User_guide.md

ActiveRun Usage

Usage

activerun [legacy input] [legacy data]
activerun -i [json input]
activerun -r [restart file]

• Legacy Input: Row-specified Data
• Json Input: Input with json format. A json with default value will be created if input not found.

Sample Input File

Legacy Input

kT 1.0
dt 0.000005             # absolute timestep
stepstauB 1             # step for tauB (not tauR)
zeta(stokes) 1          # zeta when radius=1.0
overlap(a) 0.0000001
PeR 0.05
brownrot 1              # not work
browntrans 1            # not work
PeS 0.0
attraction 1            # not work
swimattract 1           # not work
morse 1
HS 0                    # not work
Rg(a) 0.1
kappa 30
Um(kT) 5 
output 10000
swimstart 0
spstart 0
mincellL 2

Currently the type of forces need to be changed manually.

Json Input

{
    "BrownianForce":{
        "neta":0.026525823848649224,    # viscosity coeff
        "temp":1.0                      # temperature for Brownian Force
    },
    "MorseForce":{
        "Um":5.0,
        "cutoff":1.20,
        "kappa":30.0
    },
    "SwimForce":{
        "PeR":0.01,
        "brownian":true,                # not work
        "init_seed":0,                  # seed for randomize angle
        "neta":0.026525823848649224,
        "swim_start":0,
        "swim_temp":1.0
    },
    "current_step":0,
    "data_file":"data.gel",
    "dump":{
        "dump_file":"outputconfig.lammpstrj",
        "dump_step":1000
    },
    "global_seed":0,                    # random seed for whole running session
    "is_restart":false,
    "restart":{                         # configure for restart
        "restart_data":"restart.data",
        "restart_file":"restart.rst",
        "write_restart":true
    },
    "run":{
        "step":200000,                  # if start from restart file, it's the total step
        "timestep":5e-06                # absolute timestep
    },
    "thermo":{                          # thermodynamic property (currently only pressure and temperature)
        "average_range":10,             # average so many step around sample point
        "average_step":1,
        "compute_temp":true,
        "thermo_file":"pressure.output",
        "thermo_start":0,
        "thermo_step":100,              # calculate step
        "using_thermo":true
    },
    "util":{
        "cell_size":2.0,
        "neighlist_step":1,
        "np":2                          # core number 
    }
}