diff --git a/examples/reax/control.reax_c.tatb b/examples/reax/control.reax_c.tatb new file mode 100644 index 0000000000..a972ea2e16 --- /dev/null +++ b/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 diff --git a/examples/reax/ffield.reax b/examples/reax/ffield.reax index 737c3c1ccf..5d372d73b5 100644 --- a/examples/reax/ffield.reax +++ b/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 diff --git a/examples/reax/in.reax.rdx b/examples/reax/in.reax.rdx index a2a6949e40..288812fedf 100644 --- a/examples/reax/in.reax.rdx +++ b/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 diff --git a/examples/reax/in.reax.tatb b/examples/reax/in.reax.tatb index 429fff12ab..f612a2e6b9 100644 --- a/examples/reax/in.reax.tatb +++ b/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 diff --git a/examples/reax/in.reax_c.rdx b/examples/reax/in.reax_c.rdx new file mode 100644 index 0000000000..8f5e67c591 --- /dev/null +++ b/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 diff --git a/examples/reax/in.reax_c.tatb b/examples/reax/in.reax_c.tatb new file mode 100644 index 0000000000..0c959f30fe --- /dev/null +++ b/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 +