From bf8a4402cef5d2b9da6c0ffcc0c93e4f03ec0932 Mon Sep 17 00:00:00 2001 From: oywg11 Date: Sun, 4 Jun 2023 10:17:21 +0800 Subject: [PATCH] update log files in the examples --- .../aip_water_2dm/log.18May23.gr_water.g++.1 | 83 ++++++++++--------- .../aip_water_2dm/log.18May23.gr_water.g++.4 | 81 +++++++++--------- .../log.18May23.gr_water.opt.g++.1 | 83 ++++++++++--------- .../log.18May23.gr_water.opt.g++.4 | 81 +++++++++--------- 4 files changed, 174 insertions(+), 154 deletions(-) diff --git a/examples/PACKAGES/interlayer/aip_water_2dm/log.18May23.gr_water.g++.1 b/examples/PACKAGES/interlayer/aip_water_2dm/log.18May23.gr_water.g++.1 index 6e13280f70..c8268c72f6 100644 --- a/examples/PACKAGES/interlayer/aip_water_2dm/log.18May23.gr_water.g++.1 +++ b/examples/PACKAGES/interlayer/aip_water_2dm/log.18May23.gr_water.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (23 Jun 2022) +LAMMPS (23 Jun 2022 - Update 4) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:98) using 1 OpenMP thread(s) per MPI task # Initialization @@ -29,8 +29,8 @@ Finding 1-2 1-3 1-4 neighbors ... 1 = max # of 1-3 neighbors 1 = max # of 1-4 neighbors 2 = max # of special neighbors - special bonds CPU = 0.005 seconds - read_data CPU = 0.020 seconds + special bonds CPU = 0.000 seconds + read_data CPU = 0.012 seconds mass 1 12.0107 # carbon mass (g/mole) mass 2 15.9994 # oxygen mass (g/mole) mass 3 1.008 # hydrogen mass (g/mole) @@ -41,14 +41,14 @@ group water molecule 2 144 atoms in group water ######################## Potential defition ############################## # Interlayer potential -pair_style hybrid/overlay ilp/water/2dm 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5 +pair_style hybrid/overlay aip/water/2dm 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5 #################################################################### pair_coeff 1 1 none -pair_coeff 2 2 lj/cut/tip4p/long 8.0313e-3 3.1589 # O-O +pair_coeff 2 2 lj/cut/tip4p/long 8.0313e-3 3.1589 # O-O pair_coeff 2 3 lj/cut/tip4p/long 0.0 0.0 # O-H -pair_coeff 3 3 lj/cut/tip4p/long 0.0 0.0 # H-H -pair_coeff * * ilp/water/2dm COH.ILP C Ow Hw # C-water -Reading ilp/water/2dm potential file COH.ILP with DATE: 2023-05-17 +pair_coeff 3 3 lj/cut/tip4p/long 0.0 0.0 # H-H +pair_coeff * * aip/water/2dm COH.aip.water.2dm C Ow Hw # C-H2O +Reading aip/water/2dm potential file COH.aip.water.2dm with DATE: 2022-12-02 # bond and angle bond_style harmonic bond_coeff 1 0.0 0.9572 @@ -62,7 +62,7 @@ neigh_modify every 1 delay 5 check yes page 1000000 one 100000 #################################################################### # Calculate pair energy compute 1 all pair lj/cut/tip4p/long -compute 2 all pair ilp/water/2dm +compute 2 all pair aip/water/2dm compute wt water temp variable TIP4P equal c_1 variable EILP equal c_2 # total interlayer energy @@ -72,18 +72,18 @@ thermo_style custom step etotal pe ke v_TIP4P v_EILP v_temp_wt thermo 100 thermo_modify lost error -fix subf gr setforce 0.0 0.0 0.0 -fix 1 water shake 0.0001 20 100 b 1 a 1 +fix subf gr setforce 0.0 0.0 0.0 +fix 1 water shake 0.0001 20 100 b 1 a 1 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 48 = # of frozen angles - find clusters CPU = 0.001 seconds + find clusters CPU = 0.000 seconds -timestep 1e-3 -velocity water create 300.0 12345 dist gaussian mom yes rot yes -fix 2 water nve -run 1000 +timestep 1e-3 +velocity water create 300.0 12345 dist gaussian mom yes rot yes +fix 2 water nve +run 1000 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE @@ -91,22 +91,24 @@ Your simulation uses code contributions which should be cited: - ilp/graphene/hbn potential doi:10.1021/acs.nanolett.8b02848 @Article{Ouyang2018 - author = {W. Ouyang, D. Mandelli, M. Urbakh, and O. Hod}, + author = {W. Ouyang and D. Mandelli and M. Urbakh and O. Hod}, title = {Nanoserpents: Graphene Nanoribbon Motion on Two-Dimensional Hexagonal Materials}, journal = {Nano Letters}, volume = 18, - pages = {6009} + pages = 6009, year = 2018, } -- ilp/tmd potential doi/10.1021/acs.jctc.1c00782 +- ilp/tmd potential doi:10.1021/acs.jctc.1c00782 @Article{Ouyang2021 - author = {W. Ouyang, R. Sofer, X. Gao, J. Hermann, A. Tkatchenko, L. Kronik, M. Urbakh, and O. Hod}, - title = {Anisotropic Interlayer Force Field for Transition Metal Dichalcogenides: The Case of Molybdenum Disulfide}, - journal = {J. Chem. Theory Comput.}, - volume = 17, - pages = {7237–7245} - year = 2021, + author = {W. Ouyang and R. Sofer and X. Gao and J. Hermann and + A. Tkatchenko and L. Kronik and M. Urbakh and O. Hod}, + title = {Anisotropic Interlayer Force Field for Transition + Metal Dichalcogenides: The Case of Molybdenum Disulfide}, + journal = {J.~Chem.\ Theory Comput.}, + volume = 17, + pages = {7237--7245} + year = 2021, } - ilp/water/2dm potential doi/10.1021/acs.jpcc.2c08464 @@ -132,6 +134,8 @@ PPPM initialization ... using single precision MKL FFT 3d grid and FFT values/proc = 84320 48000 WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:239) +WARNING: Communication cutoff 0 is shorter than a bond length based estimate of 3.4358. This may lead to errors. (../comm.cpp:727) +WARNING: Increasing communication cutoff to 11.6118 for TIP4P pair style (../pair_lj_cut_tip4p_long.cpp:484) Neighbor list info ... update every 1 steps, delay 5 steps, check yes max neighbors/atom: 100000, page size: 1000000 @@ -139,7 +143,7 @@ Neighbor list info ... ghost atom cutoff = 18 binsize = 9, bins = 6 5 23 3 neighbor lists, perpetual/occasional/extra = 3 0 0 - (1) pair ilp/water/2dm, perpetual + (1) pair aip/water/2dm, perpetual attributes: full, newton on, ghost pair build: full/bin/ghost stencil: full/ghost/bin/3d @@ -154,10 +158,11 @@ Neighbor list info ... pair build: half/bin/newton stencil: half/bin/3d bin: standard +WARNING: Communication cutoff adjusted to 18 (../comm.cpp:736) SHAKE stats (type/ave/delta/count) on step 0 Bond: 1 0.957201 2.19705e-06 96 Angle: 1 104.52 0.000203056 48 -Per MPI rank memory allocation (min/avg/max) = 33.53 | 33.53 | 33.53 Mbytes +Per MPI rank memory allocation (min/avg/max) = 32.9 | 32.9 | 32.9 Mbytes Step TotEng PotEng KinEng v_TIP4P v_EILP v_temp_wt 0 -16.131263 -19.815178 3.6839141 189.37246 -1.903543 300 SHAKE stats (type/ave/delta/count) on step 100 @@ -200,22 +205,22 @@ SHAKE stats (type/ave/delta/count) on step 1000 Bond: 1 0.9572 1.00586e-06 96 Angle: 1 104.52 0.000111712 48 1000 -17.498465 -20.331545 2.8330804 188.87473 -1.812177 230.71225 -Loop time of 20.801 on 1 procs for 1000 steps with 936 atoms +Loop time of 20.3334 on 1 procs for 1000 steps with 936 atoms -Performance: 4.154 ns/day, 5.778 hours/ns, 48.075 timesteps/s -99.9% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 4.249 ns/day, 5.648 hours/ns, 49.180 timesteps/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 | 16.429 | 16.429 | 16.429 | 0.0 | 78.98 -Bond | 0.0010991 | 0.0010991 | 0.0010991 | 0.0 | 0.01 -Kspace | 3.4769 | 3.4769 | 3.4769 | 0.0 | 16.72 -Neigh | 0.83359 | 0.83359 | 0.83359 | 0.0 | 4.01 -Comm | 0.028825 | 0.028825 | 0.028825 | 0.0 | 0.14 -Output | 0.00046349 | 0.00046349 | 0.00046349 | 0.0 | 0.00 -Modify | 0.01943 | 0.01943 | 0.01943 | 0.0 | 0.09 -Other | | 0.01154 | | | 0.06 +Pair | 16.179 | 16.179 | 16.179 | 0.0 | 79.57 +Bond | 0.00021103 | 0.00021103 | 0.00021103 | 0.0 | 0.00 +Kspace | 3.3118 | 3.3118 | 3.3118 | 0.0 | 16.29 +Neigh | 0.79017 | 0.79017 | 0.79017 | 0.0 | 3.89 +Comm | 0.026379 | 0.026379 | 0.026379 | 0.0 | 0.13 +Output | 0.00046496 | 0.00046496 | 0.00046496 | 0.0 | 0.00 +Modify | 0.017013 | 0.017013 | 0.017013 | 0.0 | 0.08 +Other | | 0.008835 | | | 0.04 Nlocal: 936 ave 936 max 936 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -231,4 +236,4 @@ Ave neighs/atom = 460.87821 Ave special neighs/atom = 0.30769231 Neighbor list builds = 28 Dangerous builds = 0 -Total wall time: 0:00:21 +Total wall time: 0:00:20 diff --git a/examples/PACKAGES/interlayer/aip_water_2dm/log.18May23.gr_water.g++.4 b/examples/PACKAGES/interlayer/aip_water_2dm/log.18May23.gr_water.g++.4 index 078ca76e2e..ab28c96657 100644 --- a/examples/PACKAGES/interlayer/aip_water_2dm/log.18May23.gr_water.g++.4 +++ b/examples/PACKAGES/interlayer/aip_water_2dm/log.18May23.gr_water.g++.4 @@ -1,4 +1,4 @@ -LAMMPS (23 Jun 2022) +LAMMPS (23 Jun 2022 - Update 4) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:98) using 1 OpenMP thread(s) per MPI task # Initialization @@ -29,8 +29,8 @@ Finding 1-2 1-3 1-4 neighbors ... 1 = max # of 1-3 neighbors 1 = max # of 1-4 neighbors 2 = max # of special neighbors - special bonds CPU = 0.003 seconds - read_data CPU = 0.018 seconds + special bonds CPU = 0.001 seconds + read_data CPU = 0.017 seconds mass 1 12.0107 # carbon mass (g/mole) mass 2 15.9994 # oxygen mass (g/mole) mass 3 1.008 # hydrogen mass (g/mole) @@ -41,14 +41,14 @@ group water molecule 2 144 atoms in group water ######################## Potential defition ############################## # Interlayer potential -pair_style hybrid/overlay ilp/water/2dm 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5 +pair_style hybrid/overlay aip/water/2dm 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5 #################################################################### pair_coeff 1 1 none -pair_coeff 2 2 lj/cut/tip4p/long 8.0313e-3 3.1589 # O-O +pair_coeff 2 2 lj/cut/tip4p/long 8.0313e-3 3.1589 # O-O pair_coeff 2 3 lj/cut/tip4p/long 0.0 0.0 # O-H -pair_coeff 3 3 lj/cut/tip4p/long 0.0 0.0 # H-H -pair_coeff * * ilp/water/2dm COH.ILP C Ow Hw # C-water -Reading ilp/water/2dm potential file COH.ILP with DATE: 2023-05-17 +pair_coeff 3 3 lj/cut/tip4p/long 0.0 0.0 # H-H +pair_coeff * * aip/water/2dm COH.aip.water.2dm C Ow Hw # C-H2O +Reading aip/water/2dm potential file COH.aip.water.2dm with DATE: 2022-12-02 # bond and angle bond_style harmonic bond_coeff 1 0.0 0.9572 @@ -62,7 +62,7 @@ neigh_modify every 1 delay 5 check yes page 1000000 one 100000 #################################################################### # Calculate pair energy compute 1 all pair lj/cut/tip4p/long -compute 2 all pair ilp/water/2dm +compute 2 all pair aip/water/2dm compute wt water temp variable TIP4P equal c_1 variable EILP equal c_2 # total interlayer energy @@ -72,18 +72,18 @@ thermo_style custom step etotal pe ke v_TIP4P v_EILP v_temp_wt thermo 100 thermo_modify lost error -fix subf gr setforce 0.0 0.0 0.0 -fix 1 water shake 0.0001 20 100 b 1 a 1 +fix subf gr setforce 0.0 0.0 0.0 +fix 1 water shake 0.0001 20 100 b 1 a 1 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 48 = # of frozen angles - find clusters CPU = 0.001 seconds + find clusters CPU = 0.000 seconds -timestep 1e-3 -velocity water create 300.0 12345 dist gaussian mom yes rot yes -fix 2 water nve -run 1000 +timestep 1e-3 +velocity water create 300.0 12345 dist gaussian mom yes rot yes +fix 2 water nve +run 1000 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE @@ -91,22 +91,24 @@ Your simulation uses code contributions which should be cited: - ilp/graphene/hbn potential doi:10.1021/acs.nanolett.8b02848 @Article{Ouyang2018 - author = {W. Ouyang, D. Mandelli, M. Urbakh, and O. Hod}, + author = {W. Ouyang and D. Mandelli and M. Urbakh and O. Hod}, title = {Nanoserpents: Graphene Nanoribbon Motion on Two-Dimensional Hexagonal Materials}, journal = {Nano Letters}, volume = 18, - pages = {6009} + pages = 6009, year = 2018, } -- ilp/tmd potential doi/10.1021/acs.jctc.1c00782 +- ilp/tmd potential doi:10.1021/acs.jctc.1c00782 @Article{Ouyang2021 - author = {W. Ouyang, R. Sofer, X. Gao, J. Hermann, A. Tkatchenko, L. Kronik, M. Urbakh, and O. Hod}, - title = {Anisotropic Interlayer Force Field for Transition Metal Dichalcogenides: The Case of Molybdenum Disulfide}, - journal = {J. Chem. Theory Comput.}, - volume = 17, - pages = {7237–7245} - year = 2021, + author = {W. Ouyang and R. Sofer and X. Gao and J. Hermann and + A. Tkatchenko and L. Kronik and M. Urbakh and O. Hod}, + title = {Anisotropic Interlayer Force Field for Transition + Metal Dichalcogenides: The Case of Molybdenum Disulfide}, + journal = {J.~Chem.\ Theory Comput.}, + volume = 17, + pages = {7237--7245} + year = 2021, } - ilp/water/2dm potential doi/10.1021/acs.jpcc.2c08464 @@ -132,6 +134,8 @@ PPPM initialization ... using single precision MKL FFT 3d grid and FFT values/proc = 30685 12480 WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:239) +WARNING: Communication cutoff 0 is shorter than a bond length based estimate of 3.4358. This may lead to errors. (../comm.cpp:727) +WARNING: Increasing communication cutoff to 11.6118 for TIP4P pair style (../pair_lj_cut_tip4p_long.cpp:484) Neighbor list info ... update every 1 steps, delay 5 steps, check yes max neighbors/atom: 100000, page size: 1000000 @@ -139,7 +143,7 @@ Neighbor list info ... ghost atom cutoff = 18 binsize = 9, bins = 6 5 23 3 neighbor lists, perpetual/occasional/extra = 3 0 0 - (1) pair ilp/water/2dm, perpetual + (1) pair aip/water/2dm, perpetual attributes: full, newton on, ghost pair build: full/bin/ghost stencil: full/ghost/bin/3d @@ -154,10 +158,11 @@ Neighbor list info ... pair build: half/bin/newton stencil: half/bin/3d bin: standard +WARNING: Communication cutoff adjusted to 18 (../comm.cpp:736) SHAKE stats (type/ave/delta/count) on step 0 Bond: 1 0.957201 2.19705e-06 96 Angle: 1 104.52 0.000203056 48 -Per MPI rank memory allocation (min/avg/max) = 25.84 | 25.88 | 25.92 Mbytes +Per MPI rank memory allocation (min/avg/max) = 25.22 | 25.25 | 25.29 Mbytes Step TotEng PotEng KinEng v_TIP4P v_EILP v_temp_wt 0 -16.131263 -19.815178 3.6839141 189.37246 -1.903543 300 SHAKE stats (type/ave/delta/count) on step 100 @@ -200,22 +205,22 @@ SHAKE stats (type/ave/delta/count) on step 1000 Bond: 1 0.9572 1.00568e-06 96 Angle: 1 104.52 0.000111707 48 1000 -17.498474 -20.331607 2.833133 188.87466 -1.8121689 230.71654 -Loop time of 9.42273 on 4 procs for 1000 steps with 936 atoms +Loop time of 9.05361 on 4 procs for 1000 steps with 936 atoms -Performance: 9.169 ns/day, 2.617 hours/ns, 106.126 timesteps/s -97.1% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 9.543 ns/day, 2.515 hours/ns, 110.453 timesteps/s +99.6% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 2.2328 | 4.3228 | 7.5931 | 103.1 | 45.88 -Bond | 0.00084131 | 0.00088983 | 0.00095229 | 0.0 | 0.01 -Kspace | 1.3979 | 4.6476 | 6.7252 | 98.8 | 49.32 -Neigh | 0.34367 | 0.34371 | 0.34376 | 0.0 | 3.65 -Comm | 0.042806 | 0.062908 | 0.075887 | 5.4 | 0.67 -Output | 0.00037677 | 0.00041431 | 0.0004619 | 0.0 | 0.00 -Modify | 0.028432 | 0.031138 | 0.034528 | 1.3 | 0.33 -Other | | 0.01321 | | | 0.14 +Pair | 2.462 | 4.2266 | 7.1075 | 89.3 | 46.68 +Bond | 0.00018424 | 0.00019878 | 0.00022125 | 0.0 | 0.00 +Kspace | 1.4698 | 4.338 | 6.1001 | 87.8 | 47.91 +Neigh | 0.39462 | 0.39489 | 0.39518 | 0.0 | 4.36 +Comm | 0.043753 | 0.055826 | 0.062746 | 