From 4078c7897e442a64ec27f161f52a2479dfd4b259 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 8 Dec 2018 15:00:14 -0500 Subject: [PATCH 1/9] fix permissions --- src/MAKE/MACHINES/Makefile.cori2 | 0 1 file changed, 0 insertions(+), 0 deletions(-) mode change 100755 => 100644 src/MAKE/MACHINES/Makefile.cori2 diff --git a/src/MAKE/MACHINES/Makefile.cori2 b/src/MAKE/MACHINES/Makefile.cori2 old mode 100755 new mode 100644 From 802bf4bc1fa89c3197f323ee064d97afbd735252 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 8 Dec 2018 15:00:33 -0500 Subject: [PATCH 2/9] update .gitignore for recently added files --- src/.gitignore | 44 ++++++++++++++++++++++++++++++++++++++++++-- 1 file changed, 42 insertions(+), 2 deletions(-) diff --git a/src/.gitignore b/src/.gitignore index acba20b79d..13aeee4d6e 100644 --- a/src/.gitignore +++ b/src/.gitignore @@ -225,6 +225,10 @@ /atom_vec_template.h /body_nparticle.cpp /body_nparticle.h +/body_rounded_polygon.cpp +/body_rounded_polygon.h +/body_rounded_polyhedron.cpp +/body_rounded_polyhedron.h /bond_class2.cpp /bond_class2.h /bond_fene.cpp @@ -309,8 +313,12 @@ /compute_pressure_cylinder.h /compute_pressure_grem.cpp /compute_pressure_grem.h +/compute_ptm_atom.cpp +/compute_ptm_atom.h /compute_rigid_local.cpp /compute_rigid_local.h +/compute_smd_triangle_vertices.cpp +/compute_smd_triangle_vertices.h /compute_spec_atom.cpp /compute_spec_atom.h /compute_stress_mop.cpp @@ -421,6 +429,8 @@ /fix_bond_react.h /fix_bond_swap.cpp /fix_bond_swap.h +/fix_client_md.cpp +/fix_client_md.h /fix_cmap.cpp /fix_cmap.h /fix_deposit.cpp @@ -445,6 +455,8 @@ /fix_ehex.h /fix_event.cpp /fix_event.h +/fix_event_hyper.cpp +/fix_event_hyper.h /fix_event_prd.cpp /fix_event_prd.h /fix_event_tad.cpp @@ -463,6 +475,12 @@ /fix_gpu.h /fix_grem.cpp /fix_grem.h +/fix_hyper.cpp +/fix_hyper.h +/fix_hyper_global.cpp +/fix_hyper_global.h +/fix_hyper_local.cpp +/fix_hyper_local.h /fix_imd.cpp /fix_imd.h /fix_ipi.cpp @@ -626,6 +644,10 @@ /fix_ttm.h /fix_tune_kspace.cpp /fix_tune_kspace.h +/fix_wall_body_polygon.cpp +/fix_wall_body_polygon.h +/fix_wall_body_polyhedron.cpp +/fix_wall_body_polyhedron.h /fix_wall_colloid.cpp /fix_wall_colloid.h /fix_wall_ees.cpp @@ -647,6 +669,8 @@ /group_ndx.h /ndx_group.cpp /ndx_group.h +/hyper.cpp +/hyper.h /improper_class2.cpp /improper_class2.h /improper_cossq.cpp @@ -671,6 +695,8 @@ /lj_sdk_common.h /math_complex.h /math_vector.h +/message.cpp +/message.h /mgpt_*.cpp /mgpt_*.h /msm.cpp @@ -688,8 +714,14 @@ /pair_airebo.h /pair_airebo_morse.cpp /pair_airebo_morse.h -/pair_body.cpp -/pair_body.h +/pair_atm.cpp +/pair_atm.h +/pair_body_nparticle.cpp +/pair_body_nparticle.h +/pair_body_rounded_polygon.cpp +/pair_body_rounded_polygon.h +/pair_body_rounded_polyhedron.cpp +/pair_body_rounded_polyhedron.h /pair_bop.cpp /pair_bop.h /pair_born_coul_long.cpp @@ -1028,6 +1060,14 @@ /remap_wrap.h /restart_mpiio.cpp /restart_mpiio.h +/scafacos.cpp +/scafacos.h +/server.cpp +/server.h +/server_mc.cpp +/server_mc.h +/server_md.cpp +/server_md.h /smd_kernels.h /smd_material_models.cpp /smd_material_models.h From 8f95cdcb2727eaa747ba0605a29cdba48e121e83 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 9 Dec 2018 16:24:06 -0500 Subject: [PATCH 3/9] small update to the fix rigid/meso command docs --- doc/src/fix_rigid_meso.txt | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/doc/src/fix_rigid_meso.txt b/doc/src/fix_rigid_meso.txt index d86d359f1d..0819fdb2fb 100644 --- a/doc/src/fix_rigid_meso.txt +++ b/doc/src/fix_rigid_meso.txt @@ -160,7 +160,7 @@ unaffected by interactions with other particles. Note that if you expect a rigid body not to move or rotate by using these keywords, you must insure its initial center-of-mass translational or angular velocity is 0.0. Otherwise the initial translational or angular -momentum the body has will persist. +momentum, the body has, will persist. An xflag, yflag, or zflag set to {off} means turn off the component of force or torque in that dimension. A setting of {on} means turn on @@ -287,9 +287,10 @@ bodies. The number of columns is 28. Thus for each rigid body, 28 values are stored: the xyz coords of the center of mass (COM), the xyz components of the COM velocity, the xyz components of the force acting on the COM, the components of the 4-vector quaternion representing the -orientation of the rigid body, the xyz components of the angular momentum +orientation of the rigid body, the xyz components of the angular velocity of the body around its COM, the xyz components of the torque acting on the -COM, the 3 principal components of the moment of inertia and the xyz image +COM, the 3 principal components of the moment of inertia, the xyz components +of the angular momentum of the body around its COM, and the xyz image flags of the COM. The center of mass (COM) for each body is similar to unwrapped From b6b813459bddedaa11faee95debeb8c89c77bbae Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 10 Dec 2018 11:04:52 -0500 Subject: [PATCH 4/9] update example logfiles for USER-DRUDE package --- .../butane/log.27Nov18.butane.lang.g++.1 | 193 ++++++++++++ .../butane/log.27Nov18.butane.lang.g++.4 | 193 ++++++++++++ .../drude/butane/log.27Nov18.butane.nh.g++.1 | 199 ++++++++++++ .../drude/butane/log.27Nov18.butane.nh.g++.4 | 199 ++++++++++++ .../butane/log.butane.lang.18Jul15.linux.1 | 171 ----------- .../butane/log.butane.lang.18Jul15.linux.4 | 171 ----------- .../butane/log.butane.nh.18Jul15.linux.3 | 177 ----------- .../butane/log.butane.nh.18Jul15.linux.4 | 177 ----------- .../ethanol/log.27Nov18.ethanol.lang.g++.1 | 277 +++++++++++++++++ .../ethanol/log.27Nov18.ethanol.lang.g++.4 | 277 +++++++++++++++++ .../ethanol/log.27Nov18.ethanol.nh.g++.1 | 286 ++++++++++++++++++ .../ethanol/log.27Nov18.ethanol.nh.g++.4 | 286 ++++++++++++++++++ .../ethanol/log.ethanol.lang.8Jul15.linux.1 | 254 ---------------- .../ethanol/log.ethanol.lang.8Jul15.linux.4 | 254 ---------------- .../ethanol/log.ethanol.nh.8Jul15.linux.1 | 263 ---------------- .../ethanol/log.ethanol.nh.8Jul15.linux.4 | 263 ---------------- .../swm4-ndp/log.27Nov18.swm4-ndp.lang.g++.1 | 246 +++++++++++++++ .../swm4-ndp/log.27Nov18.swm4-ndp.lang.g++.4 | 246 +++++++++++++++ .../swm4-ndp/log.27Nov18.swm4-ndp.nh.g++.1 | 252 +++++++++++++++ .../swm4-ndp/log.27Nov18.swm4-ndp.nh.g++.4 | 252 +++++++++++++++ .../swm4-ndp/log.swm4-ndp.lang.8Jul15.linux.1 | 230 -------------- .../swm4-ndp/log.swm4-ndp.lang.8Jul15.linux.4 | 230 -------------- .../swm4-ndp/log.swm4-ndp.nh.8Jul15.linux.1 | 236 --------------- .../swm4-ndp/log.swm4-ndp.nh.8Jul15.linux.4 | 236 --------------- .../toluene/log.27Nov18.toluene.lang.g++.1 | 14 + .../toluene/log.27Nov18.toluene.lang.g++.4 | 14 + .../toluene/log.27Nov18.toluene.nh.g++.1 | 14 + .../toluene/log.27Nov18.toluene.nh.g++.4 | 14 + .../toluene/log.toluene.lang.11Aug17.linux.1 | 251 --------------- .../toluene/log.toluene.lang.11Aug17.linux.4 | 251 --------------- .../toluene/log.toluene.nh.11Aug17.linux.1 | 259 ---------------- .../toluene/log.toluene.nh.11Aug17.linux.4 | 259 ---------------- 32 files changed, 2962 insertions(+), 3682 deletions(-) create mode 100644 examples/USER/drude/butane/log.27Nov18.butane.lang.g++.1 create mode 100644 examples/USER/drude/butane/log.27Nov18.butane.lang.g++.4 create mode 100644 examples/USER/drude/butane/log.27Nov18.butane.nh.g++.1 create mode 100644 examples/USER/drude/butane/log.27Nov18.butane.nh.g++.4 delete mode 100644 examples/USER/drude/butane/log.butane.lang.18Jul15.linux.1 delete mode 100644 examples/USER/drude/butane/log.butane.lang.18Jul15.linux.4 delete mode 100644 examples/USER/drude/butane/log.butane.nh.18Jul15.linux.3 delete mode 100644 examples/USER/drude/butane/log.butane.nh.18Jul15.linux.4 create mode 100644 examples/USER/drude/ethanol/log.27Nov18.ethanol.lang.g++.1 create mode 100644 examples/USER/drude/ethanol/log.27Nov18.ethanol.lang.g++.4 create mode 100644 examples/USER/drude/ethanol/log.27Nov18.ethanol.nh.g++.1 create mode 100644 examples/USER/drude/ethanol/log.27Nov18.ethanol.nh.g++.4 delete mode 100644 examples/USER/drude/ethanol/log.ethanol.lang.8Jul15.linux.1 delete mode 100644 examples/USER/drude/ethanol/log.ethanol.lang.8Jul15.linux.4 delete mode 100644 examples/USER/drude/ethanol/log.ethanol.nh.8Jul15.linux.1 delete mode 100644 examples/USER/drude/ethanol/log.ethanol.nh.8Jul15.linux.4 create mode 100644 examples/USER/drude/swm4-ndp/log.27Nov18.swm4-ndp.lang.g++.1 create mode 100644 examples/USER/drude/swm4-ndp/log.27Nov18.swm4-ndp.lang.g++.4 create mode 100644 examples/USER/drude/swm4-ndp/log.27Nov18.swm4-ndp.nh.g++.1 create mode 100644 examples/USER/drude/swm4-ndp/log.27Nov18.swm4-ndp.nh.g++.4 delete mode 100644 examples/USER/drude/swm4-ndp/log.swm4-ndp.lang.8Jul15.linux.1 delete mode 100644 examples/USER/drude/swm4-ndp/log.swm4-ndp.lang.8Jul15.linux.4 delete mode 100644 examples/USER/drude/swm4-ndp/log.swm4-ndp.nh.8Jul15.linux.1 delete mode 100644 examples/USER/drude/swm4-ndp/log.swm4-ndp.nh.8Jul15.linux.4 create mode 100644 