Modified pair_styles reax and reax/c

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5153 f3b2605a-c512-4ea7-a41b-209d697bcdaa

examples/reax/control.reax_c.tatb

@@ -0,0 +1,21 @@
+simulation_name         reax.tatb  ! output files will carry this name + their specific extension
+
+tabulate_long_range     0 ! denotes the granularity of long range tabulation, 0 means no tabulation
+energy_update_freq      1 
+remove_CoM_vel          500 ! remove the trans. & rot. vel around the CoM every 'this many' steps
+
+nbrhood_cutoff          4.0  ! near neighbors cutoff for bond calculations in A
+hbond_cutoff            10.0  ! cutoff distance for hydrogen bond interactions
+bond_graph_cutoff       0.3  ! bond strength cutoff for bond graphs
+thb_cutoff              0.001 ! cutoff value for three body interactions
+q_err                   1e-6  ! average per atom error norm allowed in GMRES convergence
+
+geo_format              0    ! 0: xyz, 1: pdb, 2: bgf
+write_freq              0    ! write trajectory after so many steps
+traj_compress           0    ! 0: no compression  1: uses zlib to compress trajectory output
+traj_title              TATB ! (no white spaces)
+atom_info               0    ! 0: no atom info, 1: print basic atom info in the trajectory file
+atom_forces             0    ! 0: basic atom format, 1: print force on each atom in the trajectory file
+atom_velocities         0    ! 0: basic atom format, 1: print the velocity of each atom in the trajectory file
+bond_info               0    ! 0: do not print bonds, 1: print bonds in the trajectory file
+angle_info              0    ! 0: do not print angles, 1: print angles in the trajectory file 

examples/reax/ffield.reax

@@ -1,4 +1,4 @@
-Reactive MD-force field [Strachan et al, JCP 122 054502 (2005).]                
+Reactive MD-force field
  39       ! Number of general parameters                                        
    50.0000 !Overcoordination parameter                                          
     9.5469 !Overcoordination parameter                                          

examples/reax/in.reax.rdx

@@ -6,16 +6,33 @@ units		real
 atom_style	charge
 read_data	data.rdx
 
-pair_style	reax 10.0 1.0e-6
+pair_style	reax 10.0 0 1.0e-6
 pair_coeff	* * ffield.reax 1 2 3 4
 
+compute reax all pair reax
+
+variable eb  	 equal c_reax[1]
+variable ea  	 equal c_reax[2]
+variable elp 	 equal c_reax[3]
+variable emol 	 equal c_reax[4]
+variable ev 	 equal c_reax[5]
+variable epen 	 equal c_reax[6]
+variable ecoa 	 equal c_reax[7]
+variable ehb 	 equal c_reax[8]
+variable et 	 equal c_reax[9]
+variable eco 	 equal c_reax[10]
+variable ew 	 equal c_reax[11]
+variable ep 	 equal c_reax[12]
+variable efi 	 equal c_reax[13]
+variable eqeq 	 equal c_reax[14]
+
 neighbor	2.5 bin
 neigh_modify	every 10 delay 0 check no
 
 fix		1 all nve
 
 thermo		10
-thermo_modify	format float %15.14g
+thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
 
 timestep	1.0
 

examples/reax/in.reax.tatb

@@ -6,21 +6,41 @@ units		real
 atom_style	charge
 read_data	data.tatb
 
-pair_style	reax 10.0 1.0e-6
+# N.B. to match reax/c, set hbnewflag = 1
+#     reax args: hbcut hbnewflag precision
+#pair_style	reax 10.0 1 1.0e-6
+pair_style	reax 10.0 0 1.0e-6
 pair_coeff	* * ffield.reax 1 2 3 4
 
+compute reax all pair reax
+
+variable eb  	 equal c_reax[1]
+variable ea  	 equal c_reax[2]
+variable elp 	 equal c_reax[3]
+variable emol 	 equal c_reax[4]
+variable ev 	 equal c_reax[5]
+variable epen 	 equal c_reax[6]
+variable ecoa 	 equal c_reax[7]
+variable ehb 	 equal c_reax[8]
+variable et 	 equal c_reax[9]
+variable eco 	 equal c_reax[10]
+variable ew 	 equal c_reax[11]
+variable ep 	 equal c_reax[12]
+variable efi 	 equal c_reax[13]
+variable eqeq 	 equal c_reax[14]
+
 neighbor	2.5 bin
 neigh_modify	delay 0 every 5 check no
 
 fix		1 all nve
 
 thermo		1
-thermo_style	custom step temp evdwl ecoul pe ke etotal press
+thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
 
 timestep	0.0625
 
-dump		1 all atom 25 dump.reax.tatb
-dump_modify	1 scale no
+dump		1 all custom 100 dump.reax.tatb id type q x y z
+
 fix 		2 all reax/bonds 25 bonds.reax.tatb
 
 run		25

examples/reax/in.reax_c.rdx

@@ -0,0 +1,42 @@
+# REAX potential for RDX system
+# this run is equivalent to reax/in.reax.rdx
+
+units		real
+
+atom_style	charge
+read_data	data.rdx
+
+pair_style      reax/c NULL
+pair_coeff      * * ffield.reax 1 2 3 4
+
+compute reax all pair reax/c
+
+variable eb  	 equal c_reax[1]
+variable ea  	 equal c_reax[2]
+variable elp 	 equal c_reax[3]
+variable emol 	 equal c_reax[4]
+variable ev 	 equal c_reax[5]
+variable epen 	 equal c_reax[6]
+variable ecoa 	 equal c_reax[7]
+variable ehb 	 equal c_reax[8]
+variable et 	 equal c_reax[9]
+variable eco 	 equal c_reax[10]
+variable ew 	 equal c_reax[11]
+variable ep 	 equal c_reax[12]
+variable efi 	 equal c_reax[13]
+variable eqeq 	 equal c_reax[14]
+
+neighbor	2.5 bin
+neigh_modify	every 10 delay 0 check no
+
+fix		1 all nve
+fix             2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
+
+thermo		10
+thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
+
+timestep	1.0
+
+dump		1 all atom 10 dump.reax.rdx
+
+run		100

examples/reax/in.reax_c.tatb

@@ -0,0 +1,44 @@
+# REAX potential for TATB system
+# this run is equivalent to reax/in.reax.tatb,
+#    if hbnewflag = 1 in in.reax.tatb
+
+units		real
+
+atom_style	charge
+read_data	data.tatb
+
+pair_style      reax/c control.reax_c.tatb
+pair_coeff      * * ffield.reax 1 2 3 4
+
+compute reax all pair reax/c
+
+variable eb  	 equal c_reax[1]
+variable ea  	 equal c_reax[2]
+variable elp 	 equal c_reax[3]
+variable emol 	 equal c_reax[4]
+variable ev 	 equal c_reax[5]
+variable epen 	 equal c_reax[6]
+variable ecoa 	 equal c_reax[7]
+variable ehb 	 equal c_reax[8]
+variable et 	 equal c_reax[9]
+variable eco 	 equal c_reax[10]
+variable ew 	 equal c_reax[11]
+variable ep 	 equal c_reax[12]
+variable efi 	 equal c_reax[13]
+variable eqeq 	 equal c_reax[14]
+
+neighbor	2.5 bin
+neigh_modify	delay 0 every 5 check no
+
+fix		1 all nve
+fix             2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
+
+thermo		1
+thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
+
+timestep	0.0625
+
+dump		1 all custom 100 dump.reax.tatb id type q x y z
+
+run		25
+