rename some examples folders

examples/USER-MISC/cnp/in.cnp

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+# Generation and relaxation of a partial dislocation in Cu perfect FCC crystal
+
+# Initialization
+units           metal
+boundary        p p p
+atom_style      atomic
+
+# create simulation box and system
+lattice         fcc 3.615  origin 0.01 0.01 0.01 orient x -1 -1 2 orient y 1 1 1 orient z -1 1 0 
+region          mdbox  block 0 3 0.0 14.0 0 84 units lattice
+region          system block 0 3 1.1 13.1 0 84 units lattice
+create_box      2 mdbox
+create_atoms    1 region system
+
+# Define atoms mass and force field
+mass            *  63.54                     
+pair_style      eam/alloy
+pair_coeff      * * Cu_Mishin1.eam Cu Cu
+
+# Delete a plane of atoms along the z direction to generate a partial dislocation
+region          dislocation_atoms block 0 3 7 14 41.9 42.1 units lattice
+delete_atoms    region dislocation_atoms
+region          quarter_up block 0 3 7 11 0 84 units lattice
+group           middle region quarter_up
+
+# specify simulation parameters
+timestep        0.004
+
+# Relax configuration using conjugate gradient
+#min_style cg
+#minimize 1.0e-4 1.0e-6 100 1000
+
+# Setup calculations 
+compute         1 all cnp/atom 3.086
+compute         2 all cna/atom 3.086
+compute         3 all centro/atom fcc
+compute         4 all coord/atom cutoff 3.086
+dump            1 all custom 100 dump.lammpstrj id type xu yu zu c_1 c_2 c_3 c_4 
+
+### Set up thermo display
+thermo          10
+thermo_style    custom step atoms temp press pe ke etotal
+
+# Relax the system performing a langevin dynamics (freeze motion along y 111 direction)
+fix             1 all nve
+fix             2 all langevin 50 1 0.1 699483
+fix             3 all setforce NULL 0.0 NULL
+fix             4 middle setforce 0.0  0.0 0.0
+run             100
+unfix           4
+run             200