Lammps 问题集锦

1、Results of time averaging in a variable?

Hi - I’d like to run an equilibration NPT, take the average box shape, and then use it to run an NVE, in a single lammps input file.  Is there any way to get the results of the time averaged box shape (e.g. as computed by “fix ave/time”) in a variable, so I can use it in a change box command?  All I’ve been able to get from the documentation and searching the mailing list is how to write it to a file.   thanks, Noam   On Nov 6, 2017, at 9:33 AM, Axel Kohlmeyer <akohlmey@gmail> wrote:   ​from the fix ave/time documentation:   ​Restart, fix_modify, output, run start/stop, minimize info:   No information about this fix is written to binary restart files. None of the fix_modify options are relevant to this fix.   **This fix produces a global scalar or global vector or global array which can be accessed by various output commands. The values can only be accessed on timesteps that are multiples of Nfreq since that is when averaging is performed.**

2、ERROR: Dihedral charmm is incompatible with Pair style

Hi dear all   I want to calculate my system potential energy from 200 to 1800 kelvin. I use EAM and L-J potential for my system but I see this error   ERROR: Dihedral charmm is incompatible with Pair style (../dihedral_charmm.cpp:402) Last command: minimize        0 0 100000 1000000    what is your guide to solve this ( change pair style ? what pair style? ....)   best   Ehsan     this is my input command ------------------------------------------------  units           real atom_style      full   neighbor        1 bin neigh_modify    delay 2 every 1   bond_style      harmonic angle_style     charmm dihedral_style  charmm     read_data       256b.data pair_style     hybrid lj/cut 14.0 eam dihedral_coeff  1 3.1 2 180 0.5   pair_coeff      2*2 2*2 eam Au_u3.eam   pair_coeff      1 2 lj/cut 0.048427138 1.41964710735663 pair_coeff      1 1 lj/cut 0.10492547 1.7155   pair_modify     mix arithmetic   kspace_style    none      group           CA type 1   fix             1 CA setforce 0.0 0.0 0.0   thermo          200 thermo_style    custom step temp pe etotal press vol ke enthalpy evdwl epair ebond eangle edihed   minimize        0 0 100000 1000000   special_bonds   charmm dump            npt all dcd 5000 ionized-npt.dcd fix             2 all npt temp 298.0 298.0 100.0 y 1.0 1.0 500 run             4000000 unfix           2 undump          npt   fix             3 all nvt temp 298.0 298.0 100.0 fix             4 all shake 1e-6 500 0 m 1.0 a 17 velocity        all create 180.0 12345678 rot yes mom yes dist gaussian velocity        CA create 0.0 12345678  rot yes mom yes dist gaussian   timestep        0.5   restart         10 ionized.restart1 ionized.restart2 dump            1 all dcd 5000 ionized.dcd #dump_modify    1 image yes scale yes   run             10000000 ------------------------------------------------  I read manual but I not found charmm dihedral style that compatible with EAM and L-J pair style my system that I work on it is a gold nano cluster based on graphene sheet and I want to measure thermodynamics properties during heating from 200 to 1800 kelvin and cooling from 1800 to 200 kelvin I set EAM potential between gold nano particle and Lennard-Jones potential between graphene and gold nano particles   I want to see when temperature increase, my system potential energy how much change ----------------------------------------------------- ...and why do you need dihedrals with EAM and LJ potentials?

转载于:https://wwwblogs/Simulation-Campus/p/8830958.html