ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

start of clean up

Browse Source
This commit is contained in:
Tom Swinburne
2020-04-17 18:11:59 +02:00
parent 6904e1e6ef
commit 0ea2eabbb2
11 changed files with 383 additions and 1437 deletions
Download Patch File Download Diff File Expand all files Collapse all files

0
examples/USER/pafi/Fe.eam.fs → examples/USER/misc/pafi/Fe_M07.eam.fs
View File

3
examples/USER/pafi/README → examples/USER/misc/pafi/README
View File

@ -26,6 +26,5 @@ make machine # for binary (machine= e.g. mpi)
To run the example from this folder:
```
mpirun -np NPROCS /path/to/lammps/src/lmp_machine < pafi.lammps
mpirun -np NPROCS /path/to/lammps/src/lmp_machine -in in.pafi.lammps
```

9
examples/USER/pafi/pafi.lammps → examples/USER/misc/pafi/in.pafi.lammps
View File

@ -1,6 +1,7 @@
units metal
atom_style atomic
atom_modify map array sort 0 0.0
neigh_modify every 2 delay 10 check yes page 1000000 one 100000
## read in path data using fix property/atom
fix pa all property/atom d_nx d_ny d_nz d_dnx d_dny d_dnz d_ddnx d_ddny d_ddnz
@ -9,7 +10,8 @@ run 0
## EAM potential
pair_style eam/fs
pair_coeff * * ../Fe.eam.fs Fe
pair_coeff * * Fe_M07.eam.fs Fe
mass * 55.85
thermo 100
@ -23,7 +25,7 @@ compute pa all property/atom d_nx d_ny d_nz d_dnx d_dny d_dnz d_ddnx d_ddny d_dd
run 0
## fix name group-id hp compute-id temperature damp seed overdamped 0/1 com 0/1
fix hp all hp pa 400.0 0.1 434 overdamped 1 com 1
fix hp all pafi pa 1000.1 0.05 434 overdamped 1 com 1
run 0
variable dn equal f_hp[4]*f_hp[4] # should be zero
fix af all ave/time 1 1000 1000 f_hp[1] f_hp[2] f_hp[3] v_dn
@ -46,3 +48,4 @@ unfix hp
minimize 0 0 1000 1000
print "energy=${pe}"
write_data final.dat

