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Merge branch 'develop' into mala

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Lenz Fiedler
2025-01-15 13:19:15 +01:00
committed by GitHub
parent bf0f149445 ffa4765b15
commit c3ca6a8e56
30 changed files with 57965 additions and 3 deletions
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# Point dipoles in a 3d box with an external potential (ignoring dipolar interactions)
units lj
atom_style hybrid sphere dipole
dimension 3
boundary s s s
region box block -2 2 -2 2 -2 2
create_box 1 box
create_atoms 1 random 100 12345 NULL
# need both mass settings due to hybrid atom style
mass 1 1.0
set group all mass 1.0
set group all diameter 0.1
set group all dipole/random 98934 0.01
pair_style none
comm_modify cutoff 3.0
velocity all create 0.0 87287 mom yes rot yes
fix 1 all nve/sphere update dipole
###############################################################################################################
## Yukawa potential
#fix 2 all efield/lepton "A*exp(-B*r)/r; r=abs(sqrt(x^2+y^2+z^2)); A = 0.1; B = 5" step 1e-8
## Gradually increasing uniform field
#variable E equal ramp(0,1)
#fix 2 all efield/lepton "-v_E*(x+y+z)"
## Linear gradient field
fix 2 all efield/lepton "-1/6*x^3" step 1e-6
fix_modify 2 energy yes
###############################################################################################################
timestep 1e-3
compute erot all erotate/sphere
variable etotal equal "ke + c_erot + pe" # thermo etotal doesn't include erot
thermo_style custom step temp ke c_erot pe v_etotal
thermo 500
thermo_modify norm no
#dump 1 all custom 500 dump.dipole id x y z diameter mux muy muz fx fy fz tqx tqy tqz
run 10000

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LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-283-g742c869534-modified)
using 1 OpenMP thread(s) per MPI task
# Point dipoles in a 3d box with an external potential (ignoring dipolar interactions)
units lj
atom_style hybrid sphere dipole
WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:132)
dimension 3
boundary s s s
region box block -2 2 -2 2 -2 2
create_box 1 box
Created orthogonal box = (-2 -2 -2) to (2 2 2)
1 by 1 by 1 MPI processor grid
create_atoms 1 random 100 12345 NULL
Created 100 atoms
using lattice units in orthogonal box = (-2.0004 -2.0004 -2.0004) to (2.0004 2.0004 2.0004)
create_atoms CPU = 0.000 seconds
# need both mass settings due to hybrid atom style
mass 1 1.0
set group all mass 1.0
Setting atom values ...
100 settings made for mass
set group all diameter 0.1
Setting atom values ...
100 settings made for diameter
set group all dipole/random 98934 0.01
Setting atom values ...
100 settings made for dipole/random
pair_style none
comm_modify cutoff 3.0
velocity all create 0.0 87287 mom yes rot yes
fix 1 all nve/sphere update dipole
###############################################################################################################
## Yukawa potential
#fix 2 all efield/lepton "A*exp(-B*r)/r; r=abs(sqrt(x^2+y^2+z^2)); A = 0.1; B = 5" step 1e-8
## Gradually increasing uniform field
#variable E equal ramp(0,1)
#fix 2 all efield/lepton "-v_E*(x+y+z)"
## Linear gradient field
fix 2 all efield/lepton "-1/6*x^3" step 1e-6
fix_modify 2 energy yes
###############################################################################################################
