Dear Sir,
Below is my input script for radiation damage on iron. I wanted to obeserv how temp/rescale work with simulation for this reason i used f_2 and f_3 in dump but it is giving me the error.
(ERROR: Dump custom fix does not compute per-atom info (src/dump_custom.cpp:1399)
Last command: dump 1 interior custom 100 test_init_col.dump type x y z c_3 c_2 f_3 f_2)
Can anybody help me about this?
-------------- Initialize Simulation ------------
echo both
units metal # set ‘metal’ units (Angstrom,ps timescale)
dimension 3
boundary p p p # periodic BCs
atom_style atomic
neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes # neighbor command modifies potential’s natural cutoff_needed?
----------------------- ATOM DEFINITION ----------------------------
read_data Fe_core.lmp
write_dump all atom all_atom.lammpstrj
--------------- Creat Atoms / Geometry -----------------------
mass 1 55.847
region rPKA sphere 0 62.713 62.713 1.4 # Create spherical region ‘rpka’ at x, y, x with radius
------------------Define Interatomic Potential -----------------
pair_style eam/alloy # Finnis-Sinclair EAM Potential from NIST
pair_coeff * * FeNiCr.eam.alloy Fe #Fe # Applies Fe coefficients to all atom pairs # Fe-Fe
Groups
region rallatoms block INF INF INF INF INF INF # define region of entire domain
region rinterior block 3 118.380 5 118.380 5 INF # define inner box region used for simulation domain
region rexterior block 3 118.380 5 118.380 5 INF side out # define thermostat region outside of simulation domain
group interior region rinterior # define group called ‘interior’ comprised of region ‘rinterior’
group exterior region rexterior
group PKA region rPKA
--------------Initialization----------------
compute 1 all temp
compute 2 interior coord/atom cutoff 2.2
compute 3 interior ke/atom
set PKA velocities to correspond to ~ 3000 Ang/ps
velocity PKA set 3000 NULL NULL units box
set timestep to smaller value for initial phase of collision (.01 fs for .2 ps)
reset_timestep 0
timestep 0.00001
thermo 100
thermo_style custom step temp pe etotal press # ‘custom’ specifies what thermo info is printed
fix 1 all nve # specifiy constant NVE interation to update position andn velocity for atoms in ther group each timestep
fix 2 exterior temp/rescale 1 300.0 300.0 0.5 1.0 region rexterior # set atoms in exterior group temperature to 100k by rescalling velocities.
fix 3 interior temp/rescale 1 300.0 300.0 0.5 1.0 region rinterior # set atoms in interior group temperature to 100k by rescalling velocities.
dump 1 interior custom 100 test_init_col.dump type x y z c_3 c_2 f_3 f_2
dump 2 PKA custom 100 PKA_traj_init_col.dump type x y z c_3 c_2 f_3 f_2
run 20000 # run the collisional phase for .2 ps
undump 1
undump 2
run intermediate phase with intermediate timestep (.1 fs for 1 ps)
timestep 0.0001
thermo 100
thermo_style custom step temp pe etotal press # ‘custom’ specifies what thermo info is printed
fix 1 all nve # specifiy constant NVE interation to update position andn velocity for atoms in ther group each timestep
fix 2 exterior temp/rescale 1 300.0 300.0 0.5 1.0 region rexterior # set atoms in exterior group temperature to 100k by rescalling velocities.
fix 3 interior temp/rescale 1 300.0 300.0 0.5 1.0 region rinterior # set atoms in interior group temperature to 100k by rescalling velocities.
dump 3 interior custom 100 test_inter_evolve.dump type x y z c_3 c_2 f_3 f_2
dump 4 PKA custom 100 PKA_traj_inter_evolve.dump type x y z c_3 c_2 f_3 f_2
run 10000 # run the collisional phase for 1 ps
undump 3 # close the previous dumps
undump 4
run intermediate phase with intermediate timestep (.1 fs for 30 ps)
timestep 0.001
thermo 100
thermo_style custom step temp pe etotal press # ‘custom’ specifies what thermo info is printed
fix 1 all nve # specifiy constant NVE interation to update position andn velocity for atoms in ther group each timestep
fix 2 exterior temp/rescale 1 300.0 300.0 0.5 1.0 region rexterior # set atoms in exterior group temperature to 100k by rescalling velocities.
fix 3 interior temp/rescale 1 300.0 300.0 0.5 1.0 region rinterior # set atoms in interior group temperature to 100k by rescalling velocities.
dump 5 interior custom 100 test_final_evolve.dump type x y z c_3 c_2 f_3 f_2
dump 6 PKA custom 100 PKA_traj_final_evolve.dump type x y z c_3 c_2 f_3 f_2
run 30000 # run the collisional phase for 30 ps