examples/USER/drude/toluene/log.27Nov18.toluene.lang.g++.1 create mode 100644 examples/USER/drude/toluene/log.27Nov18.toluene.lang.g++.4 create mode 100644 examples/USER/drude/toluene/log.27Nov18.toluene.nh.g++.1 create mode 100644 examples/USER/drude/toluene/log.27Nov18.toluene.nh.g++.4 delete mode 100644 examples/USER/drude/toluene/log.toluene.lang.11Aug17.linux.1 delete mode 100644 examples/USER/drude/toluene/log.toluene.lang.11Aug17.linux.4 delete mode 100644 examples/USER/drude/toluene/log.toluene.nh.11Aug17.linux.1 delete mode 100644 examples/USER/drude/toluene/log.toluene.nh.11Aug17.linux.4 diff --git a/examples/USER/drude/butane/log.27Nov18.butane.lang.g++.1 b/examples/USER/drude/butane/log.27Nov18.butane.lang.g++.1 new file mode 100644 index 0000000000..0302966447 --- /dev/null +++ b/examples/USER/drude/butane/log.27Nov18.butane.lang.g++.1 @@ -0,0 +1,193 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# 250 butane system for drude polarizability example (Langevin) + +units real +boundary p p p + +atom_style full +bond_style harmonic +angle_style harmonic +dihedral_style opls +special_bonds lj/coul 0.0 0.0 0.5 + +pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.089 8.0 +pair_modify mix geometric tail yes +kspace_style pppm 1.0e-4 + +read_data data.butane + orthogonal box = (-19.1 -19.0999 -19.1) to (19.1 19.1 19.1) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 4500 atoms + scanning bonds ... + 5 = max bonds/atom + scanning angles ... + 6 = max angles/atom + scanning dihedrals ... + 9 = max dihedrals/atom + reading bonds ... + 4250 bonds + reading angles ... + 6000 angles + reading dihedrals ... + 6750 dihedrals + 5 = max # of 1-2 neighbors + 8 = max # of 1-3 neighbors + 12 = max # of 1-4 neighbors + 17 = max # of special neighbors + +comm_modify vel yes + +group gBUTANE molecule 1:250 +4500 atoms in group gBUTANE +group gCORES type 1 2 3 +3500 atoms in group gCORES +group gDRUDES type 4 5 +1000 atoms in group gDRUDES + +pair_coeff 1 1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H +pair_coeff 1 2 lj/cut/coul/long 0.065997 3.500000 # C3H C2H +pair_coeff 1 3 lj/cut/coul/long 0.044496 2.958040 # C3H H +pair_coeff 2 2 lj/cut/coul/long 0.065997 3.500000 # C2H C2H +pair_coeff 2 3 lj/cut/coul/long 0.044496 2.958040 # C2H H +pair_coeff 3 3 lj/cut/coul/long 0.029999 2.500000 # H H +pair_coeff * 4*5 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes +pair_coeff 1 * thole 1.368000 +pair_coeff 2 * thole 1.368000 +pair_coeff 4 * thole 1.368000 +pair_coeff 5 * thole 1.368000 + +neighbor 2.0 bin + +variable vTEMP equal 260.0 +variable vTEMP_D equal 1.0 +variable vPRESS equal 1.0 + +velocity gCORES create ${vTEMP} 12345 +velocity gCORES create 260 12345 +velocity gDRUDES create ${vTEMP_D} 12345 +velocity gDRUDES create 1 12345 + +fix fDRUDE all drude C C N D D + +fix fSHAKE gCORES shake 0.0001 20 0 b 2 4 + 0 = # of size 2 clusters + 500 = # of size 3 clusters + 500 = # of size 4 clusters + 0 = # of frozen angles + +fix fLANG all langevin/drude ${vTEMP} 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes +fix fLANG all langevin/drude 260 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes +fix fLANG all langevin/drude 260 100.0 200611 1 20.0 260514 zero yes +fix fNPH all nve + +compute cTEMP all temp/drude + +thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2] +thermo 50 + +timestep 0.5 +run 2000 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) + G vector (1/distance) = 0.367867 + grid = 36 36 36 + stencil order = 5 + estimated absolute RMS force accuracy = 0.031354 + estimated relative force accuracy = 9.44215e-05 + using double precision FFTs + 3d grid and FFT values/proc = 79507 46656 +Rebuild special list taking Drude particles into account +Old max number of 1-2 to 1-4 neighbors: 17 +New max number of 1-2 to 1-4 neighbors: 17 (+0) +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10 + ghost atom cutoff = 10 + binsize = 5, bins = 8 8 8 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) pair thole, perpetual, skip from (1) + attributes: half, newton on + pair build: skip + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 26.29 | 26.29 | 26.29 Mbytes +Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2] + 0 0 6535.5187 2714.74 248.45112 3820.7787 3724.3278 140.75328 1.4735401 0 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-146.38102 55742.797 264.67477 1.4395372 + 1300 48.015128 3286.0631 2125.3364 194.50931 1160.7267 236.69229 1272.7247 218.49151 0 -995.46842 595298.38 -594870.1 434.46496 55742.797 266.83295 1.451771 + 1350 49.79655 3247.1808 2087.4518 191.04214 1159.7291 215.07571 1301.219 211.43766 0 -995.15128 595297.24 -594870.09 1501.3496 55742.797 262.07016 1.44305 + 1400 51.624074 3194.7716 2041.9251 186.87557 1152.8466 236.94802 1261.0635 209.14663 0 -982.03995 595297.35 -594869.63 346.64925 55742.797 256.31352 1.5208162 + 1450 53.450535 3229.6083 2087.4545 191.04239 1142.1538 246.85361 1264.077 205.22437 0 -1003.5382 595299.44 -594869.9 278.1536 55742.797 262.08335 1.4087832 + 1500 55.288627 3249.6608 2089.8541 191.262 1159.8067 238.99337 1274.9502 206.61799 0 -988.99015 595297.98 -594869.75 636.34142 55742.797 262.36618 1.4595924 + 1550 57.093174 3273.2213 2122.5463 194.25397 1150.675 230.16428 1274.9965 195.7686 0 -979.24728 595298.84 -594869.85 528.01943 55742.797 266.47594 1.4678006 + 1600 58.978489 3288.6787 2120.7284 194.0876 1167.9503 229.10278 1274.2494 205.30619 0 -969.94195 595298.85 -594869.62 1126.6579 55742.797 266.23416 1.5026913 + 1650 60.803467 3286.3327 2148.1031 196.59291 1138.2295 234.18582 1256.2009 214.69184 0 -995.41699 595298.38 -594869.81 -457.07393 55742.797 269.67989 1.4977223 + 1700 62.624963 3296.9487 2092.8432 191.53556 1204.1055 238.05554 1313.8592 213.47968 0 -989.09874 595297.16 -594869.35 981.42569 55742.797 262.7423 1.4593707 + 1750 64.39829 3310.3958 2097.6547 191.97591 1212.7411 243.56621 1309.681 210.07115 0 -978.63733 595297.78 -594869.72 -41.877565 55742.797 263.31945 1.5344885 + 1800 66.216881 3229.7417 2079.7567 190.33789 1149.985 226.57585 1276.3941 202.60118 0 -984.26122 595298.62 -594869.94 515.97995 55742.797 261.07174 1.5239416 + 1850 68.038292 3199.6375 2033.1459 186.0721 1166.4916 242.84458 1267.7768 212.87764 0 -984.52187 595296.72 -594869.21 440.77319 55742.797 255.22287 1.4839954 + 1900 69.841965 3155.3872 2019.0731 184.78417 1136.3141 213.38104 1263.0105 213.0042 0 -980.43253 595296.92 -594869.57 469.76979 55742.797 253.48524 1.3965366 + 1950 71.702563 3191.9366 2051.5475 187.75621 1140.3891 211.61608 1278.9441 206.1048 0 -984.04544 595297.56 -594869.79 758.07165 55742.797 257.54478 1.4655839 + 2000 73.520102 3214.3938 2041.9357 186.87654 1172.4582 237.13198 1275.4194 218.0467 0 -985.25597 595296.76 -594869.64 375.81502 55742.797 256.33161 1.4761528 +Loop time of 73.5201 on 1 procs for 2000 steps with 4500 atoms + +Performance: 1.175 ns/day, 20.422 hours/ns, 27.203 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 50.346 | 50.346 | 50.346 | 0.0 | 68.48 +Bond | 3.3227 | 3.3227 | 3.3227 | 0.0 | 4.52 +Kspace | 16.003 | 16.003 | 16.003 | 0.0 | 21.77 +Neigh | 1.3495 | 1.3495 | 1.3495 | 0.0 | 1.84 +Comm | 0.33013 | 0.33013 | 0.33013 | 0.0 | 0.45 +Output | 0.0044131 | 0.0044131 | 0.0044131 | 0.0 | 0.01 +Modify | 2.1068 | 2.1068 | 2.1068 | 0.0 | 2.87 +Other | | 0.05755 | | | 0.08 + +Nlocal: 4500 ave 4500 max 4500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 8703 ave 8703 max 8703 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 860806 ave 860806 max 860806 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 860806 +Ave neighs/atom = 191.29 +Ave special neighs/atom = 13.3333 +Neighbor list builds = 28 +Dangerous builds = 0 +Total wall time: 0:01:13 diff --git a/examples/USER/drude/butane/log.27Nov18.butane.lang.g++.4 b/examples/USER/drude/butane/log.27Nov18.butane.lang.g++.4 new file mode 100644 index 0000000000..3a0f60f3cb --- /dev/null +++ b/examples/USER/drude/butane/log.27Nov18.butane.lang.g++.4 @@ -0,0 +1,193 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# 250 butane system for drude polarizability example (Langevin) + +units real +boundary p p p + +atom_style full +bond_style harmonic +angle_style harmonic +dihedral_style opls +special_bonds lj/coul 0.0 0.0 0.5 + +pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.089 8.0 +pair_modify mix geometric tail yes +kspace_style pppm 1.0e-4 + +read_data data.butane + orthogonal box = (-19.1 -19.0999 -19.1) to (19.1 19.1 19.1) + 2 by 1 by 2 MPI processor grid + reading atoms ... + 4500 atoms + scanning bonds ... + 5 = max bonds/atom + scanning angles ... + 6 = max angles/atom + scanning dihedrals ... + 9 = max dihedrals/atom + reading bonds ... + 4250 bonds + reading angles ... + 6000 angles + reading dihedrals ... + 6750 dihedrals + 5 = max # of 1-2 neighbors + 8 = max # of 1-3 neighbors + 12 = max # of 1-4 neighbors + 17 = max # of special neighbors + +comm_modify vel yes + +group gBUTANE molecule 1:250 +4500 atoms in group gBUTANE +group