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Merged
pull merged 5 commits into from
Aug 1, 2026
Merged

[pull] develop from lammps:develop #178

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c1d745b
Update MBX to v1.4.0
Miniland1333 Jul 21, 2026
e34aa63
Update examples for MBX v1.4.0
Miniland1333 Jul 22, 2026
7ae7065
Update MBX tar to v1.4.0
Miniland1333 Jul 30, 2026
4e96ab9
Merge remote-tracking branch 'upstream/develop' into mbx-v1.4.0
Miniland1333 Jul 30, 2026
2cb47c3
Merge pull request #5117 from Miniland1333/mbx-v1.4.0
akohlmey Jul 31, 2026
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4 changes: 2 additions & 2 deletions cmake/Modules/Packages/MBX.cmake
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Original file line number Diff line number Diff line change
Expand Up @@ -34,8 +34,8 @@ if(CONFIGURE_REQUEST_PIC)
list(APPEND MBX_CONFIG_FLAGS ${CONFIGURE_REQUEST_PIC})
endif()

set(MBXLIB_URL "https://github.com/paesanilab/MBX/releases/download/v1.3.12/mbx-1.3.12.tar.gz" CACHE STRING "URL for MBX tarball")
set(MBXLIB_SHA256 "0f3600d0841e1736abec3fe6a38c8ff673523fe4494169db2839ddaa9bb618bf" CACHE STRING "SHA256 checksum of MBX tarball")
set(MBXLIB_URL "https://github.com/paesanilab/MBX/releases/download/v1.4.0/mbx-1.4.0.tar.gz" CACHE STRING "URL for MBX tarball")
set(MBXLIB_SHA256 "219de5af7cd81bdf8c3394c3aeee923cf4de7dd322769441a35c7cf4950bf912" CACHE STRING "SHA256 checksum of MBX tarball")

mark_as_advanced(MBXLIB_URL)
mark_as_advanced(MBXLIB_SHA256)
Expand Down
30 changes: 15 additions & 15 deletions ...KAGES/mbx/256h2o/log.23Mar26.256h2o.g++.1 → ...KAGES/mbx/256h2o/log.21Jul26.256h2o.g++.1
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
LAMMPS (11 Feb 2026 - Development - patch_11Feb2026-274-gb4dcbc8748)
LAMMPS (4 Jul 2026 - Development - c1d745b79e)
using 1 OpenMP thread(s) per MPI task
processors * * * map xyz

Expand Down Expand Up @@ -32,7 +32,7 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.011 seconds
read_data CPU = 0.031 seconds

pair_style mbx 9.0

Expand Down Expand Up @@ -96,7 +96,7 @@ Your simulation uses code contributions which should be cited:
pages = {054802},
year = {2023},
doi = {10.1063/5.0156036},
version = {1.3.12}
version = {1.4.0}
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Expand All @@ -114,7 +114,7 @@ Neighbor list info ...
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 8.503 | 8.503 | 8.503 Mbytes
Per MPI rank memory allocation (min/avg/max) = 9.816 | 9.816 | 9.816 Mbytes
Step Time Temp TotEng KinEng PotEng Enthalpy Density Lx Ly Lz Volume Pxx Pyy Pzz Press
0 0 298 -1731.1398 681.31183 -2412.4517 -1661.3647 1.0085627 19.655164 19.655164 19.655164 7593.2911 2461.8369 -310.60204 -260.99809 630.07893
1 0.5 305.62775 -1731.7838 698.75101 -2430.5349 -1604.1604 1.0085626 19.655165 19.655165 19.655165 7593.2915 3142.813 -49.500427 364.05582 1152.4561
Expand Down Expand Up @@ -217,21 +217,21 @@ Per MPI rank memory allocation (min/avg/max) = 8.503 | 8.503 | 8.503 Mbytes
98 49 297.63541 -1717.5994 680.47828 -2398.0777 -1491.6173 1.0071865 19.664113 19.664113 19.664113 7603.6664 701.28196 384.3734 5027.9366 2037.864
99 49.5 302.89083 -1717.5771 692.49365 -2410.0708 -1566.0823 1.0071606 19.664281 19.664281 19.664281 7603.8614 -486.15579 46.29196 4538.2141 1366.1168
100 50 303.33647 -1717.3173 693.51249 -2410.8298 -1645.0949 1.0071346 19.66445 19.66445 19.66445 7604.0583 -1621.9658 -60.918855 3636.6481 651.25445
Loop time of 77.6656 on 1 procs for 100 steps with 768 atoms
Loop time of 45.7514 on 1 procs for 100 steps with 768 atoms