timestep 1e-3
compute erot all erotate/sphere
variable etotal equal "ke + c_erot + pe" # thermo etotal doesn't include erot
thermo_style custom step temp ke c_erot pe v_etotal
thermo 500
thermo_modify norm no
#dump 1 all custom 500 dump.dipole id x y z diameter mux muy muz fx fy fz tqx tqy tqz
run 10000
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2442)
Per MPI rank memory allocation (min/avg/max) = 4.273 | 4.273 | 4.273 Mbytes
Step Temp KinEng c_erot PotEng v_etotal
0 0 0 0 0.036419797 0.036419797
500 3.7159175e-06 0.00055181374 0.44262618 -0.40675701 0.036420985
1000 1.2808438e-05 0.0019020531 0.24499116 -0.21047295 0.036420259
1500 2.8343769e-05 0.0042090498 0.26504485 -0.2328336 0.036420307
2000 4.8796894e-05 0.0072463388 0.30953526 -0.28036098 0.036420618
2500 7.8933715e-05 0.011721657 0.2015076 -0.17680909 0.036420173
3000 0.00011381678 0.016901791 0.31002163 -0.29050294 0.036420476
3500 0.00015650339 0.023240753 0.27837968 -0.26520001 0.036420418
4000 0.00020429109 0.030337227 0.26201101 -0.25592795 0.036420289
4500 0.00026362339 0.039148074 0.29769952 -0.3004271 0.036420499
5000 0.00033328941 0.049493478 0.21642442 -0.22949776 0.036420131
5500 0.00040914224 0.060757622 0.28422322 -0.30856047 0.036420377
6000 0.00049425119 0.073396302 0.31767 -0.35464572 0.03642058
6500 0.00058508892 0.086885704 0.29079532 -0.34126075 0.036420276
7000 0.00069845073 0.10371993 0.25776048 -0.32506015 0.036420262
7500 0.0008215656 0.12200249 0.27033777 -0.35591972 0.036420539
8000 0.00095528125 0.14185927 0.33943527 -0.44487406 0.036420479
8500 0.0011052502 0.16412965 0.26727165 -0.39498109 0.036420218
9000 0.0012738298 0.18916373 0.31082058 -0.46356382 0.036420485
9500 0.001464197 0.21743325 0.25669856 -0.43771158 0.036420224
10000 0.0016627654 0.24692067 0.36273185 -0.57323194 0.036420578
Loop time of 0.84714 on 1 procs for 10000 steps with 100 atoms
Performance: 1019901.911 tau/day, 11804.420 timesteps/s, 1.180 Matom-step/s
62.3% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 9.21e-07 | 9.21e-07 | 9.21e-07 | 0.0 | 0.00
Comm | 0.00094138 | 0.00094138 | 0.00094138 | 0.0 | 0.11
Output | 0.0001983 | 0.0001983 | 0.0001983 | 0.0 | 0.02
Modify | 0.84105 | 0.84105 | 0.84105 | 0.0 | 99.28
Other | | 0.004946 | | | 0.58
Nlocal: 100 ave 100 max 100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 5
Dangerous builds = 0
Total wall time: 0:00:00

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LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-283-g742c869534-modified)
using 1 OpenMP thread(s) per MPI task
# Point dipoles in a 3d box with an external potential (ignoring dipolar interactions)
units lj
atom_style hybrid sphere dipole
WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:132)
dimension 3
boundary s s s
region box block -2 2 -2 2 -2 2
create_box 1 box
Created orthogonal box = (-2 -2 -2) to (2 2 2)
1 by 2 by 2 MPI processor grid
create_atoms 1 random 100 12345 NULL
Created 100 atoms
using lattice units in orthogonal box = (-2.0004 -2.0004 -2.0004) to (2.0004 2.0004 2.0004)
create_atoms CPU = 0.000 seconds
# need both mass settings due to hybrid atom style
mass 1 1.0
set group all mass 1.0
Setting atom values ...
100 settings made for mass
set group all diameter 0.1
Setting atom values ...
100 settings made for diameter
set group all dipole/random 98934 0.01
Setting atom values ...