gCORES type 1 2 3 +3500 atoms in group gCORES +group gDRUDES type 4 5 +1000 atoms in group gDRUDES + +pair_coeff 1 1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H +pair_coeff 1 2 lj/cut/coul/long 0.065997 3.500000 # C3H C2H +pair_coeff 1 3 lj/cut/coul/long 0.044496 2.958040 # C3H H +pair_coeff 2 2 lj/cut/coul/long 0.065997 3.500000 # C2H C2H +pair_coeff 2 3 lj/cut/coul/long 0.044496 2.958040 # C2H H +pair_coeff 3 3 lj/cut/coul/long 0.029999 2.500000 # H H +pair_coeff * 4*5 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes +pair_coeff 1 * thole 1.368000 +pair_coeff 2 * thole 1.368000 +pair_coeff 4 * thole 1.368000 +pair_coeff 5 * thole 1.368000 + +neighbor 2.0 bin + +variable vTEMP equal 260.0 +variable vTEMP_D equal 1.0 +variable vPRESS equal 1.0 + +velocity gCORES create ${vTEMP} 12345 +velocity gCORES create 260 12345 +velocity gDRUDES create ${vTEMP_D} 12345 +velocity gDRUDES create 1 12345 + +fix fDRUDE all drude C C N D D + +fix fSHAKE gCORES shake 0.0001 20 0 b 2 4 + 0 = # of size 2 clusters + 500 = # of size 3 clusters + 500 = # of size 4 clusters + 0 = # of frozen angles + +fix fLANG all langevin/drude ${vTEMP} 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes +fix fLANG all langevin/drude 260 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes +fix fLANG all langevin/drude 260 100.0 200611 1 20.0 260514 zero yes +fix fNPH all nve + +compute cTEMP all temp/drude + +thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2] +thermo 50 + +timestep 0.5 +run 2000 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) + G vector (1/distance) = 0.367867 + grid = 36 36 36 + stencil order = 5 + estimated absolute RMS force accuracy = 0.031354 + estimated relative force accuracy = 9.44215e-05 + using double precision FFTs + 3d grid and FFT values/proc = 26875 11664 +Rebuild special list taking Drude particles into account +Old max number of 1-2 to 1-4 neighbors: 17 +New max number of 1-2 to 1-4 neighbors: 17 (+0) +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10 + ghost atom cutoff = 10 + binsize = 5, bins = 8 8 8 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) pair thole, perpetual, skip from (1) + attributes: half, newton on + pair build: skip + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 16.75 | 17.03 | 17.13 Mbytes +Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2] + 0 0 6535.5187 2714.74 248.45112 3820.7787 3724.3278 140.75328 1.4735401 0 -518.77975 595169.42 -594696.41 4439.7916 55742.797 334.61375 18.435655 + 50 0.60067916 3418.0026 2021.3092 184.98882 1396.6934 835.43668 808.1357 113.8069 0 -759.89265 595242.48 -594843.28 3040.8412 55742.797 197.07838 152.67751 + 100 1.1808443 2892.8432 1932.7674 176.88554 960.07578 363.31823 924.84568 164.52097 0 -931.84989 595306.29 -594867.05 1694.4336 55742.797 224.44681 49.87859 + 150 1.7504072 2833.9225 1947.7257 178.2545 886.19681 243.64601 972.03324 186.73658 0 -941.85405 595295.47 -594869.83 4603.775 55742.797 239.63159 14.40403 + 200 2.3280952 2870.6299 1920.2424 175.73925 950.38759 226.3737 1061.7175 186.27763 0 -950.17253 595296.43 -594870.24 2606.5041 55742.797 239.64552 5.1468097 + 250 2.9009523 2894.0913 1933.574 176.95936 960.51728 215.18824 1118.0957 195.43563 0 -993.95102 595296.54 -594870.8 1812.6379 55742.797 242.26101 2.6446653 + 300 3.4866827 2959.1219 1970.1936 180.31075 988.92834 209.63552 1155.4811 193.64322 0 -996.9511 595297.92 -594870.8 3371.5528 55742.797 247.17325 1.8304564 + 350 4.1206505 2988.7765 1988.8664 182.01968 999.91007 217.65998 1148.4029 204.96757 0 -996.5586 595296.05 -594870.61 3021.4005 55742.797 249.63956 1.5179762 + 400 4.7467482 3014.5638 1983.6589 181.54309 1030.9049 225.81008 1174.5083 214.70193 0 -1012.492 595298.89 -594870.51 668.28879 55742.797 249.02834 1.40089 + 450 5.3385043 3065.528 2028.5299 185.64965 1036.9981 206.85828 1232.536 204.7453 0 -1034.5447 595297.52 -594870.12 1276.895 55742.797 254.65283 1.4568976 + 500 5.8841732 3087.3359 1998.9143 182.93925 1088.4216 209.84037 1244.2781 211.45124 0 -1004.5214 595297.9 -594870.53 1811.1357 55742.797 250.95893 1.3696214 + 550 6.495003 3082.7524 2000.662 183.0992 1082.0904 218.46927 1229.7948 204.12764 0 -997.16039 595297.23 -594870.37 2005.0512 55742.797 251.16775 1.399994 + 600 7.0529547 3089.1148 2008.9702 183.85957 1080.1445 215.63956 1239.6501 205.6559 0 -1008.3414 595297.61 -594870.07 1579.3906 55742.797 252.19307 1.453043 + 650 7.6147993 3094.7607 1984.215 181.59398 1110.5457 217.2587 1270.5436 217.11567 0 -1021.7236 595297.37 -594870.02 922.17911 55742.797 249.09972 1.3970954 + 700 8.1847589 3085.7974 1977.7443 181.00179 1108.0531 226.89107 1263.0937 209.93619 0 -1019.8382 595298.21 -594870.24 1358.6744 55742.797 248.27153 1.4348071 + 750 8.7551639 3098.7075 1990.5214 182.17114 1108.186 210.53964 1263.8112 208.67005 0 -1002.6807 595298.31 -594870.47 1389.4827 55742.797 249.86686 1.4670711 + 800 9.3312614 3106.7743 2001.1286 183.14191 1105.6457 223.39008 1267.3688 200.94765 0 -1014.1025 595298.4 -594870.36 498.96153 55742.797 251.20537 1.4561965 + 850 9.9120548 3162.1905 2015.7594 184.4809 1146.4311 238.91403 1296.3319 216.49567 0 -1033.2993 595298.07 -594870.08 -146.24973 55742.797 253.06241 1.4124079 + 900 10.506582 3151.6622 2017.7351 184.66172 1133.9272 225.66798 1259.6857 214.41352 0 -993.82625 595298.42 -594870.44 855.52595 55742.797 253.32946 1.3630807 + 950 11.073148 3108.5571 1984.4638 181.61676 1124.0933 219.09683 1258.9728 215.5009 0 -998.11162 595299.1 -594870.46 742.29532 55742.797 249.13228 1.3937456 + 1000 11.712476 3151.1431 2010.1073 183.96363 1141.0358 234.62673 1262.3296 218.152 0 -1001.9319 595297.94 -594870.08 -15.429859 55742.797 252.31702 1.5039719 + 1050 12.416933 3154.9906 2025.2409 185.34864 1129.7498 240.28475 1245.2732 211.12104 0 -994.07995 595297.56 -594870.41 220.34341 55742.797 254.21036 1.5313366 + 1100 13.000971 3146.7058 2015.0512 184.41609 1131.6546 217.69098 1255.773 216.52818 0 -985.5434 595297.52 -594870.32 245.54987 55742.797 252.9731 1.4117211 + 1150 13.566174 3184.3315 2097.0388 191.91954 1087.2926 210.06417 1226.6616 216.15719 0 -994.73562 595299.65 -594870.51 960.8241 55742.797 263.29333 1.3975188 + 1200 14.098352 3181.1191 2062.3454 188.74443 1118.7737 228.90526 1255.3357 202.92363 0 -997.73355 595299.52 -594870.18 341.31357 55742.797 258.91222 1.4415835 + 1250 14.653097 3174.3638 2030.9146 185.8679 1143.4492 239.32477 1267.7689 201.40964 0 -992.67835 595297.78 -594870.16 399.69023 55742.797 254.97189 1.4037218 + 1300 15.198202 3181.4157 2020.4604 184.91114 1160.9553 213.94195 1283.8134 212.79399 0 -977.52401 595298.12 -594870.19 141.81633 55742.797 253.64065 1.447907 + 1350 15.763844 3221.4526 2077.8786 190.16601 1143.574 237.97099 1261.8854 206.43835 0 -991.01514 595298.43 -594870.14 293.86155 55742.797 260.85797 1.4643006 + 1400 16.36341 3273.4082 2117.3713 193.78035 1156.0369 241.63847 1257.3077 215.03947 0 -986.42491 595298.6 -594870.13 881.28305 55742.797 265.82788 1.4598428 + 1450 16.907335 3277.2159 2086.1619 190.92409 1191.054 245.42292 1289.0177 220.33432 0 -991.71405 595297.92 -594869.93 24.577369 55742.797 261.91752 1.4173689 + 1500 17.461373 3277.8652 2139.2814 195.78556 1138.5838 230.79453 1253.5268 210.7018 0 -984.94169 595298.66 -594870.16 612.24618 55742.797 268.59444 1.432741 + 1550 17.996041 3247.9903 2120.4397 194.06118 1127.5505 237.85251 1244.2413 207.38138 0 -989.02975 595297.17 -594870.07 908.40409 55742.797 266.20105 1.4941148 + 1600 18.546506 3263.2065 2095.2604 191.75678 1167.9461 222.27478 1287.0828 217.80256 0 -988.01164 595299.17 -594870.37 372.09439 55742.797 263.06244 1.4165997 + 1650 19.087156 3279.007 2102.6708 192.43497 1176.3363 228.35925 1287.432 218.78886 0 -987.87117 595299.94 -594870.32 -277.43091 55742.797 263.9961 1.4129192 + 1700 19.665064 3297.4084 2103.7436 192.53316 1193.6648 248.40926 1304.8649 202.53258 0 -989.5236 595297.12 -594869.74 1158.9952 55742.797 264.11122 1.4655993 + 1750 20.367483 3280.0391 2075.6964 189.9663 1204.3427 240.06411 1311.9499 213.18798 0 -987.79028 595296.5 -594869.56 437.83034 55742.797 260.60055 1.4183112 + 1800 20.942509 3272.2429 2082.8406 190.62013 1189.4023 235.68331 1306.7318 216.11438 0 -997.06553 595297.79 -594869.86 1293.8956 55742.797 261.49937 1.4181999 + 1850 21.546463 3288.8649 2088.0429 191.09624 1200.822 239.22801 1297.8732 214.15066 0 -979.04152 595298.01 -594869.39 217.43385 55742.797 262.15237 1.4245994 + 1900 22.118972 3213.0018 2032.382 186.00219 1180.6198 222.35796 1278.9261 222.52754 0 -969.8068 595296.01 -594869.39 563.16684 55742.797 255.16077 1.393322 + 1950 22.701752 3228.1804 2084.1556 190.74048 1144.0248 232.43889 1247.3333 216.54358 0 -981.18306 595298.59 -594869.7 -309.06733 55742.797 261.65433 1.4460719 + 2000 23.402514 3297.5065 2091.6171 191.42335 1205.8894 238.75396 1287.293 220.47084 0 -968.78447 595297.97 -594869.81 128.84944 55742.797 262.59803 1.4363623 +Loop time of 23.4026 on 4 procs for 2000 steps with 4500 atoms + +Performance: 3.692 ns/day, 6.501 hours/ns, 85.461 timesteps/s +96.1% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 12.545 | 13.094 | 13.896 | 14.0 | 55.95 +Bond | 0.83177 | 0.90776 | 0.96459 | 5.1 | 3.88 +Kspace | 6.3904 | 7.1918 | 7.7297 | 18.8 | 30.73 +Neigh | 0.38941 | 0.38974 | 0.38988 | 0.0 | 1.67 +Comm | 0.65148 | 0.70795 | 0.7821 | 5.6 | 3.03 +Output | 0.0028274 | 0.0036304 | 0.0057163 | 2.0 | 0.02 +Modify | 1.0483 | 1.0571 | 1.0693 | 0.9 | 4.52 +Other | | 0.05109 | | | 0.22 + +Nlocal: 1125 ave 1207 max 1003 min +Histogram: 1 0 0 0 0 1 0 0 1 1 +Nghost: 5763 ave 5904 max 5656 min +Histogram: 2 0 0 0 0 0 1 0 0 1 +Neighs: 214633 ave 220347 max 204542 min +Histogram: 1 0 0 0 0 0 1 0 1 1 + +Total # of neighbors = 858532 +Ave neighs/atom = 190.785 +Ave special neighs/atom = 13.3333 +Neighbor list builds = 28 +Dangerous builds = 0 +Total wall time: 0:00:23 diff --git a/examples/USER/drude/butane/log.27Nov18.butane.nh.g++.1 b/examples/USER/drude/butane/log.27Nov18.butane.nh.g++.1 new file mode 100644 index 0000000000..fbbe14192e --- /dev/null +++ b/examples/USER/drude/butane/log.27Nov18.butane.nh.g++.1 @@ -0,0 +1,199 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# 250 butane system for drude polarizability example (Nose-Hoover) + +units real +boundary p p p + +atom_style full +bond_style harmonic +angle_style harmonic +dihedral_style opls +special_bonds lj/coul 0.0 0.0 0.5 + +pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.089 8.0 +pair_modify mix geometric tail yes +kspace_style pppm 1.0e-4 + +read_data data.butane + orthogonal box = (-19.1 -19.0999 -19.1) to (19.1 19.1 19.1) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 4500 atoms + scanning bonds ... + 5 = max bonds/atom + scanning angles ... + 6 = max angles/atom + scanning dihedrals ... + 9 = max dihedrals/atom + reading bonds ... + 4250 bonds + reading angles ... + 6000 angles + reading dihedrals ... + 6750 dihedrals + 5 = max # of 1-2 neighbors + 8 = max # of 1-3 neighbors + 12 = max # of 1-4 neighbors + 17 = max # of special neighbors + +group gBUTANE molecule 1:250 +4500 atoms in group gBUTANE +group gCORES type 1 2 3 +3500 atoms in group gCORES +group gDRUDES type 4 5 +1000 atoms in group gDRUDES + +pair_coeff 1 1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H +pair_coeff 1 2 lj/cut/coul/long 0.065997 3.500000 # C3H C2H +pair_coeff 1 3 lj/cut/coul/long 0.044496 2.958040 # C3H H +pair_coeff 2 2 lj/cut/coul/long 0.065997 3.500000 # C2H C2H +pair_coeff 2 3 lj/cut/coul/long 0.044496 2.958040 # C2H H +pair_coeff 3 3 lj/cut/coul/long 0.029999 2.500000 # H H +pair_coeff * 4*5 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes +pair_coeff 1 * thole 1.368000 +pair_coeff 2 * thole 1.368000 +pair_coeff 4 * thole 1.368000 +pair_coeff 5 * thole 1.368000 + +neighbor 2.0 bin + +variable vTEMP equal 260.0 +variable vTEMP_D equal 1.0 +variable vPRESS equal 1.0 + +velocity gCORES create ${vTEMP} 12345 +velocity gCORES create 260 12345 +velocity gDRUDES create ${vTEMP_D} 12345 +velocity gDRUDES create 1 12345 + +fix fDRUDE all drude C C N D D + +fix fSHAKE gCORES shake 0.0001 20 0 b 2 4 + 0 = # of size 2 clusters + 500 = # of size 3 clusters + 500 = # of size 4 clusters + 0 = # of frozen angles + +comm_modify vel yes +compute cTEMP_CORE gCORES temp/com +compute cTEMP all temp/drude + +fix fDIRECT all drude/transform/direct +fix fNVT1 gCORES nvt temp ${vTEMP} ${vTEMP} 100.0 +fix fNVT1 gCORES nvt temp 260 ${vTEMP} 100.0 +fix fNVT1 gCORES nvt temp 260 260 100.0 +fix fNVT2 gDRUDES nvt temp ${vTEMP_D} ${vTEMP_D} 20.0 +fix fNVT2 gDRUDES nvt temp 1 ${vTEMP_D} 20.0 +fix fNVT2 gDRUDES nvt temp 1 1 20.0 +fix fINVERSE all drude/transform/inverse + +fix fMOMENTUM all momentum 100 linear 1 1 1 + +thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2] +thermo 50 + +timestep 0.5 +run 2000 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) + G vector (1/distance) = 0.367867 + grid = 36 36 36 + stencil order = 5 + estimated absolute RMS force accuracy = 0.031354 + estimated relative force accuracy = 9.44215e-05 + using double precision FFTs + 3d grid and FFT values/proc = 79507 46656 +Rebuild special list taking Drude particles into account +Old max number of 1-2 to 1-4 neighbors: 17 +New max number of 1-2 to 1-4 neighbors: 17 (+0) +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10 + ghost atom cutoff = 10 + binsize = 5, bins = 8 8 8 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) pair thole, perpetual, skip from (1) + attributes: half, newton on + pair build: skip + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 26.29 | 26.29 | 26.29 Mbytes +Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2] + 0 0 6535.5187 2714.74 248.45112 3820.7787 3724.3278 140.75328 1.4735401 0 -518.77975 595169.42 -594696.41 4439.7916 55742.797 334.61375 18.435655 + 50 1.9199426 2090.3465 1466.1274 134.17896 624.21909 190.60044 660.09649 113.3603 0 -768.0633 595300.82 -594872.6 2826.2298 55742.797 184.22006 0.60185015 + 100 3.8672287 2131.9775 1633.3979 149.48744 498.57958 179.65934 694.88741 164.06284 0 -972.81644 595305.26 -594872.47 1226.789 55742.797 205.4291 0.16019587 + 150 5.7598403 2177.6381 1711.4959 156.63492 466.14214 134.74039 700.59918 168.27759 0 -965.58407 595300.38 -594872.27 4413.0226 55742.797 215.26856 0.12192183 + 200 7.7044377 2233.5218 1730.4556 158.3701 503.06611 188.43014 712.9189 165.88668 0 -988.5136 595295.4 -594871.06 2113.5946 55742.797 217.61368 0.22886584 + 250 9.6830325 2297.301 1773.2292 162.28471 524.07183 151.53589 821.1354 166.81416 0 -1042.1458 595297.16 -594870.43 1173.0574 55742.797 222.691 1.0389647 + 300 11.612487 2368.3956 1891.828 173.13879 476.56753 142.49028 789.96852 154.5939 0 -1037.1885 595297.25 -594870.54 2520.9226 55742.797 236.85673 3.051144 + 350 13.534112 2414.4805 1843.9331 168.75548 570.54737 181.42276 808.67959 163.12794 0 -1005.9572 595293.4 -594870.13 2879.5958 55742.797 231.57282 1.0738202 + 400 15.432559 2466.7093 1924.3089 176.11142 542.40037 167.48008 817.71904 181.25315 0 -1050.6473 595296.37 -594869.77 494.79722 55742.797 241.94266 0.38534823 + 450 17.325742 2522.7871 1875.8855 171.67974 646.90166 133.40905 944.20903 180.31147 0 -1037.0957 595295.5 -594869.43 63.401476 55742.797 235.86638 0.34369113 + 500 19.162983 2580.277 1955.7507 178.98895 624.52624 185.08446 827.39298 175.04156 0 -984.94513 595290.88 -594868.93 3484.9214 55742.797 245.79119 0.67067789 + 550 21.070935 2640.6835 1866.0349 170.77823 774.64852 176.89611 988.92025 176.49761 0 -991.07213 595292.32 -594868.91 1773.3487 55742.797 234.10561 1.7344182 + 600 22.994624 2690.8564 1876.0664 171.6963 814.79004 186.23916 1032.0131 182.3033 0 -1010.7649 595293.3 -594868.3 919.72494 55742.797 235.38014 1.7010295 + 650 24.877667 2732.1824 1963.5421 179.70202 768.64029 165.39218 949.23884 183.81872 0 -951.98446 595290.3 -594868.13 2658.9019 55742.797 246.76774 0.68037803 + 700 26.759878 2775.7295 1921.9362 175.89427 853.7933 175.21242 987.66711 186.48684 0 -918.75412 595291.36 -594868.18 670.06325 55742.797 241.62283 0.44222016 + 750 28.615888 2820.0743 2038.1503 186.53011 781.92393 168.58533 929.80575 193.62705 0 -939.93789 595298.09 -594868.25 398.72744 55742.797 256.20117 0.55407341 + 800 30.410775 2865.9592 1943.5754 177.87467 922.38383 197.16018 1009.2236 201.50387 0 -914.81706 595297.54 -594868.23 -717.10982 55742.797 244.0452 1.2420646 + 850 32.248099 2909.1134 2101.5572 192.33306 807.55624 195.1889 876.12791 184.47417 0 -876.31499 595296.17 -594868.09 -1403.423 55742.797 263.69793 1.8344087 + 900 34.102496 2938.1375 2038.9241 186.60092 899.21338 183.32678 989.0166 184.31256 0 -889.86015 595300.05 -594867.63 -1087.2756 55742.797 256.12731 1.0106116 + 950 35.940632 2965.6943 2007.942 183.76546 957.75234 227.45507 972.71509 206.37948 0 -880.42319 595299.46 -594867.83 -1848.76 55742.797 252.40652 0.53885795 + 1000 37.768527 2994.2318 2058.0187 188.34845 936.2131 170.68954 965.88084 205.36587 0 -833.14442 595294.86 -594867.44 327.63778 55742.797 258.71295 0.52143526 + 1050 39.603905 3022.9502 2095.3849 191.76817 927.56532 203.90713 935.91395 205.082 0 -845.07245 595294.32 -594866.59 -355.70498 55742.797 263.25608 0.94199109 + 1100 41.345196 3051.1765 2047.7198 187.4059 1003.4567 212.39896 989.65688 227.20813 0 -856.11279 595297.04 -594866.74 -1402.0226 55742.797 256.98382 1.677375 + 1150 43.126233 3071.8156 2127.8628 194.74053 943.95283 188.38429 926.24314 223.28057 0 -821.63214 595294.06 -594866.38 550.31162 55742.797 267.19152 1.343134 + 1200 44.919531 3087.7694 2015.2957 184.43847 1072.4737 199.90941 1034.9531 215.15479 0 -804.43316 595293.38 -594866.49 -333.57889 55742.797 253.2678 0.70913779 + 1250 46.708812 3102.5825 2176.9514 199.23308 925.63109 155.81514 956.83605 230.07299 0 -847.4765 595296.65 -594866.26 -932.66378 55742.797 273.66546 0.54750847 + 1300 48.515239 3116.8403 2087.6042 191.05609 1029.2361 209.96221 974.81036 241.13636 0 -823.38395 595292.74 -594866.03 -825.75374 55742.797 262.34482 0.76176534 + 1350 50.311301 3131.0791 2089.6528 191.24358 1041.4264 186.48162 998.11153 233.70979 