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Merge branch 'develop' into bond/react-molmap_option

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This commit is contained in:
Axel Kohlmeyer
2025-03-30 23:27:50 -04:00
parent 05521d38d9 285baf27b5
commit 935e323d08
2010 changed files with 177765 additions and 51686 deletions
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1
examples/PACKAGES/atc/elastic/Au_u3.eam Symbolic link
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../../../../potentials/Au_u3.eam

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examples/PACKAGES/dispersion/README Normal file
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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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examples/PACKAGES/dispersion/in.d2 Normal file
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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

36
examples/PACKAGES/dispersion/in.d3 Normal file
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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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examples/PACKAGES/dispersion/log.20Dec2024.d2.g++.1 Normal file
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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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examples/PACKAGES/dispersion/log.20Dec2024.d2.g++.4 Normal file
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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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examples/PACKAGES/dispersion/log.20Dec2024.d3.g++.1 Normal file
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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

484
examples/PACKAGES/dispersion/potential_files/c_ace.yace Normal file
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20005
examples/PACKAGES/dispersion/potential_files/d2.table Normal file
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File diff suppressed because it is too large Load Diff

12
examples/PACKAGES/dpd-basic/dpd_coul_slater_long/data.dpd_coul_slater_long
View File

@ -15,12 +15,12 @@ Masses
PairIJ Coeffs # dpd/coul/slater/long
1 1 78 4.5 yes 1
1 2 78 4.5 yes 1
1 3 78 4.5 yes 1
2 2 78 4.5 no 1
2 3 78 4.5 no 1
3 3 78 4.5 no 1
1 1 78 4.5 no 1
1 2 78 4.5 no 1
1 3 78 4.5 no 1
2 2 78 4.5 yes 1
2 3 78 4.5 yes 1
3 3 78 4.5 yes 1
Atoms # full

48
examples/PACKAGES/dpd-basic/dpd_coul_slater_long/in.dpd_coul_slater_long
View File

@ -10,49 +10,47 @@ variable cut_coul equal 2.0
# Initialize LAMMPS run for 3-d periodic
#-------------------------------------------------------------------------------
units lj
boundary p p p # periodic at all axes
atom_style full
dimension 3
units lj
boundary p p p # periodic at all axes
atom_style full
dimension 3
bond_style none
angle_style none
dihedral_style none
improper_style none
bond_style none
angle_style none
dihedral_style none
improper_style none
newton on
comm_modify vel yes # store info of ghost atoms btw processors
newton on
comm_modify vel yes # store info of ghost atoms btw processors
#-------------------------------------------------------------------------------
# Box creation and configuration
#-------------------------------------------------------------------------------
# Define pair style and coefficients
pair_style dpd/coul/slater/long ${T} ${cut_DPD} ${seed} ${lambda} ${cut_coul}
read_data data.dpd_coul_slater_long
pair_style dpd/coul/slater/long ${T} ${cut_DPD} ${seed} ${lambda} ${cut_coul}
# Enable long range electrostatics solver
kspace_style pppm 1e-04
kspace_style pppm 1e-04
read_data data.dpd_coul_slater_long
# Construct neighbors every steps
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
#-------------------------------------------------------------------------------
# Run the simulation
#-------------------------------------------------------------------------------
thermo_style custom step temp press vol evdwl ecoul elong pe ke fnorm fmax
thermo_modify norm no
thermo 100
thermo_style custom step temp press vol evdwl ecoul elong pe ke fnorm fmax
thermo_modify norm no
thermo 100
timestep 0.01
run_style verlet
timestep 0.01
run_style verlet
fix 1 all nve
fix 1 all nve
run 1000
unfix 1
run 1000

147
examples/PACKAGES/dpd-basic/dpd_coul_slater_long/log.19Jun24.dpd_coul_slater.g++.1
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@ -1,147 +0,0 @@
LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-262-g0aff26705c-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# DPD Ionic Fluid
variable T equal 1.0
variable cut_DPD equal 1.0
variable seed equal 165412
variable lambda equal 0.25
variable cut_coul equal 2.0
#-------------------------------------------------------------------------------
# Initialize LAMMPS run for 3-d periodic
#-------------------------------------------------------------------------------
units lj
boundary p p p # periodic at all axes
atom_style full
dimension 3
bond_style none
angle_style none
dihedral_style none
improper_style none
newton on
comm_modify vel yes # store info of ghost atoms btw processors
#-------------------------------------------------------------------------------
# Box creation and configuration
#-------------------------------------------------------------------------------
# Define pair style and coefficients
pair_style dpd/coul/slater/long ${T} ${cut_DPD} ${seed} ${lambda} ${cut_coul}
pair_style dpd/coul/slater/long 1 ${cut_DPD} ${seed} ${lambda} ${cut_coul}
pair_style dpd/coul/slater/long 1 1 ${seed} ${lambda} ${cut_coul}
pair_style dpd/coul/slater/long 1 1 165412 ${lambda} ${cut_coul}
pair_style dpd/coul/slater/long 1 1 165412 0.25 ${cut_coul}
pair_style dpd/coul/slater/long 1 1 165412 0.25 2
read_data data.dpd_coul_slater_long
Reading data file ...
orthogonal box = (0 0 0) to (5 5 5)
1 by 1 by 1 MPI processor grid
reading atoms ...
375 atoms
reading velocities ...
375 velocities
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.003 seconds
# Enable long range electrostatics solver
kspace_style pppm 1e-04
# Construct neighbors every steps
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
#-------------------------------------------------------------------------------
# Run the simulation
#-------------------------------------------------------------------------------
thermo_style custom step temp press vol evdwl ecoul elong pe ke fnorm fmax
thermo_modify norm no
thermo 100
timestep 0.01
run_style verlet
fix 1 all nve
run 1000
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 1.4828454
grid = 20 20 20
stencil order = 5
estimated absolute RMS force accuracy = 7.7240141e-05
estimated relative force accuracy = 7.7240141e-05
using double precision FFTW3
3d grid and FFT values/proc = 24389 8000
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3
ghost atom cutoff = 3
binsize = 1.5, bins = 4 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair dpd/coul/slater/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 8.359 | 8.359 | 8.359 Mbytes
Step Temp Press Volume E_vdwl E_coul E_long PotEng KinEng Fnorm Fmax
0 0.9849949 69.271905 125 4673.0443 0 -30.365103 4642.6792 552.58214 646.76798 65.851035
100 1.0614027 69.794624 125 4659.0139 0 -31.906319 4627.1075 595.44692 612.94396 60.338653
200 0.9422517 68.721098 125 4687.8862 0 -33.81531 4654.0709 528.6032 620.25627 62.726994
300 0.8956649 69.323482 125 4721.0824 0 -33.854275 4687.2281 502.46801 670.22699 73.087908
400 0.99584547 69.670416 125 4713.9086 0 -30.783633 4683.125 558.66931 607.65881 59.224652
500 1.0565931 69.497816 125 4701.2584 0 -26.80545 4674.4529 592.74873 646.18907 71.398122
600 1.0071523 70.26222 125 4659.2061 0 -29.98909 4629.217 565.01243 630.00244 58.264115
700 1.0507355 67.920078 125 4695.255 0 -32.649209 4662.6058 589.46259 651.80459 70.573524
800 0.98561942 68.279591 125 4745.7603 0 -28.98491 4716.7754 552.9325 627.14371 67.196483
900 0.96470105 70.742864 125 4706.3605 0 -30.271633 4676.0889 541.19729 644.43036 79.474998
1000 1.0204819 70.164419 125 4654.6077 0 -27.797433 4626.8103 572.49035 624.19728 71.825307
Loop time of 2.10153 on 1 procs for 1000 steps with 375 atoms
Performance: 411128.483 tau/day, 475.843 timesteps/s, 178.441 katom-step/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.1779 | 1.1779 | 1.1779 | 0.0 | 56.05
Bond | 6.507e-05 | 6.507e-05 | 6.507e-05 | 0.0 | 0.00
Kspace | 0.74636 | 0.74636 | 0.74636 | 0.0 | 35.51
Neigh | 0.12903 | 0.12903 | 0.12903 | 0.0 | 6.14
Comm | 0.039726 | 0.039726 | 0.039726 | 0.0 | 1.89
Output | 0.00027587 | 0.00027587 | 0.00027587 | 0.0 | 0.01
Modify | 0.0037596 | 0.0037596 | 0.0037596 | 0.0 | 0.18
Other | | 0.004451 | | | 0.21
Nlocal: 375 ave 375 max 375 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3613 ave 3613 max 3613 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 62354 ave 62354 max 62354 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 62354
Ave neighs/atom = 166.27733
Ave special neighs/atom = 0
Neighbor list builds = 65
Dangerous builds = 0
unfix 1
Total wall time: 0:00:02

147
examples/PACKAGES/dpd-basic/dpd_coul_slater_long/log.19Jun24.dpd_coul_slater.g++.4
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@ -1,147 +0,0 @@
LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-262-g0aff26705c-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# DPD Ionic Fluid
variable T equal 1.0
variable cut_DPD equal 1.0
variable seed equal 165412
variable lambda equal 0.25
variable cut_coul equal 2.0
#-------------------------------------------------------------------------------
# Initialize LAMMPS run for 3-d periodic
#-------------------------------------------------------------------------------
units lj
boundary p p p # periodic at all axes
atom_style full
dimension 3
bond_style none
angle_style none
dihedral_style none
improper_style none
newton on
comm_modify vel yes # store info of ghost atoms btw processors
#-------------------------------------------------------------------------------
# Box creation and configuration
#-------------------------------------------------------------------------------
# Define pair style and coefficients
pair_style dpd/coul/slater/long ${T} ${cut_DPD} ${seed} ${lambda} ${cut_coul}
pair_style dpd/coul/slater/long 1 ${cut_DPD} ${seed} ${lambda} ${cut_coul}
pair_style dpd/coul/slater/long 1 1 ${seed} ${lambda} ${cut_coul}
pair_style dpd/coul/slater/long 1 1 165412 ${lambda} ${cut_coul}
pair_style dpd/coul/slater/long 1 1 165412 0.25 ${cut_coul}
pair_style dpd/coul/slater/long 1 1 165412 0.25 2
read_data data.dpd_coul_slater_long
Reading data file ...
orthogonal box = (0 0 0) to (5 5 5)
1 by 2 by 2 MPI processor grid
reading atoms ...
375 atoms
reading velocities ...
375 velocities
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.003 seconds
# Enable long range electrostatics solver
kspace_style pppm 1e-04
# Construct neighbors every steps
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
#-------------------------------------------------------------------------------
# Run the simulation
#-------------------------------------------------------------------------------
thermo_style custom step temp press vol evdwl ecoul elong pe ke fnorm fmax
thermo_modify norm no
thermo 100
timestep 0.01
run_style verlet
fix 1 all nve
run 1000
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 1.4828454
grid = 20 20 20
stencil order = 5
estimated absolute RMS force accuracy = 7.7240141e-05
estimated relative force accuracy = 7.7240141e-05
using double precision FFTW3
3d grid and FFT values/proc = 10469 2000
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3
ghost atom cutoff = 3
binsize = 1.5, bins = 4 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair dpd/coul/slater/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 7.208 | 7.208 | 7.209 Mbytes
Step Temp Press Volume E_vdwl E_coul E_long PotEng KinEng Fnorm Fmax
0 0.9849949 69.076433 125 4673.0443 0 -30.365103 4642.6792 552.58214 613.18374 70.700582
100 0.95374867 69.110009 125 4681.1097 0 -31.260804 4649.8489 535.053 629.95109 62.05418
200 1.0076152 69.824904 125 4670.7458 0 -28.382203 4642.3636 565.27213 656.8501 72.049813
300 1.0014752 69.666331 125 4696.454 0 -26.943577 4669.5105 561.8276 631.49861 74.737274
400 0.98863876 69.731774 125 4700.7552 0 -23.816077 4676.9391 554.62634 637.74742 68.928573
500 0.95782852 68.588075 125 4698.588 0 -29.249543 4669.3385 537.3418 646.31897 68.800569
600 0.97443232 70.864079 125 4674.8821 0 -26.415644 4648.4664 546.65653 606.50755 78.664429
700 0.98783988 68.908299 125 4692.5536 0 -28.092022 4664.4616 554.17817 638.98401 69.691814
800 0.98000145 69.83977 125 4706.6365 0 -29.648365 4676.9881 549.78082 626.84362 73.133934
900 1.0526251 69.466078 125 4671.9648 0 -30.941117 4641.0237 590.52269 618.1049 62.333546
1000 0.98340746 69.527121 125 4728.2894 0 -31.869907 4696.4195 551.69159 630.14208 61.392611
Loop time of 0.928543 on 4 procs for 1000 steps with 375 atoms
Performance: 930490.137 tau/day, 1076.956 timesteps/s, 403.859 katom-step/s
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.30761 | 0.34974 | 0.38864 | 4.9 | 37.67
Bond | 8.4633e-05 | 9.0539e-05 | 9.9184e-05 | 0.0 | 0.01
Kspace | 0.39038 | 0.42976 | 0.47215 | 4.4 | 46.28
Neigh | 0.033986 | 0.035576 | 0.036791 | 0.5 | 3.83
Comm | 0.10247 | 0.10324 | 0.10481 | 0.3 | 11.12
Output | 0.00024145 | 0.00027404 | 0.00036867 | 0.0 | 0.03
Modify | 0.0022402 | 0.0025068 | 0.0026343 | 0.3 | 0.27
Other | | 0.007356 | | | 0.79
Nlocal: 93.75 ave 96 max 93 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Nghost: 2289.75 ave 2317 max 2271 min
Histogram: 1 1 0 0 1 0 0 0 0 1
Neighs: 15590.2 ave 16765 max 14540 min
Histogram: 1 0 1 0 0 1 0 0 0 1
Total # of neighbors = 62361
Ave neighs/atom = 166.296
Ave special neighs/atom = 0
Neighbor list builds = 64
Dangerous builds = 0
unfix 1
Total wall time: 0:00:00

145
examples/PACKAGES/dpd-basic/dpd_coul_slater_long/log.25Mar25.dpd_coul_slater.g++.1 Normal file
View File

@ -0,0 +1,145 @@
LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-468-gd830412228-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
# DPD Ionic Fluid
variable T equal 1.0
variable cut_DPD equal 1.0
variable seed equal 165412
variable lambda equal 0.25
variable cut_coul equal 2.0
#-------------------------------------------------------------------------------
# Initialize LAMMPS run for 3-d periodic
#-------------------------------------------------------------------------------
units lj
boundary p p p # periodic at all axes
atom_style full
dimension 3
bond_style none
angle_style none
dihedral_style none
improper_style none
newton on
comm_modify vel yes # store info of ghost atoms btw processors
#-------------------------------------------------------------------------------
# Box creation and configuration
#-------------------------------------------------------------------------------
# Define pair style and coefficients
pair_style dpd/coul/slater/long ${T} ${cut_DPD} ${seed} ${lambda} ${cut_coul}
pair_style dpd/coul/slater/long 1 ${cut_DPD} ${seed} ${lambda} ${cut_coul}
pair_style dpd/coul/slater/long 1 1 ${seed} ${lambda} ${cut_coul}
pair_style dpd/coul/slater/long 1 1 165412 ${lambda} ${cut_coul}
pair_style dpd/coul/slater/long 1 1 165412 0.25 ${cut_coul}
pair_style dpd/coul/slater/long 1 1 165412 0.25 2
# Enable long range electrostatics solver
kspace_style pppm 1e-04
read_data data.dpd_coul_slater_long
Reading data file ...
orthogonal box = (0 0 0) to (5 5 5)
1 by 1 by 1 MPI processor grid
reading atoms ...
375 atoms
reading velocities ...
375 velocities
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.004 seconds
# Construct neighbors every steps
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
#-------------------------------------------------------------------------------
# Run the simulation
#-------------------------------------------------------------------------------
thermo_style custom step temp press vol evdwl ecoul elong pe ke fnorm fmax
thermo_modify norm no
thermo 100
timestep 0.01
run_style verlet
fix 1 all nve
run 1000
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 1.4828454
grid = 20 20 20
stencil order = 5
estimated absolute RMS force accuracy = 7.7240141e-05
estimated relative force accuracy = 7.7240141e-05
using double precision KISS FFT
3d grid and FFT values/proc = 24389 8000
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3
ghost atom cutoff = 3
binsize = 1.5, bins = 4 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair dpd/coul/slater/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 8.359 | 8.359 | 8.359 Mbytes
Step Temp Press Volume E_vdwl E_coul E_long PotEng KinEng Fnorm Fmax
0 0.9849949 69.242343 125 4673.0443 -3.2653869 -30.365103 4639.4138 552.58214 646.89929 65.851035
100 1.023885 69.716134 125 4676.9465 -4.9878506 -34.092864 4637.8658 574.39949 663.35845 94.350026
200 1.0286646 69.674249 125 4636.201 -4.6314926 -33.406897 4598.1626 577.08087 614.52805 62.295431
300 0.9745797 69.689534 125 4679.9157 -4.3964184 -30.560567 4644.9588 546.73921 603.46282 60.56253
400 0.99487931 69.17085 125 4678.0362 -4.9518269 -34.446596 4638.6378 558.12729 656.99738 88.090014
500 0.97732377 69.551562 125 4684.3709 -5.0851581 -33.863212 4645.4226 548.27864 647.12533 75.851935
600 0.95396337 68.358297 125 4706.824 -4.269168 -33.634096 4668.9207 535.17345 604.31276 63.41042
700 0.99397324 68.365109 125 4669.1062 -4.700146 -35.014001 4629.3921 557.61899 633.29262 74.300913
800 1.0157864 69.263686 125 4664.1398 -4.0142381 -34.372669 4625.7529 569.85616 595.81462 67.046561
900 0.9925779 70.008922 125 4652.3023 -2.7845751 -33.095293 4616.4224 556.8362 620.13154 82.785317
1000 0.97336501 68.973657 125 4688.8002 -5.5239266 -36.42345 4646.8529 546.05777 625.66451 64.948859
Loop time of 0.755094 on 1 procs for 1000 steps with 375 atoms
Performance: 1144228.093 tau/day, 1324.338 timesteps/s, 496.627 katom-step/s
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.14421 | 0.14421 | 0.14421 | 0.0 | 19.10
Bond | 3.8885e-05 | 3.8885e-05 | 3.8885e-05 | 0.0 | 0.01
Kspace | 0.53292 | 0.53292 | 0.53292 | 0.0 | 70.58
Neigh | 0.056741 | 0.056741 | 0.056741 | 0.0 | 7.51
Comm | 0.017676 | 0.017676 | 0.017676 | 0.0 | 2.34
Output | 0.00024925 | 0.00024925 | 0.00024925 | 0.0 | 0.03
Modify | 0.0016688 | 0.0016688 | 0.0016688 | 0.0 | 0.22
Other | | 0.001588 | | | 0.21
Nlocal: 375 ave 375 max 375 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3570 ave 3570 max 3570 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 19729 ave 19729 max 19729 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 19729
Ave neighs/atom = 52.610667
Ave special neighs/atom = 0
Neighbor list builds = 66
Dangerous builds = 0
Total wall time: 0:00:00

145
examples/PACKAGES/dpd-basic/dpd_coul_slater_long/log.25Mar25.dpd_coul_slater.g++.4 Normal file
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@ -0,0 +1,145 @@
LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-468-gd830412228-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
# DPD Ionic Fluid
variable T equal 1.0
variable cut_DPD equal 1.0
variable seed equal 165412
variable lambda equal 0.25
variable cut_coul equal 2.0
#-------------------------------------------------------------------------------
# Initialize LAMMPS run for 3-d periodic
#-------------------------------------------------------------------------------
units lj
boundary p p p # periodic at all axes
atom_style full
dimension 3
bond_style none
angle_style none
dihedral_style none
improper_style none
newton on
comm_modify vel yes # store info of ghost atoms btw processors
#-------------------------------------------------------------------------------
# Box creation and configuration
#-------------------------------------------------------------------------------
# Define pair style and coefficients
pair_style dpd/coul/slater/long ${T} ${cut_DPD} ${seed} ${lambda} ${cut_coul}
pair_style dpd/coul/slater/long 1 ${cut_DPD} ${seed} ${lambda} ${cut_coul}
pair_style dpd/coul/slater/long 1 1 ${seed} ${lambda} ${cut_coul}
pair_style dpd/coul/slater/long 1 1 165412 ${lambda} ${cut_coul}
pair_style dpd/coul/slater/long 1 1 165412 0.25 ${cut_coul}
pair_style dpd/coul/slater/long 1 1 165412 0.25 2
# Enable long range electrostatics solver
kspace_style pppm 1e-04
read_data data.dpd_coul_slater_long
Reading data file ...
orthogonal box = (0 0 0) to (5 5 5)
1 by 2 by 2 MPI processor grid
reading atoms ...
375 atoms
reading velocities ...
375 velocities
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.004 seconds
# Construct neighbors every steps
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
#-------------------------------------------------------------------------------
# Run the simulation
#-------------------------------------------------------------------------------
thermo_style custom step temp press vol evdwl ecoul elong pe ke fnorm fmax
thermo_modify norm no
thermo 100
timestep 0.01
run_style verlet
fix 1 all nve
run 1000
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 1.4828454
grid = 20 20 20
stencil order = 5
estimated absolute RMS force accuracy = 7.7240141e-05
estimated relative force accuracy = 7.7240141e-05
using double precision KISS FFT
3d grid and FFT values/proc = 10469 2000
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3
ghost atom cutoff = 3
binsize = 1.5, bins = 4 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair dpd/coul/slater/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 7.208 | 7.208 | 7.209 Mbytes
Step Temp Press Volume E_vdwl E_coul E_long PotEng KinEng Fnorm Fmax
0 0.9849949 69.04687 125 4673.0443 -3.2653869 -30.365103 4639.4138 552.58214 613.14254 70.700582
100 1.0206537 69.308834 125 4676.3153 -4.5693306 -33.647673 4638.0983 572.58672 630.70953 76.020236
200 0.99990746 68.572978 125 4707.1556 -3.4977853 -33.275671 4670.3821 560.94809 633.00167 77.040049
300 0.91055241 69.390592 125 4685.5268 -2.9764038 -29.986737 4652.5637 510.8199 614.61006 62.799933
400 1.0080135 69.442971 125 4677.3078 -4.8740989 -32.908722 4639.525 565.49557 649.20121 61.033612
500 0.99500653 68.275189 125 4718.6774 -4.2475783 -35.206868 4679.223 558.19867 657.3073 74.738502
600 1.052925 70.601712 125 4703.6749 -2.8511316 -34.085418 4666.7383 590.69094 641.70441 59.043346
700 0.96467445 69.502018 125 4720.4257 -4.3345734 -34.310005 4681.7811 541.18237 656.24965 72.433637
800 1.0657358 70.960958 125 4685.5637 -5.8903418 -35.207202 4644.4661 597.87781 595.54446 61.462159
900 1.0273388 68.735518 125 4693.5106 -2.4175829 -28.602387 4662.4906 576.33707 598.80294 71.747886
1000 0.9702835 69.885576 125 4701.4385 -3.6513555 -29.487331 4668.2999 544.32904 666.55262 73.231425
Loop time of 0.270344 on 4 procs for 1000 steps with 375 atoms
Performance: 3195929.791 tau/day, 3698.993 timesteps/s, 1.387 Matom-step/s
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.031268 | 0.035485 | 0.039491 | 1.6 | 13.13
Bond | 3.3378e-05 | 3.4848e-05 | 3.5667e-05 | 0.0 | 0.01
Kspace | 0.18632 | 0.19083 | 0.19556 | 0.8 | 70.59
Neigh | 0.012413 | 0.012991 | 0.013598 | 0.4 | 4.81
Comm | 0.028195 | 0.028407 | 0.028626 | 0.1 | 10.51
Output | 0.00013369 | 0.00015738 | 0.00022498 | 0.0 | 0.06
Modify | 0.00055373 | 0.00059062 | 0.00068807 | 0.0 | 0.22
Other | | 0.001846 | | | 0.68
Nlocal: 93.75 ave 95 max 92 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Nghost: 2286 ave 2307 max 2269 min
Histogram: 1 0 1 0 0 1 0 0 0 1
Neighs: 4945 ave 5443 max 4513 min
Histogram: 1 0 1 0 0 1 0 0 0 1
Total # of neighbors = 19780
Ave neighs/atom = 52.746667
Ave special neighs/atom = 0
Neighbor list builds = 66
Dangerous builds = 0
Total wall time: 0:00:00

4
examples/PACKAGES/eff/Auger-Adamantane/in.adamantane_ionized.nve
View File

@ -16,7 +16,7 @@ comm_modify vel yes
compute effTemp all temp/eff
thermo 1000
thermo_style custom step pe temp press
thermo_style custom step pe temp etotal press
thermo_modify temp effTemp
# Minimization
@ -36,7 +36,7 @@ undump 2
#velocity all create 300.0 4928459 dist uniform
# NVE
timestep 0.001
timestep 0.0001
fix 1 all nve/eff
dump 1 all xyz 1000 ${sname}.nve.xyz

367
examples/PACKAGES/eff/Auger-Adamantane/log.31Jan25.adamantane_ionized.nve.g++.1 Normal file
View File