100 settings made for dipole/random
pair_style none
comm_modify cutoff 3.0
velocity all create 0.0 87287 mom yes rot yes
fix 1 all nve/sphere update dipole
###############################################################################################################
## Yukawa potential
#fix 2 all efield/lepton "A*exp(-B*r)/r; r=abs(sqrt(x^2+y^2+z^2)); A = 0.1; B = 5" step 1e-8
## Gradually increasing uniform field
#variable E equal ramp(0,1)
#fix 2 all efield/lepton "-v_E*(x+y+z)"
## Linear gradient field
fix 2 all efield/lepton "-1/6*x^3" step 1e-6
fix_modify 2 energy yes
###############################################################################################################
timestep 1e-3
compute erot all erotate/sphere
variable etotal equal "ke + c_erot + pe" # thermo etotal doesn't include erot
thermo_style custom step temp ke c_erot pe v_etotal
thermo 500
thermo_modify norm no
#dump 1 all custom 500 dump.dipole id x y z diameter mux muy muz fx fy fz tqx tqy tqz
run 10000
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2442)
Per MPI rank memory allocation (min/avg/max) = 4.289 | 4.289 | 4.289 Mbytes
Step Temp KinEng c_erot PotEng v_etotal
0 0 0 0 0.036419797 0.036419797
500 3.7159175e-06 0.00055181374 0.44262618 -0.40675701 0.036420985
1000 1.2808438e-05 0.0019020531 0.24499116 -0.21047295 0.036420259
1500 2.8343769e-05 0.0042090498 0.26504485 -0.2328336 0.036420307
2000 4.8796894e-05 0.0072463388 0.30953526 -0.28036098 0.036420618
2500 7.8933715e-05 0.011721657 0.2015076 -0.17680909 0.036420173
3000 0.00011381678 0.016901791 0.31002163 -0.29050294 0.036420476
3500 0.00015650339 0.023240753 0.27837968 -0.26520001 0.036420418
4000 0.00020429109 0.030337227 0.26201101 -0.25592795 0.036420289
4500 0.00026362339 0.039148074 0.29769952 -0.3004271 0.036420499
5000 0.00033328941 0.049493478 0.21642442 -0.22949776 0.036420131
5500 0.00040914224 0.060757622 0.28422322 -0.30856047 0.036420377
6000 0.00049425119 0.073396302 0.31767 -0.35464572 0.03642058
6500 0.00058508892 0.086885704 0.29079532 -0.34126075 0.036420276
7000 0.00069845073 0.10371993 0.25776048 -0.32506015 0.036420262
7500 0.0008215656 0.12200249 0.27033777 -0.35591972 0.036420539
8000 0.00095528125 0.14185927 0.33943527 -0.44487406 0.036420479
8500 0.0011052502 0.16412965 0.26727165 -0.39498109 0.036420218
9000 0.0012738298 0.18916373 0.31082058 -0.46356382 0.036420485
9500 0.001464197 0.21743325 0.25669856 -0.43771158 0.036420224
10000 0.0016627654 0.24692067 0.36273185 -0.57323194 0.036420578
Loop time of 0.985035 on 4 procs for 10000 steps with 100 atoms
Performance: 877125.838 tau/day, 10151.919 timesteps/s, 1.015 Matom-step/s
67.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 7.22e-07 | 8.9125e-07 | 1.031e-06 | 0.0 | 0.00
Comm | 0.09818 | 0.1024 | 0.10798 | 1.1 | 10.40
Output | 0.00021634 | 0.00028668 | 0.00044312 | 0.0 | 0.03
Modify | 0.773 | 0.81845 | 0.84055 | 3.0 | 83.09
Other | | 0.06389 | | | 6.49
Nlocal: 25 ave 30 max 23 min
Histogram: 2 1 0 0 0 0 0 0 0 1
Nghost: 75 ave 77 max 70 min
Histogram: 1 0 0 0 0 0 0 0 1 2
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 5
Dangerous builds = 0
Total wall time: 0:00:00

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To run these examples, one needs to compile LAMMPS with the ML-PACE (-DPKG_ML-PACE=ON) and the EXTRA-PAIR packages (-DPKG_EXTRA-PAIR=ON).
These examples show how to combine a short-ranged ML potential with a dispersion correction scheme. Here we combine a general-purpose ACE potential for carbon (10.1021/acs.jctc.2c01149), with two different dispersion correction schemes:
- D2 (a pure two-body potential, here tabulated)
- D3 (a many-body potential, implemented in LAMMPS).

