Hi lammps users,

I am running a loop in my lammps input file, it operates creating or deleting atoms at the beginning of each loop session. The problem is the simulation is still running, but just give me no out put files after 900 runs in the first loop. I am using the current lammps-17Nov16 version with rigid and MISC package compiled. I tried to run the simulation on two different clusters but still got the same problem.

I tried to run with only loop or only create_atoms, the results were able to output normally. I think there should be something wrong with the input file here. I also tried with “thermo modify flush”, but still didn’t work.

I appreciate you help in advance.

Best,

Dan

# 3-d micelle DPD simulation

dimension 3

boundary p p p

units lj

atom_style full

timestep 0.006

read_data 24HM_s70_bilyer.data

#read_restart RS2.restart

neighbor 0.5 bin

#neigh_modify delay 2

comm_modify cutoff 30 vel yes

# Force-field parameters

# define masses and interaction coefficient

mass * 1

# Bonded interactions

bond_style harmonic

bond_coeff 1 50 0.18

bond_coeff 2 50.0 0.7

bond_coeff 3 50.0 0.7

bond_coeff 4 1754.8 0.42

angle_style hybrid harmonic cosine/squared

angle_coeff 1 harmonic 50 180.0

angle_coeff 2 harmonic 3 180.0

angle_coeff 3 harmonic 1.5 120.0

angle_coeff 4 harmonic 3 180.0

angle_coeff 5 cosine/squared 13.7 130.0

angle_coeff 6 harmonic 2.25 120.0

# Non-bonded interactions

pair_style hybrid/overlay dpd 0.8 1.0 81096

pair_coeff 1 1 dpd 25 4.5 1.0

pair_coeff 1 2 dpd 100 4.5 1.0

pair_coeff 1 3 dpd 100 4.5 1.0

pair_coeff 1 4 dpd 20 4.5 1.0

pair_coeff 1 5 dpd 26.3 4.5 1.0

pair_coeff 1 6 dpd 33.7 4.5 1.0

pair_coeff 1 7 dpd 26.3 4.5 1.0

pair_coeff 1 8 dpd 20 4.5 1.0

pair_coeff 1 9 dpd 26.3 4.5 1.0

pair_coeff 2 2 dpd 25 4.5 1.0

pair_coeff 2 3 dpd 26.3 4.5 1.0

pair_coeff 2 4 dpd 100 4.5 1.0

pair_coeff 2 5 dpd 33.7 4.5 1.0

pair_coeff 2 6 dpd 26.3 4.5 1.0

pair_coeff 2 7 dpd 33.7 4.5 1.0

pair_coeff 2 8 dpd 100 4.5 1.0

pair_coeff 2 9 dpd 33.7 4.5 1.0

pair_coeff 3 3 dpd 25 4.5 1.0

pair_coeff 3 4 dpd 100 4.5 1.0

pair_coeff 3 5 dpd 33.7 4.5 1.0

pair_coeff 3 6 dpd 26.3 4.5 1.0

pair_coeff 3 7 dpd 33.7 4.5 1.0

pair_coeff 3 8 dpd 100 4.5 1.0

pair_coeff 3 9 dpd 33.7 4.5 1.0

pair_coeff 4 4 dpd 25 4.5 1.0

pair_coeff 4 5 dpd 26.3 4.5 1.0

pair_coeff 4 6 dpd 33.7 4.5 1.0

pair_coeff 4 7 dpd 26.3 4.5 1.0

pair_coeff 4 8 dpd 25 4.5 1.0

pair_coeff 4 9 dpd 26.3 4.5 1.0

pair_coeff 5 5 dpd 25 4.5 1.0

pair_coeff 5 6 dpd 100 4.5 1.0

pair_coeff 5 7 dpd 26.3 4.5 1.0

pair_coeff 5 8 dpd 26.3 4.5 1.0

pair_coeff 5 9 dpd 25 4.5 1.0

pair_coeff 6 6 dpd 25 4.5 1.0

pair_coeff 6 7 dpd 100 4.5 1.0

pair_coeff 6 8 dpd 33.7 4.5 1.0

pair_coeff 6 9 dpd 100 4.5 1.0

pair_coeff 7 7 dpd 25 4.5 1.0

pair_coeff 7 8 dpd 26.3 4.5 1.0

pair_coeff 7 9 dpd 26.3 4.5 1.0

pair_coeff 8 8 dpd 25 4.5 1.0

pair_coeff 8 9 dpd 0.0 4.5 1.0 #ligand and receptor

pair_coeff 9 9 dpd 25 4.5 1.0

# Groups

group protein type 1

fix 10 protein rigid molecule

group bilayer type 5 6 9

group water type 7

group head type 5 9

region allregion block -35 35 -35 35 -20 10 side in units box

region inner block -33 33 -33 33 INF INF side out units box

region bound intersect 2 allregion inner units box

region upperall block -34 34 -34 34 -7 -6.5 side in units box

region lowerall block -34 34 -34 34 -3 -2.5 side in units box

region upper intersect 2 upperall inner

region lower intersect 2 lowerall inner

region inside block -5 5 -5 5 -20 10 side in units box

group ball region bound

group lfix intersect ball head

# create initial velocities

velocity all create 0.8 2984 dist gaussian

# Output

thermo 10

thermo_modify lost ignore flush yes

restart 10000 RS1.restart RS2.restart

dump 1 all dcd 1000 dpd.dcd

# N-varied DPD

fix 1 all nve/limit 0.02

run 1000

# definie local density of lipid and water

variable lcd equal 1.0 #lower critical density

variable ucd equal 1.8 #upper critical density

molecule lipidmolu lipidu.mol

molecule lipidmoll lipidl.mol

# run boundary loop

variable a loop 400000

label loop

# calculate density for if statement

variable lipidden equal count(bilayer,inside)/13/100/2

variable boundden equal count(bilayer,bound)/13/276/2

variable waterden equal count(water,bound)/276

variable lipidD equal ({lipidden}-{ucd})/{lipidden}
variable waterI equal floor((1-{lipidD})*276*30*3)

variable waterD equal ({lcd}-{lipidden})*26/{waterden}
if "{waterD} < 1" then &

“variable lipidI equal floor({waterD}*276*30*3/26)" &
else &
"variable lipidI equal floor(({lcd}-${lipidden})*276)”

if “{lipidden} < {lcd}” then &

“delete_atoms porosity inside {waterD} 32071 mol yes" &
"create_atoms 0 random {lipidI} 49380 upper mol lipidmolu 67432” &

“create_atoms 0 random {lipidI} 24523 lower mol lipidmoll 76525" &
elif "{lipidden} > {ucd}" &
"delete_atoms porosity inside {lipidD} 73680 mol yes” &

“create_atoms 7 random ${waterI} 90723 inside” &

run 1500

next a

jump in-DPD_NV.ligand loop