git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11164 f3b2605a-c512-4ea7-a41b-209d697bcdaa

examples/deposit/in.deposit.molecule.shake

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+# sample surface deposition script for molecules
+
+units		lj
+atom_style      bond
+boundary        p p f
+
+lattice		fcc 1.0
+region          box block 0 5 0 5 0 10
+create_box      3 box "bond types" 1 "extra bond per atom" 1
+
+region		substrate block INF INF INF INF INF 3
+create_atoms	1 region substrate
+
+pair_style	lj/cut 2.5
+pair_coeff	* * 1.0 1.0
+pair_coeff	1 2 1.0 1.0 5.0
+mass		* 1.0
+
+bond_style	harmonic
+bond_coeff      1 5.0 1.0
+
+neigh_modify	delay 0
+
+group		addatoms type 2
+region          mobile block 0 5 0 5 2 INF
+group		mobile region mobile
+
+compute		add addatoms temp
+compute_modify	add dynamic yes extra 0
+
+fix		1 addatoms nve
+fix		2 mobile langevin 0.1 0.1 0.1 587283
+fix		3 mobile nve
+
+molecule        dimer molecule.dimer.shake
+region          slab block 0 5 0 5 8 9
+fix		4 addatoms deposit 100 0 100 12345 region slab near 1.0 &
+                mol dimer vz -1.0 -1.0 shake 6
+fix		5 addatoms wall/reflect zhi EDGE
+fix             6 all shake 0.0001 20 1000 b 1 mol dimer
+
+thermo_style	custom step atoms temp epair etotal press
+thermo          100
+thermo_modify	temp add lost/bond ignore lost warn
+
+#dump		1 all atom 50 dump.deposit.atom
+
+#dump		1 all image 50 image.*.jpg type type &
+#		axes yes 0.8 0.02 view 80 -30
+#dump_modify	1 pad 5
+
+#dump		1 all movie 50 tmp.mpg type type &
+#		axes yes 0.8 0.02 view 80 -30
+#dump_modify	1 pad 5
+
+run             10000