Skip to content

Deal with warning in tutorial 4 #53

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 2 commits into from
Dec 30, 2024
Merged

Deal with warning in tutorial 4 #53

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
1955000
deal with warning in tutorial 4
simongravelle Dec 29, 2024
c43f6c7
simplified minimization tutorial 4
simongravelle Dec 30, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
Binary file modified figures/NANOSHEAR-equilibration.png
View file
Open in desktop
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
2 changes: 1 addition & 1 deletion files/tutorial4/equilibrate.lmp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@ pair_style lj/cut/tip4p/long O H O-H H-O-H 0.1546 12.0
kspace_style pppm/tip4p 1.0e-5
kspace_modify slab 3.0

read_data minimize.data
read_data create.data

include parameters.inc
include groups.inc
Expand Down
18 changes: 0 additions & 18 deletions files/tutorial4/minimize.lmp
View file
Open in desktop

This file was deleted.

13 changes: 6 additions & 7 deletions files/tutorial4/solution/create.log
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,14 +1,13 @@
using 8 OpenMP thread(s) per MPI task
using multi-threaded neighbor list subroutines
WARNING: Detected non-ASCII characters in input. Will try to continue by replacing with ASCII equivalents where known. (src/input.cpp:478)
Lattice spacing in x,y,z = 4.04 4.04 4.04
Created orthogonal box = (-12.12 -12.12 -20.2) to (12.12 12.12 20.2)
1 by 1 by 1 MPI processor grid
Created 432 atoms
using lattice units in orthogonal box = (-12.12 -12.12 -20.2) to (12.12 12.12 20.2)
create_atoms CPU = 0.006 seconds
Read molecule template h2omol:
# Water molecule.
# LAMMPS Input File (License CC BY 4.0)
1 molecules
0 fragments
3 atoms with max type 2
Expand All @@ -21,7 +20,7 @@ Created 1944 atoms
create_atoms CPU = 0.002 seconds
Created 15 atoms
using lattice units in orthogonal box = (-12.12 -12.12 -20.2) to (12.12 12.12 20.2)
create_atoms CPU = 0.004 seconds
create_atoms CPU = 0.005 seconds
Created 15 atoms
using lattice units in orthogonal box = (-12.12 -12.12 -20.2) to (12.12 12.12 20.2)
create_atoms CPU = 0.004 seconds
Expand Down Expand Up @@ -63,7 +62,7 @@ PPPM initialization ...
estimated relative force accuracy = 1.0535666e-05
using double precision KISS FFT
3d grid and FFT values/proc = 39375 19440
WARNING: Communication cutoff 0 is shorter than a bond length based estimate of 3.4358. This may lead to errors. (src/comm.cpp:731)
WARNING: Communication cutoff 0 is shorter than a bond length based estimate of 3.4358. This may lead to errors. (src/comm.cpp:730)
WARNING: Increasing communication cutoff to 15.1118 for TIP4P pair style (src/KSPACE/pair_lj_cut_tip4p_long.cpp:497)
Generated 9 of 10 mixed pair_coeff terms from geometric mixing rule
Last active /omp style is kspace_style pppm/tip4p/omp
Expand All @@ -86,9 +85,9 @@ Setting up Verlet run ...
Per MPI rank memory allocation (min/avg/max) = 19.16 | 19.16 | 19.16 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 501411.03 0 501411.03 6165751.9
Loop time of 0.000133443 on 8 procs for 0 steps with 1680 atoms
Loop time of 3.207e-06 on 8 procs for 0 steps with 1680 atoms

81.7% CPU use with 1 MPI tasks x 8 OpenMP threads
155.9% CPU use with 1 MPI tasks x 8 OpenMP threads

MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
Expand All @@ -100,7 +99,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.0001334 | | |100.00
Other | | 3.207e-06 | | |100.00

Nlocal: 1680 ave 1680 max 1680 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Expand Down
9,138 changes: 4,569 additions & 4,569 deletions files/tutorial4/solution/equilibrate.data
View file
Open in desktop

Large diffs are not rendered by default.

46 changes: 16 additions & 30 deletions files/tutorial4/solution/equilibrate.ipynb
View file
Open in desktop

Large diffs are not rendered by default.

24 changes: 23 additions & 1 deletion files/tutorial4/solution/equilibrate.lmp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -12,16 +12,34 @@ pair_style lj/cut/tip4p/long O H O-H H-O-H 0.1546 12.0
kspace_style pppm/tip4p 1.0e-5
kspace_modify slab 3.0

read_data minimize.data
read_data create.data

include parameters.inc
include groups.inc

fix myshk H2O shake 1.0e-5 200 0 b O-H a H-O-H kbond 2000

dump mydmp all image 1 myimage-*.ppm type type &
shiny 0.1 box no 0.01 view 90 0 zoom 1.8
dump_modify mydmp backcolor white &
acolor O red adiam O 2 &
acolor H white adiam H 1 &
acolor Na+ blue adiam Na+ 2.5 &
acolor Cl- cyan adiam Cl- 3 &
acolor WALL gray adiam WALL 3

thermo 1
thermo_style custom step temp etotal press

minimize 1.0e-6 1.0e-6 1000 1000
reset_timestep 0

fix mynvt all nvt temp 300 300 100
fix myshk H2O shake 1.0e-5 200 0 b O-H a H-O-H
fix myrct all recenter NULL NULL 0
timestep 1.0

undump mydmp
dump mydmp all image 250 myimage-*.ppm type type &
shiny 0.1 box no 0.01 view 90 0 zoom 1.8
dump_modify mydmp backcolor white &
Expand All @@ -41,3 +59,7 @@ thermo_style custom step temp etotal press v_deltaz
run 30000

write_data equilibrate.data nocoeff




Loading