@ -0,0 +1,367 @@
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
variable sname index adamantane_ionized
units electron
newton on
boundary f f f
atom_style electron
read_data data.${sname}
read_data data.adamantane_ionized
Reading data file ...
orthogonal box = (-50 -50 -50) to (50 50 50)
1 by 1 by 1 MPI processor grid
reading atoms ...
101 atoms
read_data CPU = 0.038 seconds
pair_style eff/cut 100.0
pair_coeff * *
comm_modify vel yes
compute effTemp all temp/eff
thermo 1000
thermo_style custom step pe temp etotal press
thermo_modify temp effTemp
# Minimization
min_style cg
dump 1 all xyz 500 ${sname}.min.xyz
dump 1 all xyz 500 adamantane_ionized.min.xyz
compute 1 all property/atom spin eradius erforce
dump 2 all custom 500 ${sname}.min.lammpstrj id type x y z c_1[1] c_1[2] fx fy fz c_1[3]
dump 2 all custom 500 adamantane_ionized.min.lammpstrj id type x y z c_1[1] c_1[2] fx fy fz c_1[3]
min_modify line quadratic
minimize 0.0 1.0e-5 10000 100000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- EFF package: doi:10.1002/jcc.21637
@Article{Jaramillo-Botero11,
author = {A. Jaramillo-Botero and J. Su and A. Qi and Goddard, III, W. A.},
title = {Large-Scale, Long-Term Nonadiabatic Electron Molecular Dynamics for Describing Material Properties and Phenomena in Extreme Environments},
journal = {J.~Comp.\ Chem.},
year = 2011,
volume = 32,
number = 3,
pages = {497--512}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 102
ghost atom cutoff = 102
binsize = 51, bins = 2 2 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair eff/cut, 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) = 5.222 | 5.222 | 5.222 Mbytes
Step PotEng Temp TotEng Press
0 -320.50186 0 -320.50186 -45590269
571 -324.30072 0 -324.30072 21193099
Loop time of 2.61846 on 1 procs for 571 steps with 101 atoms
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-320.501859657303 -324.30071870307 -324.30071870307
Force two-norm initial, final = 2.8135352 2.2777398
Force max component initial, final = 1.7194878 2.093044
Final line search alpha, max atom move = 2.2781994e-09 4.7683716e-09
Iterations, force evaluations = 571 5621
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.602 | 2.602 | 2.602 | 0.0 | 99.37
Neigh | 2.5097e-05 | 2.5097e-05 | 2.5097e-05 | 0.0 | 0.00
Comm | 0.00046417 | 0.00046417 | 0.00046417 | 0.0 | 0.02
Output | 0.00029579 | 0.00029579 | 0.00029579 | 0.0 | 0.01
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.0157 | | | 0.60
Nlocal: 101 ave 101 max 101 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: 5050 ave 5050 max 5050 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 5050
Ave neighs/atom = 50
Neighbor list builds = 1
Dangerous builds = 0
undump 1
undump 2
#restart timestep
# set velocities for nve
#velocity all create 300.0 4928459 dist uniform
# NVE
timestep 0.0001
fix 1 all nve/eff
dump 1 all xyz 1000 ${sname}.nve.xyz
dump 1 all xyz 1000 adamantane_ionized.nve.xyz
dump 2 all custom 1000 ${sname}.nve.lammpstrj id type x y z c_1[1] c_1[2] fx fy fz c_1[3]
dump 2 all custom 1000 adamantane_ionized.nve.lammpstrj id type x y z c_1[1] c_1[2] fx fy fz c_1[3]
#restart 1000 ${sname}.nve.restart1 ${sname}.nve.restart2
run 200000
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 4.097 | 4.097 | 4.097 Mbytes
Step PotEng Temp TotEng Press
571 -324.30072 0 -324.30072 21193099
1000 -324.00833 75606.318 -315.02966 1.9184325e+08
2000 -322.45879 62558.11 -315.02966 1.4564261e+08
3000 -322.01495 58820.681 -315.02966 1.3051251e+08
4000 -321.3178 52950.225 -315.02966 75989118
5000 -320.89488 49388.959 -315.02966 55413771
6000 -320.97564 50069.086 -315.02966 67105302
7000 -320.9772 50082.172 -315.02966 90728737
8000 -320.76927 48331.305 -315.02966 1.1054849e+08
9000 -320.40821 45290.936 -315.02966 1.1325434e+08
10000 -320.10216 42713.788 -315.02966 1.0766253e+08
11000 -320.00263 41875.679 -315.02966 1.0831982e+08
12000 -319.92006 41180.36 -315.02966 1.0888686e+08
13000 -319.85913 40667.331 -315.02966 1.0763265e+08
14000 -319.86056 40679.317 -315.02966 1.1159571e+08
15000 -319.79071 40091.129 -315.02966 1.1261281e+08
16000 -319.7393 39658.231 -315.02966 1.0983394e+08
17000 -319.74963 39745.211 -315.02966 1.12573e+08
18000 -319.70347 39356.518 -315.02966 1.1249278e+08
19000 -319.68924 39236.684 -315.02966 1.084432e+08
20000 -319.74747 39727.04 -315.02966 1.109151e+08
21000 -319.76264 39854.793 -315.02966 1.0990745e+08
22000 -319.7997 40166.86 -315.02966 1.0446598e+08
23000 -319.91061 41100.771 -315.02966 1.0605289e+08
24000 -319.98762 41749.299 -315.02966 1.0312843e+08
25000 -320.06842 42429.669 -315.02966 96790253
26000 -320.2321 43807.92 -315.02966 98941422
27000 -320.43008 45475.083 -315.02966 99172853
28000 -320.75368 48199.998 -315.02966 1.0304506e+08
29000 -321.43727 53956.239 -315.02966 1.2359013e+08
30000 -322.86003 65936.838 -315.02966 1.6426506e+08
31000 -325.85698 91173.108 -315.02966 2.3460809e+08
32000 -323.96663 75255.122 -315.02967 1.4386254e+08
33000 -324.31173 78161.078 -315.02966 1.9611146e+08
34000 -321.81048 57098.954 -315.02966 1.3183304e+08
35000 -321.11553 51247.011 -315.02966 1.1860383e+08
36000 -320.7006 47753.061 -315.02966 1.0988072e+08
37000 -320.42875 45463.834 -315.02966 1.0486186e+08
38000 -320.37522 45013.139 -315.02966 1.0667734e+08
39000 -320.16625 43253.419 -315.02966 1.0141734e+08
40000 -320.09034 42614.247 -315.02966 1.0082579e+08
41000 -320.21558 43668.822 -315.02966 1.0548768e+08
42000 -320.19431 43489.747 -315.02966 1.0242614e+08
43000 -320.35932 44879.232 -315.02966 1.0646487e+08
44000 -320.67457 47533.878 -315.02966 1.1366565e+08
45000 -320.83512 48885.757 -315.02966 1.111537e+08
46000 -321.16647 51675.946 -315.02966 1.1302624e+08
47000 -321.38122 53484.331 -315.02966 1.0507686e+08
48000 -321.06774 50844.617 -315.02966 74672082
49000 -322.49756 62884.615 -315.02966 1.044115e+08
50000 -325.97731 92186.422 -315.02966 2.2498335e+08
51000 -320.66106 47420.072 -315.02966 34605338
52000 -323.2278 69033.706 -315.02966 1.4817693e+08
53000 -322.82489 65640.939 -315.02966 1.6065307e+08
54000 -321.95574 58322.133 -315.02966 1.3860454e+08
55000 -321.41375 53758.198 -315.02966 1.1831887e+08
56000 -320.82121 48768.626 -315.02966 97374067
57000 -320.39876 45211.333 -315.02966 85881342
58000 -320.26394 44076.088 -315.02966 80873235
59000 -320.06828 42428.515 -315.02966 75885502
60000 -320.12912 42940.809 -315.02966 83005858
61000 -320.34086 44723.765 -315.02966 90748569
62000 -320.3942 45172.977 -315.02966 93992240
63000 -320.63122 47168.811 -315.02966 1.0726441e+08
64000 -320.86235 49115.084 -315.02966 1.1515294e+08
65000 -320.95075 49859.439 -315.02966 1.1705259e+08
66000 -321.28995 52715.744 -315.02966 1.3144493e+08
67000 -321.69035 56087.363 -315.02966 1.4188253e+08
68000 -322.28755 61116.149 -315.02966 1.5220904e+08
69000 -323.31574 69774.213 -315.02966 1.5914511e+08
70000 -322.98352 66976.685 -315.02966 1.0382488e+08
71000 -323.42006 70652.696 -315.02966 1.1257889e+08
72000 -322.38839 61965.354 -315.02966 1.213394e+08
73000 -321.62733 55556.719 -315.02966 1.2062207e+08
74000 -321.10333 51144.304 -315.02966 1.0628135e+08
75000 -320.84916 49004.001 -315.02966 1.0188029e+08
76000 -320.51651 46202.858 -315.02966 94118114
77000 -320.47427 45847.17 -315.02966 91437540
78000 -320.52773 46297.312 -315.02966 95165197
79000 -320.43972 45556.265 -315.02966 95366722
80000 -320.58645 46791.792 -315.02966 1.0182068e+08
81000 -320.75509 48211.862 -315.02966 1.0907204e+08
82000 -320.77091 48345.056 -315.02966 1.1257336e+08
83000 -321.02219 50461.057 -315.02966 1.2376776e+08
84000 -321.20064 51963.656 -315.02966 1.2909546e+08
85000 -321.2856 52679.138 -315.02966 1.3104703e+08
86000 -321.67229 55935.33 -315.02966 1.4072532e+08
87000 -322.11917 59698.307 -315.02966 1.4404812e+08
88000 -324.23523 77516.896 -315.02966 1.9731217e+08
89000 -320.62579 47123.095 -315.02966 75893884
90000 -324.35107 78492.385 -315.02966 2.1044355e+08
91000 -322.47803 62720.127 -315.02966 1.5538903e+08
92000 -321.71623 56305.3 -315.02966 1.3227964e+08
93000 -321.22259 52148.564 -315.02966 1.1511464e+08
94000 -320.89326 49375.312 -315.02966 1.0320494e+08
95000 -320.60652 46960.796 -315.02966 93163389
96000 -320.42504 45432.671 -315.02966 82638699
97000 -320.35025 44802.889 -315.02966 77728012
98000 -320.38016 45054.714 -315.02966 76753988
99000 -320.64823 47312.019 -315.02966 79089183
100000 -321.20665 52014.291 -315.02966 90654215
101000 -322.45176 62498.949 -315.02966 1.1671692e+08
102000 -325.27551 86276.757 -315.02966 1.7450838e+08
103000 -324.86597 82828.164 -315.02967 1.5358223e+08
104000 -323.50288 71350.092 -315.02966 1.3914499e+08
105000 -321.83206 57280.642 -315.02966 1.1374062e+08
106000 -321.23029 52213.369 -315.02966 1.0154377e+08
107000 -320.79552 48552.352 -315.02966 93581739
108000 -320.85374 49042.571 -315.02966 1.0230141e+08
109000 -320.711 47840.638 -315.02966 98035102
110000 -320.92927 49678.547 -315.02966 1.0291687e+08
111000 -321.37088 53397.184 -315.02966 1.161465e+08
112000 -321.64623 55715.825 -315.02966 1.2178973e+08
113000 -323.29623 69609.916 -315.02966 1.5738912e+08
114000 -326.43458 96036.881 -315.02966 2.2117147e+08
115000 -326.29249 94840.366 -315.02967 2.1727072e+08
116000 -323.49398 71275.138 -315.02966 1.6236371e+08
117000 -321.69956 56164.918 -315.02966 1.2248665e+08
118000 -321.03061 50531.902 -315.02966 1.114646e+08
119000 -320.58664 46793.421 -315.02966 1.0201646e+08
120000 -320.31068 44469.633 -315.02966 92788900
121000 -320.33764 44696.673 -315.02966 96573809
122000 -320.29533 44340.406 -315.02966 96276795
123000 -320.48178 45910.447 -315.02966 96702563
124000 -320.99926 50267.91 -315.02966 1.1042709e+08
125000 -321.72882 56411.316 -315.02966 1.2653574e+08
126000 -323.76935 73593.887 -315.02966 1.6411768e+08
127000 -323.84136 74200.288 -315.02967 1.2684596e+08
128000 -325.27771 86295.322 -315.02966 1.7908195e+08
129000 -322.44151 62412.6 -315.02966 1.2334056e+08
130000 -321.33424 53088.672 -315.02966 1.0110915e+08
131000 -320.74694 48143.276 -315.02966 87343006
132000 -320.58456 46775.879 -315.02966 84619630
133000 -320.42884 45464.64 -315.02966 80256772
134000 -320.41844 45377.068 -315.02966 79998095
135000 -320.67167 47509.417 -315.02966 88059739
136000 -320.94223 49787.695 -315.02966 94538899
137000 -321.61703 55469.964 -315.02966 1.1016475e+08
138000 -323.12933 68204.503 -315.02966 1.4202379e+08
139000 -326.08028 93053.485 -315.02966 1.894649e+08
140000 -326.22688 94287.865 -315.02967 1.9082785e+08
141000 -323.43485 70777.215 -315.02966 1.4698731e+08
142000 -321.79035 56929.435 -315.02966 1.1785802e+08
143000 -321.17113 51715.2 -315.02966 1.0630317e+08
144000 -320.72407 47950.681 -315.02966 94302254
145000 -320.53771 46381.4 -315.02966 89962864
146000 -320.57538 46698.572 -315.02966 90769921
147000 -320.65873 47400.459 -315.02966 88297290
148000 -321.05389 50727.942 -315.02966 95860956
149000 -321.86647 57570.413 -315.02966 1.1210695e+08
150000 -323.71338 73122.627 -315.02966 1.4277977e+08
151000 -325.52965 88416.746 -315.02967 1.7216009e+08
152000 -325.82817 90930.57 -315.02966 1.8312663e+08
153000 -322.5891 63655.44 -315.02966 1.2089115e+08
154000 -321.32957 53049.334 -315.02966 96494848
155000 -320.66612 47462.65 -315.02966 81236441
156000 -320.47196 45827.713 -315.02966 78679995
157000 -320.33169 44646.581 -315.02966 75407967
158000 -320.42358 45420.371 -315.02966 76161171
159000 -320.79103 48514.483 -315.02966 84173108
160000 -321.27968 52629.281 -315.02966 92130817
161000 -322.50401 62938.95 -315.02966 1.138272e+08
162000 -325.40267 87347.575 -315.02966 1.6576028e+08
163000 -323.59983 72166.432 -315.02967 1.1072655e+08
164000 -324.04378 75904.823 -315.02966 1.4709858e+08
165000 -322.01605 58829.972 -315.02966 1.0400742e+08
166000 -321.15747 51600.213 -315.02966 82397014
167000 -320.8409 48934.422 -315.02966 73988066
168000 -320.58861 46810.029 -315.02966 64925698
169000 -320.54312 46426.959 -315.02966 61942158
170000 -320.68604 47630.438 -315.02966 64309567
171000 -320.77008 48338.134 -315.02966 63324927
172000 -321.08474 50987.727 -315.02966 69721832
173000 -321.6134 55439.431 -315.02966 80485473
174000 -322.41904 62223.44 -315.02966 94329801
175000 -324.95819 83604.705 -315.02966 1.5681125e+08
176000 -321.71907 56329.278 -315.02966 45217519
177000 -324.24577 77605.673 -315.02966 1.5164385e+08
178000 -322.34082 61564.766 -315.02966 1.0677988e+08
179000 -321.3229 52993.228 -315.02966 80528491
180000 -320.91614 49567.992 -315.02966 70928167
181000 -320.79771 48570.793 -315.02966 70105356
182000 -320.43289 45498.72 -315.02966 62263793
183000 -320.59821 46890.81 -315.02966 67986358
184000 -320.64879 47316.739 -315.02966 70175355
185000 -320.52287 46256.459 -315.02966 68704646
186000 -320.94252 49790.187 -315.02966 81368769
187000 -321.10174 51130.914 -315.02966 84251825
188000 -321.38014 53475.167 -315.02966 91376642
189000 -322.14722 59934.547 -315.02966 1.1198813e+08
190000 -322.9004 66276.794 -315.02966 1.2823518e+08
191000 -323.63455 72458.807 -315.02966 1.6144592e+08
192000 -324.3348 78355.338 -315.02966 1.5544396e+08
193000 -321.63344 55608.185 -315.02966 85813641
194000 -323.54261 71684.651 -315.02966 1.4340251e+08
195000 -323.1577 68443.449 -315.02966 1.5089288e+08
196000 -322.90055 66278.083 -315.02966 1.4392954e+08
197000 -322.45751 62547.374 -315.02966 1.2607137e+08
198000 -322.18257 60232.201 -315.02966 1.137101e+08
199000 -322.24297 60740.76 -315.02966 1.0950975e+08
200000 -322.47749 62715.575 -315.02966 1.070732e+08
200571 -323.24897 69211.97 -315.02966 1.1694375e+08
Loop time of 86.0986 on 1 procs for 200000 steps with 101 atoms
Performance: 20070.020 fs/day, 0.001 hours/fs, 2322.919 timesteps/s, 234.615 katom-step/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 85.691 | 85.691 | 85.691 | 0.0 | 99.53
Neigh | 0.0010104 | 0.0010104 | 0.0010104 | 0.0 | 0.00
Comm | 0.016762 | 0.016762 | 0.016762 | 0.0 | 0.02
Output | 0.061098 | 0.061098 | 0.061098 | 0.0 | 0.07
Modify | 0.22948 | 0.22948 | 0.22948 | 0.0 | 0.27
Other | | 0.09905 | | | 0.12
Nlocal: 101 ave 101 max 101 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: 5050 ave 5050 max 5050 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 5050
Ave neighs/atom = 50
Neighbor list builds = 46
Dangerous builds = 0
unfix 1
undump 1
undump 2
Total wall time: 0:01:28

367
examples/PACKAGES/eff/Auger-Adamantane/log.31Jan25.adamantane_ionized.nve.g++.4 Normal file
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@ -0,0 +1,367 @@
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
variable sname index adamantane_ionized
units electron
newton on
boundary f f f
atom_style electron
read_data data.${sname}
read_data data.adamantane_ionized
Reading data file ...
orthogonal box = (-50 -50 -50) to (50 50 50)
1 by 2 by 2 MPI processor grid
reading atoms ...
101 atoms
read_data CPU = 0.001 seconds
pair_style eff/cut 100.0
pair_coeff * *
comm_modify vel yes
compute effTemp all temp/eff
thermo 1000
thermo_style custom step pe temp etotal press
thermo_modify temp effTemp
# Minimization
min_style cg
dump 1 all xyz 500 ${sname}.min.xyz
dump 1 all xyz 500 adamantane_ionized.min.xyz
compute 1 all property/atom spin eradius erforce
dump 2 all custom 500 ${sname}.min.lammpstrj id type x y z c_1[1] c_1[2] fx fy fz c_1[3]
dump 2 all custom 500 adamantane_ionized.min.lammpstrj id type x y z c_1[1] c_1[2] fx fy fz c_1[3]
min_modify line quadratic
minimize 0.0 1.0e-5 10000 100000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- EFF package: doi:10.1002/jcc.21637
@Article{Jaramillo-Botero11,
author = {A. Jaramillo-Botero and J. Su and A. Qi and Goddard, III, W. A.},
title = {Large-Scale, Long-Term Nonadiabatic Electron Molecular Dynamics for Describing Material Properties and Phenomena in Extreme Environments},
journal = {J.~Comp.\ Chem.},
year = 2011,
volume = 32,
number = 3,
pages = {497--512}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 102
ghost atom cutoff = 102
binsize = 51, bins = 2 2 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair eff/cut, 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) = 5.253 | 5.253 | 5.253 Mbytes
Step PotEng Temp TotEng Press
0 -320.50186 0 -320.50186 -45590269
493 -324.31743 0 -324.31743 20971271
Loop time of 0.883439 on 4 procs for 493 steps with 101 atoms
99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-320.501859657306 -324.317430790588 -324.317430790588
Force two-norm initial, final = 2.8135352 1.2148731
Force max component initial, final = 1.7194878 1.1232786
Final line search alpha, max atom move = 4.245048e-09 4.7683716e-09
Iterations, force evaluations = 493 3804
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.24614 | 0.45831 | 0.84299 | 34.7 | 51.88
Neigh | 1.1159e-05 | 1.2751e-05 | 1.5479e-05 | 0.0 | 0.00
Comm | 0.019423 | 0.40607 | 0.62032 | 37.1 | 45.97
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.01905 | | | 2.16
Nlocal: 25.25 ave 30 max 17 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 75.75 ave 84 max 71 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Neighs: 1262.5 ave 2394 max 663 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Total # of neighbors = 5050
Ave neighs/atom = 50
Neighbor list builds = 1
Dangerous builds = 0
undump 1
undump 2
#restart timestep
# set velocities for nve
#velocity all create 300.0 4928459 dist uniform
# NVE
timestep 0.0001
fix 1 all nve/eff
dump 1 all xyz 1000 ${sname}.nve.xyz
dump 1 all xyz 1000 adamantane_ionized.nve.xyz
dump 2 all custom 1000 ${sname}.nve.lammpstrj id type x y z c_1[1] c_1[2] fx fy fz c_1[3]
dump 2 all custom 1000 adamantane_ionized.nve.lammpstrj id type x y z c_1[1] c_1[2] fx fy fz c_1[3]
#restart 1000 ${sname}.nve.restart1 ${sname}.nve.restart2
run 200000
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 4.128 | 4.128 | 4.128 Mbytes
Step PotEng Temp TotEng Press
493 -324.31743 0 -324.31743 20971271
1000 -324.2963 3994.2535 -323.82196 29875505
2000 -324.14448 2715.8412 -323.82196 24005899
3000 -323.9446 1032.7299 -323.82196 16224812
4000 -323.83425 103.47941 -323.82196 11886177
5000 -323.87559 451.59681 -323.82196 13395168
6000 -324.05446 1957.8271 -323.82196 20034811
7000 -324.24814 3588.7467 -323.82196 28092249
8000 -324.3149 4150.7958 -323.82197 31632418
9000 -324.25366 3635.1689 -323.82196 27760974
10000 -324.05069 1926.0777 -323.82196 19436396
11000 -323.88484 529.46541 -323.82196 13264080
12000 -323.86286 344.37477 -323.82196 12741952
13000 -324.00393 1532.3029 -323.82196 17720089
14000 -324.20987 3266.4109 -323.82196 25528615
15000 -324.34308 4388.1934 -323.82196 30700580
16000 -324.30475 4065.4216 -323.82196 29168176
17000 -324.12375 2541.2612 -323.82196 21928164
18000 -323.93619 961.92262 -323.82196 14363951
19000 -323.87105 413.39974 -323.82196 11446320
20000 -323.9713 1257.5055 -323.82196 15118972
21000 -324.16564 2894.0212 -323.82196 22749979
22000 -324.32073 4199.9228 -323.82196 29044099
23000 -324.34614 4413.8921 -323.82196 29514541
24000 -324.20431 3219.6717 -323.82196 23595226
25000 -324.01211 1601.1964 -323.82196 15812197
26000 -323.90577 705.76969 -323.82196 11992491
27000 -323.95668 1134.4631 -323.82196 14679820
28000 -324.12645 2564.0146 -323.82196 21299092
29000 -324.29158 3954.5234 -323.82196 28120074
30000 -324.32731 4255.3405 -323.82196 31311574
31000 -324.27771 3837.6901 -323.82196 28270491
32000 -324.09259 2278.8862 -323.82196 21338356
33000 -323.95465 1117.2898 -323.82196 15833338
34000 -323.95469 1117.6477 -323.82196 16034624
35000 -324.08796 2239.9037 -323.82196 22076527
36000 -324.26866 3761.5323 -323.82196 29147703
37000 -324.3502 4448.1533 -323.82196 33380564
38000 -324.29459 3979.8076 -323.82196 31533851
39000 -324.1694 2925.6774 -323.82196 25161011
40000 -324.01365 1614.1815 -323.82196 19145060
41000 -323.97015 1247.8234 -323.82196 16994462
42000 -324.04755 1899.62 -323.82196 19654332
43000 -324.22071 3357.7354 -323.82196 25666317
44000 -324.35528 4490.9023 -323.82196 30318540
45000 -324.35807 4514.3651 -323.82196 30645986
46000 -324.24462 3559.0921 -323.82196 25690532
47000 -324.09319 2283.909 -323.82196 18529309
48000 -324.00266 1521.597 -323.82196 14177383
49000 -324.04261 1858.0104 -323.82196 15780869
50000 -324.19619 3151.2862 -323.82196 21070555
51000 -324.32727 4255.0227 -323.82196 26451705
52000 -324.3917 4797.6094 -323.82196 28066000
53000 -324.30169 4039.6086 -323.82196 24214730
54000 -324.14884 2752.5491 -323.82196 17848175
55000 -324.02946 1747.258 -323.82196 13686029
56000 -324.05031 1922.825 -323.82196 14113758
57000 -324.16944 2925.9624 -323.82196 18723794
58000 -324.30745 4088.1772 -323.82196 24387592
59000 -324.36463 4569.6324 -323.82196 27059420
60000 -324.32147 4206.1707 -323.82196 25012812
61000 -324.18133 3026.1579 -323.82196 19500659
62000 -324.07027 2090.9001 -323.82196 14626096
63000 -324.04536 1881.129 -323.82196 13606034
64000 -324.14417 2713.2333 -323.82196 17524492
65000 -324.28817 3925.7771 -323.82196 23261363
66000 -324.37816 4683.5409 -323.82196 26852878
67000 -324.34311 4388.4452 -323.82196 25854003
68000 -324.24346 3549.2763 -323.82196 20818195
69000 -324.1067 2397.6992 -323.82196 15550338
70000 -324.05471 1959.908 -323.82196 13178617
71000 -324.12382 2541.8769 -323.82196 15655087
72000 -324.25986 3687.3615 -323.82196 20831733
73000 -324.37345 4643.9165 -323.82196 25082640
74000 -324.38407 4733.3013 -323.82196 25377064
75000 -324.28752 3920.3485 -323.82196 21185087
76000 -324.14479 2718.409 -323.82196 15093238
77000 -324.06273 2027.4447 -323.82196 11357895
78000 -324.1027 2363.9918 -323.82196 12682184
79000 -324.24431 3556.4784 -323.82196 17923460
80000 -324.37329 4642.461 -323.82197 22977159
81000 -324.40875 4941.1418 -323.82196 24175202
82000 -324.33677 4334.993 -323.82196 20418362
83000 -324.18471 3054.6117 -323.82196 14173787
84000 -324.08262 2194.902 -323.82196 10107358
85000 -324.07536 2133.7765 -323.82196 9748952.1
86000 -324.18707 3074.432 -323.82196 13462472
87000 -324.32091 4201.5211 -323.82196 19096674
88000 -324.44557 5251.2038 -323.82196 22573960
89000 -324.39988 4866.4678 -323.82196 21348490
90000 -324.25685 3662.0864 -323.82196 15903121
91000 -324.0755 2135.0001 -323.82196 10233161
92000 -324.06354 2034.2765 -323.82196 7509452
93000 -324.15185 2777.9236 -323.82196 9750370.3
94000 -324.30478 4065.6146 -323.82196 15561885
95000 -324.42696 5094.5186 -323.82196 20667693
96000 -324.44094 5212.1846 -323.82196 21153174
97000 -324.33283 4301.8232 -323.82196 16435314
98000 -324.1883 3084.8099 -323.82196 10336860
99000 -324.09656 2312.304 -323.82196 6808669.9
100000 -324.13298 2619.0245 -323.82196 7675912.4
101000 -324.25984 3687.2237 -323.82196 11868042
102000 -324.40322 4894.6055 -323.82196 17007266
103000 -324.44333 5232.3546 -323.82196 19025190
104000 -324.39727 4844.4421 -323.82196 15980570
105000 -324.25 3604.3886 -323.82196 9668044.1
106000 -324.08507 2215.5839 -323.82196 4405958.8
107000 -324.11835 2495.8211 -323.82196 3436936.2
108000 -324.21008 3268.2404 -323.82196 6028268.3
109000 -324.34118 4372.1743 -323.82196 10939013
110000 -324.40282 4891.1987 -323.82196 14333667
111000 -324.45353 5318.1927 -323.82196 13380345
112000 -324.33795 4344.9374 -323.82196 7923709.9
113000 -324.19654 3154.2192 -323.82196 1970263.7
114000 -324.12867 2582.7343 -323.82196 -1481413.1
115000 -324.17132 2941.8126 -323.82196 -290956.43
116000 -324.33613 4329.6247 -323.82196 5245770.9
117000 -324.41548 4997.8222 -323.82196 10354303
118000 -324.48518 5584.7558 -323.82196 11795673
119000 -324.41046 4955.5092 -323.82196 8031391.3
120000 -324.24749 3583.2536 -323.82196 1845177.6
121000 -324.14124 2688.5331 -323.82196 -2784584.1
122000 -324.14467 2717.4458 -323.82196 -2261498.4
123000 -324.28472 3896.7771 -323.82196 3080452.1
124000 -324.43687 5177.9121 -323.82196 9819540.9
125000 -324.51452 5831.8132 -323.82196 13180239
126000 -324.47691 5515.0823 -323.82196 11018721
127000 -324.31812 4178.0163 -323.82196 4976672.9
128000 -324.16884 2920.9366 -323.82196 -186371.44
129000 -324.13025 2596.0395 -323.82196 -1883126.3
130000 -324.22275 3374.922 -323.82196 1526423.1
131000 -324.41343 4980.5335 -323.82196 8415685
132000 -324.45089 5296.046 -323.82196 13250300
133000 -324.51148 5806.2229 -323.82196 12827560
134000 -324.39463 4822.239 -323.82196 7049805.8
135000 -324.20254 3204.6979 -323.82196 -187723.51
136000 -324.1379 2660.4388 -323.82196 -3970679.9
137000 -324.18473 3054.7443 -323.82196 -2351010.9
138000 -324.35172 4460.9406 -323.82196 3024494.5
139000 -324.48743 5603.6722 -323.82196 8652609.2
140000 -324.53668 6018.4343 -323.82196 9612584.9
141000 -324.43638 5173.8016 -323.82196 4805500.8
142000 -324.28353 3886.746 -323.82196 -2740880.4
143000 -324.14169 2692.2995 -323.82196 -8310197.6
144000 -324.13063 2599.1788 -323.82196 -9603391.1
145000 -324.27459 3811.4423 -323.82196 -5690559.8
146000 -324.4342 5155.4519 -323.82196 431484.28
147000 -324.55834 6200.7798 -323.82196 4166801.6
148000 -324.51567 5841.5105 -323.82196 2299540.9
149000 -324.34424 4397.967 -323.82196 -4487220.6
150000 -324.20348 3212.6032 -323.82196 -10852097
151000 -324.13211 2611.6979 -323.82196 -12942852
152000 -324.20634 3236.7635 -323.82196 -10732036
153000 -324.35827 4516.0788 -323.82196 -4665668.3
154000 -324.5074 5771.8121 -323.82196 1703175.2
155000 -324.51881 5867.9505 -323.82196 2959605.5
156000 -324.44762 5268.4581 -323.82196 -1706620
157000 -324.25179 3619.4025 -323.82196 -8511782.3
158000 -324.13478 2634.1695 -323.82196 -11767435
159000 -324.17085 2937.9043 -323.82196 -10356431
160000 -324.28946 3936.6179 -323.82196 -5252437.9
161000 -324.47596 5507.0864 -323.82196 1737812.2
162000 -324.52686 5935.7476 -323.82196 5782720.9
163000 -324.5121 5811.4236 -323.82196 4273238.8
164000 -324.35265 4468.7315 -323.82196 -1590319.8
165000 -324.19582 3148.1193 -323.82196 -6770200.2
166000 -324.15306 2788.0507 -323.82196 -8385908.5
167000 -324.24186 3535.8588 -323.82196 -4776412.5
168000 -324.4 4867.4913 -323.82196 2207883.7
169000 -324.52732 5939.6216 -323.82196 7770368.9
170000 -324.53787 6028.4604 -323.82196 8163057.7
171000 -324.42167 5049.9129 -323.82196 2893037
172000 -324.25784 3670.3642 -323.82196 -4020286
173000 -324.16815 2915.1362 -323.82196 -7461767.8
174000 -324.21774 3332.737 -323.82196 -5214520.3
175000 -324.37502 4657.1185 -323.82196 -81968.156
176000 -324.5128 5817.2882 -323.82196 5130806.8
177000 -324.4983 5695.2281 -323.82196 6394017.7
178000 -324.47309 5482.9629 -323.82196 2466372.3
179000 -324.31526 4153.8777 -323.82196 -4378953.5
180000 -324.2046 3222.0434 -323.82196 -9221400.9
181000 -324.21978 3349.8648 -323.82196 -9338327.2
182000 -324.33867 4351.0162 -323.82196 -5586765.2
183000 -324.44483 5244.9523 -323.82196 -706564.21
184000 -324.54787 6112.6128 -323.82196 1971109.1
185000 -324.49436 5662.0508 -323.82196 -1239.0449
186000 -324.38425 4734.8404 -323.82196 -5595239.9
187000 -324.25734 3666.1954 -323.82196 -10793981
188000 -324.21303 3293.0496 -323.82196 -11574584
189000 -324.28662 3912.7067 -323.82196 -8579023.4
190000 -324.4316 5133.5815 -323.82196 -2888022.8
191000 -324.51735 5855.6722 -323.82196 1558206.4
192000 -324.55207 6147.9783 -323.82196 1897782.9
193000 -324.43491 5161.4381 -323.82196 -1998628.2
194000 -324.28751 3920.2514 -323.82196 -6841627.4
195000 -324.24114 3529.7564 -323.82196 -8565471.5
196000 -324.30158 4038.6851 -323.82196 -5634096.8
197000 -324.44261 5226.2386 -323.82196 443851.89
198000 -324.53354 5991.9831 -323.82196 5993350.1
199000 -324.5697 6296.4193 -323.82196 7393255.8
200000 -324.46863 5445.3485 -323.82196 4272906.2
200493 -324.39372 4814.6196 -323.82196 1812660.2
Loop time of 42.6156 on 4 procs for 200000 steps with 101 atoms
Performance: 40548.540 fs/day, 0.001 hours/fs, 4693.118 timesteps/s, 474.005 katom-step/s
100.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 11.576 | 22.615 | 40.956 | 235.7 | 53.07
Neigh | 1.9114e-05 | 2.3629e-05 | 2.5892e-05 | 0.0 | 0.00
Comm | 0.99241 | 19.433 | 30.581 | 255.9 | 45.60
Output | 0.03344 | 0.035732 | 0.037864 | 0.8 | 0.08
Modify | 0.066393 | 0.082377 | 0.09318 | 3.4 | 0.19
Other | | 0.4486 | | | 1.05
Nlocal: 25.25 ave 31 max 21 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Nghost: 75.75 ave 80 max 70 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Neighs: 1262.5 ave 2143 max 476 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Total # of neighbors = 5050
Ave neighs/atom = 50
Neighbor list builds = 2
Dangerous builds = 0
unfix 1
undump 1
undump 2
Total wall time: 0:00:43