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atom_style atomic
units metal
boundary p p p
atom_modify sort 0 0.0
lattice sc 1.0
region box block 0 10 0 10 0 10
create_box 1 box
create_atoms 1 region box
variable l equal 47.6
change_box all x final 0 $l y final 0 $l z final 0 $l remap
region world block INF INF INF INF INF INF
### interactions
pair_style hybrid/overlay pace table linear 10000
pair_coeff * * pace potential_files/c_ace.yace C
pair_coeff * * table potential_files/d2.table D2 9.0
mass 1 12.011000
velocity all create 200 1234
compute c1 all pair pace
compute c2 all pair table
# calculate the e/atom for each pair style individually
variable dUpace equal c_c1/atoms
variable dUd2 equal c_c2/atoms
### run
timestep 0.001
fix 1 all nvt temp 200.0 200.0 0.01
thermo_style custom step temp pe press etotal v_dUpace v_dUd2
thermo 10
run 100

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atom_style atomic
units metal
boundary p p p
atom_modify sort 0 0.0
lattice sc 1.0
region box block 0 10 0 10 0 10
create_box 1 box
create_atoms 1 region box
variable l equal 47.6
change_box all x final 0 $l y final 0 $l z final 0 $l remap
region world block INF INF INF INF INF INF
### interactions
pair_style hybrid/overlay pace dispersion/d3 bj pbe 16.0 16.0
pair_coeff * * pace potential_files/c_ace.yace C
pair_coeff * * dispersion/d3 C
mass 1 12.011000
velocity all create 200 1234
compute c1 all pair pace
compute c2 all pair dispersion/d3
# calculate the e/atom for each pair style individually
variable Upace equal c_c1/atoms
variable Ud3 equal c_c2/atoms
### run
timestep 0.001
fix 1 all nvt temp 200.0 200.0 0.01
thermo_style custom step temp pe press etotal v_Upace v_Ud3
thermo 10
run 100

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LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-125-g095d33dafb)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
atom_style atomic
units metal
boundary p p p
atom_modify sort 0 0.0
lattice sc 1.0
Lattice spacing in x,y,z = 1 1 1
region box block 0 10 0 10 0 10
create_box 1 box
Created orthogonal box = (0 0 0) to (10 10 10)
1 by 1 by 1 MPI processor grid
create_atoms 1 region box
Created 1000 atoms
using lattice units in orthogonal box = (0 0 0) to (10 10 10)
create_atoms CPU = 0.000 seconds
variable l equal 47.6
change_box all x final 0 $l y final 0 $l z final 0 $l remap
change_box all x final 0 47.6 y final 0 $l z final 0 $l remap
change_box all x final 0 47.6 y final 0 47.6 z final 0 $l remap
change_box all x final 0 47.6 y final 0 47.6 z final 0 47.6 remap
Changing box ...
orthogonal box = (0 0 0) to (47.6 10 10)
orthogonal box = (0 0 0) to (47.6 47.6 10)
orthogonal box = (0 0 0) to (47.6 47.6 47.6)
region world block INF INF INF INF INF INF
### interactions
pair_style hybrid/overlay pace table linear 10000
ACE version: 2023.11.25
Recursive evaluator is used
pair_coeff * * pace potential_files/c_ace.yace C
Loading potential_files/c_ace.yace
Total number of basis functions
C: 20 (r=1) 455 (r>1)
Mapping LAMMPS atom type #1(C) -> ACE species type #0
pair_coeff * * table potential_files/d2.table D2 9.0
Reading pair table potential file potential_files/d2.table with DATE: 2021-12-16
WARNING: 8063 of 20000 force values in table D2 are inconsistent with -dE/dr.