3.1 | 0.62 +Output | 0.00048755 | 0.00053971 | 0.00062785 | 0.0 | 0.01 +Modify | 0.027255 | 0.028664 | 0.030278 | 0.7 | 0.32 +Other | | 0.008904 | | | 0.10 Nlocal: 234 ave 302 max 198 min Histogram: 2 0 0 1 0 0 0 0 0 1 diff --git a/examples/PACKAGES/interlayer/aip_water_2dm/log.18May23.gr_water.opt.g++.1 b/examples/PACKAGES/interlayer/aip_water_2dm/log.18May23.gr_water.opt.g++.1 index c6a11d209d..c795e85d56 100644 --- a/examples/PACKAGES/interlayer/aip_water_2dm/log.18May23.gr_water.opt.g++.1 +++ b/examples/PACKAGES/interlayer/aip_water_2dm/log.18May23.gr_water.opt.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (23 Jun 2022) +LAMMPS (23 Jun 2022 - Update 4) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:98) using 1 OpenMP thread(s) per MPI task # Initialization @@ -29,8 +29,8 @@ Finding 1-2 1-3 1-4 neighbors ... 1 = max # of 1-3 neighbors 1 = max # of 1-4 neighbors 2 = max # of special neighbors - special bonds CPU = 0.005 seconds - read_data CPU = 0.020 seconds + special bonds CPU = 0.000 seconds + read_data CPU = 0.012 seconds mass 1 12.0107 # carbon mass (g/mole) mass 2 15.9994 # oxygen mass (g/mole) mass 3 1.008 # hydrogen mass (g/mole) @@ -41,14 +41,14 @@ group water molecule 2 144 atoms in group water ######################## Potential defition ############################## # Interlayer potential -pair_style hybrid/overlay ilp/water/2dm/opt 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5 +pair_style hybrid/overlay aip/water/2dm/opt 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5 #################################################################### pair_coeff 1 1 none -pair_coeff 2 2 lj/cut/tip4p/long 8.0313e-3 3.1589 # O-O +pair_coeff 2 2 lj/cut/tip4p/long 8.0313e-3 3.1589 # O-O pair_coeff 2 3 lj/cut/tip4p/long 0.0 0.0 # O-H -pair_coeff 3 3 lj/cut/tip4p/long 0.0 0.0 # H-H -pair_coeff * * ilp/water/2dm/opt COH.ILP C Ow Hw # C-water -Reading ilp/water/2dm potential file COH.ILP with DATE: 2023-05-17 +pair_coeff 3 3 lj/cut/tip4p/long 0.0 0.0 # H-H +pair_coeff * * aip/water/2dm/opt COH.aip.water.2dm C Ow Hw # C-H2O +Reading aip/water/2dm potential file COH.aip.water.2dm with DATE: 2022-12-02 # bond and angle bond_style harmonic bond_coeff 1 0.0 0.9572 @@ -62,7 +62,7 @@ neigh_modify every 1 delay 5 check yes page 1000000 one 100000 #################################################################### # Calculate pair energy compute 1 all pair lj/cut/tip4p/long -compute 2 all pair ilp/water/2dm/opt +compute 2 all pair aip/water/2dm/opt compute wt water temp variable TIP4P equal c_1 variable EILP equal c_2 # total interlayer energy @@ -72,18 +72,18 @@ thermo_style custom step etotal pe ke v_TIP4P v_EILP v_temp_wt thermo 100 thermo_modify lost error -fix subf gr setforce 0.0 0.0 0.0 -fix 1 water shake 0.0001 20 100 b 1 a 1 +fix subf gr setforce 0.0 0.0 0.0 +fix 1 water shake 0.0001 20 100 b 1 a 1 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 48 = # of frozen angles - find clusters CPU = 0.001 seconds + find clusters CPU = 0.000 seconds -timestep 1e-3 -velocity water create 300.0 12345 dist gaussian mom yes rot yes -fix 2 water nve -run 1000 +timestep 1e-3 +velocity water create 300.0 12345 dist gaussian mom yes rot yes +fix 2 water nve +run 1000 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE @@ -91,22 +91,24 @@ Your simulation uses code contributions which should be cited: - ilp/graphene/hbn potential doi:10.1021/acs.nanolett.8b02848 @Article{Ouyang2018 - author = {W. Ouyang, D. Mandelli, M. Urbakh, and O. Hod}, + author = {W. Ouyang and D. Mandelli and M. Urbakh and O. Hod}, title = {Nanoserpents: Graphene Nanoribbon Motion on Two-Dimensional Hexagonal Materials}, journal = {Nano Letters}, volume = 18, - pages = {6009} + pages = 6009, year = 2018, } -- ilp/tmd potential doi/10.1021/acs.jctc.1c00782 +- ilp/tmd potential doi:10.1021/acs.jctc.1c00782 @Article{Ouyang2021 - author = {W. Ouyang, R. Sofer, X. Gao, J. Hermann, A. Tkatchenko, L. Kronik, M. Urbakh, and O. Hod}, - title = {Anisotropic Interlayer Force Field for Transition Metal Dichalcogenides: The Case of Molybdenum Disulfide}, - journal = {J. Chem. Theory Comput.