90
examples/PACKAGES/eff/Be-solid/log.01Feb25.Be-solid.spe.g++.4 Normal file
View File

@ -0,0 +1,90 @@
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
variable sname index Be-solid
units electron
newton on
boundary p p p
atom_style electron
read_data data.${sname}
read_data data.Be-solid
Reading data file ...
orthogonal box = (0 0 0) to (64.288 63.628618 63.225)
2 by 2 by 1 MPI processor grid
reading atoms ...
20160 atoms
read_data CPU = 0.060 seconds
pair_style eff/cut 31.6125
pair_coeff * *
comm_modify vel yes
neigh_modify one 10000 page 100000
compute effTemp all temp/eff
thermo 10
thermo_style custom step etotal pe ke temp press
thermo_modify temp effTemp
compute 1 all property/atom spin eradius
dump 1 all custom 1 ${sname}.spe.lammpstrj id type x y z c_1[1] c_1[2]
dump 1 all custom 1 Be-solid.spe.lammpstrj id type x y z c_1[1] c_1[2]
fix 1 all nve/eff
run 0
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- EFF package: doi:10.1002/jcc.21637
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 10000, page size: 100000
master list distance cutoff = 33.6125
ghost atom cutoff = 33.6125
binsize = 16.80625, bins = 4 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair eff/cut, 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) = 152.2 | 157 | 161.7 Mbytes
Step TotEng PotEng KinEng Temp Press
0 -49308.807 -49308.807 0 0 1.7906684e+11
Loop time of 2.49575e-06 on 4 procs for 0 steps with 20160 atoms
140.2% 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 | 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 | | 2.496e-06 | | |100.00
Nlocal: 5040 ave 5040 max 5040 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 97370 ave 97370 max 97370 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 3.11643e+07 ave 3.241e+07 max 2.99372e+07 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Total # of neighbors = 1.2465734e+08
Ave neighs/atom = 6183.4
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:03

118
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LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
variable sname index SiC
variable nstep equal 100
units electron
newton on
boundary p p p
atom_style electron
read_data data.${sname}
read_data data.SiC
Reading data file ...
orthogonal box = (0 0 0) to (41.1 41.1 41.1)
1 by 2 by 2 MPI processor grid
reading atoms ...
5000 atoms
read_data CPU = 0.016 seconds
pair_style eff/cut 20.0 limit/eradius pressure/evirials ecp 1 Si 2 C
pair_coeff * *
pair_coeff 1 s 0.320852 2.283269 0.814857
pair_coeff 2 p 22.721015 0.728733 1.103199 17.695345 6.693621
comm_modify vel yes
neigh_modify one 4000 page 40000
compute energies all pair eff/cut
variable eke equal c_energies[1]
variable epauli equal c_energies[2]
variable ecoul equal c_energies[3]
variable erres equal c_energies[4]
variable etotalnew equal c_energies[1]+c_energies[2]+c_energies[3]+c_energies[4]
thermo ${nstep}
thermo 100
thermo_style custom step etotal pe ke v_etotalnew v_eke v_epauli v_ecoul v_erres
thermo_modify format float %16.8f
thermo_modify lost warn norm yes flush yes
# Minimization
min_style cg
dump 1 all xyz ${nstep} ${sname}.min.xyz
dump 1 all xyz 100 ${sname}.min.xyz
dump 1 all xyz 100 SiC.min.xyz
compute 1 all property/atom spin eradius erforce
dump 2 all custom ${nstep} ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
dump 2 all custom 100 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
dump 2 all custom 100 SiC.min.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
dump 3 all custom ${nstep} ${sname}.data.restart id type q c_1[1] c_1[2] x y z
dump 3 all custom 100 ${sname}.data.restart id type q c_1[1] c_1[2] x y z
dump 3 all custom 100 SiC.data.restart id type q c_1[1] c_1[2] x y z
min_modify line quadratic
minimize 0 1e-8 100000 1000000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- EFF package: doi:10.1002/jcc.21637
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 4000, page size: 40000
master list distance cutoff = 22
ghost atom cutoff = 22
binsize = 11, bins = 4 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair eff/cut, 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) = 20.12 | 20.7 | 21.34 Mbytes
Step TotEng PotEng KinEng v_etotalnew v_eke v_epauli v_ecoul v_erres
0 -0.61266585 -0.61266585 0.00000000 -3063.32924433 2666.66666667 2055.59661323 -7785.59252422 0.00000000
27 -0.87995767 -0.87995767 0.00000000 -4399.78836066 2569.46885777 446.25650389 -7415.51372232 0.00000000
Loop time of 7.78522 on 4 procs for 27 steps with 5000 atoms
99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = force tolerance
Energy initial, next-to-last, final =
-0.612665848866385 -0.879957672127075 -0.879957672129693
Force two-norm initial, final = 254.76567 6.2598998e-09
Force max component initial, final = 2.9077051 3.4450958e-10
Final line search alpha, max atom move = 1 3.4450958e-10
Iterations, force evaluations = 27 37
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 6.976 | 7.3573 | 7.6627 | 10.1 | 94.50
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.11037 | 0.41578 | 0.79718 | 42.4 | 5.34
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.0121 | | | 0.16
Nlocal: 1250 ave 1250 max 1250 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 25192 ave 25192 max 25192 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 1.9985e+06 ave 2.14947e+06 max 1.84582e+06 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Total # of neighbors = 7994000
Ave neighs/atom = 1598.8
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:08

11
examples/PACKAGES/eff/ECP/SiH4/log.01Feb25.SiH4.ang.g++.4 Normal file
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LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
# Created 2011-01-07
# General parameters
variable sname index SiH4.ang
log ${sname}.log
log SiH4.ang.log

11
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@ -0,0 +1,11 @@
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
# Created 2011-01-07
# General parameters
variable sname index SiH4
log ${sname}.log
log SiH4.log

95
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LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
variable sname index h_atom.ang
units real
newton on
boundary p p p
atom_style electron
read_data data.${sname}
read_data data.h_atom.ang
Reading data file ...
orthogonal box = (-0.529177 -0.529177 -0.529177) to (0.529177 0.529177 0.529177)
1 by 2 by 2 MPI processor grid
reading atoms ...
4 atoms
read_data CPU = 0.000 seconds
pair_style eff/cut 0.529177249
pair_coeff * *
comm_modify vel yes
timestep 0.0001
compute energies all pair eff/cut
variable eke equal c_energies[1]
variable epauli equal c_energies[2]
variable estatics equal c_energies[3]
variable errestrain equal c_energies[4]
compute peratom all stress/atom NULL
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
compute effTemp all temp/eff
compute effPress all pressure effTemp
thermo 1
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
thermo_modify temp effTemp press effPress
run 0
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- EFF package: doi:10.1002/jcc.21637
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.5291772
ghost atom cutoff = 2.5291772
binsize = 1.2645886, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair eff/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:1202)
Per MPI rank memory allocation (min/avg/max) = 4.35 | 4.35 | 4.35 Mbytes
Step TotEng PotEng KinEng v_eke v_epauli v_estatics v_errestrain Temp Press v_press
0 367.03102 367.03102 0 1882.5288 389.88475 -1905.3825 0 0 29191582 29191582
Loop time of 2.124e-06 on 4 procs for 0 steps with 4 atoms
70.6% 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 | 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 | | 2.124e-06 | | |100.00
Nlocal: 1 ave 4 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Nghost: 549 ave 550 max 546 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 121.5 ave 486 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Total # of neighbors = 486
Ave neighs/atom = 121.5
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

94
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@ -0,0 +1,94 @@
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
variable sname index h_atom.bohr
units electron
newton on
boundary p p p
atom_style electron
read_data data.${sname}
read_data data.h_atom.bohr
Reading data file ...
orthogonal box = (-1 -1 -1) to (1 1 1)
1 by 2 by 2 MPI processor grid
reading atoms ...
2 atoms
read_data CPU = 0.001 seconds
pair_style eff/cut 1.0
pair_coeff * *
comm_modify vel yes
compute energies all pair eff/cut
variable eke equal c_energies[1]
variable epauli equal c_energies[2]
variable estatics equal c_energies[3]
variable errestrain equal c_energies[4]
compute peratom all stress/atom NULL
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
compute effTemp all temp/eff
compute effPress all pressure effTemp
thermo 1
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
thermo_modify temp effTemp press effPress
run 0
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- EFF package: doi:10.1002/jcc.21637
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3
ghost atom cutoff = 3
binsize = 1.5, bins = 2 2 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair eff/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:1202)
Per MPI rank memory allocation (min/avg/max) = 4.301 | 4.301 | 4.301 Mbytes
Step TotEng PotEng KinEng v_eke v_epauli v_estatics v_errestrain Temp Press v_press
0 -0.095769122 -0.095769122 0 1.5 0 -1.5957691 0 0 0 0
Loop time of 2.4135e-06 on 4 procs for 0 steps with 2 atoms
0.0% 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 | 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 | | 2.414e-06 | | |100.00
Nlocal: 0.5 ave 2 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Nghost: 159.5 ave 160 max 158 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 9.25 ave 37 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Total # of neighbors = 37
Ave neighs/atom = 18.5
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

381
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@ -0,0 +1,381 @@
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
variable sname index h2
units electron
newton on
boundary p p p
atom_style electron
read_data data.${sname}
read_data data.h2
Reading data file ...
orthogonal box = (0 0 0) to (12.895936 12.895936 12.895936)
1 by 2 by 2 MPI processor grid
reading atoms ...
128 atoms
read_data CPU = 0.001 seconds
pair_style eff/cut 6.447968 pressure/evirials
pair_coeff * *
comm_modify vel yes
min_style cg
min_modify line quadratic
minimize 0 1.0e-6 1000 2000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- EFF package: doi:10.1002/jcc.21637
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.447968
ghost atom cutoff = 8.447968
binsize = 4.223984, bins = 4 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair eff/cut, 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) = 5.473 | 5.473 | 5.473 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -25.681592 0 -25.681592 4.1596728e+10
43 0 -29.402735 0 -29.402735 5.8094784e+10
Loop time of 0.00763171 on 4 procs for 43 steps with 128 atoms
97.4% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = force tolerance
Energy initial, next-to-last, final =
-25.6815917951629 -29.4027346945036 -29.4027347455099
Force two-norm initial, final = 0.90233034 1.9851971e-07
Force max component initial, final = 0.10428109 2.0171202e-08
Final line search alpha, max atom move = 1 2.0171202e-08
Iterations, force evaluations = 43 49
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0027162 | 0.0036134 | 0.0039713 | 0.9 | 47.35
Neigh | 4.3664e-05 | 4.9777e-05 | 5.6567e-05 | 0.0 | 0.65
Comm | 0.0030668 | 0.0034209 | 0.004339 | 0.9 | 44.82
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.0005477 | | | 7.18
Nlocal: 32 ave 32 max 32 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 928 ave 928 max 928 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 2416 ave 2579 max 2253 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 9664
Ave neighs/atom = 75.5
Neighbor list builds = 1
Dangerous builds = 0
region part block INF 2.0 INF 2.0 INF 5.0 units box
group sub id < 32
31 atoms in group sub
compute effTemp all temp/eff
compute effPress all pressure effTemp
compute regionT sub temp/region/eff part
compute peratom all stress/atom NULL
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
thermo 100
thermo_style custom step etotal pe ke temp press v_press c_regionT
thermo_modify temp effTemp press effPress
#velocity all create 300.0 4928459 rot yes dist gaussian
fix 3 all temp/rescale/eff 10 0.0 300.0 0.02 1.0
fix 1 all nve/eff
run 10000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 4.723 | 4.723 | 4.723 Mbytes
Step TotEng PotEng KinEng Temp Press v_press c_regionT
43 -29.402735 -29.402735 0 0 5.8094784e+10 5.8094784e+10 0
100 -29.402222 -29.402734 0.00051174152 1.71 5.811788e+10 5.8115522e+10 0.84298014
200 -29.401297 -29.402706 0.0014095337 4.71 5.8200069e+10 5.8193571e+10 2.2642129
300 -29.400299 -29.402606 0.0023073258 7.71 5.8313355e+10 5.8302716e+10 3.5188104
400 -29.399185 -29.40239 0.003205118 10.71 5.8450303e+10 5.8435537e+10 4.4975076
500 -29.397917 -29.40202 0.0041029101 13.71 5.8606915e+10 5.8588085e+10 5.0938111
600 -29.396468 -29.401468 0.0050007023 16.71 5.8780191e+10 5.8757458e+10 5.214099
700 -29.394823 -29.400721 0.0058984944 19.71 5.8967293e+10 5.8940983e+10 4.7987742
800 -29.392986 -29.399782 0.0067962866 22.71 5.9165038e+10 5.9135736e+10 3.8586623
900 -29.390985 -29.398679 0.0076940787 25.71 5.936952e+10 5.9338162e+10 2.5267164
1000 -29.388873 -29.397465 0.0085918709 28.71 5.9575808e+10 5.9543743e+10 1.1129096
1100 -29.386732 -29.396221 0.009489663 31.71 5.9777799e+10 5.9746754e+10 0.12904766
1200 -29.38466 -29.395047 0.010387455 34.71 5.9968346e+10 5.9940231e+10 0.23254239
1300 -29.382761 -29.394047 0.011285247 37.71 6.0139768e+10 6.0116306e+10 2.0555958
1400 -29.381123 -29.393306 0.012183039 40.71 6.0284712e+10 6.0267009e+10 5.9623931
1500 -29.379789 -29.39287 0.013080832 43.71 6.0397168e+10 6.0385416e+10 11.867131
1600 -29.378749 -29.392728 0.013978624 46.71 6.0473266e+10 6.0466731e+10 19.241519
1700 -29.377937 -29.392813 0.014876416 49.71 6.051158e+10 6.0508871e+10 27.309028
1800 -29.377239 -29.393013 0.015774208 52.71 6.0512895e+10 6.0512343e+10 35.292057
1900 -29.376517 -29.393189 0.016672 55.71 6.0479626e+10 6.0479611e+10 42.576307
2000 -29.375623 -29.393193 0.017569792 58.71 6.0415141e+10 6.0414287e+10 48.751559
2100 -29.374415 -29.392882 0.018467585 61.71 6.0323201e+10 6.0320436e+10 53.567423
2200 -29.372763 -29.392128 0.019365377 64.71 6.0207563e+10 6.0202104e+10 56.859803
2300 -29.370562 -29.390825 0.020263169 67.71 6.0071772e+10 6.0063077e+10 58.484447
2400 -29.367733 -29.388894 0.021160961 70.71 5.9919081e+10 5.9906793e+10 58.272649
2500 -29.36423 -29.386289 0.022058753 73.71 5.9752468e+10 5.9736389e+10 56.015194
2600 -29.360049 -29.383005 0.022956545 76.71 5.9574736e+10 5.9554816e+10 51.483979
2700 -29.355237 -29.379092 0.023854337 79.71 5.9388664e+10 5.9365044e+10 44.512157
2800 -29.349911 -29.374664 0.02475213 82.71 5.9197231e+10 5.9170319e+10 35.165882
2900 -29.344268 -29.369918 0.025649922 85.71 5.9003898e+10 5.8974484e+10 24.034217
3000 -29.338593 -29.365141 0.026547714 88.71 5.8812903e+10 5.8782274e+10 12.596437
3100 -29.333256 -29.360702 0.027445506 91.71 5.8629493e+10 5.8599437e+10 3.4545231
3200 -29.328661 -29.357004 0.028343298 94.71 5.8459894e+10 5.8432478e+10 0.016534267
3300 -29.325167 -29.354408 0.02924109 97.71 5.8310843e+10 5.828792e+10 5.3243002
3400 -29.322991 -29.35313 0.030138882 100.71 5.8188646e+10 5.8171288e+10 20.462635
3500 -29.322131 -29.353168 0.031036675 103.71 5.8098076e+10 5.8086277e+10 43.783703
3600 -29.322365 -29.3543 0.031934467 106.71 5.8041579e+10 5.8034437e+10 71.730426
3700 -29.323314 -29.356147 0.032832259 109.71 5.8019147e+10 5.8015336e+10 100.55288
3800 -29.32453 -29.35826 0.033730051 112.71 5.8028749e+10 5.8026989e+10 127.58755
3900 -29.325571 -29.360199 0.034627843 115.71 5.8067003e+10 5.8066317e+10 151.55747
4000 -29.326051 -29.361577 0.035525635 118.71 5.8129753e+10 5.8129529e+10 172.22883
4100 -29.325653 -29.362076 0.036423427 121.71 5.8212438e+10 5.8212365e+10 189.92431
4200 -29.324129 -29.36145 0.03732122 124.71 5.8310227e+10 5.8310175e+10 205.15122
4300 -29.321298 -29.359517 0.038219012 127.71 5.8417974e+10 5.8417851e+10 218.38021
4400 -29.317038 -29.356155 0.039116804 130.71 5.853006e+10 5.8529625e+10 229.92521
4500 -29.311285 -29.3513 0.040014596 133.71 5.8640135e+10 5.8638756e+10 239.8628
4600 -29.304036 -29.344948 0.040912388 136.71 5.8740796e+10 5.8737084e+10 247.94642
4700 -29.295358 -29.337168 0.04181018 139.71 5.8823225e+10 5.8814498e+10 253.48762
4800 -29.285407 -29.328115 0.042707973 142.71 5.8876834e+10 5.8858342e+10 255.20199
4900 -29.274456 -29.318062 0.043605765 145.71 5.8889029e+10 5.8852994e+10 251.07158
5000 -29.262921 -29.307424 0.044503557 148.71 5.8845331e+10 5.8780052e+10 238.3896
5100 -29.251383 -29.296784 0.045401349 151.71 5.8730207e+10 5.8619991e+10 214.32208
5200 -29.240581 -29.286881 0.046299141 154.71 5.8529067e+10 5.8356259e+10 177.37505
5300 -29.231338 -29.278535 0.047196933 157.71 5.8231557e+10 5.7981728e+10 129.63824
5400 -29.2244 -29.272495 0.048094725 160.71 5.783545e+10 5.7504658e+10 78.320218
5500 -29.220236 -29.269228 0.048992518 163.71 5.734924e+10 5.6948969e+10 34.221251
5600 -29.218882 -29.268773 0.04989031 166.71 5.6791455e+10 5.6346643e+10 6.9175951
5700 -29.219941 -29.270729 0.050788102 169.71 5.6186504e+10 5.5727327e+10 0.29716744
5800 -29.222711 -29.274397 0.051685894 172.71 5.5559255e+10 5.5112403e+10 12.070047
5900 -29.226384 -29.278968 0.052583686 175.71 5.4930986e+10 5.4515116e+10 36.620819
6000 -29.230194 -29.283676 0.053481478 178.71 5.4317798e+10 5.394343e+10 68.124786
6100 -29.233502 -29.287881 0.05437927 181.71 5.373093e+10 5.3402599e+10 102.15151
6200 -29.235817 -29.291094 0.055277063 184.71 5.317797e+10 5.2896659e+10 135.88236
6300 -29.236796 -29.29297 0.056174855 187.71 5.266419e+10 5.2429163e+10 167.68481
6400 -29.236229 -29.293302 0.057072647 190.71 5.2193678e+10 5.2003557e+10 196.5624
6500 -29.234036 -29.292006 0.057970439 193.71 5.1770207e+10 5.1623395e+10 221.67578
6600 -29.230262 -29.28913 0.058868231 196.71 5.1397868e+10 5.1292425e+10 241.95867
6700 -29.225101 -29.284867 0.059766023 199.71 5.1081526e+10 5.1014513e+10 255.81687
6800 -29.218918 -29.279582 0.060663816 202.71 5.0827088e+10 5.0793357e+10 260.95381
6900 -29.212279 -29.27384 0.061561608 205.71 5.0641515e+10 5.0632006e+10 254.493
7000 -29.20597 -29.26843 0.0624594 208.71 5.0532428e+10 5.0532428e+10 233.71509
7100 -29.200973 -29.264331 0.063357192 211.71 5.0507114e+10 5.0495687e+10 197.6792
7200 -29.198346 -29.262601 0.064254984 214.71 5.0570894e+10 5.0523214e+10 149.34022
7300 -29.199011 -29.264163 0.065152776 217.71 5.0725246e+10 5.061858e+10 96.508036
7400 -29.203489 -29.26954 0.066050568 220.71 5.0966567e+10 5.0787531e+10 49.67303
7500 -29.211725 -29.278674 0.066948361 223.71 5.1286493e+10 5.103478e+10 17.246635
7600 -29.223104 -29.29095 0.067846153 226.71 5.167383e+10 5.1359868e+10 1.9485991
7700 -29.236642 -29.305386 0.068743945 229.71 5.2117092e+10 5.1756034e+10 1.0837556
7800 -29.251244 -29.320885 0.069641737 232.71 5.2606457e+10 5.2212741e+10 9.4375813
7900 -29.265892 -29.336432 0.070539529 235.71 5.3134616e+10 5.2719209e+10 21.964752
8000 -29.279741 -29.351178 0.071437321 238.71 5.3696722e+10 5.3266678e+10 34.999087
8100 -29.292137 -29.364472 0.072335113 241.71 5.4289899e+10 5.3849048e+10 46.31642
8200 -29.3026 -29.375833 0.073232906 244.71 5.4912636e+10 5.4462542e+10 54.747327
8300 -29.310798 -29.384928 0.074130698 247.71 5.5564256e+10 5.510506e+10 59.766256
8400 -29.316514 -29.391542 0.07502849 250.71 5.6244467e+10 5.5775533e+10 61.201976
8500 -29.319632 -29.395559 0.075926282 253.71 5.6952997e+10 5.6473403e+10 59.079366
8600 -29.32013 -29.396954 0.076824074 256.71 5.7689238e+10 5.719821e+10 53.567555
8700 -29.318072 -29.395794 0.077721866 259.71 5.845187e+10 5.7949231e+10 45.014327
8800 -29.313622 -29.392241 0.078619658 262.71 5.923839e+10 5.8725125e+10 34.059265
8900 -29.307054 -29.386572 0.079517451 265.71 6.0044529e+10 5.9523495e+10 21.822776
9000 -29.298773 -29.379188 0.080415243 268.71 6.0863509e+10 6.0340317e+10 10.151211
9100 -29.289324 -29.370637 0.081313035 271.71 6.1685216e+10 6.1169112e+10 1.8420489
9200 -29.279397 -29.361608 0.082210827 274.71 6.2495436e+10 6.1999812e+10 0.66834686
9300 -29.269795 -29.352904 0.083108619 277.71 6.3275527e+10 6.2817393e+10 10.912705
9400 -29.261351 -29.345358 0.084006411 280.71 6.400305e+10 6.3600785e+10 36.169722
9500 -29.254801 -29.339705 0.084904204 283.71 6.4653796e+10 6.4323113e+10 77.605603
9600 -29.250616 -29.336418 0.085801996 286.71 6.520517e+10 6.4954574e+10 132.59334
9700 -29.248872 -29.335572 0.086699788 289.71 6.5640092e+10 6.5468097e+10 194.91905
9800 -29.249212 -29.33681 0.08759758 292.71 6.59499e+10 6.5845645e+10 256.81628
9900 -29.250911 -29.339406 0.088495372 295.71 6.6135085e+10 6.6081884e+10 311.59173
10000 -29.253024 -29.342417 0.089393164 298.71 6.6203807e+10 6.6183517e+10 355.23319
10043 -29.253759 -29.343588 0.089828702 300.16536 6.6201159e+10 6.6189815e+10 370.38327
Loop time of 1.04131 on 4 procs for 10000 steps with 128 atoms
Performance: 829720.937 fs/day, 0.000 hours/fs, 9603.252 timesteps/s, 1.229 Matom-step/s
90.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.43097 | 0.51117 | 0.59532 | 10.4 | 49.09
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.40178 | 0.48688 | 0.56619 | 10.6 | 46.76
Output | 0.0046624 | 0.0047434 | 0.0049664 | 0.2 | 0.46
Modify | 0.0074002 | 0.007613 | 0.0078044 | 0.2 | 0.73
Other | | 0.0309 | | | 2.97
Nlocal: 32 ave 32 max 32 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 928 ave 928 max 928 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 2480 ave 2645 max 2315 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 9920
Ave neighs/atom = 77.5
Neighbor list builds = 0
Dangerous builds = 0
unfix 3
#compute 1 all property/atom spin eradius
#fix 1 all npt/eff temp 3000.0 3000.0 0.1 iso 1e7 1e7 1.0 drag 0.5
#dump 1 all custom 100 dump.file id type q c_1[1] c_1[2] x y z
#fix 1 all nve/eff
run 10000
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 5.473 | 5.473 | 5.473 Mbytes
Step TotEng PotEng KinEng Temp Press v_press c_regionT
10043 -29.253759 -29.343588 0.089828702 300.16536 6.6201159e+10 6.6189815e+10 370.38327
10100 -29.253759 -29.344838 0.091079452 304.34478 6.6176296e+10 6.6172538e+10 389.80019
10200 -29.253759 -29.345711 0.091951632 307.2592 6.6052925e+10 6.6052773e+10 409.04715
10300 -29.253759 -29.344222 0.09046268 302.28382 6.5835973e+10 6.5829924e+10 406.94188
10400 -29.253759 -29.339884 0.086124587 287.78795 6.5537696e+10 6.5519727e+10 382.65817
10500 -29.253759 -29.33263 0.078870586 263.54848 6.5173326e+10 6.5140691e+10 337.96709
10600 -29.253759 -29.32285 0.069091456 230.87122 6.476052e+10 6.4713236e+10 277.25232
10700 -29.253759 -29.311365 0.057605907 192.4919 6.4318542e+10 6.4258684e+10 207.17514
10800 -29.253759 -29.299325 0.045566125 152.26061 6.3867235e+10 6.379814e+10 136.00177
10900 -29.253759 -29.288069 0.034309769 114.64714 6.3425834e+10 6.3351345e+10 72.65992
11000 -29.253759 -29.278938 0.025178778 84.135657 6.3011735e+10 6.2935563e+10 25.640652
11100 -29.253759 -29.273091 0.01933168 64.597401 6.2639343e+10 6.2564598e+10 1.8969587
11200 -29.253759 -29.271337 0.01757805 58.737592 6.2319122e+10 6.224804e+10 5.9017765
11300 -29.253759 -29.27402 0.02026083 67.702184 6.2056961e+10 6.1990807e+10 39.010867
11400 -29.253759 -29.280964 0.02720461 90.905038 6.1853928e+10 6.1793041e+10 99.231156
11500 -29.253759 -29.291496 0.037737065 126.09956 6.1706426e+10 6.1650353e+10 181.43067
11600 -29.253759 -29.304538 0.050778773 169.67883 6.1606742e+10 6.1554398e+10 277.95525
11700 -29.253759 -29.318745 0.064985916 217.15243 6.1543891e+10 6.1493702e+10 379.55439
11800 -29.253759 -29.332682 0.078922995 263.72361 6.1504653e+10 6.1454647e+10 476.47604
11900 -29.253759 -29.344999 0.091239641 304.88006 6.1474696e+10 6.1422513e+10 559.5746
12000 -29.253759 -29.354586 0.10082711 336.91689 6.1439645e+10 6.1382484e+10 621.28769
12100 -29.253759 -29.360694 0.10693515 357.32707 6.1386022e+10 6.1320551e+10 656.36975
12200 -29.253759 -29.362996 0.10923714 365.01925 6.1301987e+10 6.1224243e+10 662.31507
12300 -29.253759 -29.361599 0.10783979 360.34996 6.1177837e+10 6.1083188e+10 639.45046
12400 -29.253759 -29.357 0.10324072 344.98202 6.1006282e+10 6.0889481e+10 590.72007
12500 -29.253759 -29.350003 0.096243698 321.60127 6.0782503e+10 6.0637874e+10 521.21754
12600 -29.253759 -29.341604 0.087845122 293.53717 6.0504033e+10 6.032581e+10 437.54122
12700 -29.253759 -29.332866 0.079107181 264.33907 6.017052e+10 5.995332e+10 347.0566
12800 -29.253759 -29.324792 0.071033241 237.35975 5.9783407e+10 5.9522812e+10 257.14865
12900 -29.253759 -29.318218 0.064459023 215.3918 5.9345591e+10 5.9038771e+10 174.53724
13000 -29.253759 -29.313729 0.059970255 200.39245 5.8861097e+10 5.8507403e+10 104.71393
13100 -29.253759 -29.311613 0.057853612 193.31962 5.8334792e+10 5.7936245e+10 51.540581
13200 -29.253759 -29.311843 0.05808372 194.08853 5.777218e+10 5.7333762e+10 17.031706
13300 -29.253759 -29.314104 0.060345047 201.64482 5.7179263e+10 5.6708972e+10 1.3240561
13400 -29.253759 -29.317843 0.064084089 214.13895 5.6562484e+10 5.6071106e+10 2.82093
13500 -29.253759 -29.322344 0.068584649 229.17771 5.5928737e+10 5.542933e+10 18.484961
13600 -29.253759 -29.326816 0.073057273 244.12312 5.528542e+10 5.4792545e+10 44.242832
13700 -29.253759 -29.330492 0.076733214 256.40639 5.4640519e+10 5.4169259e+10 75.458518
13800 -29.253759 -29.332712 0.07895342 263.82528 5.4002682e+10 5.3567542e+10 107.42845
13900 -29.253759 -29.333003 0.079244028 264.79635 5.3381274e+10 5.2995036e+10 135.85235
14000 -29.253759 -29.33113 0.077371384 258.53885 5.2786371e+10 5.2459011e+10 157.23725
14100 -29.253759 -29.327131 0.073371666 245.17367 5.2228695e+10 5.196645e+10 169.19917
14200 -29.253759 -29.321311 0.06755247 225.72865 5.1719461e+10 5.1524114e+10 170.63669
14300 -29.253759 -29.314225 0.060466227 202.04975 5.1270133e+10 5.1138601e+10 161.76275
14400 -29.253759 -29.306617 0.052857773 176.62587 5.089211e+10 5.0816349e+10 143.99448
14500 -29.253759 -29.29935 0.045590774 152.34297 5.059633e+10 5.0563589e+10 119.71531
14600 -29.253759 -29.293319 0.039559773 132.1902 5.0392837e+10 5.0386251e+10 91.93698
14700 -29.253759 -29.289355 0.035596197 118.94579 5.029032e+10 5.0289808e+10 63.900552
14800 -29.253759 -29.288137 0.034377629 114.8739 5.029568e+10 5.0279104e+10 38.66315
14900 -29.253759 -29.290109 0.036349691 121.46361 5.0413636e+10 5.0358148e+10 18.71998
15000 -29.253759 -29.295428 0.041669069 139.23847 5.0646422e+10 5.0529927e+10 5.7077538
15100 -29.253759 -29.303933 0.050174363 167.65917 5.099359e+10 5.079623e+10 0.22655448
15200 -29.253759 -29.315148 0.061388837 205.13268 5.1451944e+10 5.1157502e+10 1.802684
15300 -29.253759 -29.328315 0.074555888 249.13079 5.2015605e+10 5.1612742e+10 8.997261
15400 -29.253759 -29.342464 0.088704628 296.40923 5.2676201e+10 5.2159429e+10 19.646426
15500 -29.253759 -29.356499 0.10273965 343.30769 5.3423173e+10 5.2793473e+10 31.201748
15600 -29.253759 -29.369305 0.11554633 386.10162 5.4244166e+10 5.3509204e+10 41.12616
15700 -29.253759 -29.37986 0.1261011 421.37071 5.5125447e+10 5.429932e+10 47.293231
15800 -29.253759 -29.387334 0.13357524 446.34577 5.6052334e+10 5.5154866e+10 48.336756
15900 -29.253759 -29.39118 0.13742108 459.19674 5.7009617e+10 5.6065206e+10 43.903332
16000 -29.253759 -29.39119 0.13743084 459.22936 5.798194e+10 5.7018034e+10 34.771959
16100 -29.253759 -29.38752 0.13376082 446.96588 5.8954112e+10 5.7999411e+10 22.820321
16200 -29.253759 -29.380676 0.12691686 424.09659 5.9911355e+10 5.8993881e+10 10.835339
16300 -29.253759 -29.37146 0.11770099 393.30145 6.083948e+10 5.9984681e+10 2.1841693
16400 -29.253759 -29.360882 0.10712336 357.956 6.1725019e+10 6.095406e+10 0.37905177
16500 -29.253759 -29.350047 0.096287961 321.74918 6.255531e+10 6.1883732e+10 8.5837627
16600 -29.253759 -29.340023 0.086263871 288.25337 6.3318582e+10 6.2755451e+10 29.119377
16700 -29.253759 -29.331716 0.077957034 260.49582 6.4004055e+10 6.3551677e+10 63.031437
16800 -29.253759 -29.325757 0.071998194 240.58417 6.460208e+10 6.4256316e+10 109.77858
16900 -29.253759 -29.322421 0.06866219 229.43681 6.5104343e+10 6.4855474e+10 167.09379
17000 -29.253759 -29.32159 0.067830842 226.65884 6.5504142e+10 6.5338169e+10 231.05378
17100 -29.253759 -29.322766 0.06900694 230.58881 6.5796723e+10 6.5696949e+10 296.37046
17200 -29.253759 -29.325139 0.071380489 238.52009 6.5979662e+10 6.5928378e+10 356.89258
17300 -29.253759 -29.3277 0.073941262 247.07699 6.6053264e+10 6.6033329e+10 406.27733
17400 -29.253759 -29.329384 0.075624794 252.70257 6.6020907e+10 6.6017081e+10 438.765
17500 -29.253759 -29.329232 0.075473164 252.19589 6.5889298e+10 6.5889197e+10 449.9672
17600 -29.253759 -29.326547 0.072788435 243.22479 6.5668557e+10 6.566317e+10 437.56505
17700 -29.253759 -29.321015 0.067255999 224.73798 6.537209e+10 6.5355863e+10 401.81223
17800 -29.253759 -29.312777 0.059017856 197.20998 6.5016192e+10 6.4986737e+10 345.75083
17900 -29.253759 -29.302441 0.048681923 162.67214 6.461938e+10 6.4576898e+10 275.07707
18000 -29.253759 -29.291021 0.037262252 124.51296 6.4201459e+10 6.4148001e+10 197.63846
18100 -29.253759 -29.279814 0.026055453 87.065095 6.3782375e+10 6.3721066e+10 122.59764
18200 -29.253759 -29.270228 0.016469061 55.031873 6.3380961e+10 6.3315275e+10 59.354773
18300 -29.253759 -29.263585 0.009826229 32.834645 6.3013664e+10 6.2946844e+10 16.367993
18400 -29.253759 -29.260935 0.0071761426 23.9793 6.2693422e+10 6.2628079e+10 0.04021999
18500 -29.253759 -29.262899 0.0091396789 30.540517 6.2428791e+10 6.2366686e+10 13.840884
18600 -29.253759 -29.269574 0.01581463 52.84507 6.2223448e+10 6.2165441e+10 57.800802
18700 -29.253759 -29.280514 0.026755117 89.403044 6.2076104e+10 6.2022224e+10 128.46082
18800 -29.253759 -29.294786 0.041027472 137.09456 6.1980858e+10 6.1930427e+10 219.28144
18900 -29.253759 -29.311091 0.057332365 191.57786 6.1927902e+10 6.1879682e+10 321.44654
19000 -29.253759 -29.327932 0.074172828 247.85078 6.1904521e+10 6.1856811e+10 424.935
19100 -29.253759 -29.343801 0.090041852 300.87761 6.1896231e+10 6.1846902e+10 519.70032
19200 -29.253759 -29.357361 0.10360217 346.18982 6.1887942e+10 6.1834406e+10 596.79434
19300 -29.253759 -29.367593 0.11383425 380.38063 6.1865031e+10 6.1804149e+10 649.29447
19400 -29.253759 -29.373894 0.12013535 401.43594 6.1814231e+10 6.1742208e+10 672.93539
19500 -29.253759 -29.37612 0.12236075 408.87221 6.1724294e+10 6.1636603e+10 666.39687
19600 -29.253759 -29.374566 0.12080701 403.68034 6.1586396e+10 6.1477781e+10 631.24827
19700 -29.253759 -29.369903 0.11614425 388.09956 6.1394308e+10 6.1258917e+10 571.59167
19800 -29.253759 -29.363069 0.10931013 365.26317 6.1144351e+10 6.0976023e+10 493.47418
19900 -29.253759 -29.35514 0.10138144 338.76918 6.0835203e+10 6.0627905e+10 404.15587
20000 -29.253759 -29.347199 0.093439728 312.23172 6.0467587e+10 6.0215993e+10 311.32317
20043 -29.253759 -29.344026 0.090267282 301.63089 6.0292085e+10 6.002012e+10 272.18496
Loop time of 1.02899 on 4 procs for 10000 steps with 128 atoms
Performance: 839654.865 fs/day, 0.000 hours/fs, 9718.228 timesteps/s, 1.244 Matom-step/s
91.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.42341 | 0.50618 | 0.59534 | 10.4 | 49.19
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.39233 | 0.48231 | 0.56438 | 10.7 | 46.87
Output | 0.0047128 | 0.0048033 | 0.0050386 | 0.2 | 0.47
Modify | 0.0052563 | 0.0055253 | 0.0058241 | 0.3 | 0.54
Other | | 0.03018 | | | 2.93
Nlocal: 32 ave 32 max 32 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 928 ave 928 max 928 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 2416 ave 2582 max 2250 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 9664
Ave neighs/atom = 75.5
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:02