0 -801.36955 595290.06 -594865.57 684.79541 55742.797 262.36803 1.3871258 + 1400 52.135502 3138.996 2186.2583 200.08485 952.73772 168.60362 957.20176 227.71916 0 -826.52254 595291.08 -594865.34 1796.7314 55742.797 274.47405 1.5135697 + 1450 53.920154 3139.5791 2010.7381 184.02136 1128.841 192.80138 1074.5202 245.37245 0 -807.31625 595288.01 -594864.55 -16.506503 55742.797 252.6314 0.8772328 + 1500 55.713369 3143.899 2099.4529 192.14047 1044.4461 186.04036 980.83507 242.01351 0 -784.81179 595285 -594864.63 2343.8872 55742.797 263.89144 0.6124176 + 1550 57.492258 3149.7317 2086.0668 190.91539 1063.6649 165.80538 1056.0892 230.89557 0 -813.37736 595289.09 -594864.84 2260.7336 55742.797 262.17651 0.69483863 + 1600 59.30172 3156.5347 2013.4253 184.26729 1143.1093 210.65899 1098.2888 243.95147 0 -835.61974 595290.47 -594864.64 -838.56538 55742.797 252.86557 1.1543025 + 1650 61.139585 3160.0034 2081.0689 190.45799 1078.9345 212.2197 1005.7495 250.37949 0 -813.72039 595289.15 -594864.85 796.20008 55742.797 261.22489 1.5557795 + 1700 62.942445 3155.5695 2113.3768 193.41478 1042.1927 146.0358 1019.0909 249.77844 0 -798.16322 595290.59 -594865.14 359.703 55742.797 265.47004 1.0739924 + 1750 64.762126 3151.7963 2063.5473 188.85442 1088.249 224.89092 997.01992 247.37169 0 -807.87664 595291.82 -594864.98 -1081.2896 55742.797 259.34344 0.69485895 + 1800 66.592646 3150.4284 2097.9263 192.00076 1052.5021 202.22769 974.42253 248.58755 0 -799.53819 595291.61 -594864.8 94.59915 55742.797 263.68436 0.65251966 + 1850 68.418504 3153.4497 2106.6304 192.79735 1046.8193 177.57201 971.73173 249.90467 0 -777.13268 595289.76 -594865.02 881.42667 55742.797 264.65056 0.99601086 + 1900 70.216536 3159.2067 2092.2719 191.48328 1066.9348 198.78887 969.41481 260.03017 0 -787.26086 595290.41 -594864.45 606.42691 55742.797 262.6612 1.4839999 + 1950 72.044671 3164.5166 2059.5681 188.49025 1104.9485 214.12266 1000.4479 263.39571 0 -799.45144 595291.13 -594864.69 -1248.7635 55742.797 258.62997 1.2624764 + 2000 73.841754 3171.2996 2080.1586 190.37468 1091.1409 179.21893 996.41501 248.41662 0 -760.00915 595292.04 -594864.94 940.6962 55742.797 261.39988 0.78376244 +Loop time of 73.8418 on 1 procs for 2000 steps with 4500 atoms + +Performance: 1.170 ns/day, 20.512 hours/ns, 27.085 timesteps/s +98.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 48.171 | 48.171 | 48.171 | 0.0 | 65.23 +Bond | 3.3962 | 3.3962 | 3.3962 | 0.0 | 4.60 +Kspace | 16.344 | 16.344 | 16.344 | 0.0 | 22.13 +Neigh | 1.6599 | 1.6599 | 1.6599 | 0.0 | 2.25 +Comm | 0.35976 | 0.35976 | 0.35976 | 0.0 | 0.49 +Output | 0.0045705 | 0.0045705 | 0.0045705 | 0.0 | 0.01 +Modify | 3.8475 | 3.8475 | 3.8475 | 0.0 | 5.21 +Other | | 0.05927 | | | 0.08 + +Nlocal: 4500 ave 4500 max 4500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 10103 ave 10103 max 10103 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 774433 ave 774433 max 774433 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 774433 +Ave neighs/atom = 172.096 +Ave special neighs/atom = 13.3333 +Neighbor list builds = 35 +Dangerous builds = 0 +Total wall time: 0:01:14 diff --git a/examples/USER/drude/butane/log.27Nov18.butane.nh.g++.4 b/examples/USER/drude/butane/log.27Nov18.butane.nh.g++.4 new file mode 100644 index 0000000000..d91bba57b1 --- /dev/null +++ b/examples/USER/drude/butane/log.27Nov18.butane.nh.g++.4 @@ -0,0 +1,199 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# 250 butane system for drude polarizability example (Nose-Hoover) + +units real +boundary p p p + +atom_style full +bond_style harmonic +angle_style harmonic +dihedral_style opls +special_bonds lj/coul 0.0 0.0 0.5 + +pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.089 8.0 +pair_modify mix geometric tail yes +kspace_style pppm 1.0e-4 + +read_data data.butane + orthogonal box = (-19.1 -19.0999 -19.1) to (19.1 19.1 19.1) + 2 by 1 by 2 MPI processor grid + reading atoms ... + 4500 atoms + scanning bonds ... + 5 = max bonds/atom + scanning angles ... + 6 = max angles/atom + scanning dihedrals ... + 9 = max dihedrals/atom + reading bonds ... + 4250 bonds + reading angles ... + 6000 angles + reading dihedrals ... + 6750 dihedrals + 5 = max # of 1-2 neighbors + 8 = max # of 1-3 neighbors + 12 = max # of 1-4 neighbors + 17 = max # of special neighbors + +group gBUTANE molecule 1:250 +4500 atoms in group gBUTANE +group gCORES type 1 2 3 +3500 atoms in group gCORES +group gDRUDES type 4 5 +1000 atoms in group gDRUDES + +pair_coeff 1 1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H +pair_coeff 1 2 lj/cut/coul/long 0.065997 3.500000 # C3H C2H +pair_coeff 1 3 lj/cut/coul/long 0.044496 2.958040 # C3H H +pair_coeff 2 2 lj/cut/coul/long 0.065997 3.500000 # C2H C2H +pair_coeff 2 3 lj/cut/coul/long 0.044496 2.958040 # C2H H +pair_coeff 3 3 lj/cut/coul/long 0.029999 2.500000 # H H +pair_coeff * 4*5 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes +pair_coeff 1 * thole 1.368000 +pair_coeff 2 * thole 1.368000 +pair_coeff 4 * thole 1.368000 +pair_coeff 5 * thole 1.368000 + +neighbor 2.0 bin + +variable vTEMP equal 260.0 +variable vTEMP_D equal 1.0 +variable vPRESS equal 1.0 + +velocity gCORES create ${vTEMP} 12345 +velocity gCORES create 260 12345 +velocity gDRUDES create ${vTEMP_D} 12345 +velocity gDRUDES create 1 12345 + +fix fDRUDE all drude C C N D D + +fix fSHAKE gCORES shake 0.0001 20 0 b 2 4 + 0 = # of size 2 clusters + 500 = # of size 3 clusters + 500 = # of size 4 clusters + 0 = # of frozen angles + +comm_modify vel yes +compute cTEMP_CORE gCORES temp/com +compute cTEMP all temp/drude + +fix fDIRECT all drude/transform/direct +fix fNVT1 gCORES nvt temp ${vTEMP} ${vTEMP} 100.0 +fix fNVT1 gCORES nvt temp 260 ${vTEMP} 100.0 +fix fNVT1 gCORES nvt temp 260 260 100.0 +fix fNVT2 gDRUDES nvt temp ${vTEMP_D} ${vTEMP_D} 20.0 +fix fNVT2 gDRUDES nvt temp 1 ${vTEMP_D} 20.0 +fix fNVT2 gDRUDES nvt temp 1 1 20.0 +fix fINVERSE all drude/transform/inverse + +fix fMOMENTUM all momentum 100 linear 1 1 1 + +thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2] +thermo 50 + +timestep 0.5 +run 2000 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) + G vector (1/distance) = 0.367867 + grid = 36 36 36 + stencil order = 5 + estimated absolute RMS force accuracy = 0.031354 + estimated relative force accuracy = 9.44215e-05 + using double precision FFTs + 3d grid and FFT values/proc = 26875 11664 +Rebuild special list taking Drude particles into account +Old max number of 1-2 to 1-4 neighbors: 17 +New max number of 1-2 to 1-4 neighbors: 17 (+0) +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10 + ghost atom cutoff = 10 + binsize = 5, bins = 8 8 8 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) pair thole, perpetual, skip from (1) + attributes: half, newton on + pair build: skip + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 16.75 | 17.03 | 17.13 Mbytes +Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2] + 0 0 6535.5187 2714.74 248.45112 3820.7787 3724.3278 140.75328 1.4735401 0 -518.77975 595169.42 -594696.41 4439.7916 55742.797 334.61375 18.435655 + 50 0.63524747 2090.3465 1466.1274 134.17896 624.2191 190.60044 660.09649 113.3603 0 -768.0633 595300.82 -594872.6 2826.2298 55742.797 184.22006 0.60185015 + 100 1.2804167 2131.9774 1633.3979 149.48744 498.57955 179.65934 694.88741 164.06284 0 -972.81644 595305.26 -594872.47 1226.789 55742.797 205.4291 0.16019587 + 150 1.9264774 2177.6381 1711.4959 156.63492 466.14218 134.74039 700.59917 168.27759 0 -965.58407 595300.38 -594872.27 4413.0227 55742.797 215.26856 0.12192187 + 200 2.5798194 2233.5217 1730.4557 158.3701 503.06601 188.43014 712.9189 165.88668 0 -988.5136 595295.4 -594871.06 2113.5944 55742.797 217.61368 0.22886584 + 250 3.234822 2297.3011 1773.2292 162.28471 524.07191 151.5359 821.1354 166.81416 0 -1042.1458 595297.16 -594870.43 1173.0577 55742.797 222.691 1.0389643 + 300 3.9885037 2368.3956 1891.828 173.13879 476.56759 142.49027 789.96852 154.5939 0 -1037.1885 595297.25 -594870.54 2520.9227 55742.797 236.85673 3.0511439 + 350 4.7276039 2414.4804 1843.9331 168.75548 570.54727 181.42277 808.6796 163.12794 0 -1005.9572 595293.4 -594870.13 2879.5954 55742.797 231.57282 1.0738212 + 400 5.3416793 2466.7094 1924.3089 176.11142 542.40044 167.48008 817.71904 181.25315 0 -1050.6473 595296.37 -594869.77 494.79737 55742.797 241.94266 0.38534799 + 450 6.0018888 2522.7872 1875.8855 171.67974 646.90169 133.40906 944.20903 180.31147 0 -1037.0957 595295.5 -594869.43 63.40141 55742.797 235.86638 0.34369111 + 500 6.6298664 2580.2771 1955.7507 178.98895 624.52635 185.08445 827.39297 175.04156 0 -984.94513 595290.88 -594868.93 3484.9216 55742.797 245.79119 0.67067791 + 550 7.2369561 2640.6835 1866.035 170.77823 774.64858 176.89609 988.92025 176.49761 0 -991.07212 595292.32 -594868.91 1773.3486 55742.797 234.10561 1.7344207 + 600 7.8453741 2690.8569 1876.0664 171.6963 814.7905 186.23916 1032.0131 182.3033 0 -1010.7649 595293.3 -594868.3 919.72487 55742.797 235.38014 1.7010285 + 650 8.4387105 2732.1825 1963.5421 179.70202 