Performance: 0.056 ns/day, 431.476 hours/ns, 1.288 timesteps/s, 988.854 atom-step/s
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 0.094 ns/day, 254.175 hours/ns, 2.186 timesteps/s, 1.679 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 | 77.483 | 77.483 | 77.483 | 0.0 | 99.77
Bond | 0.00015614 | 0.00015614 | 0.00015614 | 0.0 | 0.00
Neigh | 0.012615 | 0.012615 | 0.012615 | 0.0 | 0.02
Comm | 0.0062873 | 0.0062873 | 0.0062873 | 0.0 | 0.01
Output | 0.0064041 | 0.0064041 | 0.0064041 | 0.0 | 0.01
Modify | 0.1554 | 0.1554 | 0.1554 | 0.0 | 0.20
Other | | 0.001316 | | | 0.00
Pair | 45.644 | 45.644 | 45.644 | 0.0 | 99.77
Bond | 0.00015895 | 0.00015895 | 0.00015895 | 0.0 | 0.00
Neigh | 0.0094953 | 0.0094953 | 0.0094953 | 0.0 | 0.02
Comm | 0.0037601 | 0.0037601 | 0.0037601 | 0.0 | 0.01
Output | 0.0060363 | 0.0060363 | 0.0060363 | 0.0 | 0.01
Modify | 0.086685 | 0.086685 | 0.086685 | 0.0 | 0.19
Other | | 0.001 | | | 0.00

Nlocal: 768 ave 768 max 768 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Expand All @@ -248,4 +248,4 @@ Dangerous builds = 0

# write_data final.data
# write_restart restart.new
Total wall time: 0:01:18
Total wall time: 0:00:46
30 changes: 15 additions & 15 deletions ...2o_dipole/log.23Mar26.256h2o_dipole.g++.1 → ...2o_dipole/log.21Jul26.256h2o_dipole.g++.1
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
LAMMPS (11 Feb 2026 - Development - patch_11Feb2026-273-ge995714d19-modified)
LAMMPS (4 Jul 2026 - Development - c1d745b79e)
using 1 OpenMP thread(s) per MPI task
processors * * * map xyz

Expand Down Expand Up @@ -32,7 +32,7 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.034 seconds
read_data CPU = 0.049 seconds

pair_style mbx 9.0

Expand Down Expand Up @@ -113,7 +113,7 @@ Your simulation uses code contributions which should be cited:
pages = {054802},
year = {2023},
doi = {10.1063/5.0156036},
version = {1.3.12}
version = {1.4.0}
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Expand All @@ -131,7 +131,7 @@ Neighbor list info ...
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 8.503 | 8.503 | 8.503 Mbytes
Per MPI rank memory allocation (min/avg/max) = 9.816 | 9.816 | 9.816 Mbytes
Step Time Temp TotEng KinEng PotEng Enthalpy Density Lx Ly Lz Volume Pxx Pyy Pzz Press
0 0 298 -1731.1398 681.31183 -2412.4517 -1661.3647 1.0085627 19.655164 19.655164 19.655164 7593.2911 2461.8369 -310.60204 -260.99809 630.07893
1 0.5 305.62775 -1731.7838 698.75101 -2430.5349 -1604.1604 1.0085626 19.655165 19.655165 19.655165 7593.2915 3142.813 -49.500427 364.05582 1152.4561
Expand Down Expand Up @@ -234,21 +234,21 @@ Per MPI rank memory allocation (min/avg/max) = 8.503 | 8.503 | 8.503 Mbytes
98 49 297.63541 -1717.5994 680.47828 -2398.0777 -1491.6173 1.0071865 19.664113 19.664113 19.664113 7603.6664 701.28196 384.3734 5027.9366 2037.864
99 49.5 302.89083 -1717.5771 692.49365 -2410.0708 -1566.0823 1.0071606 19.664281 19.664281 19.664281 7603.8614 -486.15579 46.29196 4538.2141 1366.1168
100 50 303.33647 -1717.3173 693.51249 -2410.8298 -1645.0949 1.0071346 19.66445 19.66445 19.66445 7604.0583 -1621.9658 -60.918855 3636.6481 651.25445
Loop time of 78.3853 on 1 procs for 100 steps with 768 atoms
Loop time of 45.7765 on 1 procs for 100 steps with 768 atoms