}, - volume = 17, - pages = {7237–7245} - year = 2021, + author = {W. Ouyang and R. Sofer and X. Gao and J. Hermann and + A. Tkatchenko and L. Kronik and M. Urbakh and O. Hod}, + title = {Anisotropic Interlayer Force Field for Transition + Metal Dichalcogenides: The Case of Molybdenum Disulfide}, + journal = {J.~Chem.\ Theory Comput.}, + volume = 17, + pages = {7237--7245} + year = 2021, } - ilp/water/2dm potential doi/10.1021/acs.jpcc.2c08464 @@ -149,6 +151,8 @@ PPPM initialization ... using single precision MKL FFT 3d grid and FFT values/proc = 84320 48000 WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:239) +WARNING: Communication cutoff 0 is shorter than a bond length based estimate of 3.4358. This may lead to errors. (../comm.cpp:727) +WARNING: Increasing communication cutoff to 11.6118 for TIP4P pair style (../pair_lj_cut_tip4p_long.cpp:484) Neighbor list info ... update every 1 steps, delay 5 steps, check yes max neighbors/atom: 100000, page size: 1000000 @@ -156,7 +160,7 @@ Neighbor list info ... ghost atom cutoff = 18 binsize = 9, bins = 6 5 23 3 neighbor lists, perpetual/occasional/extra = 3 0 0 - (1) pair ilp/water/2dm/opt, perpetual + (1) pair aip/water/2dm/opt, perpetual attributes: full, newton on pair build: full/bin stencil: full/bin/3d @@ -171,10 +175,11 @@ Neighbor list info ... pair build: halffull/newton stencil: none bin: none +WARNING: Communication cutoff adjusted to 18 (../comm.cpp:736) SHAKE stats (type/ave/delta/count) on step 0 Bond: 1 0.957201 2.19705e-06 96 Angle: 1 104.52 0.000203056 48 -Per MPI rank memory allocation (min/avg/max) = 25.89 | 25.89 | 25.89 Mbytes +Per MPI rank memory allocation (min/avg/max) = 25.27 | 25.27 | 25.27 Mbytes Step TotEng PotEng KinEng v_TIP4P v_EILP v_temp_wt 0 -16.131263 -19.815178 3.6839141 189.37246 -1.903543 300 SHAKE stats (type/ave/delta/count) on step 100 @@ -217,22 +222,22 @@ SHAKE stats (type/ave/delta/count) on step 1000 Bond: 1 0.9572 1.00586e-06 96 Angle: 1 104.52 0.000111711 48 1000 -17.498466 -20.331547 2.8330808 188.87473 -1.8121768 230.71228 -Loop time of 8.95265 on 1 procs for 1000 steps with 936 atoms +Loop time of 8.11929 on 1 procs for 1000 steps with 936 atoms -Performance: 9.651 ns/day, 2.487 hours/ns, 111.699 timesteps/s -100.0% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 10.641 ns/day, 2.255 hours/ns, 123.163 timesteps/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 | 5.2127 | 5.2127 | 5.2127 | 0.0 | 58.23 -Bond | 0.00083377 | 0.00083377 | 0.00083377 | 0.0 | 0.01 -Kspace | 3.5005 | 3.5005 | 3.5005 | 0.0 | 39.10 -Neigh | 0.17946 | 0.17946 | 0.17946 | 0.0 | 2.00 -Comm | 0.028553 | 0.028553 | 0.028553 | 0.0 | 0.32 -Output | 0.00035446 | 0.00035446 | 0.00035446 | 0.0 | 0.00 -Modify | 0.01889 | 0.01889 | 0.01889 | 0.0 | 0.21 -Other | | 0.01135 | | | 0.13 +Pair | 4.6849 | 4.6849 | 4.6849 | 0.0 | 57.70 +Bond | 0.00017678 | 0.00017678 | 0.00017678 | 0.0 | 0.00 +Kspace | 3.2098 | 3.2098 | 3.2098 | 0.0 | 39.53 +Neigh | 0.17546 | 0.17546 | 0.17546 | 0.0 | 2.16 +Comm | 0.024693 | 0.024693 | 0.024693 | 0.0 | 0.30 +Output | 0.00037798 | 0.00037798 | 0.00037798 | 0.0 | 0.00 +Modify | 0.015853 | 0.015853 | 0.015853 | 0.0 | 0.20 +Other | | 0.007983 | | | 0.10 Nlocal: 936 ave 936 max 936 