From 8705a14b3572eafd146375d02b83802c5fd6a9f6 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 13 Jan 2025 16:18:24 -0500 Subject: [PATCH] create logs for example input --- examples/LEPTON/in.efield-lepton | 55 +++++---- .../LEPTON/log.13Jan25.efield-lepton.g++.1 | 115 ++++++++++++++++++ .../LEPTON/log.13Jan25.efield-lepton.g++.4 | 115 ++++++++++++++++++ 3 files changed, 258 insertions(+), 27 deletions(-) create mode 100644 examples/LEPTON/log.13Jan25.efield-lepton.g++.1 create mode 100644 examples/LEPTON/log.13Jan25.efield-lepton.g++.4 diff --git a/examples/LEPTON/in.efield-lepton b/examples/LEPTON/in.efield-lepton index 04ac5954ba..00ba8fa112 100644 --- a/examples/LEPTON/in.efield-lepton +++ b/examples/LEPTON/in.efield-lepton @@ -1,49 +1,50 @@ # Point dipoles in a 3d box with an external potential (ignoring dipolar interactions) -units lj -atom_style hybrid sphere dipole -dimension 3 -boundary s s s -region box block -2 2 -2 2 -2 2 +units lj +atom_style hybrid sphere dipole +dimension 3 +boundary s s s +region box block -2 2 -2 2 -2 2 -create_box 1 box -create_atoms 1 random 100 12345 NULL +create_box 1 box +create_atoms 1 random 100 12345 NULL # need both mass settings due to hybrid atom style -mass 1 1.0 -set group all mass 1.0 -set group all diameter 0.1 +mass 1 1.0 +set group all mass 1.0 +set group all diameter 0.1 -set group all dipole/random 98934 0.01 -pair_style none +set group all dipole/random 98934 0.01 +pair_style none +comm_modify cutoff 3.0 -velocity all create 0.0 87287 mom yes rot yes +velocity all create 0.0 87287 mom yes rot yes -fix 1 all nve/sphere update dipole +fix 1 all nve/sphere update dipole ############################################################################################################### ## Yukawa potential -#fix 2 all efield/lepton "A*exp(-B*r)/r; r=abs(sqrt(x^2+y^2+z^2)); A = 0.1; B = 5" step 1e-8 +#fix 2 all efield/lepton "A*exp(-B*r)/r; r=abs(sqrt(x^2+y^2+z^2)); A = 0.1; B = 5" step 1e-8 ## Gradually increasing uniform field -#variable E equal ramp(0,1) -#fix 2 all efield/lepton "-v_E*(x+y+z)" +#variable E equal ramp(0,1) +#fix 2 all efield/lepton "-v_E*(x+y+z)" ## Linear gradient field -fix 2 all efield/lepton "-1/6*x^3" step 1e-6 +fix 2 all efield/lepton "-1/6*x^3" step 1e-6 -fix_modify 2 energy yes +fix_modify 2 energy yes ############################################################################################################### -timestep 1e-3 +timestep 1e-3 -compute erot all erotate/sphere -variable etotal equal "ke + c_erot + pe" # thermo etotal doesn't include erot -thermo_style custom step temp ke c_erot pe v_etotal -thermo 500 -thermo_modify norm no +compute erot all erotate/sphere +variable etotal equal "ke + c_erot + pe" # thermo etotal doesn't include erot +thermo_style custom step temp ke c_erot pe v_etotal +thermo 500 +thermo_modify norm no -#dump 1 all custom 500 dump.dipole id x y z diameter mux muy muz fx fy fz tqx tqy tqz +#dump 1 all custom 500 dump.dipole id x y z diameter mux muy muz fx fy fz tqx tqy tqz -run 10000 +run 10000 diff --git a/examples/LEPTON/log.13Jan25.efield-lepton.g++.1 b/examples/LEPTON/log.13Jan25.efield-lepton.g++.1 new file mode 100644 index 0000000000..8954e045ab --- /dev/null +++ b/examples/LEPTON/log.13Jan25.efield-lepton.g++.1 @@ -0,0 +1,115 @@ +LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-283-g742c869534-modified) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 3d box with an external potential (ignoring dipolar interactions) + +units lj +atom_style hybrid sphere dipole +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:132) +dimension 3 +boundary s s s +region box block -2 2 -2 2 -2 2 + +create_box 1 box +Created orthogonal box = (-2 -2 -2) to (2 2 2) + 1 by 1 by 1 MPI processor grid +create_atoms 1 random 100 12345 NULL +Created 100 atoms + using lattice units in orthogonal box = (-2.0004 -2.0004 -2.0004) to (2.0004 2.0004 2.0004) + create_atoms CPU = 0.000 seconds + +# need