WARNING: Should only be flagged at inflection points (src/pair_table.cpp:466)
WARNING: 2386 of 20000 distance values in table 1e-06 with relative error
WARNING: over D2 to re-computed values (src/pair_table.cpp:474)
mass 1 12.011000
velocity all create 200 1234
compute c1 all pair pace
compute c2 all pair table
# calculate the e/atom for each pair style individually
variable dUpace equal c_c1/atoms
variable dUd2 equal c_c2/atoms
### run
timestep 0.001
fix 1 all nvt temp 200.0 200.0 0.01
thermo_style custom step temp pe press etotal v_dUpace v_dUd2
thermo 10
run 100
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 11
ghost atom cutoff = 11
binsize = 5.5, bins = 9 9 9
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair pace, perpetual
attributes: full, newton on, cut 7.5
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) pair table, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.735 | 3.735 | 3.735 Mbytes
Step Temp PotEng Press TotEng v_dUpace v_dUd2
0 200 -262.26589 -9971.6713 -236.43971 -0.2577066 -0.0045592958
10 198.01563 -261.95164 -9936.5218 -236.38171 -0.25738489 -0.004566747
20 199.80384 -261.06484 -9826.0969 -235.26399 -0.25647577 -0.0045890709
30 200.79867 -259.7549 -9655.8924 -233.82559 -0.25512792 -0.0046269853
40 194.7303 -258.36397 -9450.9508 -233.21827 -0.25368377 -0.004680203
50 197.08802 -257.40377 -9200.5727 -231.95362 -0.25265301 -0.0047507608
60 204.21755 -257.66495 -8919.2309 -231.29416 -0.25282305 -0.0048419012
70 216.81983 -260.19034 -8702.5441 -232.19221 -0.25523198 -0.0049583602
80 242.71952 -266.40641 -8617.9868 -235.06383 -0.26129243 -0.0051139831
90 294.45869 -279.46195 -8724.2954 -241.43824 -0.27411961 -0.0053423377
100 400.44323 -307.29577 -9070.6387 -255.58618 -0.30165815 -0.0056376175
Loop time of 2.66184 on 1 procs for 100 steps with 1000 atoms
Performance: 3.246 ns/day, 7.394 hours/ns, 37.568 timesteps/s, 37.568 katom-step/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.6584 | 2.6584 | 2.6584 | 0.0 | 99.87
Neigh | 0.0012861 | 0.0012861 | 0.0012861 | 0.0 | 0.05
Comm | 0.00064617 | 0.00064617 | 0.00064617 | 0.0 | 0.02
Output | 0.00024173 | 0.00024173 | 0.00024173 | 0.0 | 0.01
Modify | 0.00099328 | 0.00099328 | 0.00099328 | 0.0 | 0.04
Other | | 0.0002431 | | | 0.01
Nlocal: 1000 ave 1000 max 1000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2375 ave 2375 max 2375 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 26027 ave 26027 max 26027 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 17736 ave 17736 max 17736 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 26027
Ave neighs/atom = 26.027
Neighbor list builds = 1
Dangerous builds = 0
Total wall time: 0:00:02

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LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-125-g095d33dafb)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
atom_style atomic
units metal
boundary p p p
atom_modify sort 0 0.0
lattice sc 1.0
Lattice spacing in x,y,z = 1 1 1
region box block 0 10 0 10 0 10
create_box 1 box
Created orthogonal box = (0 0 0) to (10 10 10)
1 by 2 by 2 MPI processor grid
create_atoms 1 region box
Created 1000 atoms
using lattice units in orthogonal box = (0 0 0) to (10 10 10)
create_atoms CPU = 0.000 seconds
variable l equal 47.6
change_box all x final 0 $l y final 0 $l z final 0 $l remap
change_box all x final 0 47.6 y final 0 $l z final 0 $l remap
change_box all x final 0 47.6 y final 0 47.6 z final 0 $l remap
change_box all x final 0 47.6 y final 0 47.6 z final 0 47.6 remap
Changing box ...
orthogonal box = (0 0 0) to (47.6 10 10)
orthogonal box = (0 0 0) to (47.6 47.6 10)
orthogonal box = (0 0 0) to (47.6 47.6 47.6)
region world block INF INF INF INF INF INF
### interactions
pair_style hybrid/overlay pace table linear 10000
ACE version: 2023.11.25
Recursive evaluator is used
pair_coeff * * pace potential_files/c_ace.yace C
Loading potential_files/c_ace.yace
Total number of basis functions
C: 20 (r=1) 455 (r>1)
Mapping LAMMPS atom type #1(C) -> ACE species type #0
pair_coeff * * table potential_files/d2.table D2 9.0
Reading pair table potential file potential_files/d2.table with DATE: 2021-12-16
WARNING: 8063 of 20000 force values in table D2 are inconsistent with -dE/dr.