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -248,4 +253,4 @@ Ave neighs/atom = 460.87821 Ave special neighs/atom = 0.30769231 Neighbor list builds = 28 Dangerous builds = 0 -Total wall time: 0:00:09 +Total wall time: 0:00:08 diff --git a/examples/PACKAGES/interlayer/aip_water_2dm/log.18May23.gr_water.opt.g++.4 b/examples/PACKAGES/interlayer/aip_water_2dm/log.18May23.gr_water.opt.g++.4 index 852c429323..f885c5708d 100644 --- a/examples/PACKAGES/interlayer/aip_water_2dm/log.18May23.gr_water.opt.g++.4 +++ b/examples/PACKAGES/interlayer/aip_water_2dm/log.18May23.gr_water.opt.g++.4 @@ -1,4 +1,4 @@ -LAMMPS (23 Jun 2022) +LAMMPS (23 Jun 2022 - Update 4) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:98) using 1 OpenMP thread(s) per MPI task # Initialization @@ -29,8 +29,8 @@ Finding 1-2 1-3 1-4 neighbors ... 1 = max # of 1-3 neighbors 1 = max # of 1-4 neighbors 2 = max # of special neighbors - special bonds CPU = 0.003 seconds - read_data CPU = 0.017 seconds + special bonds CPU = 0.001 seconds + read_data CPU = 0.014 seconds mass 1 12.0107 # carbon mass (g/mole) mass 2 15.9994 # oxygen mass (g/mole) mass 3 1.008 # hydrogen mass (g/mole) @@ -41,14 +41,14 @@ group water molecule 2 144 atoms in group water ######################## Potential defition ############################## # Interlayer potential -pair_style hybrid/overlay ilp/water/2dm/opt 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5 +pair_style hybrid/overlay aip/water/2dm/opt 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5 #################################################################### pair_coeff 1 1 none -pair_coeff 2 2 lj/cut/tip4p/long 8.0313e-3 3.1589 # O-O +pair_coeff 2 2 lj/cut/tip4p/long 8.0313e-3 3.1589 # O-O pair_coeff 2 3 lj/cut/tip4p/long 0.0 0.0 # O-H -pair_coeff 3 3 lj/cut/tip4p/long 0.0 0.0 # H-H -pair_coeff * * ilp/water/2dm/opt COH.ILP C Ow Hw # C-water -Reading ilp/water/2dm potential file COH.ILP with DATE: 2023-05-17 +pair_coeff 3 3 lj/cut/tip4p/long 0.0 0.0 # H-H +pair_coeff * * aip/water/2dm/opt COH.aip.water.2dm C Ow Hw # C-H2O +Reading aip/water/2dm potential file COH.aip.water.2dm with DATE: 2022-12-02 # bond and angle bond_style harmonic bond_coeff 1 0.0 0.9572 @@ -62,7 +62,7 @@ neigh_modify every 1 delay 5 check yes page 1000000 one 100000 #################################################################### # Calculate pair energy compute 1 all pair lj/cut/tip4p/long -compute 2 all pair ilp/water/2dm/opt +compute 2 all pair aip/water/2dm/opt compute wt water temp variable TIP4P equal c_1 variable EILP equal c_2 # total interlayer energy @@ -72,18 +72,18 @@ thermo_style custom step etotal pe ke v_TIP4P v_EILP v_temp_wt thermo 100 thermo_modify lost error -fix subf gr setforce 0.0 0.0 0.0 -fix 1 water shake 0.0001 20 100 b 1 a 1 +fix subf gr setforce 0.0 0.0 0.0 +fix 1 water shake 0.0001 20 100 b 1 a 1 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 48 = # of frozen angles - find clusters CPU = 0.001 seconds + find clusters CPU = 0.000 seconds -timestep 1e-3 -velocity water create 300.0 12345 dist gaussian mom yes rot yes -fix 2 water nve -run 1000 +timestep 1e-3 +velocity water create 300.0 12345 dist gaussian mom yes rot yes +fix 2 water nve +run 1000 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE @@ -91,22 +91,24 @@ Your simulation uses code contributions which should be cited: - ilp/graphene/hbn potential doi:10.1021/acs.nanolett.8b02848 @Article{Ouyang2018 - author = {W. Ouyang, D. Mandelli, M. Urbakh, and O. Hod}, + author = {W. Ouyang and D. Mandelli and M. Urbakh and O. Hod}, title = {Nanoserpents: Graphene Nanoribbon Motion on Two-Dimensional Hexagonal Materials}, journal = {Nano Letters}, volume = 18, - pages = {6009} + pages = 6009, year = 2018, } -- ilp/tmd potential doi/10.1021/acs.jctc.1c00782 +- ilp/tmd potential doi:10.1021/acs.jctc.1c00782 @Article{Ouyang2021 - author = {W. Ouyang, R. Sofer, X. Gao, J. Hermann, A. Tkatchenko, L. Kronik, M. Urbakh, and O. Hod}, - title = {Anisotropic Interlayer Force Field for Transition Metal Dichalcogenides: The Case of Molybdenum Disulfide}, - journal = {J. Chem. Theory Comput.