Performance: 0.055 ns/day, 435.474 hours/ns, 1.276 timesteps/s, 979.776 atom-step/s
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 0.094 ns/day, 254.314 hours/ns, 2.185 timesteps/s, 1.678 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 | 78.18 | 78.18 | 78.18 | 0.0 | 99.74
Bond | 0.00014684 | 0.00014684 | 0.00014684 | 0.0 | 0.00
Neigh | 0.012459 | 0.012459 | 0.012459 | 0.0 | 0.02
Comm | 0.0060721 | 0.0060721 | 0.0060721 | 0.0 | 0.01
Output | 0.035904 | 0.035904 | 0.035904 | 0.0 | 0.05
Modify | 0.14956 | 0.14956 | 0.14956 | 0.0 | 0.19
Other | | 0.001389 | | | 0.00
Pair | 45.648 | 45.648 | 45.648 | 0.0 | 99.72
Bond | 0.00015921 | 0.00015921 | 0.00015921 | 0.0 | 0.00
Neigh | 0.009499 | 0.009499 | 0.009499 | 0.0 | 0.02
Comm | 0.0035636 | 0.0035636 | 0.0035636 | 0.0 | 0.01
Output | 0.027889 | 0.027889 | 0.027889 | 0.0 | 0.06
Modify | 0.086798 | 0.086798 | 0.086798 | 0.0 | 0.19
Other | | 0.0008758 | | | 0.00

Nlocal: 768 ave 768 max 768 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Expand All @@ -265,4 +265,4 @@ Dangerous builds = 0

# write_data final.data
# write_restart restart.new
Total wall time: 0:01:19
Total wall time: 0:00:46
28 changes: 14 additions & 14 deletions ...ff_lammps+1_h2o_mbx/log.23Mar26.mof.g++.1 → ...ff_lammps+1_h2o_mbx/log.21Jul26.mof.g++.1
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
LAMMPS (11 Feb 2026 - Development - patch_11Feb2026-274-gb4dcbc8748)
LAMMPS (4 Jul 2026 - Development - c1d745b79e)
using 1 OpenMP thread(s) per MPI task
# Depositing TIP3P water into MOF with QeQ charges obtained with Ongari scheme

Expand Down Expand Up @@ -42,7 +42,7 @@ Finding 1-2 1-3 1-4 neighbors ...
25 = max # of 1-4 neighbors
24 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.081 seconds
read_data CPU = 0.091 seconds