WARNING: Should only be flagged at inflection points (src/pair_table.cpp:466)
WARNING: 2386 of 20000 distance values in table 1e-06 with relative error
WARNING: over D2 to re-computed values (src/pair_table.cpp:474)
mass 1 12.011000
velocity all create 200 1234
compute c1 all pair pace
compute c2 all pair table
# calculate the e/atom for each pair style individually
variable dUpace equal c_c1/atoms
variable dUd2 equal c_c2/atoms
### run
timestep 0.001
fix 1 all nvt temp 200.0 200.0 0.01
thermo_style custom step temp pe press etotal v_dUpace v_dUd2
thermo 10
run 100
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 11
ghost atom cutoff = 11
binsize = 5.5, bins = 9 9 9
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair pace, perpetual
attributes: full, newton on, cut 7.5
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) pair table, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.655 | 3.655 | 3.655 Mbytes
Step Temp PotEng Press TotEng v_dUpace v_dUd2
0 200 -262.26589 -9971.6713 -236.43971 -0.2577066 -0.0045592958
10 198.00622 -261.95011 -9934.5046 -236.38139 -0.25738304 -0.0045670733
20 199.81545 -261.06219 -9818.4051 -235.25985 -0.25647183 -0.0045903655
30 200.85902 -259.76256 -9639.9086 -233.82546 -0.25513263 -0.0046299265
40 195.00229 -258.4153 -9425.3772 -233.23448 -0.25372979 -0.0046855071
50 198.00573 -257.57066 -9164.7658 -232.00201 -0.25281159 -0.0047590772
60 206.26759 -258.09159 -8877.0162 -231.45607 -0.25323684 -0.0048547477
70 219.81939 -261.10607 -8668.5789 -232.7206 -0.25612771 -0.0049783595
80 250.27428 -268.27862 -8601.1343 -235.96048 -0.2631332 -0.0051454143
90 308.88167 -283.24793 -8745.8792 -243.36177 -0.27785093 -0.0053969977
100 427.60692 -315.05776 -9147.2389 -259.8405 -0.30933434 -0.0057234269
Loop time of 0.69628 on 4 procs for 100 steps with 1000 atoms
Performance: 12.409 ns/day, 1.934 hours/ns, 143.620 timesteps/s, 143.620 katom-step/s
99.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.67839 | 0.68307 | 0.69054 | 0.6 | 98.10
Neigh | 0.00034181 | 0.00034811 | 0.00036188 | 0.0 | 0.05
Comm | 0.0045334 | 0.012031 | 0.016704 | 4.4 | 1.73
Output | 0.00015123 | 0.00017175 | 0.0002318 | 0.0 | 0.02
Modify | 0.00041346 | 0.00043062 | 0.00044327 | 0.0 | 0.06
Other | | 0.0002301 | | | 0.03
Nlocal: 250 ave 261 max 246 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Nghost: 1250 ave 1254 max 1239 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 6501 ave 6778 max 6320 min
Histogram: 1 0 2 0 0 0 0 0 0 1
FullNghs: 4421.5 ave 4595 max 4332 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Total # of neighbors = 26004
Ave neighs/atom = 26.004
Neighbor list builds = 1
Dangerous builds = 0
Total wall time: 0:00:00

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LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-125-g095d33dafb)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
atom_style atomic
units metal
boundary p p p
atom_modify sort 0 0.0
lattice sc 1.0
Lattice spacing in x,y,z = 1 1 1
region box block 0 10 0 10 0 10
create_box 1 box
Created orthogonal box = (0 0 0) to (10 10 10)
1 by 1 by 1 MPI processor grid
create_atoms 1 region box
Created 1000 atoms
using lattice units in orthogonal box = (0 0 0) to (10 10 10)
create_atoms CPU = 0.000 seconds
variable l equal 47.6
change_box all x final 0 $l y final 0 $l z final 0 $l remap
change_box all x final 0 47.6 y final 0 $l z final 0 $l remap
change_box all x final 0 47.6 y final 0 47.6 z final 0 $l remap
change_box all x final 0 47.6 y final 0 47.6 z final 0 47.6 remap
Changing box ...