161
examples/PACKAGES/eff/H_plasma/log.01Feb25.h2bulk.npt.g++.4 Normal file
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@ -0,0 +1,161 @@
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
variable sname index h2bulk
units electron
newton on
boundary p p p
atom_style electron
read_data data.${sname}
read_data data.h2bulk
Reading data file ...
orthogonal box = (0 0 0) to (61.255694 61.255694 61.255694)
1 by 2 by 2 MPI processor grid
reading atoms ...
13718 atoms
read_data CPU = 0.048 seconds
pair_style eff/cut 30.627847
pair_coeff * *
neigh_modify one 20000 page 200000
comm_modify vel yes
compute effTemp all temp/eff
thermo 100
thermo_style custom step pe temp press vol
thermo_modify temp effTemp
# structure minimization
dump 1 all xyz 1 ${sname}.min.xyz
dump 1 all xyz 1 h2bulk.min.xyz
min_style cg
minimize 0 1.0e-4 1 10000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- EFF package: doi:10.1002/jcc.21637
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 20000, page size: 200000
master list distance cutoff = 32.627847
ghost atom cutoff = 32.627847
binsize = 16.313924, bins = 4 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair eff/cut, 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) = 87.11 | 93.61 | 100.1 Mbytes
Step PotEng Temp Press Volume
0 -2871.4801 0 2.8596879e+10 229847.29
1 -2872.8077 0 2.8046824e+10 229847.29
Loop time of 1.02378 on 4 procs for 1 steps with 13718 atoms
100.0% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = max iterations
Energy initial, next-to-last, final =
-2871.48013813359 -2871.48013813359 -2872.8076730722
Force two-norm initial, final = 5.4264823 5.0563616
Force max component initial, final = 0.21424475 0.19518835
Final line search alpha, max atom move = 0.046675588 0.0091105311
Iterations, force evaluations = 1 1
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.7704 | 0.89228 | 1.0165 | 11.0 | 87.16
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0028288 | 0.12705 | 0.24891 | 29.2 | 12.41
Output | 0.0037898 | 0.0038794 | 0.0039584 | 0.1 | 0.38
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.0005774 | | | 0.06
Nlocal: 3429.5 ave 3800 max 3078 min
Histogram: 1 0 0 0 2 0 0 0 0 1
Nghost: 65600.5 ave 67122 max 64060 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Neighs: 1.49352e+07 ave 1.64494e+07 max 1.33918e+07 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Total # of neighbors = 59740807
Ave neighs/atom = 4354.9211
Neighbor list builds = 0
Dangerous builds = 0
undump 1
# create initial velocities according to temp, w/out e radial dof
velocity all create 20000.0 4928459 rot yes dist gaussian
# npt
fix 1 all npt/eff temp 20000.0 20000.0 1.0 iso 1e9 1e9 1.0
variable density equal 11.2058851*mass(all)
thermo_style custom step pe temp press vol v_density
WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:904)
thermo_modify temp effTemp
dump 2 all xyz 10000 ${sname}.npt.xyz
dump 2 all xyz 10000 h2bulk.npt.xyz
compute 1 all property/atom spin eradius
dump 3 all custom 10000 ${sname}.npt.lammpstrj id type x y z c_1[1] c_1[2]
dump 3 all custom 10000 h2bulk.npt.lammpstrj id type x y z c_1[1] c_1[2]
thermo 1
run 10
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 79.61 | 86.11 | 92.6 Mbytes
Step PotEng Temp Press Volume v_density
1 -2872.8077 40002.916 1.392533e+11 229847.29 154332.61
2 -2872.8075 40002.808 1.3925254e+11 229847.72 154332.61
3 -2872.8072 40002.493 1.3925022e+11 229849.01 154332.61
4 -2872.8068 40001.97 1.3924633e+11 229851.15 154332.61
5 -2872.8064 40001.241 1.3924088e+11 229854.15 154332.61
6 -2872.8058 40000.304 1.3923386e+11 229858.01 154332.61
7 -2872.8052 39999.161 1.3922528e+11 229862.72 154332.61
8 -2872.8045 39997.81 1.3921514e+11 229868.29 154332.61
9 -2872.8037 39996.253 1.3920343e+11 229874.72 154332.61
10 -2872.8028 39994.488 1.3919016e+11 229882.01 154332.61
11 -2872.8018 39992.517 1.3917533e+11 229890.15 154332.61
Loop time of 10.5538 on 4 procs for 10 steps with 13718 atoms
Performance: 81.866 fs/day, 0.293 hours/fs, 0.948 timesteps/s, 12.998 katom-step/s
100.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 8.6596 | 9.2995 | 10.519 | 24.8 | 88.12
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.029706 | 1.2492 | 1.8893 | 67.7 | 11.84
Output | 0.00056676 | 0.00059312 | 0.00063847 | 0.0 | 0.01
Modify | 0.0017284 | 0.0019179 | 0.0020891 | 0.4 | 0.02
Other | | 0.002503 | | | 0.02
Nlocal: 3429.5 ave 3800 max 3078 min
Histogram: 1 0 0 0 2 0 0 0 0 1
Nghost: 65600.5 ave 67122 max 64060 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Neighs: 1.49356e+07 ave 1.64691e+07 max 1.33702e+07 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Total # of neighbors = 59742327
Ave neighs/atom = 4355.0319
Neighbor list builds = 0
Dangerous builds = 0
unfix 1
undump 2
undump 3
Total wall time: 0:00:14

161
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@ -0,0 +1,161 @@
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
variable sname index h2bulk.ang
units real
newton on
boundary p p p
atom_style electron
read_data data.${sname}
read_data data.h2bulk.ang
Reading data file ...
orthogonal box = (0 0 0) to (32.41512 32.41512 32.41512)
1 by 2 by 2 MPI processor grid
reading atoms ...
13718 atoms
read_data CPU = 0.039 seconds
pair_style eff/cut 16.207559818252903 limit/eradius pressure/evirials
pair_coeff * *
neigh_modify one 10000 page 100000
comm_modify vel yes
compute peratom all stress/atom NULL
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
compute effTemp all temp/eff
compute effPress all pressure effTemp
compute energies all pair eff/cut
variable eke equal c_energies[1]
variable epauli equal c_energies[2]
variable ecoul equal c_energies[3]
variable erres equal c_energies[4]
thermo 10
thermo_style custom step etotal pe ke v_eke v_epauli v_ecoul v_erres press v_press temp
thermo_modify temp effTemp press effPress flush yes
# structure minimization
min_style cg
minimize 0 1.0e-4 10 10
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- EFF package: doi:10.1002/jcc.21637
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 10000, page size: 100000
master list distance cutoff = 18.20756
ghost atom cutoff = 18.20756
binsize = 9.1037799, bins = 4 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair eff/cut, 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) = 99.9 | 106.9 | 113.6 Mbytes
Step TotEng PotEng KinEng v_eke v_epauli v_ecoul v_erres Press v_press Temp
0 -1801882.2 -1801882.2 0 1941449.2 111650.99 -3854982.4 0 169191.44 169191.44 0
10 -1812982.2 -1812982.2 0 2023531 93131.746 -3929644.9 0 204251.79 204251.79 0
Loop time of 11.8971 on 4 procs for 10 steps with 13718 atoms
99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = max force evaluations
Energy initial, next-to-last, final =
-1801882.20439777 -1811783.39715666 -1812982.21160594
Force two-norm initial, final = 4976.0965 945.50616
Force max component initial, final = 134.44103 23.528388
Final line search alpha, max atom move = 0.0010624281 0.024997221
Iterations, force evaluations = 10 10
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 9.9682 | 10.823 | 11.655 | 22.1 | 90.97
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.23254 | 1.0651 | 1.9201 | 70.3 | 8.95
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.009102 | | | 0.08
Nlocal: 3429.5 ave 3800 max 3078 min
Histogram: 1 0 0 0 2 0 0 0 0 1
Nghost: 75372.5 ave 75724 max 75002 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Neighs: 1.74322e+07 ave 1.91106e+07 max 1.57195e+07 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Total # of neighbors = 69728955
Ave neighs/atom = 5083.0263
Neighbor list builds = 0
Dangerous builds = 0
timestep 0.001
velocity all create 20000.0 4928459 rot yes mom yes dist gaussian
# nve
fix 1 all nve/eff
#fix 2 all imd 8888 trate 1 unwrap on nowait on
compute peatom all pe/atom
compute keatom all ke/atom/eff
dump 2 all xyz 1000 ${sname}.nve.xyz
dump 2 all xyz 1000 h2bulk.ang.nve.xyz
compute 1 all property/atom spin eradius
dump 3 all custom 1000 ${sname}.nve.lammpstrj id type x y z c_1[1] c_1[2] c_peatom c_keatom
dump 3 all custom 1000 h2bulk.ang.nve.lammpstrj id type x y z c_1[1] c_1[2] c_peatom c_keatom
run 10
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 101 | 105.7 | 110.5 Mbytes
Step TotEng PotEng KinEng v_eke v_epauli v_ecoul v_erres Press v_press Temp
10 -995226.78 -1812982.2 817755.43 2023531 93131.746 -3929644.9 0 1301774.2 1301774.2 40002.916
20 -995226.78 -1812951.8 817725.06 2023530.9 93136.224 -3929618.9 0 1301757.1 1301757.1 40001.431
Loop time of 9.29954 on 4 procs for 10 steps with 13718 atoms
Performance: 0.000 ns/day, 258320.521 hours/ns, 1.075 timesteps/s, 14.751 katom-step/s
99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 8.5126 | 8.8333 | 9.1491 | 9.5 | 94.99
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.14252 | 0.45853 | 0.77938 | 41.7 | 4.93
Output | 0.0046943 | 0.0047097 | 0.0047198 | 0.0 | 0.05
Modify | 0.00051144 | 0.00055804 | 0.00059726 | 0.0 | 0.01
Other | | 0.002462 | | | 0.03
Nlocal: 3429.5 ave 3610 max 3249 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 75372.5 ave 75553 max 75192 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 1.74471e+07 ave 1.82017e+07 max 1.66315e+07 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Total # of neighbors = 69788395
Ave neighs/atom = 5087.3593
Neighbor list builds = 0
Dangerous builds = 0
unfix 1
#unfix 2
undump 2
undump 3
Total wall time: 0:00:24

150
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@ -0,0 +1,150 @@
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
variable sname index h2bulk
units electron
newton on
boundary p p p
atom_style electron
read_data data.${sname}
read_data data.h2bulk
Reading data file ...
orthogonal box = (0 0 0) to (61.255694 61.255694 61.255694)
1 by 2 by 2 MPI processor grid
reading atoms ...
13718 atoms
read_data CPU = 0.036 seconds
pair_style eff/cut 30.627847
pair_coeff * *
neigh_modify one 10000 page 100000
comm_modify vel yes
compute effTemp all temp/eff
thermo 10
thermo_style custom step pe temp press
thermo_modify temp effTemp
# structure minimization
min_style cg
minimize 0 1.0e-4 10 10
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- EFF package: doi:10.1002/jcc.21637
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 10000, page size: 100000
master list distance cutoff = 32.627847
ghost atom cutoff = 32.627847
binsize = 16.313924, bins = 4 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair eff/cut, 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) = 86.33 | 92.54 | 98.55 Mbytes
Step PotEng Temp Press
0 -2871.4801 0 2.8596879e+10
10 -2882.3401 0 2.1869586e+10
Loop time of 11.6123 on 4 procs for 10 steps with 13718 atoms
100.0% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = max force evaluations
Energy initial, next-to-last, final =
-2871.48013813359 -2881.24844591398 -2882.34005034714
Force two-norm initial, final = 5.4264823 1.3218657
Force max component initial, final = 0.21424475 0.025681865
Final line search alpha, max atom move = 0.4402147 0.011305535
Iterations, force evaluations = 10 10
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 9.2083 | 10.221 | 11.528 | 31.2 | 88.02
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.07895 | 1.3856 | 2.3982 | 84.8 | 11.93
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.005564 | | | 0.05
Nlocal: 3429.5 ave 3800 max 3078 min
Histogram: 1 0 0 0 2 0 0 0 0 1
Nghost: 65600.5 ave 67122 max 64060 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Neighs: 1.49352e+07 ave 1.64494e+07 max 1.33918e+07 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Total # of neighbors = 59740807
Ave neighs/atom = 4354.9211
Neighbor list builds = 0
Dangerous builds = 0
timestep 0.001
velocity all create 20000.0 4928459 rot yes mom yes dist gaussian
# nve
fix 1 all nve/eff
#fix 2 all imd 8888 trate 1 unwrap on nowait on
compute peatom all pe/atom
compute keatom all ke/atom/eff
dump 2 all xyz 1000 ${sname}.nve.xyz
dump 2 all xyz 1000 h2bulk.nve.xyz
compute 1 all property/atom spin eradius
dump 3 all custom 1000 ${sname}.nve.lammpstrj id type x y z c_1[1] c_1[2] c_peatom c_keatom
dump 3 all custom 1000 h2bulk.nve.lammpstrj id type x y z c_1[1] c_1[2] c_peatom c_keatom
run 10
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 82.52 | 87.21 | 91.69 Mbytes
Step PotEng Temp Press
10 -2882.3401 40002.916 1.3307606e+11
20 -2882.2908 40001.405 1.3306905e+11
Loop time of 9.25154 on 4 procs for 10 steps with 13718 atoms
Performance: 93.390 fs/day, 0.257 hours/fs, 1.081 timesteps/s, 14.828 katom-step/s
100.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 8.2948 | 8.675 | 8.9946 | 10.1 | 93.77
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.2531 | 0.57292 | 0.9531 | 39.5 | 6.19
Output | 3.7757e-05 | 5.7819e-05 | 7.5679e-05 | 0.0 | 0.00
Modify | 0.0005098 | 0.0005357 | 0.00055895 | 0.0 | 0.01
Other | | 0.002988 | | | 0.03
Nlocal: 3429.5 ave 3610 max 3249 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 65600.5 ave 66951 max 64250 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 1.49409e+07 ave 1.56765e+07 max 1.41457e+07 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Total # of neighbors = 59763523
Ave neighs/atom = 4356.577
Neighbor list builds = 0
Dangerous builds = 0
unfix 1
#unfix 2
undump 2
undump 3
Total wall time: 0:00:23

111
examples/PACKAGES/eff/Li-dendritic/log.01Feb25.Li-dendritic.min.g++.4 Normal file
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@ -0,0 +1,111 @@
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
variable sname index Li-dendritic
units electron
newton on
boundary p p p
atom_style electron
read_data data.${sname}
read_data data.Li-dendritic
Reading data file ...
orthogonal box = (0 0 0) to (100.224 100.224 100.224)
1 by 2 by 2 MPI processor grid
reading atoms ...
3456 atoms
read_data CPU = 0.023 seconds
#read_restart ${sname}.min.restart2
pair_style eff/cut 50.112
pair_coeff * *
comm_modify vel yes
compute effTemp all temp/eff
thermo 10
thermo_style custom step etotal pe ke temp press
thermo_modify temp effTemp
compute 1 all property/atom spin eradius
dump 1 all custom 10 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z
dump 1 all custom 10 Li-dendritic.min.lammpstrj id type q c_1[1] c_1[2] x y z
dump 2 all xyz 10 ${sname}.min.xyz
dump 2 all xyz 10 Li-dendritic.min.xyz
restart 10 ${sname}.nve.restart1 ${sname}.nve.restart2
restart 10 Li-dendritic.nve.restart1 ${sname}.nve.restart2
restart 10 Li-dendritic.nve.restart1 Li-dendritic.nve.restart2
#min_style cg
#min_modify line quadratic dmax 2.0
#minimize 0.0 1.0e-5 10000 100000
velocity all create 300.0 4928459 rot yes dist gaussian
fix 1 all nve/eff
run 100
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- EFF package: doi:10.1002/jcc.21637
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 52.112
ghost atom cutoff = 52.112
binsize = 26.056, bins = 4 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair eff/cut, 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) = 11.4 | 11.59 | 11.78 Mbytes
Step TotEng PotEng KinEng Temp Press
0 -5167.408 -5172.3316 4.9236061 1201.0429 -1.5761339e+09
10 -5167.408 -5172.3292 4.9211748 1200.4498 -1.5762759e+09
20 -5167.408 -5172.3219 4.9139105 1198.6778 -1.5767007e+09
30 -5167.408 -5172.3099 4.9019017 1195.7484 -1.5774041e+09
40 -5167.408 -5172.2933 4.885295 1191.6974 -1.5783794e+09
50 -5167.408 -5172.2723 4.8642936 1186.5744 -1.5796171e+09
60 -5167.408 -5172.2471 4.839155 1180.4422 -1.5811053e+09
70 -5167.408 -5172.2182 4.8101883 1173.3762 -1.5828297e+09
80 -5167.408 -5172.1857 4.7777514 1165.4637 -1.5847737e+09
90 -5167.408 -5172.1502 4.7422469 1156.8029 -1.5869184e+09
100 -5167.408 -5172.1121 4.7041183 1147.502 -1.5892434e+09
Loop time of 9.14099 on 4 procs for 100 steps with 3456 atoms
Performance: 945.193 fs/day, 0.025 hours/fs, 10.940 timesteps/s, 37.808 katom-step/s
99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 7.0683 | 7.7216 | 8.7585 | 22.7 | 84.47
Neigh | 0.24686 | 0.25299 | 0.2618 | 1.2 | 2.77
Comm | 0.079533 | 1.1252 | 1.784 | 60.0 | 12.31
Output | 0.035036 | 0.03505 | 0.03506 | 0.0 | 0.38
Modify | 0.0014139 | 0.0014999 | 0.0015446 | 0.1 | 0.02
Other | | 0.004642 | | | 0.05
Nlocal: 864 ave 888 max 851 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Nghost: 17185 ave 17198 max 17161 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Neighs: 890568 ave 965810 max 799750 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Total # of neighbors = 3562272
Ave neighs/atom = 1030.75
Neighbor list builds = 10
Dangerous builds = 0
Total wall time: 0:00:09