768.64035 165.39219 949.23884 183.81872 0 -951.98446 595290.3 -594868.13 2658.9017 55742.797 246.76774 0.68037827 + 700 9.0765064 2775.7294 1921.9362 175.89427 853.79318 175.21242 987.66712 186.48684 0 -918.75413 595291.36 -594868.18 670.06264 55742.797 241.62283 0.44222019 + 750 9.6925657 2820.0741 2038.1504 186.53011 781.92376 168.58531 929.80574 193.62706 0 -939.9379 595298.09 -594868.25 398.72752 55742.797 256.20117 0.55407442 + 800 10.302839 2865.959 1943.5754 177.87467 922.38359 197.16019 1009.2236 201.50386 0 -914.81706 595297.54 -594868.23 -717.10975 55742.797 244.0452 1.2420644 + 850 10.916842 2909.1138 2101.5572 192.33306 807.55656 195.18897 876.12792 184.47417 0 -876.31499 595296.17 -594868.09 -1403.4232 55742.797 263.69793 1.8344028 + 900 11.513051 2938.1376 2038.9242 186.60093 899.21343 183.32681 989.01659 184.31258 0 -889.86018 595300.05 -594867.63 -1087.2761 55742.797 256.12732 1.0106144 + 950 12.11419 2965.6942 2007.942 183.76546 957.75216 227.45503 972.71506 206.37949 0 -880.4232 595299.46 -594867.83 -1848.7603 55742.797 252.40653 0.53885876 + 1000 12.740639 2994.2317 2058.0187 188.34845 936.21302 170.68957 965.88085 205.36589 0 -833.14441 595294.86 -594867.44 327.6391 55742.797 258.71295 0.52143283 + 1050 13.346812 3022.9501 2095.3848 191.76817 927.56526 203.90712 935.91396 205.08197 0 -845.07232 595294.32 -594866.59 -355.70418 55742.797 263.25608 0.94198602 + 1100 13.938097 3051.1769 2047.7199 187.4059 1003.457 212.39892 989.65684 227.20812 0 -856.11277 595297.04 -594866.74 -1402.022 55742.797 256.98383 1.6773742 + 1150 14.508841 3071.8157 2127.8626 194.74051 943.95311 188.38445 926.24309 223.28071 0 -821.63207 595294.06 -594866.38 550.31236 55742.797 267.1915 1.3431353 + 1200 15.110682 3087.7694 2015.2955 184.43845 1072.4739 199.90932 1034.9531 215.15511 0 -804.43314 595293.38 -594866.49 -333.57793 55742.797 253.26777 0.70913778 + 1250 15.728746 3102.5825 2176.9518 199.23312 925.63076 155.81519 956.83624 230.0728 0 -847.47674 595296.65 -594866.26 -932.66685 55742.797 273.66551 0.54750805 + 1300 16.365541 3116.8403 2087.6045 191.05612 1029.2357 209.96201 974.81053 241.13608 0 -823.38398 595292.74 -594866.03 -825.75383 55742.797 262.34486 0.76175709 + 1350 16.943579 3131.0787 2089.6524 191.24354 1041.4264 186.48189 998.11168 233.71019 0 -801.37003 595290.06 -594865.57 684.79151 55742.797 262.36797 1.3871293 + 1400 17.542898 3138.996 2186.2582 200.08483 952.73785 168.60338 957.20178 227.71944 0 -826.52269 595291.08 -594865.34 1796.7295 55742.797 274.47403 1.5135537 + 1450 18.144658 3139.5791 2010.7377 184.02132 1128.8414 192.8015 1074.5205 245.37206 0 -807.3159 595288.01 -594864.55 -16.504608 55742.797 252.63135 0.87723467 + 1500 18.759382 3143.8991 2099.4529 192.14048 1044.4462 186.04014 980.83524 242.01309 0 -784.81131 595285 -594864.63 2343.8986 55742.797 263.89145 0.61241549 + 1550 19.331644 3149.7316 2086.068 190.9155 1063.6635 165.80546 1056.0893 230.89463 0 -813.37768 595289.09 -594864.84 2260.7364 55742.797 262.17666 0.69483626 + 1600 19.91757 3156.535 2013.4276 184.2675 1143.1073 210.65881 1098.2892 243.94955 0 -835.62037 595290.47 -594864.64 -838.57356 55742.797 252.86585 1.1542996 + 1650 20.503137 3160.0031 2081.0656 190.45768 1078.9375 212.2197 1005.7509 250.38023 0 -813.71955 595289.15 -594864.85 796.21731 55742.797 261.22447 1.5557945 + 1700 21.130273 3155.5677 2113.3761 193.41472 1042.1916 146.036 1019.0909 249.77802 0 -798.16357 595290.59 -594865.14 359.69262 55742.797 265.46995 1.074008 + 1750 21.735444 3151.796 2063.5487 188.85455 1088.2472 224.89093 997.02075 247.36817 0 -807.87592 595291.82 -594864.98 -1081.2667 55742.797 259.34362 0.69484916 + 1800 22.302735 3150.4232 2097.9294 192.00105 1052.4938 202.22751 974.42358 248.58229 0 -799.53722 595291.6 -594864.8 94.58692 55742.797 263.68474 0.65252808 + 1850 22.902581 3153.4477 2106.6272 192.79706 1046.8205 177.57166 971.73469 249.90348 0 -777.13298 595289.76 -594865.02 881.42516 55742.797 264.65016 0.99601444 + 1900 23.480426 3159.2037 2092.2693 191.48304 1066.9343 198.78895 969.41309 260.03288 0 -787.26163 595290.41 -594864.45 606.40366 55742.797 262.66088 1.4839893 + 1950 24.086136 3164.5139 2059.5653 188.48999 1104.9485 214.12027 1000.4493 263.39543 0 -799.45067 595291.13 -594864.69 -1248.7209 55742.797 258.62963 1.2624825 + 2000 24.655188 3171.2963 2080.1555 190.37439 1091.1408 179.21892 996.41486 248.41626 0 -760.00877 595292.04 -594864.94 940.70366 55742.797 261.39948 0.7837686 +Loop time of 24.6553 on 4 procs for 2000 steps with 4500 atoms + +Performance: 3.504 ns/day, 6.849 hours/ns, 81.119 timesteps/s +96.3% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 11.825 | 12.439 | 13.012 | 12.2 | 50.45 +Bond | 0.82239 | 0.89713 | 0.95859 | 5.7 | 3.64 +Kspace | 6.6353 | 7.2001 | 7.8139 | 15.7 | 29.20 +Neigh | 0.44976 | 0.44994 | 0.45003 | 0.0 | 1.82 +Comm | 0.55452 | 0.62432 | 0.70013 | 6.6 | 2.53 +Output | 0.003664 | 0.0043042 | 0.0061252 | 1.6 | 0.02 +Modify | 2.9457 | 2.959 | 2.9736 | 0.7 | 12.00 +Other | | 0.08099 | | | 0.33 + +Nlocal: 1125 ave 1166 max 1096 min +Histogram: 2 0 0 0 0 0 1 0 0 1 +Nghost: 5867.25 ave 5956 max 5793 min +Histogram: 1 1 0 0 0 0 1 0 0 1 +Neighs: 193608 ave 200510 max 186198 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 774433 +Ave neighs/atom = 172.096 +Ave special neighs/atom = 13.3333 +Neighbor list builds = 35 +Dangerous builds = 0 +Total wall time: 0:00:24 diff --git a/examples/USER/drude/butane/log.butane.lang.18Jul15.linux.1 b/examples/USER/drude/butane/log.butane.lang.18Jul15.linux.1 deleted file mode 100644 index a46d9b7cd5..0000000000 --- a/examples/USER/drude/butane/log.butane.lang.18Jul15.linux.1 +++ /dev/null @@ -1,171 +0,0 @@ -LAMMPS (18 Jul 2015) -# 250 butane system for drude polarizability example (Langevin) - -units real -boundary p p p - -atom_style full -bond_style harmonic -angle_style harmonic -dihedral_style opls -special_bonds lj/coul 0.0 0.0 0.5 - -pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.089 8.0 -pair_modify mix geometric tail yes -kspace_style pppm 1.0e-4 - -read_data data.butane - orthogonal box = (-19.1 -19.0999 -19.1) to (19.1 19.1 19.1) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 4500 atoms - scanning bonds ... - 5 = max bonds/atom - scanning angles ... - 6 = max angles/atom - scanning dihedrals ... - 9 = max dihedrals/atom - reading bonds ... - 4250 bonds - reading angles ... - 6000 angles - reading dihedrals ... - 6750 dihedrals - 5 = max # of 1-2 neighbors - 8 = max # of 1-3 neighbors - 12 = max # of 1-4 neighbors - 17 = max # of special neighbors - -comm_modify vel yes - -group gBUTANE molecule 1:250 -4500 atoms in group gBUTANE -group gCORES type 1 2 3 -3500 atoms in group gCORES -group gDRUDES type 4 5 -1000 atoms in group gDRUDES - -pair_coeff 1 1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H -pair_coeff 1 2 lj/cut/coul/long 0.065997 3.500000 # C3H C2H -pair_coeff 1 3 lj/cut/coul/long 0.044496 2.958040 # C3H H -pair_coeff 2 2 lj/cut/coul/long 0.065997 3.500000 # C2H C2H -pair_coeff 2 3 lj/cut/coul/long 0.044496 2.958040 # C2H H -pair_coeff 3 3 lj/cut/coul/long 0.029999 2.500000 # H H -pair_coeff * 4*5 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes -pair_coeff 1 * thole 1.368000 -pair_coeff 2 * thole 1.368000 -pair_coeff 4 * thole 1.368000 -pair_coeff 5 * thole 1.368000 - -neighbor 2.0 bin - -variable vTEMP equal 260.0 -variable vTEMP_D equal 1.0 -variable vPRESS equal 1.0 - -velocity gCORES create ${vTEMP} 12345 -velocity gCORES create 260 12345 -velocity gDRUDES create ${vTEMP_D} 12345 -velocity gDRUDES create 1 12345 - -fix fDRUDE all drude C C N D D - -fix fSHAKE gCORES shake 0.0001 20 0 b 2 4 - 0 = # of size 2 clusters - 500 = # of size 3 clusters - 500 = # of size 4 clusters - 0 = # of frozen angles - -fix fLANG all langevin/drude ${vTEMP} 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes -fix fLANG all langevin/drude 260 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes -fix fLANG all langevin/drude 260 100.0 200611 1 20.0 260514 zero yes -fix fNPH all nve - -compute cTEMP all temp/drude - -thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2] -thermo 50 - -timestep 0.5 -run 2000 -PPPM initialization ... - G vector (1/distance) = 0.367867 - grid = 36 36 36 - stencil order = 5 - estimated absolute RMS force accuracy = 0.031354 - estimated relative force accuracy = 9.44215e-05 - using double precision FFTs - 3d grid and FFT values/proc = 79507 46656 -Rebuild special list taking Drude particles into account -Old max number of 1-2 to 1-4 neighbors: 17 -New max number of 1-2 to 1-4 neighbors: 17 (+0) -Neighbor list info ... - 2 neighbor list requests - update every 1 steps, delay 10 steps, check yes - master list distance cutoff = 10 - ghost atom cutoff = 10 -Memory usage per processor = 20.1567 Mbytes -Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume cTEMP[1] cTEMP[2] - 0 0 6535.5187 2714.74 248.45112 3820.7787 3724.3278 140.75328 1.4735401 0 -518.77975 595169.42 -594696.41 -353319.1 55742.797 334.61375 