group mof type 1 2 3 4 5 6 7 8 9 10 11
888 atoms in group mof
Expand Down Expand Up @@ -299,7 +299,7 @@ Your simulation uses code contributions which should be cited:
pages = {054802},
year = {2023},
doi = {10.1063/5.0156036},
version = {1.3.12}
version = {1.4.0}
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Expand Down Expand Up @@ -334,7 +334,7 @@ Neighbor list info ...
bin: none
WARNING: Inconsistent image flags
For more information see https://docs.lammps.org/err0027 (src/domain.cpp:1052)
Per MPI rank memory allocation (min/avg/max) = 21.26 | 21.26 | 21.26 Mbytes
Per MPI rank memory allocation (min/avg/max) = 22.57 | 22.57 | 22.57 Mbytes
Step Time Temp E_vdwl E_coul E_pair E_bond E_angle E_dihed E_impro E_mol E_long E_tail v_e1bpip v_e2bpip v_e3bpip v_e4bpip v_edisp v_ebuck v_eele v_etot PotEng TotEng
0 0 298.15 -8176.5335 11692.335 3515.8017 333.85691 4108.0644 1369.7935 5.4245589 5817.1394 0 -23.891377 0.45689944 0 0 0 -2.3771962e-06 0 -7923.955 -1.1954777 9332.9411 10123.909
1 0.2 298.02821 -8176.4176 11692.427 3516.0089 333.6563 4108.171 1369.9997 5.4284001 5817.2554 0 -23.891377 0.47083048 0 0 0 -2.3321913e-06 0 -7923.993 -1.1939972 9333.2643 10123.91
Expand Down Expand Up @@ -437,21 +437,21 @@ Per MPI rank memory allocation (min/avg/max) = 21.26 | 21.26 | 21.26 Mbytes
98 19.6 421.74162 -8167.4074 11699.395 3531.9875 492.04515 3449.5823 1355.5035 49.729018 5346.86 0 -23.891377 0.39659715 0 0 0 -3.227711e-06 0 -7902.8475 -0.53532385 8878.8475 9997.6947
99 19.8 415.57236 -8166.5618 11699.438 3532.8765 503.65243 3452.4595 1353.7593 50.195047 5360.0662 0 -23.891377 0.43664364 0 0 0 -3.1607943e-06 0 -7901.8367 -0.53029933 8892.9427 9995.4233
100 20 410.14444 -8165.7119 11699.51 3533.7979 513.26482 3455.2638 1352.1124 50.678742 5371.3198 0 -23.891377 0.48982774 0 0 0 -3.0911163e-06 0 -7900.8651 -0.52529645 8905.1177 9993.1984
Loop time of 32.7372 on 1 procs for 100 steps with 891 atoms
Loop time of 18.0736 on 1 procs for 100 steps with 891 atoms

Performance: 0.053 ns/day, 454.683 hours/ns, 3.055 timesteps/s, 2.722 katom-step/s
98.0% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 0.096 ns/day, 251.022 hours/ns, 5.533 timesteps/s, 4.930 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 | 32.64 | 32.64 | 32.64 | 0.0 | 99.70
Bond | 0.036319 | 0.036319 | 0.036319 | 0.0 | 0.11
Pair | 18.002 | 18.002 | 18.002 | 0.0 | 99.60
Bond | 0.031661 | 0.031661 | 0.031661 | 0.0 | 0.18
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0023362 | 0.0023362 | 0.0023362 | 0.0 | 0.01
Output | 0.0076394 | 0.0076394 | 0.0076394 | 0.0 | 0.02
Modify | 0.050201 | 0.050201 | 0.050201 | 0.0 | 0.15
Other | | 0.001155 | | | 0.00
Comm | 0.0021185 | 0.0021185 | 0.0021185 | 0.0 | 0.01
Output | 0.00712 | 0.00712 | 0.00712 | 0.0 | 0.04
Modify | 0.030078 | 0.030078 | 0.030078 | 0.0 | 0.17
Other | | 0.0007133 | | | 0.00

Nlocal: 891 ave 891 max 891 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Expand All @@ -468,4 +468,4 @@ Dangerous builds = 0

# write_data final.data nocoeff
# write_restart restart.inter
Total wall time: 0:00:33
Total wall time: 0:00:18
30 changes: 15 additions & 15 deletions ...S/mbx/na+_slab/log.23Mar26.na+_slab.g++.1 → ...S/mbx/na+_slab/log.21Jul26.na+_slab.g++.1
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
LAMMPS (11 Feb 2026 - Development - patch_11Feb2026-274-gb4dcbc8748)
LAMMPS (4 Jul 2026 - Development - c1d745b79e)
using 1 OpenMP thread(s) per MPI task
processors * * * map xyz