178
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@ -0,0 +1,178 @@
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
variable sname index Li-dendritic
units electron
newton on
boundary p p p
atom_style electron
read_data data.${sname}
read_data data.Li-dendritic
Reading data file ...
orthogonal box = (0 0 0) to (100.224 100.224 100.224)
1 by 2 by 2 MPI processor grid
reading atoms ...
3456 atoms
read_data CPU = 0.016 seconds
#read_restart ${sname}.min.restart
pair_style eff/cut 50.112
pair_coeff * *
comm_modify vel yes
compute effTemp all temp/eff
compute effPress all pressure effTemp
thermo 10
thermo_style custom step pe temp press
thermo_modify temp effTemp press effPress
print "Starting minimizer"
Starting minimizer
min_style cg
compute 1 all property/atom spin eradius
#dump 1 all custom 100 ${sname}.min.lammpstrj id type x y z q c_1[1] c_1[2]
#dump 2 all xyz 100 ${sname}.min.xyz
min_modify line quadratic dmax 0.05
minimize 0 1.0e-7 100 100
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- EFF package: doi:10.1002/jcc.21637
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 52.112
ghost atom cutoff = 52.112
binsize = 26.056, bins = 4 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair eff/cut, 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) = 14.88 | 15.07 | 15.26 Mbytes
Step PotEng Temp Press
0 -5172.3316 0 -1.6720594e+09
10 -5199.5494 0 -1.6721099e+09
20 -5220.9343 0 -1.6720299e+09
30 -5238.4037 0 -1.6694987e+09
40 -5252.5928 0 -1.6515154e+09
50 -5263.7845 0 -1.5851579e+09
60 -5271.8051 0 -1.4304709e+09
70 -5275.1692 0 -1.2764647e+09
80 -5276.9804 0 -1.1135845e+09
87 -5277.5186 0 -1.0157231e+09
Loop time of 9.1237 on 4 procs for 87 steps with 3456 atoms
99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = max force evaluations
Energy initial, next-to-last, final =
-5172.33158699748 -5277.50851484438 -5277.51857905665
Force two-norm initial, final = 10.47944 0.61719987
Force max component initial, final = 0.33333431 0.020508985
Final line search alpha, max atom move = 0.48148149 0.0098746969
Iterations, force evaluations = 87 101
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 7.2296 | 8.0451 | 8.9943 | 23.5 | 88.18
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.11943 | 1.0682 | 1.8834 | 64.3 | 11.71
Output | 0.00021247 | 0.00022521 | 0.00026234 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.01011 | | | 0.11
Nlocal: 864 ave 864 max 864 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 17185 ave 17185 max 17185 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 890568 ave 968400 max 812736 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Total # of neighbors = 3562272
Ave neighs/atom = 1030.75
Neighbor list builds = 0
Dangerous builds = 0
write_restart ${sname}.min.restart
write_restart Li-dendritic.min.restart
System init for write_restart ...
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
#undump 1
#undump 2
# NVT
reset_timestep 0
timestep 0.005
print "Starting nvt"
Starting nvt
fix 1 all nvt/eff temp 300.0 300.0 0.1
dump 1 all custom 100 ${sname}.nvt.lammpstrj id type x y z c_1[1] c_1[2]
dump 1 all custom 100 Li-dendritic.nvt.lammpstrj id type x y z c_1[1] c_1[2]
dump 2 all xyz 100 ${sname}.nvt.xyz
dump 2 all xyz 100 Li-dendritic.nvt.xyz
restart 100 ${sname}.nvt.restart1 ${sname}.nvt.restart2
restart 100 Li-dendritic.nvt.restart1 ${sname}.nvt.restart2
restart 100 Li-dendritic.nvt.restart1 Li-dendritic.nvt.restart2
run 100
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 11.9 | 12.09 | 12.28 Mbytes
Step PotEng Temp Press
0 -5277.5186 0 -1.0157231e+09
10 -5277.5187 0.028803274 -1.0157155e+09
20 -5277.519 0.12372272 -1.0156917e+09
30 -5277.5195 0.29618333 -1.0156507e+09
40 -5277.5201 0.55263617 -1.0155924e+09
50 -5277.5206 0.8932531 -1.0155176e+09
60 -5277.521 1.3127021 -1.015428e+09
70 -5277.5211 1.8037418 -1.0153251e+09
80 -5277.5208 2.3644081 -1.0152094e+09
90 -5277.52 3.0093875 -1.0150781e+09
100 -5277.5187 3.7858675 -1.0149239e+09
Loop time of 8.47644 on 4 procs for 100 steps with 3456 atoms
Performance: 5096.477 fs/day, 0.005 hours/fs, 11.797 timesteps/s, 40.772 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 | 6.8234 | 7.537 | 8.2853 | 24.1 | 88.92
Neigh | 0.023585 | 0.024246 | 0.024867 | 0.4 | 0.29
Comm | 0.15595 | 0.90456 | 1.6184 | 69.6 | 10.67
Output | 0.0032476 | 0.0032612 | 0.0032984 | 0.0 | 0.04
Modify | 0.0036078 | 0.0037554 | 0.0039448 | 0.2 | 0.04
Other | | 0.003634 | | | 0.04
Nlocal: 864 ave 881 max 834 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Nghost: 17185 ave 17215 max 17168 min
Histogram: 1 1 0 1 0 0 0 0 0 1
Neighs: 890568 ave 976912 max 789323 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Total # of neighbors = 3562272
Ave neighs/atom = 1030.75
Neighbor list builds = 1
Dangerous builds = 0
undump 1
undump 2
Total wall time: 0:00:17

155
examples/PACKAGES/eff/Li-solid/log.01Feb25.Li.ang.g++.4 Normal file
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@ -0,0 +1,155 @@
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
variable sname index Li.ang
units real
newton on
boundary p p p
dielectric 1.0
atom_style electron
read_data data.${sname}
read_data data.Li.ang
Reading data file ...
orthogonal box = (0 0 0) to (22.098442 22.098442 22.098442)
1 by 2 by 2 MPI processor grid
reading atoms ...
2000 atoms
read_data CPU = 0.014 seconds
#read_restart ${sname}.min.restart
pair_style eff/cut 11.049221 limit/eradius pressure/evirials
pair_coeff * *
comm_modify vel yes
neigh_modify one 2000 page 20000
compute peratom all stress/atom NULL
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
compute effTemp all temp/eff
compute effPress all pressure effTemp
compute energies all pair eff/cut
variable eke equal c_energies[1]
variable epauli equal c_energies[2]
variable ecoul equal c_energies[3]
variable erres equal c_energies[4]
thermo 100
thermo_style custom step etotal pe ke v_eke v_epauli v_ecoul v_erres press v_press temp
thermo_modify temp effTemp press effPress flush yes
#min_style cg
#minimize 0 1e-6 100 1000
#write_restart ${sname}.min.restart
timestep 0.005
velocity all create 10.0 4928459 rot yes mom yes dist gaussian
fix 0 all temp/rescale/eff 1 10.0 3000.0 0.05 1.0
#fix 0 all langevin/eff 3000.0 3000.0 10.0 699483
fix 1 all nve/eff
run 200
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- EFF package: doi:10.1002/jcc.21637
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 20000
master list distance cutoff = 13.049221
ghost atom cutoff = 13.049221
binsize = 6.5246105, bins = 4 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair eff/cut, 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) = 6.772 | 6.887 | 7.001 Mbytes
Step TotEng PotEng KinEng v_eke v_epauli v_ecoul v_erres Press v_press Temp
0 -1934872.7 -1934932.3 59.586393 1973239.1 9338.8528 -3917510.2 0 119790.47 119790.47 40.06012
100 -1932300.8 -1934539.4 2238.5734 1864086.1 9857.8379 -3808483.3 0 -100104.15 -105089 1505
200 -1929809.8 -1934272.1 4462.2726 1834011.6 10753.334 -3779037 0 -151616.13 -158905.6 3000
Loop time of 6.61662 on 4 procs for 200 steps with 2000 atoms
Performance: 0.013 ns/day, 1837.949 hours/ns, 30.227 timesteps/s, 60.454 katom-step/s
99.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.572 | 5.9389 | 6.2372 | 9.8 | 89.76
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.37051 | 0.66886 | 1.0359 | 29.2 | 10.11
Output | 0.00076947 | 0.00078111 | 0.00081552 | 0.0 | 0.01
Modify | 0.0035517 | 0.0038042 | 0.0040517 | 0.4 | 0.06
Other | | 0.004249 | | | 0.06
Nlocal: 500 ave 500 max 500 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 10252 ave 10252 max 10252 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 424625 ave 448237 max 400021 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Total # of neighbors = 1698500
Ave neighs/atom = 849.25
Neighbor list builds = 0
Dangerous builds = 0
unfix 0
unfix 1
fix 1 all nvt/eff temp 3000.0 3000.0 100.0
compute 1 all property/atom spin eradius ervel
dump 1 all custom 500 ${sname}.nvt.lammpstrj id type q c_1[1] c_1[2] x y z vx vy vz c_1[3]
dump 1 all custom 500 Li.ang.nvt.lammpstrj id type q c_1[1] c_1[2] x y z vx vy vz c_1[3]
run 500
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 7.522 | 7.656 | 7.751 Mbytes
Step TotEng PotEng KinEng v_eke v_epauli v_ecoul v_erres Press v_press Temp
200 -1929809.8 -1934272.1 4462.2726 1834011.6 10753.334 -3779037 0 -151616.13 -158905.6 3000
300 -1929902.8 -1934223.4 4320.5724 2031898.3 11427.685 -3977549.4 0 268725.75 262717.84 2904.7345
400 -1929360.3 -1935088.8 5728.4403 1850892.1 13473.172 -3799454 0 -105609.57 -118457.31 3851.2485
500 -1929066.1 -1935648.1 6581.9291 1901305.5 14887.365 -3851840.9 0 7045.2102 -9644.887 4425.0518
600 -1929593.6 -1934406.5 4812.986 2003446.8 16194.971 -3954048.4 0 221662.39 211620.13 3235.7857
700 -1930061.3 -1933572.3 3510.9499 1811788.7 18436.004 -3763797 0 -182749.21 -186750.23 2360.4227
Loop time of 16.6082 on 4 procs for 500 steps with 2000 atoms
Performance: 0.013 ns/day, 1845.351 hours/ns, 30.106 timesteps/s, 60.211 katom-step/s
99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 12.79 | 14.632 | 16.232 | 32.8 | 88.10
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.35155 | 1.9504 | 3.7924 | 89.8 | 11.74
Output | 0.0034195 | 0.0035878 | 0.0038027 | 0.3 | 0.02
Modify | 0.01108 | 0.011237 | 0.0114 | 0.1 | 0.07
Other | | 0.01046 | | | 0.06
Nlocal: 500 ave 520 max 480 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Nghost: 10252 ave 10272 max 10232 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Neighs: 426287 ave 457559 max 396571 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Total # of neighbors = 1705148
Ave neighs/atom = 852.574
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:23

166
examples/PACKAGES/eff/Li-solid/log.01Feb25.Li.bohr.g++.4 Normal file
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@ -0,0 +1,166 @@
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
variable sname index Li.bohr
units electron
newton off
boundary p p p
dielectric 1.0
atom_style electron
read_data data.${sname}
read_data data.Li.bohr
Reading data file ...
orthogonal box = (0 0 0) to (41.76 41.76 41.76)
2 by 1 by 2 MPI processor grid
reading atoms ...
2000 atoms
read_data CPU = 0.006 seconds
pair_style eff/cut 20.88 limit/eradius pressure/evirials
pair_coeff * *
comm_modify vel yes
neigh_modify one 2000 page 20000
compute peratom all stress/atom NULL
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
compute effTemp all temp/eff
compute effPress all pressure effTemp
compute energies all pair eff/cut
variable eke equal c_energies[1]
variable epauli equal c_energies[2]
variable estatics equal c_energies[3]
variable errestrain equal c_energies[4]
thermo 10
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain press v_press temp
thermo_modify temp effTemp press effPress
min_style cg
minimize 0 1e-6 100 200
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- EFF package: doi:10.1002/jcc.21637
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 20000
master list distance cutoff = 22.88
ghost atom cutoff = 22.88
binsize = 11.44, bins = 4 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair eff/cut, perpetual
attributes: half, newton off
pair build: half/bin/atomonly/newtoff
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 9.51 | 9.51 | 9.51 Mbytes
Step TotEng PotEng KinEng v_eke v_epauli v_estatics v_errestrain Press v_press Temp
0 -3083.509 -3083.509 0 3144.5578 14.882406 -6242.9492 0 1.2112606e+10 1.2112606e+10 0
10 -3085.4657 -3085.4657 0 3062.6201 21.113244 -6169.199 0 1.797769e+09 1.797769e+09 0
20 -3085.9152 -3085.9152 0 3063.3218 21.843788 -6171.0808 0 1.9306772e+09 1.9306772e+09 0
30 -3086.103 -3086.103 0 3065.4937 21.7953 -6173.392 0 2.1693045e+09 2.1693045e+09 0
40 -3086.2065 -3086.2065 0 3062.3955 22.002457 -6170.6045 0 1.7527596e+09 1.7527596e+09 0
50 -3086.2558 -3086.2558 0 3059.7162 22.165243 -6168.1372 0 1.4005967e+09 1.4005967e+09 0
60 -3086.2823 -3086.2823 0 3061.7509 22.016476 -6170.0497 0 1.6419693e+09 1.6419693e+09 0
70 -3086.3068 -3086.3068 0 3063.1496 22.125331 -6171.5817 0 1.8371954e+09 1.8371954e+09 0
80 -3086.3286 -3086.3286 0 3063.4058 22.112083 -6171.8465 0 1.8595352e+09 1.8595352e+09 0
90 -3086.342 -3086.342 0 3062.6876 22.145517 -6171.1752 0 1.761838e+09 1.761838e+09 0
100 -3086.3493 -3086.3493 0 3061.4985 22.1758 -6170.0236 0 1.6034889e+09 1.6034889e+09 0
Loop time of 9.51021 on 4 procs for 100 steps with 2000 atoms
99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = max iterations
Energy initial, next-to-last, final =
-3083.5089570212 -3086.34842671529 -3086.34926128553
Force two-norm initial, final = 3.4238461 0.15353209
Force max component initial, final = 0.15119069 0.017560878
Final line search alpha, max atom move = 0.75419179 0.01324427
Iterations, force evaluations = 100 191
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 8.8842 | 9.0722 | 9.2808 | 5.4 | 95.39
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.04463 | 0.04473 | 0.04481 | 0.0 | 0.47
Output | 0.00071317 | 0.00073223 | 0.0007793 | 0.0 | 0.01
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.3926 | | | 4.13
Nlocal: 500 ave 500 max 500 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 10252 ave 10252 max 10252 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 648158 ave 648158 max 648158 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2592632
Ave neighs/atom = 1296.316
Neighbor list builds = 0
Dangerous builds = 0
fix 0 all temp/rescale/eff 1 0.0 3000.0 0.02 0.5
fix 1 all npt/eff temp 3000.0 3000.0 0.1 iso 1e7 1e7 1.0
compute 1 all property/atom spin eradius
dump 1 all custom 100 ${sname}.spe.lammpstrj id type q c_1[1] c_1[2] x y z
dump 1 all custom 100 Li.bohr.spe.lammpstrj id type q c_1[1] c_1[2] x y z
run 100
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 8.76 | 8.76 | 8.76 Mbytes
Step TotEng PotEng KinEng v_eke v_epauli v_estatics v_errestrain Press v_press Temp
100 -3086.3493 -3086.3493 0 3061.4985 22.1758 -6170.0236 0 1.6034889e+09 1.6034889e+09 0
110 -3085.709 -3086.35 0.64098668 3062.5195 22.168933 -6171.0384 0 1.9130428e+09 1.8610249e+09 270.41729
120 -3084.995 -3086.3497 1.3546418 3064.69 22.151949 -6173.1916 0 2.3968054e+09 2.2869572e+09 571.49172
130 -3084.2774 -3086.3449 2.0675114 3067.5683 22.125927 -6176.0391 0 2.9762332e+09 2.8088108e+09 872.23471
140 -3083.5543 -3086.3327 2.7783319 3071.0091 22.090343 -6179.4321 0 3.6318905e+09 3.4073653e+09 1172.1133
150 -3082.8209 -3086.3101 3.4891918 3074.9323 22.044189 -6183.2866 0 4.3538347e+09 4.0726292e+09 1472.0085
160 -3082.0735 -3086.274 4.2005492 3079.2855 21.986186 -6187.5458 0 5.1353281e+09 4.7979569e+09 1772.1135
170 -3081.3099 -3086.2215 4.911672 3084.0302 21.914874 -6192.1667 0 5.9710184e+09 5.5781934e+09 2072.1196
180 -3080.5276 -3086.1495 5.6218934 3089.1358 21.828679 -6197.1139 0 6.8564778e+09 6.4091119e+09 2371.7454
190 -3079.7237 -3086.0546 6.330928 3094.5768 21.725972 -6202.3574 0 7.787914e+09 7.2871001e+09 2670.8705
200 -3078.895 -3085.9337 7.0387107 3100.3318 21.605131 -6207.8707 0 8.7619059e+09 8.2089091e+09 2969.4675
Loop time of 5.34836 on 4 procs for 100 steps with 2000 atoms
Performance: 1615.450 fs/day, 0.015 hours/fs, 18.697 timesteps/s, 37.395 katom-step/s
99.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.8621 | 5.065 | 5.2272 | 5.9 | 94.70
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.02486 | 0.025085 | 0.025316 | 0.1 | 0.47
Output | 0.0016755 | 0.0018282 | 0.0019368 | 0.2 | 0.03
Modify | 0.092978 | 0.25534 | 0.4584 | 26.2 | 4.77
Other | | 0.00111 | | | 0.02
Nlocal: 500 ave 518 max 484 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Nghost: 10252 ave 10268 max 10234 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Neighs: 621113 ave 642857 max 604509 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Total # of neighbors = 2484453
Ave neighs/atom = 1242.2265
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:15

1165
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158
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@ -0,0 +1,158 @@
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
# Created 2010-12-13
# General parameters
variable sname index C2H6fc.bohr
units electron
newton on
boundary f f f
atom_style electron
read_data data.${sname}
read_data data.C2H6fc.bohr
Reading data file ...
orthogonal box = (-1000 -1000 -1000) to (1000 1000 1000)
1 by 2 by 2 MPI processor grid
reading atoms ...
22 atoms
read_data CPU = 0.000 seconds
pair_style eff/cut 1000.0
pair_coeff * *
compute energies all pair eff/cut
variable eke equal c_energies[1]
variable epauli equal c_energies[2]
variable estatics equal c_energies[3]
variable errestrain equal c_energies[4]
comm_modify vel yes
compute peratom all stress/atom NULL
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
compute effTemp all temp/eff
compute effPress all pressure effTemp
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
thermo_modify temp effTemp press effPress
# Minimization
min_style cg
dump 1 all xyz 10 ${sname}.min.xyz
dump 1 all xyz 10 C2H6fc.bohr.min.xyz
compute 1 all property/atom spin eradius erforce
dump 2 all custom 10 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
dump 2 all custom 10 C2H6fc.bohr.min.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
dump 3 all custom 10 data.${sname}.restart id type q c_1[1] c_1[2] x y z
dump 3 all custom 10 data.C2H6fc.bohr.restart id type q c_1[1] c_1[2] x y z
min_modify line quadratic
minimize 0 1e-6 1000 2000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- EFF package: doi:10.1002/jcc.21637
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1002
ghost atom cutoff = 1002
binsize = 501, bins = 4 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair eff/cut, 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) = 6.129 | 6.129 | 6.129 Mbytes
Step TotEng PotEng KinEng v_eke v_epauli v_estatics v_errestrain Temp Press v_press
0 -67.202286 -67.202286 0 65.187662 2.0185521 -134.4085 0 0 15.150502 15.150502
48 -67.202342 -67.202342 0 65.186464 2.0145106 -134.40332 0 0 -0.00017005462 -0.00017005462
Loop time of 0.00261219 on 4 procs for 48 steps with 22 atoms
100.0% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = force tolerance
Energy initial, next-to-last, final =
-67.202286382145 -67.2023415752272 -67.2023415752273
Force two-norm initial, final = 0.0096326869 5.0767445e-07
Force max component initial, final = 0.0062811481 1.588169e-07
Final line search alpha, max atom move = 1 1.588169e-07
Iterations, force evaluations = 48 94
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00010749 | 0.00066682 | 0.0010722 | 0.0 | 25.53
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0005904 | 0.0010031 | 0.0015945 | 1.2 | 38.40
Output | 0.00029404 | 0.00030533 | 0.0003226 | 0.0 | 11.69
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.0006369 | | | 24.38
Nlocal: 5.5 ave 6 max 5 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 16.5 ave 17 max 16 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 57.75 ave 92 max 13 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Total # of neighbors = 231
Ave neighs/atom = 10.5
Neighbor list builds = 0
Dangerous builds = 0
undump 1
undump 2
undump 3
fix 1 all nvt/eff temp 1 2000 1.0
dump 2 all custom 10 ${sname}.nvt.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
dump 2 all custom 10 C2H6fc.bohr.nvt.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
run 10000
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 5.738 | 5.738 | 5.738 Mbytes
Step TotEng PotEng KinEng v_eke v_epauli v_estatics v_errestrain Temp Press v_press
48 -67.202342 -67.202342 0 65.186464 2.0145106 -134.40332 0 0 -0.00017005463 -0.00017005463
10048 -67.202342 -67.202342 1.2683664e-08 65.186455 2.0144921 -134.40329 0 0.00038144568 -0.070540027 -0.070540735
Loop time of 0.194625 on 4 procs for 10000 steps with 22 atoms
Performance: 4439300.953 fs/day, 0.000 hours/fs, 51380.798 timesteps/s, 1.130 Matom-step/s
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0161 | 0.064789 | 0.10999 | 14.0 | 33.29
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.031236 | 0.07675 | 0.12576 | 13.2 | 39.43
Output | 0.01923 | 0.021471 | 0.025663 | 1.7 | 11.03
Modify | 0.011945 | 0.014438 | 0.017136 | 1.6 | 7.42
Other | | 0.01718 | | | 8.83
Nlocal: 5.5 ave 7 max 4 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Nghost: 16.5 ave 18 max 15 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Neighs: 57.75 ave 98 max 16 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Total # of neighbors = 231
Ave neighs/atom = 10.5
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

40165
examples/PACKAGES/eff/fixed-core/CH4/log.01Feb25.CH4fc.ang.g++.4 Normal file
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File diff suppressed because it is too large Load Diff

4166
examples/PACKAGES/eff/fixed-core/CH4/log.01Feb25.CH4fc.bohr.g++.4 Normal file
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File diff suppressed because it is too large Load Diff

100
examples/PACKAGES/eff/fixed-core/CH4/log.01Feb25.CH4fc.spe.ang.g++.4 Normal file
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@ -0,0 +1,100 @@
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
# Created 2010-11-28
# General parameters
variable sname index CH4fc.ang
units real
newton on
boundary p p p
atom_style electron
read_data data.${sname}
read_data data.CH4fc.ang
Reading data file ...
orthogonal box = (-529.17725 -529.17725 -529.17725) to (529.17725 529.17725 529.17725)
2 by 1 by 2 MPI processor grid
reading atoms ...
13 atoms
read_data CPU = 0.000 seconds
pair_style eff/cut 1000.0 limit/eradius pressure/evirials
pair_coeff * *
compute energies all pair eff/cut
variable eke equal c_energies[1]
variable epauli equal c_energies[2]
variable estatics equal c_energies[3]
variable errestrain equal c_energies[4]
comm_modify vel yes
timestep 0.0001
compute peratom all stress/atom NULL
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
compute effTemp all temp/eff
compute effPress all pressure effTemp
thermo 10
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
thermo_modify temp effTemp press effPress
run 0
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- EFF package: doi:10.1002/jcc.21637
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1002
ghost atom cutoff = 1002
binsize = 501, bins = 3 3 3
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair eff/cut, 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) = 4.387 | 4.387 | 4.387 Mbytes
Step TotEng PotEng KinEng v_eke v_epauli v_estatics v_errestrain Temp Press v_press
0 -17700.537 -17700.537 0 20676.282 6270.6707 -44647.489 0 0 0.21737096 0.21737096
Loop time of 2.41775e-06 on 4 procs for 0 steps with 13 atoms
113.7% 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 | 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 | | 2.418e-06 | | |100.00
Nlocal: 3.25 ave 4 max 3 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Nghost: 152.75 ave 153 max 152 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 19.5 ave 33 max 6 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Total # of neighbors = 78
Ave neighs/atom = 6
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

99
examples/PACKAGES/eff/fixed-core/CH4/log.01Feb25.CH4fc.spe.bohr.g++.4 Normal file
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@ -0,0 +1,99 @@
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
using 1 OpenMP thread(s) per MPI task
# Created 2010-11-28
# General parameters
variable sname index CH4fc.bohr
units electron
newton on
boundary p p p
atom_style electron
read_data data.${sname}
read_data data.CH4fc.bohr
Reading data file ...
orthogonal box = (-1000 -1000 -1000) to (1000 1000 1000)
1 by 2 by 2 MPI processor grid
reading atoms ...
13 atoms
read_data CPU = 0.000 seconds
pair_style eff/cut 1000.0 limit/eradius pressure/evirials
pair_coeff * *
compute energies all pair eff/cut
variable eke equal c_energies[1]
variable epauli equal c_energies[2]
variable estatics equal c_energies[3]
variable errestrain equal c_energies[4]
comm_modify vel yes
compute peratom all stress/atom NULL
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
compute effTemp all temp/eff
compute effPress all pressure effTemp
thermo 10
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
thermo_modify temp effTemp press effPress
run 0
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- EFF package: doi:10.1002/jcc.21637
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1002
ghost atom cutoff = 1002
binsize = 501, bins = 4 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair eff/cut, 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) = 4.388 | 4.388 | 4.388 Mbytes
Step TotEng PotEng KinEng v_eke v_epauli v_estatics v_errestrain Temp Press v_press
0 -28.207572 -28.207572 0 32.949786 9.9929585 -71.150317 0 0 22025.158 22025.158
Loop time of 2.353e-06 on 4 procs for 0 steps with 13 atoms
53.1% 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 | 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 | | 2.353e-06 | | |100.00
Nlocal: 3.25 ave 4 max 3 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Nghost: 152.75 ave 153 max 152 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 19.5 ave 31 max 10 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Total # of neighbors = 78
Ave neighs/atom = 6
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

13
examples/PACKAGES/imd/deca-ala-solv_imd_v3.py Normal file
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@ -0,0 +1,13 @@
"""
For use with 'in.deca-ala-solv_imd_v3'.
Tested with imdclient v0.1.4 and MDAnalysis v2.8.0
"""
from imdclient.IMD import IMDReader
import MDAnalysis as mda
u = mda.Universe('data.deca-ala-solv', "imd://localhost:5678", topology_format='DATA')
for ts in u.trajectory:
print(ts.time)
print(ts.velocities)

31
examples/PACKAGES/imd/in.deca-ala-solv_imd_v3 Normal file
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@ -0,0 +1,31 @@
#
units real
neighbor 2.5 bin
neigh_modify delay 1 every 1
atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
pair_style lj/charmm/coul/long 8 10
pair_modify mix arithmetic
special_bonds charmm
read_data data.deca-ala-solv
group peptide id <= 103
fix rigidh all shake 1e-6 100 1000 t 1 2 3 4 5 a 23
thermo 100
thermo_style multi
timestep 2.0
kspace_style pppm 1e-5
fix ensemble all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 0.2
# IMD setup. Client code available in 'deca-ala-solv_imd_v3.py'
fix comm all imd 5678 unwrap on trate 10 version 3 time on box on coordinates on velocities on forces off
run 5000000

2
examples/PACKAGES/pafi/in.pafi
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@ -9,7 +9,7 @@ read_data pafipath.4.data fix pa NULL PafiPath
## EAM potential
pair_style eam/fs
pair_coeff * * ../../../../potentials/Fe_mm.eam.fs Fe
pair_coeff * * Fe_mm.eam.fs Fe
mass * 55.85
thermo 100

11
examples/PACKAGES/pimd_bosonic/README Normal file
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@ -0,0 +1,11 @@
This directory contains example input files for the pimd/nvt/bosonic and pimd/langevin/bosonic fix commands.
The demonstrated system is that of 3 non-interacting bosons in a harmonic trap.
The input files initiate a simulation of 100 steps using 4 beads. The expected output log files are included.
The input files can be edited to provide a physically meaningful output, by extending the simulations to a few nanoseconds
and increasing the number of beads (32 beads should be enough).
The total energy can be computed by summing the potential energy and either the virial or primitive kinetic energy estimator, and averaging over time.
Notice that for pimd/langevin/bosonic the summed value of either kinetic estimator is printed across all log files.
It should be taken from a single log file, with all files providing the same output.
For pimd/nvt/bosonic, one has to sum over the output of all log files. For the potential energy, summing over log files is required for both fix commands.
The obtained energy should be compared to the analytical value of 0.00058031 Hartree.

