stop outputting files using loop in LAMMPS

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1

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})27630*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

2

If your runs are independent, I suggest
you create a script which just runs
run# 901 (or whichever one is failing)
and try that by itself, to see if you can
reproduce the problem.

Steve

3

Hi Steve,
Thanks for you response.
I tried to just run 999 steps, and the simulation finished, but if I run 1000 steps, it will get stuck at 999 steps. It’s still “running”, but not output anything.
To make the question simple, I used fix_deposit command and I still got the same issue. So I tried to run the example for fix_deposit in lammps example folder, it went without any problem for the original input file. But When I added a line “dump 2 all dcd 1000 test.dcd”, I see exactly the same issue. It won’t generate any output file after 999 steps. I tried to add command “dump_modify 2 flush yes”, the problem still exist.
Is there any conflict between fix_deposit and dum dcd? OR do you know how can I modify the input file to generate trajectories normally?

Best,
Dan

4

Hi Steve,
Thanks for you response.
I tried to just run 999 steps, and the simulation finished, but if I run
1000 steps, it will get stuck at 999 steps. It’s still “running”, but not
output anything.
To make the question simple, I used fix_deposit command and I still got
the same issue. So I tried to run the example for fix_deposit in lammps
example folder, it went without any problem for the original input file.
But When I added a line “dump 2 all dcd 1000 test.dcd”, I see exactly the
same issue. It won’t generate any output file after 999 steps. I tried to
add command “dump_modify 2 flush yes”, the problem still exist.

Is there any conflict between fix_deposit and dum dcd?

dcd format dumps only support a constant number of atoms.
​ this is a limitation of the file format.
try dump style atom or custom instead.

axel.​

5

Dear Axel,
Thank you so much for your help. I can run the simulation with dump atom style with format .lammpstrj now. But the problem is seems that I can not load that file completely in VMD, I got error message like “exceeded maximum number of bonds” or “ignoring out of range atom”. Any suggestion on which format I can use or how I can load the trajectories with newly created atoms?

Best,
Dan

6

Dear Axel,
Thank you so much for your help. I can run the simulation with dump atom
style with format .lammpstrj now. But the problem is seems that I can not
load that file completely in VMD, I got error message like “exceeded
maximum number of bonds” or “ignoring out of range atom”. Any suggestion on
which format I can use or how I can load the trajectories with newly
created atoms?

​both of these are VMD questions. there is the vmd-l mailing list for VMD
related questions, where you should post them and not here.

axel.​