # equilibrate
 
 velocity	mobile create 300.0 5812775 temp new3d
 fix		1 all nve
 fix		2 boundary setforce 0.0 0.0 0.0
 
 fix		3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
 fix_modify	3 temp new3d
 
 thermo		25
 thermo_modify	temp new3d
 
 timestep	0.001
 run		100
 
 # shear
 
 velocity	upper set 1.0 0 0
 velocity	mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes
 
 unfix		3
 fix		3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
 fix_modify	3 temp new2d
 
 dump		1 all atom 10 dump.shear
 thermo		100
 thermo_modify	temp new2d
 
 reset_timestep	0
 run		3000