57
examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/in.lmp Normal file
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@ -0,0 +1,57 @@
# Units and dimensions
units electron
dimension 3
boundary p p p
atom_style atomic
atom_modify map yes
pair_style none
# Time step (in femtoseconds)
timestep 0.5
# Temperature (in Kelvin)
variable Temp equal 17.4
# Force constant (in Hartree energies per Bohr radius squared)
variable k equal 1.2154614120000001e-08
# Number of beads
variable Nbeads equal 4
variable ibead uloop ${Nbeads} pad
variable seed equal 18889
# Create box and atoms. All distances are in Bohr
region box block -1500 1500 -1500 1500 -1500 1500
create_box 1 box
variable a loop 3
label loop
variable x1 equal -15.0+0.5*v_a
variable y1 equal 10.0-0.5*v_a
variable z1 equal 1+0.5*v_a
create_atoms 1 single ${x1} ${y1} ${z1}
next a
jump SELF loop
# Electron mass (in amu)
mass 1 0.00054858
# Initialize velocities
velocity all create ${Temp} ${seed}${ibead} mom yes rot yes dist gaussian
# Add harmonic external force
fix harm all spring/self ${k}
# Add harmonic potential energy to total energy and potential energy
fix_modify harm energy yes
# PIMD command
fix pimdb all pimd/langevin/bosonic ensemble nvt temp ${Temp} thermostat PILE_L 12345 tau 50 fixcom no
# Outputs
variable prim_kinetic equal f_pimdb[5]
variable virial equal f_pimdb[6]
thermo_style custom step pe v_virial v_prim_kinetic
thermo 1
run 100

2
examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.13Mar2025.g++ Normal file
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@ -0,0 +1,2 @@
LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified)
Running on 4 partitions of processors

238
examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.13Mar2025.g++.0 Normal file
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@ -0,0 +1,238 @@
LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified)
Processor partition = 0
using 1 OpenMP thread(s) per MPI task
# Units and dimensions
units electron
dimension 3
boundary p p p
atom_style atomic
atom_modify map yes
pair_style none
# Time step (in femtoseconds)
timestep 0.5
# Temperature (in Kelvin)
variable Temp equal 17.4
# Force constant (in Hartree energies per Bohr radius squared)
variable k equal 1.2154614120000001e-08
# Number of beads
variable Nbeads equal 4
variable ibead uloop ${Nbeads} pad
variable ibead uloop 4 pad
variable seed equal 18889
# Create box and atoms. All distances are in Bohr
region box block -1500 1500 -1500 1500 -1500 1500
create_box 1 box
Created orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
1 by 1 by 1 MPI processor grid
variable a loop 3
label loop
variable x1 equal -15.0+0.5*v_a
variable y1 equal 10.0-0.5*v_a
variable z1 equal 1+0.5*v_a
create_atoms 1 single ${x1} ${y1} ${z1}
create_atoms 1 single -14.5 ${y1} ${z1}
create_atoms 1 single -14.5 9.5 ${z1}
create_atoms 1 single -14.5 9.5 1.5
Created 1 atoms
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
create_atoms CPU = 0.000 seconds
next a
jump SELF loop
variable x1 equal -15.0+0.5*v_a
variable y1 equal 10.0-0.5*v_a
variable z1 equal 1+0.5*v_a
create_atoms 1 single ${x1} ${y1} ${z1}
create_atoms 1 single -14 ${y1} ${z1}
create_atoms 1 single -14 9 ${z1}
create_atoms 1 single -14 9 2
Created 1 atoms
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
create_atoms CPU = 0.000 seconds
next a
jump SELF loop
variable x1 equal -15.0+0.5*v_a
variable y1 equal 10.0-0.5*v_a
variable z1 equal 1+0.5*v_a
create_atoms 1 single ${x1} ${y1} ${z1}
create_atoms 1 single -13.5 ${y1} ${z1}
create_atoms 1 single -13.5 8.5 ${z1}
create_atoms 1 single -13.5 8.5 2.5
Created 1 atoms
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
create_atoms CPU = 0.000 seconds
next a
jump SELF loop
# Electron mass (in amu)
mass 1 0.00054858
# Initialize velocities
velocity all create ${Temp} ${seed}${ibead} mom yes rot yes dist gaussian
velocity all create 17.4 ${seed}${ibead} mom yes rot yes dist gaussian
velocity all create 17.4 18889${ibead} mom yes rot yes dist gaussian
velocity all create 17.4 188891 mom yes rot yes dist gaussian
# Add harmonic external force
fix harm all spring/self ${k}
fix harm all spring/self 1.215461412e-08
# Add harmonic potential energy to total energy and potential energy
fix_modify harm energy yes
# PIMD command
fix pimdb all pimd/langevin/bosonic ensemble nvt temp ${Temp} thermostat PILE_L 12345 tau 50 fixcom no
fix pimdb all pimd/langevin/bosonic ensemble nvt temp 17.4 thermostat PILE_L 12345 tau 50 fixcom no
# Outputs
variable prim_kinetic equal f_pimdb[5]
variable virial equal f_pimdb[6]
thermo_style custom step pe v_virial v_prim_kinetic
thermo 1
run 100
Initializing PI Langevin equation thermostat...
Bead ID | omega | tau | c1 | c2
0 9.11206647e-03 5.00000000e+01 9.95012479e-01 9.97505201e-02
1 9.11206647e-03 5.00000000e+01 9.95012479e-01 9.97505201e-02
2 9.11206647e-03 5.00000000e+01 9.95012479e-01 9.97505201e-02
3 9.11206647e-03 5.00000000e+01 9.95012479e-01 9.97505201e-02
PILE_L thermostat successfully initialized!
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2444)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:212)
Per MPI rank memory allocation (min/avg/max) = 2.801 | 2.801 | 2.801 Mbytes
Step PotEng v_virial v_prim_kinetic
0 0 1.3661449e-08 0.0009918329
1 1.3158398e-09 1.8742641e-09 0.00099182267
2 5.0818396e-09 7.1801177e-09 0.00099180053
3 1.2446727e-08 1.4372388e-08 0.00099176038
4 2.1754941e-08 3.1274072e-08 0.00099170266
5 3.2927703e-08 5.2470231e-08 0.00099162511
6 4.7293056e-08 7.2301291e-08 0.00099153
7 6.526455e-08 9.5440683e-08 0.00099141194
8 8.6974168e-08 1.1669162e-07 0.00099127168
9 1.1249595e-07 1.3551097e-07 0.00099109846
10 1.4190482e-07 1.6050328e-07 0.00099089759
11 1.7313555e-07 1.8645705e-07 0.0009906735
12 2.0672874e-07 2.1181418e-07 0.00099042271
13 2.4042615e-07 2.4218941e-07 0.00099012073
14 2.7524432e-07 2.7507982e-07 0.00098977876
15 3.1513375e-07 3.1771012e-07 0.00098940169
16 3.6161087e-07 3.6075963e-07 0.00098900826
17 4.0813191e-07 4.0059005e-07 0.00098859985
18 4.5194598e-07 4.3883585e-07 0.00098817535
19 4.9898075e-07 4.8036287e-07 0.00098770764
20 5.5458728e-07 5.2362451e-07 0.00098721266
21 6.1220768e-07 5.7705077e-07 0.00098670407
22 6.6573849e-07 6.3271105e-07 0.00098617081
23 7.2475089e-07 6.9382916e-07 0.00098557406
24 7.804837e-07 7.5979853e-07 0.0009849612
25 8.3194987e-07 8.232213e-07 0.00098434971
26 8.8723792e-07 8.9901705e-07 0.0009836645
27 9.3837241e-07 9.7033126e-07 0.0009830068
28 9.897077e-07 1.0444697e-06 0.00098229311
29 1.043431e-06 1.1208219e-06 0.00098150213
30 1.0900368e-06 1.1899315e-06 0.00098077686
31 1.1303314e-06 1.2560026e-06 0.00098003518
32 1.1725968e-06 1.3287355e-06 0.00097921099
33 1.2081344e-06 1.399856e-06 0.0009784037
34 1.2449387e-06 1.4769272e-06 0.00097754491
35 1.2852285e-06 1.5642459e-06 0.00097667479
36 1.3234189e-06 1.6571388e-06 0.00097572641
37 1.3666391e-06 1.7603492e-06 0.00097475881
38 1.4102743e-06 1.8666516e-06 0.00097373763
39 1.454172e-06 1.9696572e-06 0.0009727081
40 1.5031422e-06 2.0910539e-06 0.00097155807
41 1.5538491e-06 2.2198868e-06 0.00097030871
42 1.6079193e-06 2.3576614e-06 0.00096896762
43 1.6637051e-06 2.496284e-06 0.00096760456
44 1.7189714e-06 2.637657e-06 0.00096619083
45 1.7656688e-06 2.795845e-06 0.00096470693
46 1.8092153e-06 2.9727162e-06 0.00096303835
47 1.8415769e-06 3.1451673e-06 0.00096140406
48 1.8664597e-06 3.3241907e-06 0.00095971129
49 1.8940033e-06 3.5094834e-06 0.00095790964
50 1.9211844e-06 3.7049195e-06 0.00095603039
51 1.9533838e-06 3.9139587e-06 0.0009540918
52 1.9833776e-06 4.1289537e-06 0.0009520767
53 2.0106231e-06 4.3481079e-06 0.00095003676
54 2.0429292e-06 4.5702968e-06 0.00094802906
55 2.0747842e-06 4.7928135e-06 0.00094600351
56 2.1043981e-06 5.0253448e-06 0.0009438419
57 2.1474343e-06 5.2569331e-06 0.00094169256
58 2.2115003e-06 5.4997767e-06 0.00093948055
59 2.2773037e-06 5.7547729e-06 0.00093714003
60 2.3402972e-06 6.0074589e-06 0.00093480857
61 2.4107157e-06 6.2647899e-06 0.00093244785
62 2.4953095e-06 6.5384938e-06 0.00092998209
63 2.58923e-06 6.8124372e-06 0.00092751453
64 2.682021e-06 7.0913777e-06 0.00092505171
65 2.7538688e-06 7.3773956e-06 0.00092256944
66 2.8444661e-06 7.6811232e-06 0.00091984092
67 2.9532286e-06 7.9951107e-06 0.0009170037
68 3.0551339e-06 8.3096758e-06 0.00091414977
69 3.1625164e-06 8.6232285e-06 0.00091137219
70 3.2717759e-06 8.9388929e-06 0.00090857909
71 3.3924986e-06 9.2524846e-06 0.00090583473
72 3.5236727e-06 9.5688611e-06 0.00090308342
73 3.6440162e-06 9.8873586e-06 0.00090026584
74 3.7692169e-06 1.0203245e-05 0.00089755256
75 3.8946044e-06 1.0523755e-05 0.00089485804
76 4.0498738e-06 1.0848398e-05 0.00089217189
77 4.2099346e-06 1.1164286e-05 0.00088956967
78 4.3589564e-06 1.1466652e-05 0.00088700311
79 4.5069481e-06 1.177381e-05 0.00088439373
80 4.6635354e-06 1.2059606e-05 0.00088199635
81 4.8398269e-06 1.233837e-05 0.0008797438
82 5.0191539e-06 1.261531e-05 0.00087745162
83 5.205285e-06 1.2899972e-05 0.00087506863
84 5.3708116e-06 1.3160246e-05 0.00087288444
85 5.5534416e-06 1.3438712e-05 0.00087052617
86 5.7613e-06 1.372546e-05 0.00086818634
87 5.9645662e-06 1.4017631e-05 0.00086572407
88 6.1830289e-06 1.4328439e-05 0.000862992
89 6.423646e-06 1.4640964e-05 0.00086017364
90 6.688219e-06 1.4978644e-05 0.0008570595
91 6.9305603e-06 1.5307214e-05 0.00085411601
92 7.1857573e-06 1.5649328e-05 0.00085112325
93 7.4653538e-06 1.6015833e-05 0.0008479391
94 7.8132911e-06 1.6393131e-05 0.00084474237
95 8.1540941e-06 1.674573e-05 0.00084165639
96 8.4943231e-06 1.7094435e-05 0.00083858996
97 8.8504733e-06 1.7451741e-05 0.00083536142
98 9.2042324e-06 1.780703e-05 0.00083221292
99 9.5058078e-06 1.8141862e-05 0.00082913227
100 9.8087647e-06 1.8457846e-05 0.00082619877
Loop time of 0.00116399 on 1 procs for 100 steps with 3 atoms
Performance: 3711359336.904 fs/day, 0.000 hours/fs, 85911.096 timesteps/s, 257.733 katom-step/s
89.8% 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 | 1.292e-06 | 1.292e-06 | 1.292e-06 | 0.0 | 0.11
Comm | 1.2305e-05 | 1.2305e-05 | 1.2305e-05 | 0.0 | 1.06
Output | 0.00018105 | 0.00018105 | 0.00018105 | 0.0 | 15.55
Modify | 0.00090255 | 0.00090255 | 0.00090255 | 0.0 | 77.54
Other | | 6.68e-05 | | | 5.74
Nlocal: 3 ave 3 max 3 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 = 33
Dangerous builds = 0
Total wall time: 0:00:00

230
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LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified)
Processor partition = 1
using 1 OpenMP thread(s) per MPI task
# Units and dimensions
units electron
dimension 3
boundary p p p
atom_style atomic
atom_modify map yes
pair_style none
# Time step (in femtoseconds)
timestep 0.5
# Temperature (in Kelvin)
variable Temp equal 17.4
# Force constant (in Hartree energies per Bohr radius squared)
variable k equal 1.2154614120000001e-08
# Number of beads
variable Nbeads equal 4
variable ibead uloop ${Nbeads} pad
variable ibead uloop 4 pad
variable seed equal 18889
# Create box and atoms. All distances are in Bohr
region box block -1500 1500 -1500 1500 -1500 1500
create_box 1 box
Created orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
1 by 1 by 1 MPI processor grid
variable a loop 3
label loop
variable x1 equal -15.0+0.5*v_a
variable y1 equal 10.0-0.5*v_a
variable z1 equal 1+0.5*v_a
create_atoms 1 single ${x1} ${y1} ${z1}
create_atoms 1 single -14.5 ${y1} ${z1}
create_atoms 1 single -14.5 9.5 ${z1}
create_atoms 1 single -14.5 9.5 1.5
Created 1 atoms
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
create_atoms CPU = 0.000 seconds
next a
jump SELF loop
variable x1 equal -15.0+0.5*v_a
variable y1 equal 10.0-0.5*v_a
variable z1 equal 1+0.5*v_a
create_atoms 1 single ${x1} ${y1} ${z1}
create_atoms 1 single -14 ${y1} ${z1}
create_atoms 1 single -14 9 ${z1}
create_atoms 1 single -14 9 2
Created 1 atoms
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
create_atoms CPU = 0.000 seconds
next a
jump SELF loop
variable x1 equal -15.0+0.5*v_a
variable y1 equal 10.0-0.5*v_a
variable z1 equal 1+0.5*v_a
create_atoms 1 single ${x1} ${y1} ${z1}
create_atoms 1 single -13.5 ${y1} ${z1}
create_atoms 1 single -13.5 8.5 ${z1}
create_atoms 1 single -13.5 8.5 2.5
Created 1 atoms
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
create_atoms CPU = 0.000 seconds
next a
jump SELF loop
# Electron mass (in amu)
mass 1 0.00054858
# Initialize velocities
velocity all create ${Temp} ${seed}${ibead} mom yes rot yes dist gaussian
velocity all create 17.4 ${seed}${ibead} mom yes rot yes dist gaussian
velocity all create 17.4 18889${ibead} mom yes rot yes dist gaussian
velocity all create 17.4 188892 mom yes rot yes dist gaussian
# Add harmonic external force
fix harm all spring/self ${k}
fix harm all spring/self 1.215461412e-08
# Add harmonic potential energy to total energy and potential energy
fix_modify harm energy yes
# PIMD command
fix pimdb all pimd/langevin/bosonic ensemble nvt temp ${Temp} thermostat PILE_L 12345 tau 50 fixcom no
fix pimdb all pimd/langevin/bosonic ensemble nvt temp 17.4 thermostat PILE_L 12345 tau 50 fixcom no
# Outputs
variable prim_kinetic equal f_pimdb[5]
variable virial equal f_pimdb[6]
thermo_style custom step pe v_virial v_prim_kinetic
thermo 1
run 100
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2444)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:212)
Per MPI rank memory allocation (min/avg/max) = 2.801 | 2.801 | 2.801 Mbytes
Step PotEng v_virial v_prim_kinetic
0 0 1.3661449e-08 0.0009918329
1 7.3810761e-10 1.8742641e-09 0.00099182267
2 3.0654593e-09 7.1801177e-09 0.00099180053
3 6.4534507e-09 1.4372388e-08 0.00099176038
4 1.1681892e-08 3.1274072e-08 0.00099170266
5 1.8404818e-08 5.2470231e-08 0.00099162511
6 2.6171374e-08 7.2301291e-08 0.00099153
7 3.5990441e-08 9.5440683e-08 0.00099141194
8 4.9770229e-08 1.1669162e-07 0.00099127168
9 6.6159035e-08 1.3551097e-07 0.00099109846
10 8.7281867e-08 1.6050328e-07 0.00099089759
11 1.1505206e-07 1.8645705e-07 0.0009906735
12 1.4564491e-07 2.1181418e-07 0.00099042271
13 1.8674942e-07 2.4218941e-07 0.00099012073
14 2.3275077e-07 2.7507982e-07 0.00098977876
15 2.833552e-07 3.1771012e-07 0.00098940169
16 3.3078875e-07 3.6075963e-07 0.00098900826
17 3.7783787e-07 4.0059005e-07 0.00098859985
18 4.3007763e-07 4.3883585e-07 0.00098817535
19 4.8592613e-07 4.8036287e-07 0.00098770764
20 5.4429898e-07 5.2362451e-07 0.00098721266
21 6.0140068e-07 5.7705077e-07 0.00098670407
22 6.6036274e-07 6.3271105e-07 0.00098617081
23 7.3748601e-07 6.9382916e-07 0.00098557406
24 8.1086859e-07 7.5979853e-07 0.0009849612
25 8.8638234e-07 8.232213e-07 0.00098434971
26 9.8252709e-07 8.9901705e-07 0.0009836645
27 1.0768657e-06 9.7033126e-07 0.0009830068
28 1.1810654e-06 1.0444697e-06 0.00098229311
29 1.2964318e-06 1.1208219e-06 0.00098150213
30 1.4097624e-06 1.1899315e-06 0.00098077686
31 1.5368367e-06 1.2560026e-06 0.00098003518
32 1.6777082e-06 1.3287355e-06 0.00097921099
33 1.8186759e-06 1.399856e-06 0.0009784037
34 1.9730383e-06 1.4769272e-06 0.00097754491
35 2.1285065e-06 1.5642459e-06 0.00097667479
36 2.2809575e-06 1.6571388e-06 0.00097572641
37 2.4393024e-06 1.7603492e-06 0.00097475881
38 2.6212592e-06 1.8666516e-06 0.00097373763
39 2.8115312e-06 1.9696572e-06 0.0009727081
40 3.0115212e-06 2.0910539e-06 0.00097155807
41 3.2325069e-06 2.2198868e-06 0.00097030871
42 3.4582526e-06 2.3576614e-06 0.00096896762
43 3.6838101e-06 2.496284e-06 0.00096760456
44 3.9267475e-06 2.637657e-06 0.00096619083
45 4.1942569e-06 2.795845e-06 0.00096470693
46 4.4694976e-06 2.9727162e-06 0.00096303835
47 4.7570486e-06 3.1451673e-06 0.00096140406
48 5.0917213e-06 3.3241907e-06 0.00095971129
49 5.4581889e-06 3.5094834e-06 0.00095790964
50 5.8607381e-06 3.7049195e-06 0.00095603039
51 6.2673583e-06 3.9139587e-06 0.0009540918
52 6.6764632e-06 4.1289537e-06 0.0009520767
53 7.0828028e-06 4.3481079e-06 0.00095003676
54 7.4858144e-06 4.5702968e-06 0.00094802906
55 7.8711706e-06 4.7928135e-06 0.00094600351
56 8.2756726e-06 5.0253448e-06 0.0009438419
57 8.6667628e-06 5.2569331e-06 0.00094169256
58 9.0585083e-06 5.4997767e-06 0.00093948055
59 9.4634766e-06 5.7547729e-06 0.00093714003
60 9.8696653e-06 6.0074589e-06 0.00093480857
61 1.0308345e-05 6.2647899e-06 0.00093244785
62 1.0757919e-05 6.5384938e-06 0.00092998209
63 1.1183568e-05 6.8124372e-06 0.00092751453
64 1.1585073e-05 7.0913777e-06 0.00092505171
65 1.1993605e-05 7.3773956e-06 0.00092256944
66 1.2382612e-05 7.6811232e-06 0.00091984092
67 1.2768116e-05 7.9951107e-06 0.0009170037
68 1.3181941e-05 8.3096758e-06 0.00091414977
69 1.3605472e-05 8.6232285e-06 0.00091137219
70 1.4027012e-05 8.9388929e-06 0.00090857909
71 1.4471706e-05 9.2524846e-06 0.00090583473
72 1.4896833e-05 9.5688611e-06 0.00090308342
73 1.5345003e-05 9.8873586e-06 0.00090026584
74 1.5779905e-05 1.0203245e-05 0.00089755256
75 1.6189898e-05 1.0523755e-05 0.00089485804
76 1.6654778e-05 1.0848398e-05 0.00089217189
77 1.7131363e-05 1.1164286e-05 0.00088956967
78 1.7572176e-05 1.1466652e-05 0.00088700311
79 1.8000817e-05 1.177381e-05 0.00088439373
80 1.838117e-05 1.2059606e-05 0.00088199635
81 1.8762432e-05 1.233837e-05 0.0008797438
82 1.9099052e-05 1.261531e-05 0.00087745162
83 1.9507863e-05 1.2899972e-05 0.00087506863
84 1.9885648e-05 1.3160246e-05 0.00087288444
85 2.0266439e-05 1.3438712e-05 0.00087052617
86 2.0612316e-05 1.372546e-05 0.00086818634
87 2.0959061e-05 1.4017631e-05 0.00086572407
88 2.13065e-05 1.4328439e-05 0.000862992
89 2.1634898e-05 1.4640964e-05 0.00086017364
90 2.2023174e-05 1.4978644e-05 0.0008570595
91 2.2431573e-05 1.5307214e-05 0.00085411601
92 2.2872283e-05 1.5649328e-05 0.00085112325
93 2.338476e-05 1.6015833e-05 0.0008479391
94 2.3912199e-05 1.6393131e-05 0.00084474237
95 2.437725e-05 1.674573e-05 0.00084165639
96 2.4828999e-05 1.7094435e-05 0.00083858996
97 2.5286762e-05 1.7451741e-05 0.00083536142
98 2.5769956e-05 1.780703e-05 0.00083221292
99 2.624134e-05 1.8141862e-05 0.00082913227
100 2.6731735e-05 1.8457846e-05 0.00082619877
Loop time of 0.0011782 on 1 procs for 100 steps with 3 atoms
Performance: 3666606971.137 fs/day, 0.000 hours/fs, 84875.161 timesteps/s, 254.625 katom-step/s
88.4% 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 | 1.773e-06 | 1.773e-06 | 1.773e-06 | 0.0 | 0.15
Comm | 1.4979e-05 | 1.4979e-05 | 1.4979e-05 | 0.0 | 1.27
Output | 0.00021888 | 0.00021888 | 0.00021888 | 0.0 | 18.58
Modify | 0.00086503 | 0.00086503 | 0.00086503 | 0.0 | 73.42
Other | | 7.754e-05 | | | 6.58
Nlocal: 3 ave 3 max 3 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 = 44
Dangerous builds = 0
Total wall time: 0:00:00

230
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LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified)
Processor partition = 2
using 1 OpenMP thread(s) per MPI task
# Units and dimensions
units electron
dimension 3
boundary p p p
atom_style atomic
atom_modify map yes
pair_style none
# Time step (in femtoseconds)
timestep 0.5
# Temperature (in Kelvin)
variable Temp equal 17.4
# Force constant (in Hartree energies per Bohr radius squared)
variable k equal 1.2154614120000001e-08
# Number of beads
variable Nbeads equal 4
variable ibead uloop ${Nbeads} pad
variable ibead uloop 4 pad
variable seed equal 18889
# Create box and atoms. All distances are in Bohr
region box block -1500 1500 -1500 1500 -1500 1500
create_box 1 box
Created orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
1 by 1 by 1 MPI processor grid
variable a loop 3
label loop
variable x1 equal -15.0+0.5*v_a
variable y1 equal 10.0-0.5*v_a
variable z1 equal 1+0.5*v_a
create_atoms 1 single ${x1} ${y1} ${z1}
create_atoms 1 single -14.5 ${y1} ${z1}
create_atoms 1 single -14.5 9.5 ${z1}
create_atoms 1 single -14.5 9.5 1.5
Created 1 atoms
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
create_atoms CPU = 0.000 seconds
next a
jump SELF loop
variable x1 equal -15.0+0.5*v_a
variable y1 equal 10.0-0.5*v_a
variable z1 equal 1+0.5*v_a
create_atoms 1 single ${x1} ${y1} ${z1}
create_atoms 1 single -14 ${y1} ${z1}
create_atoms 1 single -14 9 ${z1}
create_atoms 1 single -14 9 2
Created 1 atoms
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
create_atoms CPU = 0.000 seconds
next a
jump SELF loop
variable x1 equal -15.0+0.5*v_a
variable y1 equal 10.0-0.5*v_a
variable z1 equal 1+0.5*v_a
create_atoms 1 single ${x1} ${y1} ${z1}
create_atoms 1 single -13.5 ${y1} ${z1}
create_atoms 1 single -13.5 8.5 ${z1}
create_atoms 1 single -13.5 8.5 2.5
Created 1 atoms
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
create_atoms CPU = 0.000 seconds
next a
jump SELF loop
# Electron mass (in amu)
mass 1 0.00054858
# Initialize velocities
velocity all create ${Temp} ${seed}${ibead} mom yes rot yes dist gaussian
velocity all create 17.4 ${seed}${ibead} mom yes rot yes dist gaussian
velocity all create 17.4 18889${ibead} mom yes rot yes dist gaussian
velocity all create 17.4 188893 mom yes rot yes dist gaussian
# Add harmonic external force
fix harm all spring/self ${k}
fix harm all spring/self 1.215461412e-08
# Add harmonic potential energy to total energy and potential energy
fix_modify harm energy yes
# PIMD command
fix pimdb all pimd/langevin/bosonic ensemble nvt temp ${Temp} thermostat PILE_L 12345 tau 50 fixcom no
fix pimdb all pimd/langevin/bosonic ensemble nvt temp 17.4 thermostat PILE_L 12345 tau 50 fixcom no
# Outputs
variable prim_kinetic equal f_pimdb[5]
variable virial equal f_pimdb[6]
thermo_style custom step pe v_virial v_prim_kinetic
thermo 1
run 100
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2444)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:212)
Per MPI rank memory allocation (min/avg/max) = 2.801 | 2.801 | 2.801 Mbytes
Step PotEng v_virial v_prim_kinetic
0 0 1.3661449e-08 0.0009918329
1 8.3480048e-10 1.8742641e-09 0.00099182267
2 2.8201389e-09 7.1801177e-09 0.00099180053
3 7.3605781e-09 1.4372388e-08 0.00099176038
4 1.4967393e-08 3.1274072e-08 0.00099170266
5 2.4978087e-08 5.2470231e-08 0.00099162511
6 3.5908849e-08 7.2301291e-08 0.00099153
7 4.8226614e-08 9.5440683e-08 0.00099141194
8 6.3621045e-08 1.1669162e-07 0.00099127168
9 8.0119736e-08 1.3551097e-07 0.00099109846
10 9.7965614e-08 1.6050328e-07 0.00099089759
11 1.1538858e-07 1.8645705e-07 0.0009906735
12 1.365443e-07 2.1181418e-07 0.00099042271
13 1.5920175e-07 2.4218941e-07 0.00099012073
14 1.8252589e-07 2.7507982e-07 0.00098977876
15 2.0858909e-07 3.1771012e-07 0.00098940169
16 2.3676046e-07 3.6075963e-07 0.00098900826
17 2.689757e-07 4.0059005e-07 0.00098859985
18 3.0022172e-07 4.3883585e-07 0.00098817535
19 3.3127637e-07 4.8036287e-07 0.00098770764
20 3.6044366e-07 5.2362451e-07 0.00098721266
21 3.8484646e-07 5.7705077e-07 0.00098670407
22 4.1435067e-07 6.3271105e-07 0.00098617081
23 4.4508994e-07 6.9382916e-07 0.00098557406
24 4.7879333e-07 7.5979853e-07 0.0009849612
25 5.0918223e-07 8.232213e-07 0.00098434971
26 5.4733661e-07 8.9901705e-07 0.0009836645
27 5.7932115e-07 9.7033126e-07 0.0009830068
28 6.1775401e-07 1.0444697e-06 0.00098229311
29 6.6883535e-07 1.1208219e-06 0.00098150213
30 7.0943445e-07 1.1899315e-06 0.00098077686
31 7.4477897e-07 1.2560026e-06 0.00098003518
32 7.8183156e-07 1.3287355e-06 0.00097921099
33 8.1987667e-07 1.399856e-06 0.0009784037
34 8.5514962e-07 1.4769272e-06 0.00097754491
35 8.9607784e-07 1.5642459e-06 0.00097667479
36 9.4986753e-07 1.6571388e-06 0.00097572641
37 1.0024729e-06 1.7603492e-06 0.00097475881
38 1.0526731e-06 1.8666516e-06 0.00097373763
39 1.103419e-06 1.9696572e-06 0.0009727081
40 1.1640352e-06 2.0910539e-06 0.00097155807
41 1.2292837e-06 2.2198868e-06 0.00097030871
42 1.3024454e-06 2.3576614e-06 0.00096896762
43 1.3788736e-06 2.496284e-06 0.00096760456
44 1.4503248e-06 2.637657e-06 0.00096619083
45 1.5334106e-06 2.795845e-06 0.00096470693
46 1.6246777e-06 2.9727162e-06 0.00096303835
47 1.715884e-06 3.1451673e-06 0.00096140406
48 1.8096683e-06 3.3241907e-06 0.00095971129
49 1.916714e-06 3.5094834e-06 0.00095790964
50 2.0374848e-06 3.7049195e-06 0.00095603039
51 2.1747488e-06 3.9139587e-06 0.0009540918
52 2.3236882e-06 4.1289537e-06 0.0009520767
53 2.4790586e-06 4.3481079e-06 0.00095003676
54 2.6478101e-06 4.5702968e-06 0.00094802906
55 2.8275135e-06 4.7928135e-06 0.00094600351
56 3.0338638e-06 5.0253448e-06 0.0009438419
57 3.2428318e-06 5.2569331e-06 0.00094169256
58 3.4414566e-06 5.4997767e-06 0.00093948055
59 3.6324968e-06 5.7547729e-06 0.00093714003
60 3.8269172e-06 6.0074589e-06 0.00093480857
61 4.0183315e-06 6.2647899e-06 0.00093244785
62 4.2263009e-06 6.5384938e-06 0.00092998209
63 4.4382735e-06 6.8124372e-06 0.00092751453
64 4.6488232e-06 7.0913777e-06 0.00092505171
65 4.8707403e-06 7.3773956e-06 0.00092256944
66 5.1178339e-06 7.6811232e-06 0.00091984092
67 5.377713e-06 7.9951107e-06 0.0009170037
68 5.63843e-06 8.3096758e-06 0.00091414977
69 5.8975743e-06 8.6232285e-06 0.00091137219
70 6.168921e-06 8.9388929e-06 0.00090857909
71 6.4488238e-06 9.2524846e-06 0.00090583473
72 6.7115203e-06 9.5688611e-06 0.00090308342
73 6.995134e-06 9.8873586e-06 0.00090026584
74 7.284199e-06 1.0203245e-05 0.00089755256
75 7.6029528e-06 1.0523755e-05 0.00089485804
76 7.9431391e-06 1.0848398e-05 0.00089217189
77 8.2768015e-06 1.1164286e-05 0.00088956967
78 8.6058917e-06 1.1466652e-05 0.00088700311
79 8.9683477e-06 1.177381e-05 0.00088439373
80 9.3324487e-06 1.2059606e-05 0.00088199635
81 9.6876036e-06 1.233837e-05 0.0008797438
82 1.0061754e-05 1.261531e-05 0.00087745162
83 1.0457019e-05 1.2899972e-05 0.00087506863
84 1.0866064e-05 1.3160246e-05 0.00087288444
85 1.1298832e-05 1.3438712e-05 0.00087052617
86 1.1762526e-05 1.372546e-05 0.00086818634
87 1.2264941e-05 1.4017631e-05 0.00086572407
88 1.2784125e-05 1.4328439e-05 0.000862992
89 1.332533e-05 1.4640964e-05 0.00086017364
90 1.3897966e-05 1.4978644e-05 0.0008570595
91 1.4473024e-05 1.5307214e-05 0.00085411601
92 1.5067033e-05 1.5649328e-05 0.00085112325
93 1.5677943e-05 1.6015833e-05 0.0008479391
94 1.6254294e-05 1.6393131e-05 0.00084474237
95 1.6791089e-05 1.674573e-05 0.00084165639
96 1.7362795e-05 1.7094435e-05 0.00083858996
97 1.7961498e-05 1.7451741e-05 0.00083536142
98 1.8568337e-05 1.780703e-05 0.00083221292
99 1.9188379e-05 1.8141862e-05 0.00082913227
100 1.9789011e-05 1.8457846e-05 0.00082619877
Loop time of 0.00116163 on 1 procs for 100 steps with 3 atoms
Performance: 3718915419.639 fs/day, 0.000 hours/fs, 86086.005 timesteps/s, 258.258 katom-step/s
89.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 1.582e-06 | 1.582e-06 | 1.582e-06 | 0.0 | 0.14
Comm | 1.3306e-05 | 1.3306e-05 | 1.3306e-05 | 0.0 | 1.15
Output | 0.00017996 | 0.00017996 | 0.00017996 | 0.0 | 15.49
Modify | 0.00090771 | 0.00090771 | 0.00090771 | 0.0 | 78.14
Other | | 5.907e-05 | | | 5.09
Nlocal: 3 ave 3 max 3 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 = 41
Dangerous builds = 0
Total wall time: 0:00:00