orthogonal box = (0 0 0) to (47.6 10 10)
orthogonal box = (0 0 0) to (47.6 47.6 10)
orthogonal box = (0 0 0) to (47.6 47.6 47.6)
region world block INF INF INF INF INF INF
### interactions
pair_style hybrid/overlay pace dispersion/d3 bj pbe 16.0 16.0
ACE version: 2023.11.25
Recursive evaluator is used
pair_coeff * * pace potential_files/c_ace.yace C
Loading potential_files/c_ace.yace
Total number of basis functions
C: 20 (r=1) 455 (r>1)
Mapping LAMMPS atom type #1(C) -> ACE species type #0
pair_coeff * * dispersion/d3 C
mass 1 12.011000
velocity all create 200 1234
compute c1 all pair pace
compute c2 all pair dispersion/d3
# calculate the e/atom for each pair style individually
variable Upace equal c_c1/atoms
variable Ud3 equal c_c2/atoms
### run
timestep 0.001
fix 1 all nvt temp 200.0 200.0 0.01
thermo_style custom step temp pe press etotal v_Upace v_Ud3
thermo 10
run 100
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 6 6 6
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair pace, perpetual
attributes: full, newton on, cut 7.5
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) pair dispersion/d3, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.225 | 4.225 | 4.225 Mbytes
Step Temp PotEng Press TotEng v_Upace v_Ud3
0 200 -269.22784 -10163.81 -243.40166 -0.2577066 -0.011521241
10 198.05578 -268.91992 -10128.61 -243.34481 -0.25738487 -0.01153505
20 199.85092 -268.05146 -10018.116 -242.24454 -0.25647561 -0.011575851
30 201.10902 -266.77119 -9847.2946 -240.80181 -0.2551274 -0.011643795
40 195.0686 -265.42225 -9641.6992 -240.23287 -0.25368339 -0.011738855
50 197.63706 -264.51951 -9390.1455 -238.99847 -0.25265765 -0.011861864
60 205.01072 -264.86268 -9107.4427 -238.38947 -0.25284579 -0.012016888
70 217.51797 -267.50863 -8890.9916 -239.42034 -0.25529813 -0.012210496
80 244.30754 -273.91051 -8806.154 -242.36286 -0.26145652 -0.01245399
90 296.72041 -287.2518 -8913.8963 -248.93603 -0.27448382 -0.012767981
100 404.07337 -315.6103 -9266.1292 -263.43195 -0.3024416 -0.013168694
Loop time of 4.52709 on 1 procs for 100 steps with 1000 atoms
Performance: 1.909 ns/day, 12.575 hours/ns, 22.089 timesteps/s, 22.089 katom-step/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.5223 | 4.5223 | 4.5223 | 0.0 | 99.89
Neigh | 0.0023631 | 0.0023631 | 0.0023631 | 0.0 | 0.05
Comm | 0.00088624 | 0.00088624 | 0.00088624 | 0.0 | 0.02
Output | 0.00027759 | 0.00027759 | 0.00027759 | 0.0 | 0.01
Modify | 0.0010211 | 0.0010211 | 0.0010211 | 0.0 | 0.02
Other | | 0.0002737 | | | 0.01
Nlocal: 1000 ave 1000 max 1000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3913 ave 3913 max 3913 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 116409 ave 116409 max 116409 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 17748 ave 17748 max 17748 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 116409
Ave neighs/atom = 116.409
Neighbor list builds = 1
Dangerous builds = 0
Total wall time: 0:00:04

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LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-125-g095d33dafb)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
atom_style atomic
units metal
boundary p p p
atom_modify sort 0 0.0
lattice sc 1.0
Lattice spacing in x,y,z = 1 1 1
region box block 0 10 0 10 0 10
create_box 1 box
Created orthogonal box = (0 0 0) to (10 10 10)
1 by 2 by 2 MPI processor grid
create_atoms 1 region box
Created 1000 atoms
using lattice units in orthogonal box = (0 0 0) to (10 10 10)
create_atoms CPU = 0.000 seconds
variable l equal 47.6
change_box all x final 0 $l y final 0 $l z final 0 $l remap
change_box all x final 0 47.6 y final 0 $l z final 0 $l remap
change_box all x final 0 47.6 y final 0 47.6 z final 0 $l remap
change_box all x final 0 47.6 y final 0 47.6 z final 0 47.6 remap
Changing box ...