}, - volume = 17, - pages = {7237–7245} - year = 2021, + author = {W. Ouyang and R. Sofer and X. Gao and J. Hermann and + A. Tkatchenko and L. Kronik and M. Urbakh and O. Hod}, + title = {Anisotropic Interlayer Force Field for Transition + Metal Dichalcogenides: The Case of Molybdenum Disulfide}, + journal = {J.~Chem.\ Theory Comput.}, + volume = 17, + pages = {7237--7245} + year = 2021, } - ilp/water/2dm potential doi/10.1021/acs.jpcc.2c08464 @@ -149,6 +151,8 @@ PPPM initialization ... using single precision MKL FFT 3d grid and FFT values/proc = 30685 12480 WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:239) +WARNING: Communication cutoff 0 is shorter than a bond length based estimate of 3.4358. This may lead to errors. (../comm.cpp:727) +WARNING: Increasing communication cutoff to 11.6118 for TIP4P pair style (../pair_lj_cut_tip4p_long.cpp:484) Neighbor list info ... update every 1 steps, delay 5 steps, check yes max neighbors/atom: 100000, page size: 1000000 @@ -156,7 +160,7 @@ Neighbor list info ... ghost atom cutoff = 18 binsize = 9, bins = 6 5 23 3 neighbor lists, perpetual/occasional/extra = 3 0 0 - (1) pair ilp/water/2dm/opt, perpetual + (1) pair aip/water/2dm/opt, perpetual attributes: full, newton on pair build: full/bin stencil: full/bin/3d @@ -171,10 +175,11 @@ Neighbor list info ... pair build: halffull/newton stencil: none bin: none +WARNING: Communication cutoff adjusted to 18 (../comm.cpp:736) SHAKE stats (type/ave/delta/count) on step 0 Bond: 1 0.957201 2.19705e-06 96 Angle: 1 104.52 0.000203056 48 -Per MPI rank memory allocation (min/avg/max) = 22.03 | 22.06 | 22.1 Mbytes +Per MPI rank memory allocation (min/avg/max) = 21.4 | 21.44 | 21.48 Mbytes Step TotEng PotEng KinEng v_TIP4P v_EILP v_temp_wt 0 -16.131263 -19.815178 3.6839141 189.37246 -1.903543 300 SHAKE stats (type/ave/delta/count) on step 100 @@ -217,22 +222,22 @@ SHAKE stats (type/ave/delta/count) on step 1000 Bond: 1 0.9572 1.00568e-06 96 Angle: 1 104.52 0.000111707 48 1000 -17.498472 -20.331605 2.8331335 188.87466 -1.8121689 230.71657 -Loop time of 4.7828 on 4 procs for 1000 steps with 936 atoms +Loop time of 4.24862 on 4 procs for 1000 steps with 936 atoms -Performance: 18.065 ns/day, 1.329 hours/ns, 209.082 timesteps/s -96.3% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 20.336 ns/day, 1.180 hours/ns, 235.370 timesteps/s +99.6% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.26735 | 1.3839 | 3.2059 | 99.7 | 28.93 -Bond | 0.00079377 | 0.00086039 | 0.00093529 | 0.0 | 0.02 -Kspace | 1.4248 | 3.2254 | 4.3332 | 64.6 | 67.44 -Neigh | 0.061885 | 0.061916 | 0.061951 | 0.0 | 1.29 -Comm | 0.044281 | 0.065185 | 0.078628 | 5.1 | 1.36 -Output | 0.0003482 | 0.0003787 | 0.00040746 | 0.0 | 0.01 -Modify | 0.028727 | 0.031529 | 0.034914 | 1.3 | 0.66 -Other | | 0.01367 | | | 0.29 +Pair | 0.25749 | 1.1806 | 2.6872 | 89.0 | 27.79 +Bond | 0.00018656 | 0.00020786 | 0.00025377 | 0.0 | 0.00 +Kspace | 1.4259 | 2.9204 | 3.8414 | 56.3 | 68.74 +Neigh | 0.057504 | 0.057852 | 0.05818 | 0.1 | 1.36 +Comm | 0.041952 | 0.053593 | 0.05876 | 3.0 | 1.26 +Output | 0.0004296 | 0.00046809 | 0.00055317 | 0.0 | 0.01 +Modify | 0.026204 | 0.027251 | 0.028382 | 0.6 | 0.64 +Other | | 0.008209 | | | 0.19 Nlocal: 234 ave 302 max 198 min Histogram: 2 0 0 1 0 0 0 0 0 1