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[lammps-users] FW: Restart not exact
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[lammps-users] FW: Restart not exact


From: "Sengupta, S." <S.Sengupta@...2493...>
Date: Fri, 6 Oct 2017 18:03:10 +0000

Dear users,

I ran a simulation using lambda_test.txt . I am trying to restart the simulation from 2950000 time steps using lambda_rst.txt. I am using the lammps 17Nov/16 version.

The thermo diagnostics for restart are not exactly matching the 2950000 time step data in the log file. I have kept the number of processors same and used the default newton setting in both the restart and original simulation.

Restart thermo

Step Temp E_pair E_mol TotEng Press Volume Density
2950000    300.44816   -37677.886    44295.361    20505.773    544.40548     224319.2    1.7848003

Original run thermo
Step Temp E_pair E_mol TotEng Press Volume Density
2950000    300.44816   -37679.196    44295.361    20504.462    548.64091     224319.2    1.7848003


As you can see, the diagnostics are not exactly the same. Is this acceptable ?

Please let me know if other files are needed.

Thanks
Soumyadipta


________________________________________
From: Sengupta, S.
Sent: 06 October 2017 17:51
To: lammps-users@lists.sourceforge.net
Subject: Restart not exact

I ran a simulation using lambda_test.txt . I am trying to restart the simulation from 2950000 time steps using lambda_rst.txt. I am using the lammps 17Nov/16 version.

The thermo diagnostics for restart are not exactly matching the 2950000 time step data in the log file. I have kept the number of processors same and used the default newton setting in both the restart and original simulation.

Restart thermo

Step Temp E_pair E_mol TotEng Press Volume Density
2950000    300.44816   -37677.886    44295.361    20505.773    544.40548     224319.2    1.7848003

Original run thermo
Step Temp E_pair E_mol TotEng Press Volume Density
2950000    300.44816   -37679.196    44295.361    20504.462    548.64091     224319.2    1.7848003


As you can see, the diagnostics are not exactly the same. Is this acceptable ?

I have attached the log file from the original simulation (log.lammps) and the restart file at 2950000 steps for your reference.

Thanks
Soumyadipta


kspace_style pppm 0.0001
kspace_modify slab 3.0

read_restart rst.lambda0.2950000


#group hydrophobic and hydrophilic

group phyl type 3 4 6 7

group phob type 1 2 5

#group water

group water id 12275:19414
group water_o id 12276:19413:3
group water_h subtract water water_o
group sulfur type 3
group oxy_c  type 2


#fix wall on top and bottom

fix wallphob phob wall/lj93 zhi EDGE 0.25 3.2 15 zlo EDGE 0.25 3.2 15

fix wallphyl phyl wall/lj93 zhi EDGE 1.5 3.2 15  zlo EDGE 1.5 3.2 15

fix_modify wallphob energy yes
fix_modify wallphyl energy yes


neighbor        2.0 bin
neigh_modify every 1 page 150000 one 5000


thermo 100
thermo_style custom step temp epair emol etotal press vol density
timestep        1.0  # femtoseconds

restart 50000 rst.lambda0


# saving trajectory

dump  Datom1 all custom 5000 dump.lambda0 id type xu yu zu ix iy iz
dump_modify Datom1 sort 1

dump  Datom2 all custom 5000 dump.lambda1 id type x y z ix iy iz
dump_modify Datom2 sort 1


#npt run

fix npt2 all npt temp 300 300 50 x 1 1 100 y 1 1 100 couple xy drag 2.0

run 5000000
unfix npt2

undump Datom1
undump Datom2

# saving trajectory production

dump  Datom3 all custom 500 unwrap.lammpstrj id type xu yu zu ix iy iz
dump_modify Datom3 sort 1

dump  Datom4 all custom 500 wrap.lammpstrj id type x y z ix iy iz
dump_modify Datom4 sort 1

#number density

compute water_o_chunk water_o chunk/atom bin/1d z lower 0.2 units box
compute water_h_chunk water_h chunk/atom bin/1d z lower 0.2 units box
compute sulfur_chunk sulfur chunk/atom bin/1d z lower 0.2 units box
compute oxy_c_chunk oxy_c chunk/atom bin/1d z lower 0.2 units box

fix water_o_density water_o ave/chunk 10 10 500 water_o_chunk density/mass density/number ave running file water_o_density.txt format %20.2g
fix water_h_density water_h ave/chunk 10 10 500 water_h_chunk density/mass density/number ave running file water_h_density.txt format %20.2g
fix sulfur_density sulfur ave/chunk 10 10 500 sulfur_chunk density/mass density/number ave running file sulfur_density.txt format %20.2g
fix oxy_c_density oxy_c ave/chunk 10 10 500 oxy_c_chunk density/mass density/number ave running file oxy_c_density.txt format %20.2g


#npt production run

fix npt3 all npt temp 300 300 50 x 1 1 100 y 1 1 100 couple xy drag 2.0

run 2000000
unfix npt3

units  real
atom_style full
boundary        p p f

pair_style lj/class2/coul/long 10 15
dielectric      1.0  
bond_style      class2
angle_style     class2
dihedral_style  class2
improper_style  class2
kspace_style pppm 0.0001
kspace_modify slab 3.0


read_data Polymer.data 


#group hydrophobic and hydrophilic

group phyl type 3 4 6 7

group phob type 1 2 5


#fix wall on top and bottom

fix wallphob phob wall/lj93 zhi EDGE 0.25 3.2 15 zlo EDGE 0.25 3.2 15

fix wallphyl phyl wall/lj93 zhi EDGE 1.5 3.2 15  zlo EDGE 1.5 3.2 15

fix_modify wallphob energy yes
fix_modify wallphyl energy yes

neighbor        2.0 bin
neigh_modify every 1 page 150000 one 5000


#minimize

minimize 1.0e-6 1.0e-6 5000 5000


velocity        all create 300.0 497 dist gaussian


thermo 100
thermo_style custom step temp epair emol etotal press vol density
timestep        1.0  # femtoseconds

restart 50000 rst.lambda0

write_data Polymer_min.data

# saving trajectory

dump  Datom all custom 1000 dump.lambda0 id type xu yu zu ix iy iz
dump_modify Datom sort 1

dump  Datom1 all custom 1000 dump.lambda1 id type x y z ix iy iz
dump_modify Datom1 sort 1

#write_dump all custom initial.lammpstrj id type xu yu zu ix iy iz modify sort id
#write_dump all custom initial_wrap.lammpstrj id type x y z ix iy iz modify sort id

#nvt run

fix nvt1 all nvt temp 300 300 50
run 500000
unfix nvt1

#annealing

# equilibration 

label loop
variable loop_ctr loop 5

fix nvt1 all nvt temp 300.0 600.0 50
run 50000 
unfix nvt1

fix nvt2 all nvt temp 600 600 50
run 50000
unfix nvt2

fix nvt3 all nvt temp 600 300 50
run 50000
unfix nvt3

next loop_ctr
jump SELF loop

#nvt run

fix nvt1 all nvt temp 300 300 50
run 200000
unfix nvt1

#npt run

fix npt1 all npt temp 300 300 50 x 1 1 100 y 1 1 100 couple xy drag 2.0

run 1500000
unfix npt1