orthogonal box = (0 0 0) to (47.6 10 10)
orthogonal box = (0 0 0) to (47.6 47.6 10)
orthogonal box = (0 0 0) to (47.6 47.6 47.6)
region world block INF INF INF INF INF INF
### interactions
pair_style hybrid/overlay pace dispersion/d3 bj pbe 16.0 16.0
ACE version: 2023.11.25
Recursive evaluator is used
pair_coeff * * pace potential_files/c_ace.yace C
Loading potential_files/c_ace.yace
Total number of basis functions
C: 20 (r=1) 455 (r>1)
Mapping LAMMPS atom type #1(C) -> ACE species type #0
pair_coeff * * dispersion/d3 C
mass 1 12.011000
velocity all create 200 1234
compute c1 all pair pace
compute c2 all pair dispersion/d3
# calculate the e/atom for each pair style individually
variable Upace equal c_c1/atoms
variable Ud3 equal c_c2/atoms
### run
timestep 0.001
fix 1 all nvt temp 200.0 200.0 0.01
thermo_style custom step temp pe press etotal v_Upace v_Ud3
thermo 10
run 100
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 6 6 6
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair pace, perpetual
attributes: full, newton on, cut 7.5
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) pair dispersion/d3, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.732 | 3.732 | 3.732 Mbytes
Step Temp PotEng Press TotEng v_Upace v_Ud3
0 200 -269.22784 -10163.81 -243.40166 -0.2577066 -0.011521241
10 198.04813 -268.91867 -10126.59 -243.34454 -0.25738301 -0.011535654
20 199.86491 -268.04994 -10010.421 -242.24121 -0.25647167 -0.011578276
30 201.18317 -266.78129 -9831.2837 -240.80233 -0.25513213 -0.011649162
40 195.35281 -265.47802 -9616.0833 -240.25194 -0.2537296 -0.011748422
50 198.56247 -264.69401 -9354.3017 -239.05347 -0.25281709 -0.011876925
60 207.17238 -265.30194 -9065.1196 -238.54959 -0.25326251 -0.012039431
70 221.05245 -268.44583 -8856.3622 -239.90114 -0.25620278 -0.012243053
80 252.00942 -275.82142 -8789.4126 -243.27922 -0.26332044 -0.012500977
90 311.21153 -291.09334 -8935.4036 -250.90632 -0.27825852 -0.012834817
100 431.24438 -323.45003 -9344.1963 -267.76306 -0.31019084 -0.013259185
Loop time of 1.20684 on 4 procs for 100 steps with 1000 atoms
Performance: 7.159 ns/day, 3.352 hours/ns, 82.861 timesteps/s, 82.861 katom-step/s
99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.2007 | 1.2019 | 1.2029 | 0.1 | 99.60
Neigh | 0.00060541 | 0.00062493 | 0.00064411 | 0.0 | 0.05
Comm | 0.0024344 | 0.0033552 | 0.0045996 | 1.4 | 0.28
Output | 0.00016956 | 0.00017999 | 0.00021054 | 0.0 | 0.01
Modify | 0.00046946 | 0.00048235 | 0.00049796 | 0.0 | 0.04
Other | | 0.0002449 | | | 0.02
Nlocal: 250 ave 261 max 246 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Nghost: 2198 ave 2202 max 2187 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 29023.2 ave 29681 max 27646 min
Histogram: 1 0 0 0 0 0 0 1 0 2
FullNghs: 4421 ave 4595 max 4331 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Total # of neighbors = 116093
Ave neighs/atom = 116.093
Neighbor list builds = 1
Dangerous builds = 0
Total wall time: 0:00:01

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