331
examples/USER/misc/pafi/log.pafi Normal file
View File

@ -0,0 +1,331 @@
LAMMPS (19 Mar 2020)
units metal
boundary p p p
atom_style atomic
## read in path data using fix property/atom
fix pa all property/atom d_nx d_ny d_nz d_dnx d_dny d_dnz d_ddnx d_ddny d_ddnz
read_data test.dat fix pa NULL PafiPath
orthogonal box = (0 0 0) to (19.9872 19.9872 19.9872)
1 by 1 by 2 MPI processor grid
reading atoms ...
687 atoms
read_data CPU = 0.00923154 secs
run 0
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:1950)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:166)
Per MPI rank memory allocation (min/avg/max) = 2.422 | 2.422 | 2.422 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 0 0 0 0
Loop time of 6.9535e-06 on 2 procs for 0 steps with 687 atoms
107.9% CPU use with 2 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
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 | | 6.954e-06 | | |100.00
Nlocal: 343.5 ave 353 max 334 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 0 ave 0 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
## EAM potential
pair_style eam/fs
pair_coeff * * Fe_M07.eam.fs Fe
mass * 55.85
thermo 100
compute pe all pe
variable pe equal pe
run 0
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 7.8
ghost atom cutoff = 7.8
binsize = 3.9, bins = 6 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair eam/fs, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.438 | 3.438 | 3.438 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -2828.1883 0 -2828.1883 3563.9872
Loop time of 1.475e-06 on 2 procs for 0 steps with 687 atoms
169.5% CPU use with 2 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
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 | | 1.475e-06 | | |100.00
Nlocal: 343.5 ave 353 max 334 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 2474.5 ave 2484 max 2465 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 28898 ave 29188 max 28608 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 57796
Ave neighs/atom = 84.1281
Neighbor list builds = 0
Dangerous builds = 0
print "energy=${pe}"
energy=-2828.18833783692
## compute property/atom to access relevant fields
compute pa all property/atom d_nx d_ny d_nz d_dnx d_dny d_dnz d_ddnx d_ddny d_ddnz
run 0
Per MPI rank memory allocation (min/avg/max) = 3.438 | 3.438 | 3.438 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -2828.1883 0 -2828.1883 3563.9872
Loop time of 1.683e-06 on 2 procs for 0 steps with 687 atoms
208.0% CPU use with 2 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
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 | | 1.683e-06 | | |100.00
Nlocal: 343.5 ave 353 max 334 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 2474.5 ave 2484 max 2465 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 28898 ave 29188 max 28608 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 57796
Ave neighs/atom = 84.1281
Neighbor list builds = 0
Dangerous builds = 0
## fix name group-id hp compute-id temperature damp seed overdamped 0/1 com 0/1
fix hp all hp pa 400.0 0.1 434 overdamped 1 com 1
fix hp compute name,style: pa,property/atom
run 0
Per MPI rank memory allocation (min/avg/max) = 4.938 | 4.938 | 4.938 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -2828.1883 0 -2828.1883 3563.9872
Loop time of 2.206e-06 on 2 procs for 0 steps with 687 atoms
294.7% CPU use with 2 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
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 | | 2.206e-06 | | |100.00
Nlocal: 343.5 ave 353 max 334 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 2474.5 ave 2484 max 2465 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 28898 ave 29188 max 28608 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 57796
Ave neighs/atom = 84.1281
Neighbor list builds = 0
Dangerous builds = 0
variable dn equal f_hp[4]*f_hp[4] # should be zero
fix af all ave/time 1 1000 1000 f_hp[1] f_hp[2] f_hp[3] v_dn
variable adn equal f_af[4] # should be zero
variable apf equal f_af[1]
run 1000
Per MPI rank memory allocation (min/avg/max) = 4.938 | 4.938 | 4.938 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -2828.1883 0 -2828.1883 3563.9872
100 0 -2787.7125 0 -2787.7125 16811.138
200 0 -2787.3136 0 -2787.3136 17302.039
300 0 -2788.1621 0 -2788.1621 16576.307
400 0 -2791.1893 0 -2791.1893 15611.421
500 0 -2787.3835 0 -2787.3835 17015.601
600 0 -2791.3402 0 -2791.3402 13819.752
700 0 -2788.5604 0 -2788.5604 15661.073
800 0 -2788.26 0 -2788.26 15554.53
900 0 -2788.2513 0 -2788.2513 16693.47
1000 0 -2790.1726 0 -2790.1726 15862.893
Loop time of 2.15129 on 2 procs for 1000 steps with 687 atoms
Performance: 40.162 ns/day, 0.598 hours/ns, 464.837 timesteps/s
98.3% CPU use with 2 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.9813 | 1.993 | 2.0047 | 0.8 | 92.64
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.058066 | 0.069807 | 0.081548 | 4.4 | 3.24
Output | 0.00018995 | 0.0002629 | 0.00033584 | 0.0 | 0.01
