Hi all,
I want to store the inherent structure position coordinates after doing conjugate gradient technique . So if I use dump command after min_style ,is it the right way to do what i need???Also sending my input file…
thanks in advance…
3d Lennard-Jones
#variable x index 1
#variable y index 1
#variable z index 1
#variable xx equal 5*$x
#variable yy equal 5*$y
#variable zz equal 5*$z
#units lj
#atom_style atomic
#lattice fcc 1.2959
#region box block 0 {xx} 0 {yy} 0 ${zz}
#create_box 2 box
#create_atoms 1 box
#set group all type/fraction 2 0.5 95392
read_data data.200000
#read_restart restart_0.59.dat
mass 1 1
mass 2 0.5
velocity all create 0.59 11152 mom yes rot yes dist gaussian
pair_style lj/cut 2.5
pair_modify shift yes
pair_coeff 1 1 1.0 1.0 2.5
pair_coeff 1 2 1.0 0.917 2.293
pair_coeff 2 2 1.0 0.833 2.083
neighbor 0.3 bin
neigh_modify delay 0 every 20 check no
fix 1 all nvt temp 0.59 0.59 100
min_style cg
minimize 1.0e-8 1.0e-10 10000 1000
thermo_style custom step fmax fnorm
thermo 1
thermo_modify flush yes
dump 2 all custom 1 200000.xyz id type xu yu zu
dump_modify 2 sort 1
#restart 1000 restart1.dat restart_0.59.dat
timestep 0.0015
run 0
…Atreyee Banerjee
NCL
Pune
India
inherent structure position coordinates
I don't know what this is, but if you just want
to dump atom coordintes during or after a minimization,
then dump will do that. The iteration count is treated
like a timestep count.
Steve
inherent structure position coordinates
I don't know what this is, but if you just want
to dump atom coordintes during or after a minimization,
then dump will do that. The iteration count is treated
like a timestep count.
Steve
After Steve told me about this feature, I've found it to be very
useful. It's cool to watch the minimization process in VMD. (It
helps me fix problems with my initial geometry.)
If it helps, here's an example from one of my simulations:
dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz
minimize 1.0e-5 1.0e-7 500 2000
write_restart system_after_min.rst
(This list of atom properties (id mol type x y z ix iy iz) is useful
for visualizing in VMD. See attached file. Incidentally, the dump
interval (in my case "50") does not seem to matter too much during
minimization, because the final frame is saved after minimization has
converged. That's probably all you care about.)
In addition to visualizing the results you can open the dump file in a
text file "traj_min.lammpstrj" in this example, and jump to the last
place in the file where "ITEM: ATOMS" appears. The atomic coordinates
will be located below. You can copy this section of the file and save
it to a separate file "struct_min.txt". If you don't care about
periodic boundary conditions you can try this command to extract the
coordinates:
sort -g < struct_min.txt | awk '{print $4" "$5" "$6}' > struct_min.dat
If you have rectangular box (size 50 in each direction), you can use:
sort -g < struct_min.txt | awk '{print $4+50*$7" "$5+50*$8"
"$6+50*$9}' > struct_min.dat
I'm sure you can also probably do something more fancy in pizza.py.
Cheers
Andrew
README_visualize.txt (2.85 KB)
That command was supposed to fit on one line.
(Grumble) Hopefully you get the idea.
Cheers