both mass settings due to hybrid atom style +mass 1 1.0 +set group all mass 1.0 +Setting atom values ... + 100 settings made for mass +set group all diameter 0.1 +Setting atom values ... + 100 settings made for diameter + +set group all dipole/random 98934 0.01 +Setting atom values ... + 100 settings made for dipole/random +pair_style none +comm_modify cutoff 3.0 + +velocity all create 0.0 87287 mom yes rot yes + +fix 1 all nve/sphere update dipole + +############################################################################################################### +## Yukawa potential +#fix 2 all efield/lepton "A*exp(-B*r)/r; r=abs(sqrt(x^2+y^2+z^2)); A = 0.1; B = 5" step 1e-8 + +## Gradually increasing uniform field +#variable E equal ramp(0,1) +#fix 2 all efield/lepton "-v_E*(x+y+z)" + +## Linear gradient field +fix 2 all efield/lepton "-1/6*x^3" step 1e-6 + +fix_modify 2 energy yes + +############################################################################################################### + +timestep 1e-3 + +compute erot all erotate/sphere +variable etotal equal "ke + c_erot + pe" # thermo etotal doesn't include erot +thermo_style custom step temp ke c_erot pe v_etotal +thermo 500 +thermo_modify norm no + +#dump 1 all custom 500 dump.dipole id x y z diameter mux muy muz fx fy fz tqx tqy tqz + +run 10000 +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2442) +Per MPI rank memory allocation (min/avg/max) = 4.273 | 4.273 | 4.273 Mbytes + Step Temp KinEng c_erot PotEng v_etotal + 0 0 0 0 0.036419797 0.036419797 + 500 3.7159175e-06 0.00055181374 0.44262618 -0.40675701 0.036420985 + 1000 1.2808438e-05 0.0019020531 0.24499116 -0.21047295 0.036420259 + 1500 2.8343769e-05 0.0042090498 0.26504485 -0.2328336 0.036420307 + 2000 4.8796894e-05 0.0072463388 0.30953526 -0.28036098 0.036420618 + 2500 7.8933715e-05 0.011721657 0.2015076 -0.17680909 0.036420173 + 3000 0.00011381678 0.016901791 0.31002163 -0.29050294 0.036420476 + 3500 0.00015650339 0.023240753 0.27837968 -0.26520001 0.036420418 + 4000 0.00020429109 0.030337227 0.26201101 -0.25592795 0.036420289 + 4500 0.00026362339 0.039148074 0.29769952 -0.3004271 0.036420499 + 5000 0.00033328941 0.049493478 0.21642442 -0.22949776 0.036420131 + 5500 0.00040914224 0.060757622 0.28422322 -0.30856047 0.036420377 + 6000 0.00049425119 0.073396302 0.31767 -0.35464572 0.03642058 + 6500 0.00058508892 0.086885704 0.29079532 -0.34126075 0.036420276 + 7000 0.00069845073 0.10371993 0.25776048 -0.32506015 0.036420262 + 7500 0.0008215656 0.12200249 0.27033777 -0.35591972 0.036420539 + 8000 0.00095528125 0.14185927 0.33943527 -0.44487406 0.036420479 + 8500 0.0011052502 0.16412965 0.26727165 -0.39498109 0.036420218 + 9000 0.0012738298 0.18916373 0.31082058 -0.46356382 0.036420485 + 9500 0.001464197 0.21743325 0.25669856 -0.43771158 0.036420224 + 10000 0.0016627654 0.24692067 0.36273185 -0.57323194 0.036420578 +Loop time of 0.84714 on 1 procs for 10000 steps with 100 atoms + +Performance: 1019901.911 tau/day, 11804.420 timesteps/s, 1.180 Matom-step/s +62.3% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 9.21e-07 | 9.21e-07 | 9.21e-07 | 0.0 | 0.00 +Comm | 0.00094138 | 0.00094138 | 0.00094138 | 0.0 | 0.11 +Output | 0.0001983 | 0.0001983 | 0.0001983 | 0.0 | 0.02 +Modify | 0.84105 | 0.84105 | 0.84105 | 0.0 | 99.28 +Other | | 0.004946 | | | 0.58 + +Nlocal: 100 ave 100 max 100 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 5 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/LEPTON/log.13Jan25.efield-lepton.g++.4 b/examples/LEPTON/log.13Jan25.efield-lepton.g++.4 new file mode 100644 index 0000000000..44243006a9 --- /dev/null +++ b/examples/LEPTON/log.13Jan25.efield-lepton.g++.4 @@ -0,0 +1,115 @@ +LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-283-g742c869534-modified) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 3d box with an external potential (ignoring dipolar interactions) + +units lj +atom_style hybrid sphere dipole +WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:132) +dimension 3 +boundary s s s +region box block -2 2 -2 2 -2 2 + +create_box 1 box +Created orthogonal box = (-2 -2 -2) to (2 2 2) + 1 by 2 by 2 MPI processor grid +create_atoms 1 random 100 12345 NULL +Created 100 atoms + using lattice units in orthogonal box = (-2.0004 -2.0004 -2.0004) to (2.0004 2.0004 2.0004) + create_atoms CPU = 0.000 seconds + +# need both mass settings due to hybrid atom style +mass 1 1.0 +set group all mass 1.0 +Setting atom values ... + 100 settings made for mass +set group all diameter 0.1 +Setting atom values ... + 100 settings made for diameter + +set group all dipole/random 98934 0.01 +Setting atom values ... + 100 settings made for dipole/random +pair_style none +comm_modify cutoff 3.0 + +velocity all create 0.0 87287 mom yes rot yes + +fix 1 all nve/sphere update dipole + +############################################################################################################### +## Yukawa potential +#fix 2 all efield/lepton "A*exp(-B*r)/r; r=abs(sqrt(x^2+y^2+z^2)); A = 0.1; B = 5" step 1e-8 + +## Gradually increasing uniform field +#variable E equal ramp(0,1) +#fix 2 all efield/lepton "-v_E*(x+y+z)" + +## Linear gradient field +fix 2 all efield/lepton "-1/6*x^3" step 1e-6 + +fix_modify 2 energy yes + +############################################################################################################### + +timestep 1e-3 + +compute erot all erotate/sphere +variable etotal equal "ke + c_erot + pe" # thermo etotal doesn't include erot +thermo_style custom step temp ke c_erot pe v_etotal +thermo 500 +thermo_modify norm no + +#dump 1 all custom 500 dump.dipole id x y z diameter mux muy muz fx fy fz tqx tqy tqz + +run 10000 +WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2442) +Per MPI rank memory allocation (min/avg/max) = 4.289 | 4.289 | 4.289 Mbytes + Step Temp KinEng c_erot PotEng v_etotal + 0 0 0 0 0.036419797 0.036419797 + 500 3.7159175e-06 0.00055181374 0.44262618 -0.40675701 0.036420985 + 1000 1.2808438e-05 0.0019020531 0.24499116 -0.21047295 0.036420259 + 1500 2.8343769e-05 0.0042090498 0.26504485 -0.2328336 0.036420307 + 2000 4.8796894e-05 0.0072463388 0.30953526 -0.28036098 0.036420618 + 2500 7.8933715e-05 0.011721657 0.2015076 -0.17680909 0.036420173 + 3000 0.00011381678 0.016901791 0.31002163 -0.29050294 0.036420476 + 3500 0.00015650339 0.023240753 0.27837968 -0.26520001 0.036420418 + 4000 0.00020429109 0.030337227 0.26201101 -0.25592795 0.036420289 + 4500 0.00026362339 0.039148074 0.29769952 -0.3004271 0.036420499 + 5000 0.00033328941 0.049493478 0.21642442 -0.22949776 0.036420131 + 5500 0.00040914224 0.060757622 0.28422322 -0.30856047 0.036420377 + 6000 0.00049425119 0.073396302 0.31767 -0.35464572 0.03642058 + 6500 0.00058508892 0.086885704 0.29079532 -0.34126075 0.036420276 + 7000 0.00069845073 0.10371993 0.25776048 -0.32506015 0.036420262 + 7500 0.0008215656 0.12200249 0.27033777 -0.35591972 0.036420539 + 8000 0.00095528125 0.14185927 0.33943527 -0.44487406 0.036420479 + 8500 0.0011052502 0.16412965 0.26727165 -0.39498109 0.036420218 + 9000 0.0012738298 0.18916373 0.31082058 -0.46356382 0.036420485 + 9500 0.001464197 0.21743325 0.25669856 -0.43771158 0.036420224 + 10000 0.0016627654 0.24692067 0.36273185 -0.57323194 0.036420578 +Loop time of 0.985035 on 4 procs for 10000 steps with 100 atoms + +Performance: 877125.838 tau/day, 10151.919 timesteps/s, 1.015 Matom-step/s +67.7% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 7.22e-07 | 8.9125e-07 | 1.031e-06 | 0.0 | 0.00 +Comm | 0.09818 | 0.1024 | 0.10798 | 1.1 | 10.40 +Output | 0.00021634 | 0.00028668 | 0.00044312 | 0.0 | 0.03 +Modify | 0.773 | 0.81845 | 0.84055 | 3.0 | 83.09 +Other | | 0.06389 | | | 6.49 + +Nlocal: 25 ave 30 max 23 min +Histogram: 2 1 0 0 0 0 0 0 0 1 +Nghost: 75 ave 77 max 70 min +Histogram: 1 0 0 0 0 0 0 0 1 2 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 5 +Dangerous builds = 0 +Total wall time: 0:00:00