230
examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.13Mar2025.g++.3 Normal file
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LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified)
Processor partition = 3
using 1 OpenMP thread(s) per MPI task
# Units and dimensions
units electron
dimension 3
boundary p p p
atom_style atomic
atom_modify map yes
pair_style none
# Time step (in femtoseconds)
timestep 0.5
# Temperature (in Kelvin)
variable Temp equal 17.4
# Force constant (in Hartree energies per Bohr radius squared)
variable k equal 1.2154614120000001e-08
# Number of beads
variable Nbeads equal 4
variable ibead uloop ${Nbeads} pad
variable ibead uloop 4 pad
variable seed equal 18889
# Create box and atoms. All distances are in Bohr
region box block -1500 1500 -1500 1500 -1500 1500
create_box 1 box
Created orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
1 by 1 by 1 MPI processor grid
variable a loop 3
label loop
variable x1 equal -15.0+0.5*v_a
variable y1 equal 10.0-0.5*v_a
variable z1 equal 1+0.5*v_a
create_atoms 1 single ${x1} ${y1} ${z1}
create_atoms 1 single -14.5 ${y1} ${z1}
create_atoms 1 single -14.5 9.5 ${z1}
create_atoms 1 single -14.5 9.5 1.5
Created 1 atoms
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
create_atoms CPU = 0.000 seconds
next a
jump SELF loop
variable x1 equal -15.0+0.5*v_a
variable y1 equal 10.0-0.5*v_a
variable z1 equal 1+0.5*v_a
create_atoms 1 single ${x1} ${y1} ${z1}
create_atoms 1 single -14 ${y1} ${z1}
create_atoms 1 single -14 9 ${z1}
create_atoms 1 single -14 9 2
Created 1 atoms
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
create_atoms CPU = 0.000 seconds
next a
jump SELF loop
variable x1 equal -15.0+0.5*v_a
variable y1 equal 10.0-0.5*v_a
variable z1 equal 1+0.5*v_a
create_atoms 1 single ${x1} ${y1} ${z1}
create_atoms 1 single -13.5 ${y1} ${z1}
create_atoms 1 single -13.5 8.5 ${z1}
create_atoms 1 single -13.5 8.5 2.5
Created 1 atoms
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
create_atoms CPU = 0.000 seconds
next a
jump SELF loop
# Electron mass (in amu)
mass 1 0.00054858
# Initialize velocities
velocity all create ${Temp} ${seed}${ibead} mom yes rot yes dist gaussian
velocity all create 17.4 ${seed}${ibead} mom yes rot yes dist gaussian
velocity all create 17.4 18889${ibead} mom yes rot yes dist gaussian
velocity all create 17.4 188894 mom yes rot yes dist gaussian
# Add harmonic external force
fix harm all spring/self ${k}
fix harm all spring/self 1.215461412e-08
# Add harmonic potential energy to total energy and potential energy
fix_modify harm energy yes
# PIMD command
fix pimdb all pimd/langevin/bosonic ensemble nvt temp ${Temp} thermostat PILE_L 12345 tau 50 fixcom no
fix pimdb all pimd/langevin/bosonic ensemble nvt temp 17.4 thermostat PILE_L 12345 tau 50 fixcom no
# Outputs
variable prim_kinetic equal f_pimdb[5]
variable virial equal f_pimdb[6]
thermo_style custom step pe v_virial v_prim_kinetic
thermo 1
run 100
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2444)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:212)
Per MPI rank memory allocation (min/avg/max) = 2.801 | 2.801 | 2.801 Mbytes
Step PotEng v_virial v_prim_kinetic
0 0 1.3661449e-08 0.0009918329
1 8.448696e-10 1.8742641e-09 0.00099182267
2 3.5286528e-09 7.1801177e-09 0.00099180053
3 8.2936659e-09 1.4372388e-08 0.00099176038
4 1.4586045e-08 3.1274072e-08 0.00099170266
5 2.4161875e-08 5.2470231e-08 0.00099162511
6 3.8801085e-08 7.2301291e-08 0.00099153
7 5.9758384e-08 9.5440683e-08 0.00099141194
8 8.5838823e-08 1.1669162e-07 0.00099127168
9 1.1684437e-07 1.3551097e-07 0.00099109846
10 1.4954974e-07 1.6050328e-07 0.00099089759
11 1.8686687e-07 1.8645705e-07 0.0009906735
12 2.2747543e-07 2.1181418e-07 0.00099042271
13 2.807392e-07 2.4218941e-07 0.00099012073
14 3.3827867e-07 2.7507982e-07 0.00098977876
15 3.9918359e-07 3.1771012e-07 0.00098940169
16 4.6034561e-07 3.6075963e-07 0.00098900826
17 5.2315136e-07 4.0059005e-07 0.00098859985
18 5.8457073e-07 4.3883585e-07 0.00098817535
19 6.5273892e-07 4.8036287e-07 0.00098770764
20 7.2150647e-07 5.2362451e-07 0.00098721266
21 8.0596691e-07 5.7705077e-07 0.00098670407
22 8.946994e-07 6.3271105e-07 0.00098617081
23 9.9120142e-07 6.9382916e-07 0.00098557406
24 1.09722e-06 7.5979853e-07 0.0009849612
25 1.2053692e-06 8.232213e-07 0.00098434971
26 1.3196547e-06 8.9901705e-07 0.0009836645
27 1.4380033e-06 9.7033126e-07 0.0009830068
28 1.5700587e-06 1.0444697e-06 0.00098229311
29 1.7089133e-06 1.1208219e-06 0.00098150213
30 1.839944e-06 1.1899315e-06 0.00098077686
31 1.9718088e-06 1.2560026e-06 0.00098003518
32 2.1244847e-06 1.3287355e-06 0.00097921099
33 2.2823018e-06 1.399856e-06 0.0009784037
34 2.4607034e-06 1.4769272e-06 0.00097754491
35 2.6410061e-06 1.5642459e-06 0.00097667479
36 2.8395019e-06 1.6571388e-06 0.00097572641
37 3.0476467e-06 1.7603492e-06 0.00097475881
38 3.2661567e-06 1.8666516e-06 0.00097373763
39 3.4857766e-06 1.9696572e-06 0.0009727081
40 3.7310241e-06 2.0910539e-06 0.00097155807
41 3.9947356e-06 2.2198868e-06 0.00097030871
42 4.2722057e-06 2.3576614e-06 0.00096896762
43 4.5444932e-06 2.496284e-06 0.00096760456
44 4.8307956e-06 2.637657e-06 0.00096619083
45 5.1356773e-06 2.795845e-06 0.00096470693
46 5.4835294e-06 2.9727162e-06 0.00096303835
47 5.8235502e-06 3.1451673e-06 0.00096140406
48 6.1541132e-06 3.3241907e-06 0.00095971129
49 6.4796693e-06 3.5094834e-06 0.00095790964
50 6.8009213e-06 3.7049195e-06 0.00095603039
51 7.1253629e-06 3.9139587e-06 0.0009540918
52 7.4712081e-06 4.1289537e-06 0.0009520767
53 7.8322309e-06 4.3481079e-06 0.00095003676
54 8.1941694e-06 4.5702968e-06 0.00094802906
55 8.579188e-06 4.7928135e-06 0.00094600351
56 8.9656493e-06 5.0253448e-06 0.0009438419
57 9.351102e-06 5.2569331e-06 0.00094169256
58 9.7645407e-06 5.4997767e-06 0.00093948055
59 1.0230434e-05 5.7547729e-06 0.00093714003
60 1.0724041e-05 6.0074589e-06 0.00093480857
61 1.1207453e-05 6.2647899e-06 0.00093244785
62 1.171285e-05 6.5384938e-06 0.00092998209
63 1.221299e-05 6.8124372e-06 0.00092751453
64 1.2743686e-05 7.0913777e-06 0.00092505171
65 1.3295725e-05 7.3773956e-06 0.00092256944
66 1.3906023e-05 7.6811232e-06 0.00091984092
67 1.4511348e-05 7.9951107e-06 0.0009170037
68 1.5116776e-05 8.3096758e-06 0.00091414977
69 1.571005e-05 8.6232285e-06 0.00091137219
70 1.6297136e-05 8.9388929e-06 0.00090857909
71 1.6849099e-05 9.2524846e-06 0.00090583473
72 1.7417168e-05 9.5688611e-06 0.00090308342
73 1.7971613e-05 9.8873586e-06 0.00090026584
74 1.8509472e-05 1.0203245e-05 0.00089755256
75 1.9047825e-05 1.0523755e-05 0.00089485804
76 1.9510646e-05 1.0848398e-05 0.00089217189
77 1.9903304e-05 1.1164286e-05 0.00088956967
78 2.0300948e-05 1.1466652e-05 0.00088700311
79 2.0696905e-05 1.177381e-05 0.00088439373
80 2.1058218e-05 1.2059606e-05 0.00088199635
81 2.139726e-05 1.233837e-05 0.0008797438
82 2.1755155e-05 1.261531e-05 0.00087745162
83 2.2051018e-05 1.2899972e-05 0.00087506863
84 2.2294567e-05 1.3160246e-05 0.00087288444
85 2.2559076e-05 1.3438712e-05 0.00087052617
86 2.2815918e-05 1.372546e-05 0.00086818634
87 2.3062616e-05 1.4017631e-05 0.00086572407
88 2.3324206e-05 1.4328439e-05 0.000862992
89 2.3559323e-05 1.4640964e-05 0.00086017364
90 2.3792776e-05 1.4978644e-05 0.0008570595
91 2.3990667e-05 1.5307214e-05 0.00085411601
92 2.4198637e-05 1.5649328e-05 0.00085112325
93 2.4419398e-05 1.6015833e-05 0.0008479391
94 2.4625252e-05 1.6393131e-05 0.00084474237
95 2.4816363e-05 1.674573e-05 0.00084165639
96 2.4982897e-05 1.7094435e-05 0.00083858996
97 2.5153682e-05 1.7451741e-05 0.00083536142
98 2.5288512e-05 1.780703e-05 0.00083221292
99 2.5384836e-05 1.8141862e-05 0.00082913227
100 2.5401412e-05 1.8457846e-05 0.00082619877
Loop time of 0.00116067 on 1 procs for 100 steps with 3 atoms
Performance: 3721997782.310 fs/day, 0.000 hours/fs, 86157.356 timesteps/s, 258.472 katom-step/s
88.3% 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 | 1.441e-06 | 1.441e-06 | 1.441e-06 | 0.0 | 0.12
Comm | 1.2111e-05 | 1.2111e-05 | 1.2111e-05 | 0.0 | 1.04
Output | 0.00018148 | 0.00018148 | 0.00018148 | 0.0 | 15.64
Modify | 0.0009054 | 0.0009054 | 0.0009054 | 0.0 | 78.01
Other | | 6.023e-05 | | | 5.19
Nlocal: 3 ave 3 max 3 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 = 42
Dangerous builds = 0
Total wall time: 0:00:00

1
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mpirun -np $NBEADS $LMP -in in.lmp -partition ${NBEADS}x1

60
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# Units and dimensions
units electron
dimension 3
boundary p p p
atom_style atomic
atom_modify map yes
pair_style none
# Time step (in femtoseconds)
timestep 0.5
# Temperature (in Kelvin)
variable Temp equal 17.4
# Number of Nose-Hoover chains
variable nhc equal 4
# Force constant (in Hartree energies per Bohr radius squared)
variable k equal 1.2154614120000001e-08
# Number of beads
variable Nbeads equal 4
variable ibead uloop ${Nbeads} pad
variable seed equal 18889
# Create box and atoms. All distances are in Bohr
region box block -1500 1500 -1500 1500 -1500 1500
create_box 1 box
variable a loop 3
label loop
variable x1 equal -15.0+0.5*v_a
variable y1 equal 10.0-0.5*v_a
variable z1 equal 1+0.5*v_a
create_atoms 1 single ${x1} ${y1} ${z1}
next a
jump SELF loop
# Electron mass (in amu)
mass 1 0.00054858
# Initialize velocities
velocity all create ${Temp} ${seed}${ibead} mom yes rot yes dist gaussian
# Add harmonic external force
fix harm all spring/self ${k}
# Add harmonic potential energy to total energy and potential energy
fix_modify harm energy yes
# PIMD command
fix pimdb all pimd/nvt/bosonic method pimd temp ${Temp} nhc ${nhc}
# Outputs
variable virial equal f_pimdb[3]
variable prim_kinetic equal f_pimdb[4]
thermo_style custom step pe v_virial v_prim_kinetic
thermo 1
run 100

2
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LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified)
Running on 4 partitions of processors

237
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LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified)
Processor partition = 0
using 1 OpenMP thread(s) per MPI task
# Units and dimensions
units electron
dimension 3
boundary p p p
atom_style atomic
atom_modify map yes
pair_style none
# Time step (in femtoseconds)
timestep 0.5
# Temperature (in Kelvin)
variable Temp equal 17.4
# Number of Nose-Hoover chains
variable nhc equal 4
# Force constant (in Hartree energies per Bohr radius squared)
variable k equal 1.2154614120000001e-08
# Number of beads
variable Nbeads equal 4
variable ibead uloop ${Nbeads} pad
variable ibead uloop 4 pad
variable seed equal 18889
# Create box and atoms. All distances are in Bohr
region box block -1500 1500 -1500 1500 -1500 1500
create_box 1 box
Created orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
1 by 1 by 1 MPI processor grid
variable a loop 3
label loop
variable x1 equal -15.0+0.5*v_a
variable y1 equal 10.0-0.5*v_a
variable z1 equal 1+0.5*v_a
create_atoms 1 single ${x1} ${y1} ${z1}
create_atoms 1 single -14.5 ${y1} ${z1}
create_atoms 1 single -14.5 9.5 ${z1}
create_atoms 1 single -14.5 9.5 1.5
Created 1 atoms
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
create_atoms CPU = 0.000 seconds
next a
jump SELF loop
variable x1 equal -15.0+0.5*v_a
variable y1 equal 10.0-0.5*v_a
variable z1 equal 1+0.5*v_a
create_atoms 1 single ${x1} ${y1} ${z1}
create_atoms 1 single -14 ${y1} ${z1}
create_atoms 1 single -14 9 ${z1}
create_atoms 1 single -14 9 2
Created 1 atoms
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
create_atoms CPU = 0.000 seconds
next a
jump SELF loop
variable x1 equal -15.0+0.5*v_a
variable y1 equal 10.0-0.5*v_a
variable z1 equal 1+0.5*v_a
create_atoms 1 single ${x1} ${y1} ${z1}
create_atoms 1 single -13.5 ${y1} ${z1}
create_atoms 1 single -13.5 8.5 ${z1}
create_atoms 1 single -13.5 8.5 2.5
Created 1 atoms
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
create_atoms CPU = 0.000 seconds
next a
jump SELF loop
# Electron mass (in amu)
mass 1 0.00054858
# Initialize velocities
velocity all create ${Temp} ${seed}${ibead} mom yes rot yes dist gaussian
velocity all create 17.4 ${seed}${ibead} mom yes rot yes dist gaussian
velocity all create 17.4 18889${ibead} mom yes rot yes dist gaussian
velocity all create 17.4 188891 mom yes rot yes dist gaussian
# Add harmonic external force
fix harm all spring/self ${k}
fix harm all spring/self 1.215461412e-08
# Add harmonic potential energy to total energy and potential energy
fix_modify harm energy yes
# PIMD command
fix pimdb all pimd/nvt/bosonic method pimd temp ${Temp} nhc ${nhc}
fix pimdb all pimd/nvt/bosonic method pimd temp 17.4 nhc ${nhc}
fix pimdb all pimd/nvt/bosonic method pimd temp 17.4 nhc 4
# Outputs
variable virial equal f_pimdb[3]
variable prim_kinetic equal f_pimdb[4]
thermo_style custom step pe v_virial v_prim_kinetic
thermo 1
run 100
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Fix pimd/nvt -P/(beta^2 * hbar^2) = -2.2139311e-05 (kcal/mol/A^2)
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2444)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:212)
Per MPI rank memory allocation (min/avg/max) = 9.176 | 9.176 | 9.176 Mbytes
Step PotEng v_virial v_prim_kinetic
0 0 0 0.00024794798
1 8.5849317e-10 4.5664581e-10 0.00024794215
2 3.4338094e-09 1.3424585e-09 0.00024793325
3 7.7255501e-09 2.6573351e-09 0.00024792129
4 1.3733112e-08 4.4011211e-09 0.00024790626
5 2.1455686e-08 6.5736113e-09 0.00024788818
6 3.0892259e-08 9.1745487e-09 0.00024786704
7 4.2041614e-08 1.2203626e-08 0.00024784285
8 5.4902328e-08 1.5660483e-08 0.0002478156
9 6.9472776e-08 1.9544712e-08 0.00024778532
10 8.5751128e-08 2.385585e-08 0.00024775199
11 1.0373535e-07 2.8593386e-08 0.00024771564
12 1.234232e-07 3.3756758e-08 0.00024767626
13 1.4481225e-07 3.9345352e-08 0.00024763386
14 1.6789985e-07 4.5358504e-08 0.00024758844
15 1.9268316e-07 5.1795501e-08 0.00024754003
16 2.1915914e-07 5.8655576e-08 0.00024748862
17 2.4732452e-07 6.5937915e-08 0.00024743423
18 2.7717588e-07 7.3641654e-08 0.00024737686
19 3.0870956e-07 8.1765876e-08 0.00024731653
20 3.4192172e-07 9.0309618e-08 0.00024725324
21 3.7680831e-07 9.9271863e-08 0.00024718701
22 4.1336509e-07 1.0865155e-07 0.00024711785
23 4.5158762e-07 1.1844756e-07 0.00024704578
24 4.9147126e-07 1.2865874e-07 0.0002469708
25 5.3301119e-07 1.3928387e-07 0.00024689293
26 5.7620236e-07 1.5032169e-07 0.00024681218
27 6.2103957e-07 1.6177089e-07 0.00024672857
28 6.675174e-07 1.7363012e-07 0.00024664212
29 7.1563024e-07 1.8589798e-07 0.00024655283
30 7.6537229e-07 1.9857299e-07 0.00024646073
31 8.1673756e-07 2.1165368e-07 0.00024636584
32 8.6971988e-07 2.2513849e-07 0.00024626816
33 9.2431288e-07 2.3902582e-07 0.00024616772
34 9.8051001e-07 2.5331402e-07 0.00024606453
35 1.0383045e-06 2.6800143e-07 0.00024595862
36 1.0976895e-06 2.8308629e-07 0.00024585001
37 1.1586578e-06 2.9856682e-07 0.0002457387
38 1.2212021e-06 3.1444121e-07 0.00024562473
39 1.2853151e-06 3.3070757e-07 0.00024550812
40 1.350989e-06 3.4736399e-07 0.00024538888
41 1.4182159e-06 3.644085e-07 0.00024526703
42 1.4869879e-06 3.8183911e-07 0.00024514261
43 1.5572969e-06 3.9965375e-07 0.00024501562
44 1.6291343e-06 4.1785034e-07 0.0002448861
45 1.7024917e-06 4.3642673e-07 0.00024475406
46 1.7773604e-06 4.5538075e-07 0.00024461954
47 1.8537315e-06 4.7471016e-07 0.00024448255
48 1.9315959e-06 4.9441271e-07 0.00024434312
49 2.0109445e-06 5.1448608e-07 0.00024420127
50 2.0917677e-06 5.3492792e-07 0.00024405703
51 2.1740562e-06 5.5573584e-07 0.00024391043
52 2.2578001e-06 5.769074e-07 0.00024376149
53 2.3429895e-06 5.9844014e-07 0.00024361023
54 2.4296146e-06 6.2033154e-07 0.00024345669
55 2.5176649e-06 6.4257904e-07 0.00024330088
56 2.6071302e-06 6.6518005e-07 0.00024314285
57 2.6980001e-06 6.8813194e-07 0.00024298261
58 2.7902637e-06 7.1143203e-07 0.0002428202
59 2.8839103e-06 7.3507763e-07 0.00024265563
60 2.9789289e-06 7.5906598e-07 0.00024248895
61 3.0753084e-06 7.833943e-07 0.00024232018
62 3.1730376e-06 8.0805977e-07 0.00024214934
63 3.2721049e-06 8.3305953e-07 0.00024197647
64 3.372499e-06 8.5839069e-07 0.00024180161
65 3.474208e-06 8.8405032e-07 0.00024162477
66 3.5772201e-06 9.1003545e-07 0.00024144598
67 3.6815235e-06 9.3634309e-07 0.00024126529
68 3.7871058e-06 9.6297021e-07 0.00024108272
69 3.893955e-06 9.8991374e-07 0.0002408983
70 4.0020586e-06 1.0171706e-06 0.00024071206
71 4.1114041e-06 1.0447376e-06 0.00024052403
72 4.2219789e-06 1.0726116e-06 0.00024033425
73 4.3337702e-06 1.1007895e-06 0.00024014274
74 4.4467651e-06 1.1292679e-06 0.00023994955
75 4.5609507e-06 1.1580437e-06 0.0002397547
76 4.6763137e-06 1.1871136e-06 0.00023955822
77 4.792841e-06 1.2164741e-06 0.00023936014
78 4.9105191e-06 1.2461221e-06 0.00023916051
79 5.0293346e-06 1.276054e-06 0.00023895935
80 5.149274e-06 1.3062666e-06 0.00023875669
81 5.2703234e-06 1.3367563e-06 0.00023855257
82 5.392469e-06 1.3675198e-06 0.00023834703
83 5.515697e-06 1.3985535e-06 0.00023814009
84 5.6399934e-06 1.4298539e-06 0.00023793178
85 5.7653439e-06 1.4614174e-06 0.00023772215
86 5.8917344e-06 1.4932406e-06 0.00023751123
87 6.0191505e-06 1.5253199e-06 0.00023729904
88 6.1475779e-06 1.5576515e-06 0.00023708563
89 6.277002e-06 1.590232e-06 0.00023687102
90 6.4074081e-06 1.6230576e-06 0.00023665526
91 6.5387817e-06 1.6561246e-06 0.00023643837
92 6.6711079e-06 1.6894294e-06 0.00023622039
93 6.8043718e-06 1.7229682e-06 0.00023600135
94 6.9385585e-06 1.7567372e-06 0.00023578129
95 7.0736529e-06 1.7907328e-06 0.00023556024
96 7.2096401e-06 1.8249512e-06 0.00023533824
97 7.3465046e-06 1.8593885e-06 0.00023511531
98 7.4842314e-06 1.8940408e-06 0.0002348915
99 7.622805e-06 1.9289045e-06 0.00023466684
100 7.76221e-06 1.9639756e-06 0.00023444136
Loop time of 0.00193128 on 1 procs for 100 steps with 3 atoms
Performance: 2236858456.568 fs/day, 0.000 hours/fs, 51779.131 timesteps/s, 155.337 katom-step/s
36.5% 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 | 1.454e-06 | 1.454e-06 | 1.454e-06 | 0.0 | 0.08
Comm | 2.3033e-05 | 2.3033e-05 | 2.3033e-05 | 0.0 | 1.19
Output | 0.00030824 | 0.00030824 | 0.00030824 | 0.0 | 15.96
Modify | 0.001541 | 0.001541 | 0.001541 | 0.0 | 79.79
Other | | 5.754e-05 | | | 2.98
Nlocal: 3 ave 3 max 3 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 = 24
Dangerous builds = 0
Total wall time: 0:00:00