18.435655 - 50 2.8944459 3475.1575 2067.5082 189.21692 1407.6493 846.00752 810.92425 115.58516 0 -764.28457 595242.38 -594842.96 3029.5187 55742.797 202.89871 152.54291 - 100 5.6009829 2975.2938 1988.4777 181.98411 986.81605 358.65377 931.63831 175.54125 0 -919.10691 595306.8 -594866.71 2010.6143 55742.797 231.36532 50.118891 - 150 8.2652578 2904.7202 1962.6821 179.62331 942.03808 234.91712 997.34884 195.22618 0 -909.31364 595293.23 -594869.37 4956.5664 55742.797 241.54715 14.313437 - 200 10.97319 2905.616 1909.813 174.78477 995.80302 228.33514 1082.3513 200.51771 0 -943.19777 595298.16 -594870.37 2973.6338 55742.797 238.34584 5.1137785 - 250 13.676164 2934.0626 1952.0155 178.6471 982.0471 212.76463 1131.5055 194.94566 0 -983.79846 595297.63 -594871 1591.8677 55742.797 244.66672 2.4161409 - 300 16.381759 2995.4781 2017.7772 184.66557 977.70088 213.25867 1133.9492 195.13329 0 -992.6543 595299.31 -594871.29 2817.7518 55742.797 253.21545 1.6812532 - 350 19.14905 3058.4882 1982.338 181.4222 1076.1502 228.54692 1197.9766 205.68279 0 -982.30502 595297.25 -594871 1408.2609 55742.797 248.83728 1.4672371 - 400 21.914272 3016.5895 1998.3531 182.8879 1018.2363 238.06518 1169.309 197.52924 0 -1014.8678 595298.98 -594870.78 1454.1926 55742.797 250.8778 1.3985907 - 450 24.629148 3014.232 1979.0496 181.12125 1035.1824 216.45567 1198.2831 197.81853 0 -1005.5029 595298.68 -594870.56 1296.2887 55742.797 248.44786 1.4025051 - 500 27.390589 3054.4694 2023.8824 185.22432 1030.587 220.97548 1197.2137 199.51957 0 -1014.3543 595298.28 -594871.05 2481.3102 55742.797 254.08894 1.4000969 - 550 30.147365 3088.0877 2020.1967 184.887 1067.8909 221.93439 1216.8427 213.27263 0 -1012.4867 595299.44 -594871.11 1697.8283 55742.797 253.63701 1.3687703 - 600 32.854639 3112.7966 2031.7038 185.94013 1081.0928 220.37419 1254.8806 208.09272 0 -1030.3329 595298.95 -594870.87 -75.358619 55742.797 255.05809 1.439614 - 650 35.725004 3155.4753 2025.6962 185.39031 1129.7792 221.82928 1284.1281 210.16702 0 -1015.1565 595299.63 -594870.82 1286.1601 55742.797 254.30974 1.4197689 - 700 38.70379 3134.5524 2054.9292 188.0657 1079.6232 225.36387 1243.5643 191.53984 0 -1010.9148 595301.25 -594871.18 700.78109 55742.797 257.97902 1.4421042 - 750 41.679769 3189.6098 2103.3042 192.49294 1086.3056 219.5641 1243.9772 203.81533 0 -1010.2161 595299.86 -594870.7 482.90086 55742.797 264.08828 1.3795515 - 800 44.637671 3173.7718 2053.4131 187.92694 1120.3587 219.52183 1256.8457 218.62858 0 -1003.175 595299.34 -594870.81 538.9293 55742.797 257.80398 1.4002525 - 850 47.531367 3221.5884 2084.0326 190.72922 1137.5559 224.32279 1277.7167 218.74781 0 -1011.3685 595298.54 -594870.4 145.40179 55742.797 261.66451 1.3777132 - 900 50.379314 3214.7916 2054.2398 188.00261 1160.5518 222.07439 1296.738 225.4151 0 -1013.6054 595300.61 -594870.68 490.09072 55742.797 257.90629 1.4047863 - 950 53.038527 3213.4974 2122.2134 194.2235 1091.284 221.85551 1252.3002 201.89089 0 -1014.1089 595300.04 -594870.69 1203.4321 55742.797 266.42418 1.4941572 - 1000 55.653448 3212.7244 2079.8287 190.34449 1132.8956 225.42816 1261.5078 204.71764 0 -986.95829 595298.68 -594870.48 790.47665 55742.797 261.10437 1.4611106 - 1050 58.290098 3216.1124 2106.2454 192.76212 1109.8669 213.54607 1261.1068 207.93437 0 -1001.5715 595299.05 -594870.2 69.145866 55742.797 264.43815 1.4332898 - 1100 60.921228 3218.0797 2082.4185 190.5815 1135.6611 236.95827 1266.8625 198.25038 0 -995.08857 595298.88 -594870.2 694.35787 55742.797 261.43907 1.4374087 - 1150 63.510285 3208.3968 2119.1968 193.94742 1089.2 210.20908 1236.1825 202.19163 0 -988.56762 595299.35 -594870.17 1528.4475 55742.797 266.08185 1.3950176 - 1200 66.140576 3219.1289 2078.071 190.18362 1141.0579 234.57015 1268.2146 206.93186 0 -997.01686 595298.32 -594869.97 939.70203 55742.797 260.89628 1.4263352 - 1250 68.774998 3268.5006 2115.3231 193.5929 1153.1775 241.50662 1262.3711 220.71001 0 -1000.1626 595298.37 -594869.62 -187.61926 55742.797 265.57695 1.4418423 - 1300 71.409732 3324.099 2138.7146 195.73368 1185.3844 242.3031 1279.7915 223.94399 0 -989.04901 595298.47 -594870.08 258.69655 55742.797 268.51674 1.4497832 - 1350 73.990336 3290.8471 2103.0993 192.47419 1187.7477 219.60844 1312.8653 221.57552 0 -993.69832 595297.61 -594870.21 1651.4259 55742.797 264.03877 1.4428477 - 1400 76.620059 3227.0141 2052.6998 187.86167 1174.3143 236.01325 1272.4804 217.65692 0 -979.6779 595297.5 -594869.66 595.11702 55742.797 257.67276 1.5108922 - 1450 79.249466 3253.5975 2107.984 192.92124 1145.6135 248.51645 1261.8304 208.79164 0 -1002.8333 595299.15 -594869.84 170.12671 55742.797 264.66781 1.4041436 - 1500 81.830899 3276.1976 2101.6206 192.33886 1174.577 242.38394 1288.61 204.9722 0 -989.7383 595298.02 -594869.67 619.26135 55742.797 263.84288 1.4691362 - 1550 84.449908 3271.9376 2117.6914 193.80965 1154.2463 234.62432 1268.5368 202.02117 0 -979.66071 595298.65 -594869.92 568.43047 55742.797 265.86458 1.4693675 - 1600 87.073373 3281.1387 2105.1447 192.66139 1175.994 219.69265 1288.3244 205.52796 0 -966.68015 595298.79 -594869.67 1351.6273 55742.797 264.27256 1.5056051 - 1650 89.695136 3287.675 2131.7955 195.10045 1155.8795 235.54527 1262.9178 220.26583 0 -991.68887 595298.56 -594869.72 -750.34342 55742.797 267.63101 1.4905169 - 1700 92.342235 3295.9626 2079.4982 190.31424 1216.4644 232.74928 1329.4691 218.51323 0 -992.04439 595297.16 -594869.38 589.94184 55742.797 261.06357 1.4590401 - 1750 94.911541 3315.2639 2097.2605 191.93983 1218.0035 241.24927 1312.3575 214.88139 0 -978.98823 595298.34 -594869.84 -92.971422 55742.797 263.26817 1.5389785 - 1800 97.525025 3241.5219 2086.8653 190.98847 1154.6566 221.03432 1282.1774 209.03793 0 -986.54668 595299 -594870.05 456.17335 55742.797 261.96332 1.5311996 - 1850 100.13804 3222.7069 2040.0335 186.70245 1182.6734 242.74754 1272.8794 221.80974 0 -982.51665 595296.99 -594869.24 279.00233 55742.797 256.09213 1.4766233 - 1900 102.70693 3190.3766 2032.3946 186.00335 1157.9819 213.06329 1268.187 220.21025 0 -971.50314 595297.54 -594869.51 499.15225 55742.797 255.16226 1.3935863 - 1950 105.30868 3208.3096 2053.9844 187.97923 1154.3252 212.46296 1277.2726 210.16078 0 -974.19087 595298.44 -594869.82 807.22906 55742.797 257.85261 1.4622515 - 2000 107.9105 3231.8811 2053.6913 187.9524 1178.1899 229.11239 1280.6492 220.1084 0 -979.25259 595297.02 -594869.45 474.05197 55742.797 257.80782 1.4833297 -Loop time of 107.911 on 1 procs for 2000 steps with 4500 atoms - -Pair time (%) = 65.8442 (61.0173) -Bond time (%) = 16.6061 (15.3887) -Kspce time (%) = 20.7451 (19.2244) -Neigh time (%) = 1.24307 (1.15195) -Comm time (%) = 0.386346 (0.358024) -Outpt time (%) = 0.00603366 (0.00559135) -Other time (%) = 3.07976 (2.854) - -Nlocal: 4500 ave 4500 max 4500 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 8739 ave 8739 max 8739 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 860638 ave 860638 max 860638 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 860638 -Ave neighs/atom = 191.253 -Ave special neighs/atom = 13.3333 -Neighbor list builds = 28 -Dangerous builds = 0 diff --git a/examples/USER/drude/butane/log.butane.lang.18Jul15.linux.4 b/examples/USER/drude/butane/log.butane.lang.18Jul15.linux.4 deleted file mode 100644 index 18e16e4975..0000000000 --- a/examples/USER/drude/butane/log.butane.lang.18Jul15.linux.4 +++ /dev/null @@ -1,171 +0,0 @@ -LAMMPS (18 Jul 2015) -# 250 butane system for drude polarizability example (Langevin) - -units real -boundary p p p - -atom_style full -bond_style harmonic -angle_style harmonic -dihedral_style opls -special_bonds lj/coul 0.0 0.0 0.5 - -pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.089 8.0 -pair_modify mix geometric tail yes -kspace_style pppm 1.0e-4 - -read_data data.butane - orthogonal box = (-19.1 -19.0999 -19.1) to (19.1 19.1 19.1) - 2 by 1 by 2 MPI processor grid - reading atoms ... - 4500 atoms - scanning bonds ... - 5 = max bonds/atom - scanning angles ... - 6 = max angles/atom - scanning dihedrals ... - 9 = max dihedrals/atom - reading bonds ... - 4250 bonds - reading angles ... - 6000 angles - reading dihedrals ... - 6750 dihedrals - 5 = max # of 1-2 neighbors - 8 = max # of 1-3 neighbors - 12 = max # of 1-4 neighbors - 17 = max # of special neighbors - -comm_modify vel yes - -group gBUTANE molecule 1:250 -4500 atoms in group gBUTANE -group gCORES type 1 2 3 -3500 atoms in group gCORES -group gDRUDES type 4 5 -1000 atoms in group gDRUDES - -pair_coeff 1 1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H -pair_coeff 1 2 lj/cut/coul/long 0.065997 3.500000 # C3H C2H -pair_coeff 1 3 lj/cut/coul/long 0.044496 2.958040 # C3H H -pair_coeff 2 2 lj/cut/coul/long 0.065997 3.500000 # C2H C2H -pair_coeff 2 3 lj/cut/coul/long 0.044496 2.958040 # C2H H -pair_coeff 3 3 lj/cut/coul/long 0.029999 2.500000 # H H -pair_coeff * 4*5 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes -pair_coeff 1 * thole 1.368000 -pair_coeff 2 * thole 1.368000 -pair_coeff 4 * thole 1.368000 -pair_coeff 5 * thole 1.368000 - -neighbor 