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peteboyd / lammps_interface

automatic generation of LAMMPS input files for molecular dynamics simulations of MOFs
MIT License
125 stars 63 forks source link

New maintainer wanted! #61

Open ltalirz opened 1 year ago

ltalirz commented 1 year ago

lammps_interface is currently effectively unmaintained.

In order to keep the package functional and improve it, a new maintainer will be needed (in my last email exchange with Pete Boyd, the original author of this package, he also expressed this intention). If you are interested in helping out with this, just let us know here and start, e.g. by taking on one of the open issues you think you can fix.

htz1992213 commented 1 year ago

I'm Interested. Will try to make PRs on bug fixes.

ltalirz commented 1 year ago

Cheers, looking forward!

kylincaster commented 1 year ago

I would like to provide some helps on this projects too.

ltalirz commented 1 year ago

see e.g. https://github.com/peteboyd/lammps_interface/issues/62 as an easy issue to start on

jaharvey8 commented 1 year ago

fixed #62

Raj123dev commented 4 months ago

VARIABLES

variable fname index pc_data.txt variable simname string pc_data # Assuming simname is a string

Initialization

units real boundary p p p atom_style molecular log log.${simname}.txt read_data ${fname}

Dreiding potential information

neighbor 0.4 bin neigh_modify every 10 one 10000

bond_style harmonic bond_coeff 1 1.61e22 3.37 bond_coeff 2 1.60e22 3.37 bond_coeff 3 1.57e22 3.76 bond_coeff 4 1.52e22 3.76

angle_style harmonic angle_coeff 1 4.17e2 90.53 angle_coeff 2 1.42e2 32.65 angle_coeff 3 1.36e2 32.65

dihedral_style opls dihedral_coeff 1 0.4109 -0.8192 0.1873 0.6718 -0.1202 dihedral_coeff 2 0.3270 0.3666 -0.1756 -0.3320 -0.06420 dihedral_coeff 3 0.4222 0.6021 0.1812 -0.4568 -0.4515 dihedral_coeff 4 0.3911 -0.7477 0.2187 0.5642 -0.2026

pair_style lj/cut pair_coeff 1 1 0.4109 -0.8192 3.76 # 1-2-3-4 pair_coeff 2 2 0.3270 0.3666 3.37 # 1-4-3-2 pair_coeff 3 3 0.4222 0.6021 3.37 # 2-1-4-3 pair_coeff 4 4 0.3911 -0.7477 3.76 # 3-2-1-4

compute csym all centro/atom fcc compute peratom all pe/atom

#####################################################

Equilibration (Langevin dynamics at 5000 K)

velocity all create 5000.0 1231 fix 1 all nve/limit 0.05 fix 2 all langevin 5000.0 5000.0 10.0 904297 thermo_style custom step temp thermo 10000 timestep 1 run 1000000 unfix 1 unfix 2 write_restart restart.${simname}.dreiding1

#####################################################

Define Settings

compute eng all pe/atom compute eatoms all reduce sum c_eng

#####################################################

Minimization

dump 1 all cfg 6 dump.comp_*.cfg mass type xs ys zs c_csym c_peratom fx fy fz

reset_timestep 0 fix 1 all nvt temp 500.0 500.0 100.0 thermo 20 thermo_style custom step pe lx ly lz press pxx pyy pzz c_eatoms min_style cg minimize 1e-25 1e-25 500000 1000000

print "All done"

help me with the above and its data file?

ltalirz commented 4 months ago

Hey @Raj123dev , this thread is about finding a new maintainer for lammps-interface.

For soliciting help with inputs, please open a separate thread