235
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LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified)
Processor partition = 1
using 1 OpenMP thread(s) per MPI task
# Units and dimensions
units electron
dimension 3
boundary p p p
atom_style atomic
atom_modify map yes
pair_style none
# Time step (in femtoseconds)
timestep 0.5
# Temperature (in Kelvin)
variable Temp equal 17.4
# Number of Nose-Hoover chains
variable nhc equal 4
# Force constant (in Hartree energies per Bohr radius squared)
variable k equal 1.2154614120000001e-08
# Number of beads
variable Nbeads equal 4
variable ibead uloop ${Nbeads} pad
variable ibead uloop 4 pad
variable seed equal 18889
# Create box and atoms. All distances are in Bohr
region box block -1500 1500 -1500 1500 -1500 1500
create_box 1 box
Created orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
1 by 1 by 1 MPI processor grid
variable a loop 3
label loop
variable x1 equal -15.0+0.5*v_a
variable y1 equal 10.0-0.5*v_a
variable z1 equal 1+0.5*v_a
create_atoms 1 single ${x1} ${y1} ${z1}
create_atoms 1 single -14.5 ${y1} ${z1}
create_atoms 1 single -14.5 9.5 ${z1}
create_atoms 1 single -14.5 9.5 1.5
Created 1 atoms
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
create_atoms CPU = 0.000 seconds
next a
jump SELF loop
variable x1 equal -15.0+0.5*v_a
variable y1 equal 10.0-0.5*v_a
variable z1 equal 1+0.5*v_a
create_atoms 1 single ${x1} ${y1} ${z1}
create_atoms 1 single -14 ${y1} ${z1}
create_atoms 1 single -14 9 ${z1}
create_atoms 1 single -14 9 2
Created 1 atoms
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
create_atoms CPU = 0.000 seconds
next a
jump SELF loop
variable x1 equal -15.0+0.5*v_a
variable y1 equal 10.0-0.5*v_a
variable z1 equal 1+0.5*v_a
create_atoms 1 single ${x1} ${y1} ${z1}
create_atoms 1 single -13.5 ${y1} ${z1}
create_atoms 1 single -13.5 8.5 ${z1}
create_atoms 1 single -13.5 8.5 2.5
Created 1 atoms
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
create_atoms CPU = 0.000 seconds
next a
jump SELF loop
# Electron mass (in amu)
mass 1 0.00054858
# Initialize velocities
velocity all create ${Temp} ${seed}${ibead} mom yes rot yes dist gaussian
velocity all create 17.4 ${seed}${ibead} mom yes rot yes dist gaussian
velocity all create 17.4 18889${ibead} mom yes rot yes dist gaussian
velocity all create 17.4 188892 mom yes rot yes dist gaussian
# Add harmonic external force
fix harm all spring/self ${k}
fix harm all spring/self 1.215461412e-08
# Add harmonic potential energy to total energy and potential energy
fix_modify harm energy yes
# PIMD command
fix pimdb all pimd/nvt/bosonic method pimd temp ${Temp} nhc ${nhc}
fix pimdb all pimd/nvt/bosonic method pimd temp 17.4 nhc ${nhc}
fix pimdb all pimd/nvt/bosonic method pimd temp 17.4 nhc 4
# Outputs
variable virial equal f_pimdb[3]
variable prim_kinetic equal f_pimdb[4]
thermo_style custom step pe v_virial v_prim_kinetic
thermo 1
run 100
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2444)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:212)
Per MPI rank memory allocation (min/avg/max) = 9.176 | 9.176 | 9.176 Mbytes
Step PotEng v_virial v_prim_kinetic
0 0 0 0.00024796164
1 8.5850843e-10 5.313724e-10 0.00024796083
2 3.4339027e-09 1.4919466e-09 0.00024795841
3 7.7257901e-09 2.8816048e-09 0.00024795438
4 1.3733516e-08 4.7001635e-09 0.00024794873
5 2.1456164e-08 6.9473741e-09 0.00024794148
6 3.0892555e-08 9.6229225e-09 0.00024793261
7 4.2041252e-08 1.2726429e-08 0.00024792214
8 5.4900553e-08 1.6257449e-08 0.00024791006
9 6.9468499e-08 2.0215473e-08 0.00024789638
10 8.5742867e-08 2.4599926e-08 0.0002478811
11 1.0372118e-07 2.9410168e-08 0.00024786422
12 1.2340069e-07 3.4645495e-08 0.00024784576
13 1.447784e-07 4.0305136e-08 0.0002478257
14 1.6785106e-07 4.6388259e-08 0.00024780406
15 1.9261515e-07 5.2893965e-08 0.00024778084
16 2.190669e-07 5.9821291e-08 0.00024775605
17 2.4720228e-07 6.7169211e-08 0.00024772969
18 2.7701701e-07 7.4936635e-08 0.00024770176
19 3.0850655e-07 8.312241e-08 0.00024767228
20 3.416661e-07 9.1725317e-08 0.00024764125
21 3.7649064e-07 1.0074408e-07 0.00024760868
22 4.1297485e-07 1.1017735e-07 0.00024757457
23 4.511132e-07 1.2002372e-07 0.00024753893
24 4.9089989e-07 1.3028173e-07 0.00024750177
25 5.3232887e-07 1.4094984e-07 0.0002474631
26 5.7539386e-07 1.5202647e-07 0.00024742293
27 6.2008832e-07 1.6350996e-07 0.00024738126
28 6.6640547e-07 1.7539859e-07 0.00024733811
29 7.1433828e-07 1.876906e-07 0.00024729348
30 7.6387949e-07 2.0038414e-07 0.00024724738
31 8.150216e-07 2.1347732e-07 0.00024719983
32 8.6775685e-07 2.2696818e-07 0.00024715084
33 9.2207727e-07 2.4085472e-07 0.0002471004
34 9.7797464e-07 2.5513485e-07 0.00024704855
35 1.0354405e-06 2.6980645e-07 0.00024699528
36 1.0944662e-06 2.8486732e-07 0.00024694061
37 1.1550427e-06 3.0031522e-07 0.00024688456
38 1.2171611e-06 3.1614785e-07 0.00024682713
39 1.2808118e-06 3.3236283e-07 0.00024676833
40 1.3459853e-06 3.4895776e-07 0.00024670818
41 1.4126717e-06 3.6593016e-07 0.0002466467
42 1.4808611e-06 3.832775e-07 0.0002465839
43 1.5505431e-06 4.009972e-07 0.00024651978
44 1.6217074e-06 4.1908663e-07 0.00024645437
45 1.6943431e-06 4.3754308e-07 0.00024638767
46 1.7684394e-06 4.5636381e-07 0.00024631971
47 1.8439852e-06 4.7554603e-07 0.0002462505
48 1.9209691e-06 4.9508689e-07 0.00024618005
49 1.9993796e-06 5.1498348e-07 0.00024610839
50 2.079205e-06 5.3523286e-07 0.00024603551
51 2.1604333e-06 5.5583202e-07 0.00024596145
52 2.2430524e-06 5.7677791e-07 0.00024588621
53 2.32705e-06 5.9806742e-07 0.00024580981
54 2.4124135e-06 6.1969741e-07 0.00024573228
55 2.4991302e-06 6.4166468e-07 0.00024565362
56 2.5871872e-06 6.6396597e-07 0.00024557386
57 2.6765714e-06 6.8659801e-07 0.00024549301
58 2.7672695e-06 7.0955745e-07 0.00024541108
59 2.859268e-06 7.328409e-07 0.00024532811
60 2.9525533e-06 7.5644494e-07 0.00024524409
61 3.0471115e-06 7.8036609e-07 0.00024515907
62 3.1429287e-06 8.0460083e-07 0.00024507304
63 3.2399907e-06 8.2914562e-07 0.00024498603
64 3.3382831e-06 8.5399683e-07 0.00024489807
65 3.4377915e-06 8.7915084e-07 0.00024480916
66 3.5385011e-06 9.0460395e-07 0.00024471933
67 3.6403972e-06 9.3035245e-07 0.0002446286
68 3.7434648e-06 9.5639257e-07 0.00024453698
69 3.8476886e-06 9.8272051e-07 0.0002444445
70 3.9530535e-06 1.0093324e-06 0.00024435118
71 4.0595439e-06 1.0362244e-06 0.00024425703
72 4.1671443e-06 1.0633926e-06 0.00024416208
73 4.275839e-06 1.0908331e-06 0.00024406635
74 4.3856121e-06 1.1185418e-06 0.00024396985
75 4.4964475e-06 1.1465147e-06 0.00024387262
76 4.6083292e-06 1.1747478e-06 0.00024377466
77 4.7212408e-06 1.2032371e-06 0.00024367601
78 4.835166e-06 1.2319783e-06 0.00024357668
79 4.9500883e-06 1.2609674e-06 0.00024347669
80 5.0659909e-06 1.2902001e-06 0.00024337607
81 5.1828572e-06 1.3196723e-06 0.00024327483
82 5.3006702e-06 1.3493797e-06 0.000243173
83 5.419413e-06 1.379318e-06 0.0002430706
84 5.5390685e-06 1.4094831e-06 0.00024296765
85 5.6596194e-06 1.4398705e-06 0.00024286417
86 5.7810485e-06 1.4704759e-06 0.00024276019
87 5.9033384e-06 1.501295e-06 0.00024265573
88 6.0264715e-06 1.5323234e-06 0.00024255081
89 6.1504303e-06 1.5635565e-06 0.00024244545
90 6.275197e-06 1.5949902e-06 0.00024233967
91 6.400754e-06 1.6266197e-06 0.0002422335
92 6.5270834e-06 1.6584408e-06 0.00024212696
93 6.6541672e-06 1.6904488e-06 0.00024202007
94 6.7819875e-06 1.7226394e-06 0.00024191285
95 6.9105262e-06 1.7550078e-06 0.00024180534
96 7.0397651e-06 1.7875497e-06 0.00024169754
97 7.169686e-06 1.8202604e-06 0.00024158948
98 7.3002707e-06 1.8531354e-06 0.00024148118
99 7.4315008e-06 1.88617e-06 0.00024137268
100 7.563358e-06 1.9193596e-06 0.00024126398
Loop time of 0.00190888 on 1 procs for 100 steps with 3 atoms
Performance: 2263110719.025 fs/day, 0.000 hours/fs, 52386.822 timesteps/s, 157.160 katom-step/s
0.0% 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 | 2.774e-06 | 2.774e-06 | 2.774e-06 | 0.0 | 0.15
Comm | 2.3215e-05 | 2.3215e-05 | 2.3215e-05 | 0.0 | 1.22
Output | 0.00042246 | 0.00042246 | 0.00042246 | 0.0 | 22.13
Modify | 0.0013744 | 0.0013744 | 0.0013744 | 0.0 | 72.00
Other | | 8.601e-05 | | | 4.51
Nlocal: 3 ave 3 max 3 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 = 23
Dangerous builds = 0
Total wall time: 0:00:00

235
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@ -0,0 +1,235 @@
LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified)
Processor partition = 2
using 1 OpenMP thread(s) per MPI task
# Units and dimensions
units electron
dimension 3
boundary p p p
atom_style atomic
atom_modify map yes
pair_style none
# Time step (in femtoseconds)
timestep 0.5
# Temperature (in Kelvin)
variable Temp equal 17.4
# Number of Nose-Hoover chains
variable nhc equal 4
# Force constant (in Hartree energies per Bohr radius squared)
variable k equal 1.2154614120000001e-08
# Number of beads
variable Nbeads equal 4
variable ibead uloop ${Nbeads} pad
variable ibead uloop 4 pad
variable seed equal 18889
# Create box and atoms. All distances are in Bohr
region box block -1500 1500 -1500 1500 -1500 1500
create_box 1 box
Created orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
1 by 1 by 1 MPI processor grid
variable a loop 3
label loop
variable x1 equal -15.0+0.5*v_a
variable y1 equal 10.0-0.5*v_a
variable z1 equal 1+0.5*v_a
create_atoms 1 single ${x1} ${y1} ${z1}
create_atoms 1 single -14.5 ${y1} ${z1}
create_atoms 1 single -14.5 9.5 ${z1}
create_atoms 1 single -14.5 9.5 1.5
Created 1 atoms
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
create_atoms CPU = 0.000 seconds
next a
jump SELF loop
variable x1 equal -15.0+0.5*v_a
variable y1 equal 10.0-0.5*v_a
variable z1 equal 1+0.5*v_a
create_atoms 1 single ${x1} ${y1} ${z1}
create_atoms 1 single -14 ${y1} ${z1}
create_atoms 1 single -14 9 ${z1}
create_atoms 1 single -14 9 2
Created 1 atoms
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
create_atoms CPU = 0.000 seconds
next a
jump SELF loop
variable x1 equal -15.0+0.5*v_a
variable y1 equal 10.0-0.5*v_a
variable z1 equal 1+0.5*v_a
create_atoms 1 single ${x1} ${y1} ${z1}
create_atoms 1 single -13.5 ${y1} ${z1}
create_atoms 1 single -13.5 8.5 ${z1}
create_atoms 1 single -13.5 8.5 2.5
Created 1 atoms
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
create_atoms CPU = 0.000 seconds
next a
jump SELF loop
# Electron mass (in amu)
mass 1 0.00054858
# Initialize velocities
velocity all create ${Temp} ${seed}${ibead} mom yes rot yes dist gaussian
velocity all create 17.4 ${seed}${ibead} mom yes rot yes dist gaussian
velocity all create 17.4 18889${ibead} mom yes rot yes dist gaussian
velocity all create 17.4 188893 mom yes rot yes dist gaussian
# Add harmonic external force
fix harm all spring/self ${k}
fix harm all spring/self 1.215461412e-08
# Add harmonic potential energy to total energy and potential energy
fix_modify harm energy yes
# PIMD command
fix pimdb all pimd/nvt/bosonic method pimd temp ${Temp} nhc ${nhc}
fix pimdb all pimd/nvt/bosonic method pimd temp 17.4 nhc ${nhc}
fix pimdb all pimd/nvt/bosonic method pimd temp 17.4 nhc 4
# Outputs
variable virial equal f_pimdb[3]
variable prim_kinetic equal f_pimdb[4]
thermo_style custom step pe v_virial v_prim_kinetic
thermo 1
run 100
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2444)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:212)
Per MPI rank memory allocation (min/avg/max) = 9.176 | 9.176 | 9.176 Mbytes
Step PotEng v_virial v_prim_kinetic
0 0 0 0.00024796164
1 8.5850845e-10 -3.6831179e-10 0.0002479594
2 3.4338783e-09 -3.0736303e-10 0.00024795267
3 7.7256433e-09 1.8277487e-10 0.00024794145
4 1.3733026e-08 1.1019528e-09 0.00024792576
5 2.145494e-08 2.449944e-09 0.00024790558
6 3.0889985e-08 4.226444e-09 0.00024788093
7 4.2036455e-08 6.4310711e-09 0.00024785181
8 5.4892332e-08 9.0633658e-09 0.00024781823
9 6.9455288e-08 1.2122792e-08 0.00024778019
10 8.572269e-08 1.5608734e-08 0.0002477377
11 1.0369159e-07 1.9520504e-08 0.00024769077
12 1.2335875e-07 2.3857331e-08 0.00024763941
13 1.4472059e-07 2.8618373e-08 0.00024758363
14 1.6777327e-07 3.3802708e-08 0.00024752344
15 1.9251262e-07 3.940934e-08 0.00024745886
16 2.1893415e-07 4.5437194e-08 0.00024738989
17 2.4703311e-07 5.1885122e-08 0.00024731656
18 2.768044e-07 5.8751899e-08 0.00024723887
19 3.0824267e-07 6.6036227e-08 0.00024715685
20 3.4134222e-07 7.3736729e-08 0.00024707051
21 3.7609709e-07 8.1851958e-08 0.00024697986
22 4.1250102e-07 9.0380389e-08 0.00024688494
23 4.5054742e-07 9.9320426e-08 0.00024678575
24 4.9022945e-07 1.086704e-07 0.00024668231
25 5.3153996e-07 1.1842856e-07 0.00024657466
26 5.744715e-07 1.285931e-07 0.00024646281
27 6.1901635e-07 1.3916212e-07 0.00024634678
28 6.6516648e-07 1.5013367e-07 0.0002462266
29 7.1291361e-07 1.6150571e-07 0.00024610229
30 7.6224914e-07 1.7327614e-07 0.00024597388
31 8.1316422e-07 1.8544279e-07 0.0002458414
32 8.6564969e-07 1.9800342e-07 0.00024570487
33 9.1969614e-07 2.109557e-07 0.00024556432
34 9.7529388e-07 2.2429727e-07 0.00024541978
35 1.0324329e-06 2.3802567e-07 0.00024527128
36 1.0911031e-06 2.5213838e-07 0.00024511886
37 1.1512938e-06 2.6663282e-07 0.00024496253
38 1.2129943e-06 2.8150634e-07 0.00024480234
39 1.2761936e-06 2.9675622e-07 0.00024463831
40 1.3408803e-06 3.1237968e-07 0.00024447049
41 1.407043e-06 3.2837388e-07 0.0002442989
42 1.4746698e-06 3.447359e-07 0.00024412359
43 1.5437487e-06 3.6146277e-07 0.00024394458
44 1.6142674e-06 3.7855146e-07 0.00024376192
45 1.6862132e-06 3.9599886e-07 0.00024357564
46 1.7595735e-06 4.1380182e-07 0.00024338577
47 1.8343351e-06 4.3195711e-07 0.00024319237
48 1.9104848e-06 4.5046147e-07 0.00024299547
49 1.9880091e-06 4.6931154e-07 0.00024279511
50 2.0668943e-06 4.8850394e-07 0.00024259132
51 2.1471263e-06 5.0803521e-07 0.00024238416
52 2.228691e-06 5.2790184e-07 0.00024217367
53 2.311574e-06 5.4810027e-07 0.00024195988
54 2.3957606e-06 5.6862687e-07 0.00024174285
55 2.481236e-06 5.8947797e-07 0.00024152261
56 2.5679851e-06 6.1064984e-07 0.00024129922
57 2.6559926e-06 6.3213871e-07 0.00024107271
58 2.7452431e-06 6.5394073e-07 0.00024084313
59 2.8357209e-06 6.7605203e-07 0.00024061054
60 2.9274101e-06 6.9846868e-07 0.00024037498
61 3.0202947e-06 7.2118669e-07 0.00024013649
62 3.1143583e-06 7.4420204e-07 0.00023989513
63 3.2095846e-06 7.6751065e-07 0.00023965094
64 3.3059569e-06 7.911084e-07 0.00023940398
65 3.4034585e-06 8.1499113e-07 0.00023915429
66 3.5020722e-06 8.3915461e-07 0.00023890193
67 3.601781e-06 8.6359461e-07 0.00023864694
68 3.7025676e-06 8.8830681e-07 0.00023838939
69 3.8044144e-06 9.132869e-07 0.00023812931
70 3.9073038e-06 9.3853048e-07 0.00023786677
71 4.0112181e-06 9.6403314e-07 0.00023760182
72 4.1161392e-06 9.8979043e-07 0.00023733451
73 4.2220491e-06 1.0157978e-06 0.0002370649
74 4.3289295e-06 1.0420509e-06 0.00023679303
75 4.4367621e-06 1.068545e-06 0.00023651897
76 4.5455283e-06 1.0952755e-06 0.00023624277
77 4.6552095e-06 1.1222378e-06 0.00023596449
78 4.7657869e-06 1.1494273e-06 0.00023568418
79 4.8772416e-06 1.1768393e-06 0.0002354019
80 4.9895545e-06 1.2044689e-06 0.00023511771
81 5.1027067e-06 1.2323116e-06 0.00023483166
82 5.2166788e-06 1.2603625e-06 0.00023454381
83 5.3314515e-06 1.2886168e-06 0.00023425422
84 5.4470054e-06 1.3170697e-06 0.00023396295
85 5.5633208e-06 1.3457162e-06 0.00023367006
86 5.6803783e-06 1.3745516e-06 0.0002333756
87 5.798158e-06 1.403571e-06 0.00023307963
88 5.9166402e-06 1.4327693e-06 0.00023278222
89 6.0358049e-06 1.4621418e-06 0.00023248341
90 6.1556323e-06 1.4916833e-06 0.00023218329
91 6.2761023e-06 1.5213889e-06 0.00023188189
92 6.3971948e-06 1.5512537e-06 0.00023157929
93 6.5188897e-06 1.5812727e-06 0.00023127554
94 6.6411667e-06 1.6114407e-06 0.0002309707
95 6.7640056e-06 1.6417527e-06 0.00023066484
96 6.8873862e-06 1.6722038e-06 0.00023035801
97 7.011288e-06 1.7027888e-06 0.00023005028
98 7.1356907e-06 1.7335027e-06 0.0002297417
99 7.2605738e-06 1.7643404e-06 0.00022943234
100 7.3859169e-06 1.7952968e-06 0.00022912226
Loop time of 0.00195857 on 1 procs for 100 steps with 3 atoms
Performance: 2205688634.372 fs/day, 0.000 hours/fs, 51057.607 timesteps/s, 153.173 katom-step/s
39.2% 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 | 1.602e-06 | 1.602e-06 | 1.602e-06 | 0.0 | 0.08
Comm | 1.6951e-05 | 1.6951e-05 | 1.6951e-05 | 0.0 | 0.87
Output | 0.00032627 | 0.00032627 | 0.00032627 | 0.0 | 16.66
Modify | 0.0015486 | 0.0015486 | 0.0015486 | 0.0 | 79.07
Other | | 6.514e-05 | | | 3.33
Nlocal: 3 ave 3 max 3 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 = 24
Dangerous builds = 0
Total wall time: 0:00:00

235
examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.13Mar2025.g++.3 Normal file
View File

@ -0,0 +1,235 @@
LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified)
Processor partition = 3
using 1 OpenMP thread(s) per MPI task
# Units and dimensions
units electron
dimension 3
boundary p p p
atom_style atomic
atom_modify map yes
pair_style none
# Time step (in femtoseconds)
timestep 0.5
# Temperature (in Kelvin)
variable Temp equal 17.4
# Number of Nose-Hoover chains
variable nhc equal 4
# Force constant (in Hartree energies per Bohr radius squared)
variable k equal 1.2154614120000001e-08
# Number of beads
variable Nbeads equal 4
variable ibead uloop ${Nbeads} pad
variable ibead uloop 4 pad
variable seed equal 18889
# Create box and atoms. All distances are in Bohr
region box block -1500 1500 -1500 1500 -1500 1500
create_box 1 box
Created orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
1 by 1 by 1 MPI processor grid
variable a loop 3
label loop
variable x1 equal -15.0+0.5*v_a
variable y1 equal 10.0-0.5*v_a
variable z1 equal 1+0.5*v_a
create_atoms 1 single ${x1} ${y1} ${z1}
create_atoms 1 single -14.5 ${y1} ${z1}
create_atoms 1 single -14.5 9.5 ${z1}
create_atoms 1 single -14.5 9.5 1.5
Created 1 atoms
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
create_atoms CPU = 0.000 seconds
next a
jump SELF loop
variable x1 equal -15.0+0.5*v_a
variable y1 equal 10.0-0.5*v_a
variable z1 equal 1+0.5*v_a
create_atoms 1 single ${x1} ${y1} ${z1}
create_atoms 1 single -14 ${y1} ${z1}
create_atoms 1 single -14 9 ${z1}
create_atoms 1 single -14 9 2
Created 1 atoms
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
create_atoms CPU = 0.000 seconds
next a
jump SELF loop
variable x1 equal -15.0+0.5*v_a
variable y1 equal 10.0-0.5*v_a
variable z1 equal 1+0.5*v_a
create_atoms 1 single ${x1} ${y1} ${z1}
create_atoms 1 single -13.5 ${y1} ${z1}
create_atoms 1 single -13.5 8.5 ${z1}
create_atoms 1 single -13.5 8.5 2.5
Created 1 atoms
using lattice units in orthogonal box = (-1500 -1500 -1500) to (1500 1500 1500)
create_atoms CPU = 0.000 seconds
next a
jump SELF loop
# Electron mass (in amu)
mass 1 0.00054858
# Initialize velocities
velocity all create ${Temp} ${seed}${ibead} mom yes rot yes dist gaussian
velocity all create 17.4 ${seed}${ibead} mom yes rot yes dist gaussian
velocity all create 17.4 18889${ibead} mom yes rot yes dist gaussian
velocity all create 17.4 188894 mom yes rot yes dist gaussian
# Add harmonic external force
fix harm all spring/self ${k}
fix harm all spring/self 1.215461412e-08
# Add harmonic potential energy to total energy and potential energy
fix_modify harm energy yes
# PIMD command
fix pimdb all pimd/nvt/bosonic method pimd temp ${Temp} nhc ${nhc}
fix pimdb all pimd/nvt/bosonic method pimd temp 17.4 nhc ${nhc}
fix pimdb all pimd/nvt/bosonic method pimd temp 17.4 nhc 4
# Outputs
variable virial equal f_pimdb[3]
variable prim_kinetic equal f_pimdb[4]
thermo_style custom step pe v_virial v_prim_kinetic
thermo 1
run 100
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2444)
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:212)
Per MPI rank memory allocation (min/avg/max) = 9.176 | 9.176 | 9.176 Mbytes
Step PotEng v_virial v_prim_kinetic
0 0 0 0.00024796164
1 8.5847879e-10 4.4463719e-10 0.00024796024
2 3.4336684e-09 1.3183829e-09 0.00024795602
3 7.7250055e-09 2.6210625e-09 0.000247949
4 1.3731669e-08 4.3524371e-09 0.00024793917
5 2.1452581e-08 6.5122035e-09 0.00024792653
6 3.0886407e-08 9.0999942e-09 0.0002479111
7 4.2031554e-08 1.2115377e-08 0.00024789287
8 5.4886174e-08 1.5557858e-08 0.00024787185
9 6.9448162e-08 1.9426875e-08 0.00024784804
10 8.5715159e-08 2.3721806e-08 0.00024782146
11 1.0368455e-07 2.8441963e-08 0.0002477921
12 1.2335346e-07 3.3586595e-08 0.00024775998
13 1.4471878e-07 3.9154888e-08 0.0002477251
14 1.6777712e-07 4.5145965e-08 0.00024768748
15 1.9252485e-07 5.1558884e-08 0.00024764712
16 2.1895809e-07 5.8392642e-08 0.00024760403
17 2.4707272e-07 6.5646173e-08 0.00024755823
18 2.7686434e-07 7.3318348e-08 0.00024750973
19 3.0832834e-07 8.1407976e-08 0.00024745854
20 3.4145982e-07 8.9913804e-08 0.00024740467
21 3.7625367e-07 9.8834518e-08 0.00024734813
22 4.127045e-07 1.0816874e-07 0.00024728895
23 4.5080671e-07 1.1791504e-07 0.00024722714
24 4.9055443e-07 1.2807191e-07 0.00024716271
25 5.3194155e-07 1.3863779e-07 0.00024709568
26 5.7496174e-07 1.4961107e-07 0.00024702607
27 6.1960841e-07 1.6099007e-07 0.00024695389
28 6.6587473e-07 1.7277305e-07 0.00024687917
29 7.1375365e-07 1.8495821e-07 0.00024680191
30 7.6323786e-07 1.975437e-07 0.00024672216
31 8.1431984e-07 2.1052759e-07 0.00024663991
32 8.6699183e-07 2.2390793e-07 0.0002465552
33 9.2124582e-07 2.3768267e-07 0.00024646805
34 9.7707361e-07 2.5184974e-07 0.00024637847
35 1.0344667e-06 2.6640698e-07 0.0002462865
36 1.0934165e-06 2.813522e-07 0.00024619215
37 1.1539141e-06 2.9668313e-07 0.00024609545
38 1.2159503e-06 3.1239747e-07 0.00024599643
39 1.2795157e-06 3.2849286e-07 0.00024589511
40 1.344601e-06 3.4496686e-07 0.00024579151
41 1.4111961e-06 3.61817e-07 0.00024568566
42 1.4792913e-06 3.7904076e-07 0.0002455776
43 1.5488762e-06 3.9663555e-07 0.00024546734
44 1.6199404e-06 4.1459874e-07 0.00024535492
45 1.6924734e-06 4.3292764e-07 0.00024524035
46 1.7664643e-06 4.5161952e-07 0.00024512369
47 1.841902e-06 4.7067159e-07 0.00024500494
48 1.9187753e-06 4.90081e-07 0.00024488415
49 1.9970729e-06 5.0984488e-07 0.00024476135
50 2.076783e-06 5.2996028e-07 0.00024463656
51 2.1578939e-06 5.5042422e-07 0.00024450981
52 2.2403935e-06 5.7123366e-07 0.00024438115
53 2.3242696e-06 5.9238553e-07 0.0002442506
54 2.4095099e-06 6.138767e-07 0.00024411819
55 2.4961017e-06 6.3570399e-07 0.00024398396
56 2.5840323e-06 6.5786419e-07 0.00024384795
57 2.6732887e-06 6.8035404e-07 0.00024371018
58 2.7638579e-06 7.0317021e-07 0.0002435707
59 2.8557265e-06 7.2630938e-07 0.00024342953
60 2.9488811e-06 7.4976814e-07 0.00024328672
61 3.0433081e-06 7.7354305e-07 0.0002431423
62 3.1389936e-06 7.9763065e-07 0.00024299631
63 3.2359238e-06 8.2202741e-07 0.00024284878
64 3.3340844e-06 8.4672977e-07 0.00024269976
65 3.4334612e-06 8.7173415e-07 0.00024254927
66 3.5340397e-06 8.970369e-07 0.00024239736
67 3.6358055e-06 9.2263435e-07 0.00024224406
68 3.7387437e-06 9.4852279e-07 0.00024208942
69 3.8428394e-06 9.7469849e-07 0.00024193348
70 3.9480777e-06 1.0011576e-06 0.00024177626
71 4.0544433e-06 1.0278964e-06 0.00024161782
72 4.1619211e-06 1.054911e-06 0.0002414582
73 4.2704954e-06 1.0821976e-06 0.00024129742
74 4.3801508e-06 1.1097521e-06 0.00024113554
75 4.4908716e-06 1.1375706e-06 0.0002409726
76 4.6026419e-06 1.1656492e-06 0.00024080863
77 4.7154459e-06 1.1939839e-06 0.00024064367
78 4.8292673e-06 1.2225706e-06 0.00024047778
79 4.9440901e-06 1.2514052e-06 0.00024031099
80 5.059898e-06 1.2804837e-06 0.00024014333
81 5.1766745e-06 1.309802e-06 0.00023997487
82 5.2944032e-06 1.3393558e-06 0.00023980562
83 5.4130674e-06 1.369141e-06 0.00023963565
84 5.5326505e-06 1.3991534e-06 0.00023946499
85 5.6531355e-06 1.4293887e-06 0.00023929369
86 5.7745057e-06 1.4598429e-06 0.00023912178
87 5.8967439e-06 1.4905114e-06 0.00023894931
88 6.0198332e-06 1.5213902e-06 0.00023877633
89 6.1437564e-06 1.5524748e-06 0.00023860287
90 6.2684962e-06 1.5837609e-06 0.00023842898
91 6.3940353e-06 1.6152441e-06 0.00023825471
92 6.5203562e-06 1.6469202e-06 0.0002380801
93 6.6474416e-06 1.6787847e-06 0.00023790518
94 6.7752739e-06 1.7108332e-06 0.00023773001
95 6.9038354e-06 1.7430613e-06 0.00023755463
96 7.0331085e-06 1.7754645e-06 0.00023737908
97 7.1630755e-06 1.8080385e-06 0.00023720341
98 7.2937187e-06 1.8407787e-06 0.00023702765
99 7.4250201e-06 1.8736806e-06 0.00023685186
100 7.5569619e-06 1.9067398e-06 0.00023667607
Loop time of 0.00197094 on 1 procs for 100 steps with 3 atoms
Performance: 2191851993.165 fs/day, 0.000 hours/fs, 50737.315 timesteps/s, 152.212 katom-step/s
37.5% 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 | 1.652e-06 | 1.652e-06 | 1.652e-06 | 0.0 | 0.08
Comm | 1.7965e-05 | 1.7965e-05 | 1.7965e-05 | 0.0 | 0.91
Output | 0.00036011 | 0.00036011 | 0.00036011 | 0.0 | 18.27
Modify | 0.0015231 | 0.0015231 | 0.0015231 | 0.0 | 77.28
Other | | 6.806e-05 | | | 3.45
Nlocal: 3 ave 3 max 3 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 = 24
Dangerous builds = 0
Total wall time: 0:00:00

1
examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/run.sh Normal file
View File

@ -0,0 +1 @@
mpirun -np $NBEADS $LMP -in in.lmp -partition ${NBEADS}x1

2
examples/PACKAGES/stressprofile/in.flat
View File

@ -32,7 +32,7 @@ fix 1 all nvt temp 0.7 0.7 0.2
#dump_modify 3 pad 3
fix 2 all recenter NULL NULL 15 units lattice
compute p1 all stress/cartesian z 0.5
compute p1 all stress/cartesian z 0.5 NULL 0
fix 3 all ave/time 100 1 100 c_p1[*] file flat.out mode vector
thermo 50

2
examples/PACKAGES/ti/in.ti_spring
View File

@ -13,7 +13,7 @@
create_atoms 1 box
pair_style eam/alloy
pair_coeff * * ../../../../potentials/Cu_mishin1.eam.alloy Cu
pair_coeff * * Cu_mishin1.eam.alloy Cu
#------------------------------------------------------------------------------#