Modify | 0.081354 | 0.081403 | 0.081452 | 0.0 | 3.78
Other | | 0.006816 | | | 0.32
Nlocal: 343.5 ave 353 max 334 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 2474.5 ave 2484 max 2465 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 28898 ave 29188 max 28608 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 57796
Ave neighs/atom = 84.1281
Neighbor list builds = 0
Dangerous builds = 0
print "Squared displacement normal to hyperplane = ${adn} A^2"
Squared displacement normal to hyperplane = 1.92841033952627e-23 A^2
print "average projected force = ${apf} eV/A"
average projected force = 0.303660991606611 eV/A
## minimize under same constraint (temperature effectively zero)
min_style fire
minimize 0 0 1000 1000
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:190)
Parameters for fire:
dmax delaystep dtgrow dtshrink alpha0 alphashrink tmax tmin integrator halfstepback
0.1 20 1.1 0.5 0.25 0.99 10 0.02 eulerimplicit yes
Per MPI rank memory allocation (min/avg/max) = 4.938 | 4.938 | 4.938 Mbytes
Step Temp E_pair E_mol TotEng Press
1000 0 -2790.1726 0 -2790.1726 15862.893
1100 0.01395318 -2828.1875 0 -2828.1862 3564.2791
1200 1.3924969e-08 -2828.1886 0 -2828.1886 3561.3085
1300 2.7246418e-10 -2828.1886 0 -2828.1886 3561.2517
1400 1.990932e-13 -2828.1886 0 -2828.1886 3561.2506
1500 3.6357963e-16 -2828.1886 0 -2828.1886 3561.2513
1600 3.7304413e-16 -2828.1886 0 -2828.1886 3561.252
1700 3.7758424e-16 -2828.1886 0 -2828.1886 3561.2527
1800 3.7938855e-16 -2828.1886 0 -2828.1886 3561.2534
1900 3.800255e-16 -2828.1886 0 -2828.1886 3561.2542
2000 3.8025411e-16 -2828.1886 0 -2828.1886 3561.2549
Loop time of 1.14675 on 2 procs for 1000 steps with 687 atoms
97.6% CPU use with 2 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = max iterations
Energy initial, next-to-last, final =
-2790.17255859 -2828.18861166 -2828.18861166
Force two-norm initial, final = 27.9307 5.03831e-07
Force max component initial, final = 2.89389 1.97794e-07
Final line search alpha, max atom move = 0 0
Iterations, force evaluations = 1000 1018
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.0279 | 1.0557 | 1.0836 | 2.7 | 92.06
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.034238 | 0.062094 | 0.089951 | 11.2 | 5.41
Output | 0.00014876 | 0.00019727 | 0.00024578 | 0.0 | 0.02
Modify | 0.017477 | 0.017529 | 0.01758 | 0.0 | 1.53
Other | | 0.01121 | | | 0.98
Nlocal: 343.5 ave 345 max 342 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 2474.5 ave 2476 max 2473 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 28901.5 ave 30125 max 27678 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 57803
Ave neighs/atom = 84.1383
Neighbor list builds = 0
Dangerous builds = 0
print "energy=${pe}"
energy=-2828.1886116623
## minimize without constraint
unfix af
unfix hp
minimize 0 0 1000 1000
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:190)
Parameters for fire:
dmax delaystep dtgrow dtshrink alpha0 alphashrink tmax tmin integrator halfstepback
0.1 20 1.1 0.5 0.25 0.99 10 0.02 eulerimplicit yes
Per MPI rank memory allocation (min/avg/max) = 4.563 | 4.563 | 4.563 Mbytes
Step Temp E_pair E_mol TotEng Press
2000 0 -2828.1886 0 -2828.1886 3561.2549
2100 0.00019671788 -2828.3784 0 -2828.3784 3831.5695
2200 1.3047007e-08 -2828.3785 0 -2828.3785 3828.431
2300 1.2837148e-11 -2828.3785 0 -2828.3785 3828.4076
2400 3.6777219e-16 -2828.3785 0 -2828.3785 3828.4068
2500 1.0710252e-18 -2828.3785 0 -2828.3785 3828.4068
2600 1.3523987e-23 -2828.3785 0 -2828.3785 3828.4068
2700 1.4824109e-25 -2828.3785 0 -2828.3785 3828.4068
2800 2.3789827e-26 -2828.3785 0 -2828.3785 3828.4068
2900 1.6175585e-25 -2828.3785 0 -2828.3785 3828.4068
3000 2.6404401e-26 -2828.3785 0 -2828.3785 3828.4068
Loop time of 1.0043 on 2 procs for 1000 steps with 687 atoms
97.4% CPU use with 2 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = max iterations
Energy initial, next-to-last, final =
-2828.18861166 -2828.37851625 -2828.37851625
Force two-norm initial, final = 0.380384 3.56702e-13
Force max component initial, final = 0.149002 3.48055e-14
Final line search alpha, max atom move = 0 0
Iterations, force evaluations = 1000 1029
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.93605 | 0.94701 | 0.95796 | 1.1 | 94.30
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.034637 | 0.04556 | 0.056484 | 5.1 | 4.54
Output | 0.00014805 | 0.00019121 | 0.00023438 | 0.0 | 0.02
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.01154 | | | 1.15
Nlocal: 343.5 ave 353 max 334 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 2474.5 ave 2484 max 2465 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 28898.5 ave 29188 max 28609 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 57797
Ave neighs/atom = 84.1295
Neighbor list builds = 0
Dangerous builds = 0
print "energy=${pe}"
energy=-2828.37851624648
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:04

1391
examples/USER/pafi/test.dat
View File

File diff suppressed because it is too large Load Diff