Expand Down Expand Up @@ -32,7 +32,7 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.057 seconds
read_data CPU = 0.063 seconds

pair_style mbx 9.0

Expand Down Expand Up @@ -96,7 +96,7 @@ Your simulation uses code contributions which should be cited:
pages = {054802},
year = {2023},
doi = {10.1063/5.0156036},
version = {1.3.12}
version = {1.4.0}
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Expand All @@ -114,7 +114,7 @@ Neighbor list info ...
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 8.784 | 8.784 | 8.784 Mbytes
Per MPI rank memory allocation (min/avg/max) = 10.1 | 10.1 | 10.1 Mbytes
Step Time Temp TotEng KinEng PotEng Enthalpy Density Lx Ly Lz Volume Pxx Pyy Pzz Press
0 0 298 -3243.6847 1361.7354 -4605.4201 -3659.9061 0.38301942 20 20 100 40000 -636.37649 -547.97788 -956.11844 -713.49094
1 0.5 295.83833 -3243.6773 1351.8575 -4595.5348 -3647.0291 0.38301942 20 20 100 40000 -636.17688 -651.22248 -786.89029 -691.42988
Expand Down Expand Up @@ -217,21 +217,21 @@ Per MPI rank memory allocation (min/avg/max) = 8.784 | 8.784 | 8.784 Mbytes
98 49 301.32967 -3269.9895 1376.9506 -4646.9401 -3899.5651 0.38301942 20 20 100 40000 -1485.9786 -248.10397 -1503.5924 -1079.225
99 49.5 301.08075 -3270.6746 1375.8131 -4646.4878 -3878.8165 0.38301942 20 20 100 40000 -1534.157 -263.76305 -1329.5294 -1042.4831
100 50 298.97024 -3271.0136 1366.169 -4637.1826 -3805.2011 0.38301942 20 20 100 40000 -1456.1214 -241.9852 -1049.0228 -915.70982
Loop time of 305.598 on 1 procs for 100 steps with 1534 atoms
Loop time of 182.424 on 1 procs for 100 steps with 1534 atoms

Performance: 0.014 ns/day, 1697.768 hours/ns, 0.327 timesteps/s, 501.966 atom-step/s
99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 0.024 ns/day, 1013.464 hours/ns, 0.548 timesteps/s, 840.900 atom-step/s
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 305.45 | 305.45 | 305.45 | 0.0 | 99.95
Bond | 0.00015109 | 0.00015109 | 0.00015109 | 0.0 | 0.00
Neigh | 0.018338 | 0.018338 | 0.018338 | 0.0 | 0.01
Comm | 0.0042832 | 0.0042832 | 0.0042832 | 0.0 | 0.00
Output | 0.0075068 | 0.0075068 | 0.0075068 | 0.0 | 0.00
Modify | 0.118 | 0.118 | 0.118 | 0.0 | 0.04
Other | | 0.001342 | | | 0.00
Pair | 182.32 | 182.32 | 182.32 | 0.0 | 99.94
Bond | 0.00015233 | 0.00015233 | 0.00015233 | 0.0 | 0.00
Neigh | 0.015411 | 0.015411 | 0.015411 | 0.0 | 0.01
Comm | 0.0027668 | 0.0027668 | 0.0027668 | 0.0 | 0.00
Output | 0.0070976 | 0.0070976 | 0.0070976 | 0.0 | 0.00
Modify | 0.080628 | 0.080628 | 0.080628 | 0.0 | 0.04
Other | | 0.0009226 | | | 0.00

Nlocal: 1534 ave 1534 max 1534 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Expand All @@ -248,4 +248,4 @@ Dangerous builds = 0

# write_data final.data
# write_restart restart.new
Total wall time: 0:05:08
Total wall time: 0:03:04