2.0 bin - -variable vTEMP equal 260.0 -variable vTEMP_D equal 1.0 -variable vPRESS equal 1.0 - -velocity gCORES create ${vTEMP} 12345 -velocity gCORES create 260 12345 -velocity gDRUDES create ${vTEMP_D} 12345 -velocity gDRUDES create 1 12345 - -fix fDRUDE all drude C C N D D - -fix fSHAKE gCORES shake 0.0001 20 0 b 2 4 - 0 = # of size 2 clusters - 500 = # of size 3 clusters - 500 = # of size 4 clusters - 0 = # of frozen angles - -fix fLANG all langevin/drude ${vTEMP} 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes -fix fLANG all langevin/drude 260 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes -fix fLANG all langevin/drude 260 100.0 200611 1 20.0 260514 zero yes -fix fNPH all nve - -compute cTEMP all temp/drude - -thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2] -thermo 50 - -timestep 0.5 -run 2000 -PPPM initialization ... - G vector (1/distance) = 0.367867 - grid = 36 36 36 - stencil order = 5 - estimated absolute RMS force accuracy = 0.031354 - estimated relative force accuracy = 9.44215e-05 - using double precision FFTs - 3d grid and FFT values/proc = 26875 11664 -Rebuild special list taking Drude particles into account -Old max number of 1-2 to 1-4 neighbors: 17 -New max number of 1-2 to 1-4 neighbors: 17 (+0) -Neighbor list info ... - 2 neighbor list requests - update every 1 steps, delay 10 steps, check yes - master list distance cutoff = 10 - ghost atom cutoff = 10 -Memory usage per processor = 14.7792 Mbytes -Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume cTEMP[1] cTEMP[2] - 0 0 6535.5187 2714.74 248.45112 3820.7787 3724.3278 140.75328 1.4735401 0 -518.77975 595169.42 -594696.41 -353319.1 55742.797 334.61375 18.435655 - 50 0.91017509 3449.6475 2040.7698 186.76984 1408.8777 836.85155 816.32124 115.24642 0 -758.7276 595242.44 -594843.26 3042.2937 55742.797 199.51659 152.7045 - 100 1.829694 2917.9137 1947.102 178.19743 970.81176 363.96553 932.94225 165.60761 0 -931.00296 595306.34 -594867.04 1697.0127 55742.797 226.24749 49.885738 - 150 2.6620312 2853.3142 1959.0731 179.29301 894.24108 244.19792 978.17893 187.28366 0 -941.03478 595295.44 -594869.82 4597.2005 55742.797 241.05848 14.405808 - 200 3.4969041 2885.6715 1928.6381 176.50762 957.03347 227.09245 1066.5297 186.6858 0 -949.52603 595296.49 -594870.24 2602.8275 55742.797 240.70211 5.1458056 - 250 4.621171 2905.8961 1939.7876 177.52802 966.10847 215.77945 1122.1238 195.98218 0 -993.52132 595296.54 -594870.79 1808.1681 55742.797 243.04306 2.643716 - 300 5.5216351 2968.5517 1974.9277 180.74402 993.624 210.11413 1158.7871 194.142 0 -996.53154 595297.91 -594870.79 3371.8618 55742.797 247.7682 1.8321312 - 350 6.3789251 2996.151 1992.9982 182.39782 1003.1527 217.80518 1150.726 205.32316 0 -996.14478 595296.05 -594870.61 3022.9945 55742.797 250.15947 1.5176819 - 400 7.208317 2991.7201 1975.3852 180.78589 1016.3349 221.46133 1169.8254 213.90874 0 -1016.9906 595298.44 -594870.31 753.59124 55742.797 247.99744 1.3743032 - 450 8.0359671 3061.6051 2009.1302 183.87421 1052.4749 212.54169 1234.7697 205.71762 0 -1028.2259 595297.95 -594870.28 996.71341 55742.797 252.23801 1.3870863 - 500 8.8456361 3127.3783 2009.8033 183.93581 1117.5749 222.16507 1246.5854 215.82607 0 -994.66665 595298.3 -594870.63 2537.6157 55742.797 252.32947 1.367397 - 550 9.6647151 3181.037 2069.9836 189.44346 1111.0534 218.00575 1246.961 212.55852 0 -992.83597 595296.16 -594869.79 1333.8768 55742.797 259.86467 1.4641506 - 600 10.484356 3194.2009 2007.5349 183.7282 1186.666 228.93838 1309.4718 215.93595 0 -995.70641 595297.81 -594869.79 1336.7994 55742.797 252.00698 1.4677515 - 650 11.30116 3145.4387 2028.2544 185.62444 1117.1843 209.73722 1277.9793 217.12799 0 -1015.2398 595297.88 -594870.3 1442.6875 55742.797 254.61499 1.4639962 - 700 12.106719 3163.3345 2053.2645 187.91335 1110.07 209.45249 1257.3108 216.7541 0 -1000.1505 595296.63 -594869.92 1093.9724 55742.797 257.76091 1.4652884 - 750 12.924665 3145.6215 2010.7195 184.01966 1134.902 224.53065 1248.3301 222.25374 0 -988.4479 595298.83 -594870.59 470.73988 55742.797 252.39115 1.5116555 - 800 13.736913 3191.2614 2043.4195 187.01234 1147.842 225.71717 1239.3564 234.89539 0 -980.97352 595299.07 -594870.22 1472.0305 55742.797 256.53524 1.4309304 - 850 14.550736 3157.6279 2004.8472 183.48223 1152.7806 217.72587 1269.3398 224.40554 0 -987.51794 595299.15 -594870.32 293.76575 55742.797 251.69397 1.4007963 - 900 15.344895 3188.5027 2077.065 190.09155 1111.4377 216.92608 1251.4141 213.7672 0 -1000.1269 595299.5 -594870.05 702.56821 55742.797 260.7853 1.3847905 - 950 16.157597 3205.6761 2090.9807 191.3651 1114.6954 223.7729 1252.7887 225.91029 0 -1016.3682 595299.15 -594870.56 -19.492925 55742.797 262.50762 1.4603579 - 1000 16.969809 3231.5931 2078.7058 190.24172 1152.8873 228.77504 1273.1611 219.28923 0 -995.58473 595296.82 -594869.57 1292.4071 55742.797 260.98775 1.3954023 - 1050 17.771785 3264.2837 2106.0113 192.7407 1158.2724 224.16481 1278.5557 212.91309 0 -985.93386 595298.71 -594870.14 1357.1588 55742.797 264.40381 1.4463397 - 1100 18.572331 3243.3355 2125.1664 194.49376 1118.1691 227.38559 1247.5134 210.61488 0 -996.85878 595299.68 -594870.17 650.53225 55742.797 266.82195 1.4240918 - 1150 19.40463 3255.4144 2096.5982 191.87922 1158.8162 234.11389 1267.4257 217.02225 0 -989.70892 595299.81 -594869.84 688.78475 55742.797 263.2133 1.4631154 - 1200 20.321045 3266.2609 2088.3727 191.12642 1177.8882 225.40174 1284.1097 225.77008 0 -985.63518 595297.81 -594869.57 182.80287 55742.797 262.21901 1.3550749 - 1250 21.233994 3277.4365 2093.1481 191.56346 1184.2884 250.33569 1267.9985 235.70102 0 -999.80819 595299.96 -594869.9 780.87528 55742.797 262.80001 1.4077597 - 1300 22.113268 3280.4141 2121.4996 194.15818 1158.9145 228.23585 1259.7304 230.65174 0 -989.06345 595298.99 -594869.63 932.19341 55742.797 266.34543 1.4646736 - 1350 23.007421 3272.2214 2088.047 191.09662 1184.1744 224.66504 1284.656 217.03214 0 -970.5252 595297.72 -594869.37 63.097535 55742.797 262.16781 1.3823451 - 1400 23.903494 3239.3096 2099.1837 192.11584 1140.1259 221.3215 1252.8691 215.64014 0 -978.70393 595298.89 -594869.89 1125.3057 55742.797 263.59141 1.3221979 - 1450 24.833224 3226.293 2042.7354 186.94973 1183.5576 241.40449 1273.025 233.66813 0 -994.70934 595299.55 -594869.38 -412.31857 55742.797 256.45155 1.4245996 - 1500 25.736203 3245.4596 2097.0431 191.91994 1148.4164 250.3854 1248.1507 212.36871 0 -990.48467 595297.36 -594869.36 245.49743 55742.797 263.28349 1.4252034 - 1550 26.633033 3308.5518 2113.8467 193.45778 1194.7051 234.5293 1286.7563 233.20552 0 -987.36764 595297.06 -594869.48 1324.7098 55742.797 265.37419 1.4864431 - 1600 27.530123 3319.786 2130.8949 195.01803 1188.8911 234.06508 1292.3987 225.94876 0 -992.81161 595299.1 -594869.81 343.14209 55742.797 267.51024 1.5104547 - 1650 28.41116 3239.0425 2066.8485 189.15654 1172.194 219.46922 1303.0071 210.00869 0 -989.28577 595298.63 -594869.64 -505.97551 55742.797 259.48305 1.4300292 - 1700 29.313339 3281.3023 2054.581 188.03383 1226.7213 224.72686 1339.1948 208.65914 0 -974.24634 595297.79 -594869.4 331.11846 55742.797 257.92342 1.4735531 - 1750 30.216241 3237.8348 2043.3835 187.00904 1194.4513 238.16066 1281.9383 221.74494 0 -976.72731 595299.4 -594870.06 612.69867 55742.797 256.53793 1.4116726 - 1800 31.113153 3242.1274 2087.94 191.08683 1154.1873 240.53142 1256.6966 210.49591 0 -983.16111 595299.34 -594869.72 -8.1277769 55742.797 262.14149 1.4166426 - 1850 31.993161 3249.8016 2079.8947 190.35052 1169.9069 233.21641 1269.4077 215.23716 0 -975.12835 595296.5 -594869.33 1156.1724 55742.797 261.13101 1.4122227 - 1900 32.891621 3251.9579 2097.6037 191.97124 1154.3541 243.13703 1228.3357 235.37914 0 -983.06313 595300.37 -594869.8 293.60486 55742.797 263.33664 1.4715416 - 1950 33.791255 3202.0703 2076.0894 190.00227 1125.9809 233.71337 1217.6976 227.58496 0 -981.8352 595298.07 -594869.25 -544.65606 55742.797 260.61868 1.5018224 - 2000 34.690323 3215.7987 2015.5993 184.46625 1200.1994 242.43605 1281.6846 227.48326 0 -980.70325 595298.82 -594869.52 248.82508 55742.797 253.04055 1.4169879 -Loop time of 34.6904 on 4 procs for 2000 steps with 4500 atoms - -Pair time (%) = 16.514 (47.6038) -Bond time (%) = 4.35555 (12.5555) -Kspce time (%) = 10.6198 (30.613) -Neigh time (%) = 0.393407 (1.13405) -Comm time (%) = 1.18699 (3.42165) -Outpt time (%) = 0.00467861 (0.0134867) -Other time (%) = 1.6161 (4.65863) - -Nlocal: 1125 ave 1219 max 1009 min -Histogram: 1 0 0 0 0 1 1 0 0 1 -Nghost: 5768 ave 5890 max 5664 min -Histogram: 1 1 0 0 0 0 1 0 0 1 -Neighs: 215002 ave 223956 max 206872 min -Histogram: 2 0 0 0 0 0 0 0 1 1 - -Total # of neighbors = 860008 -Ave neighs/atom = 191.113 -Ave special neighs/atom = 13.3333 -Neighbor list builds = 29 -Dangerous builds = 0 diff --git a/examples/USER/drude/butane/log.butane.nh.18Jul15.linux.3 b/examples/USER/drude/butane/log.butane.nh.18Jul15.linux.3 deleted file mode 100644 index 26ef8dad2c..0000000000 --- a/examples/USER/drude/butane/log.butane.nh.18Jul15.linux.3 +++ /dev/null @@ -1,177 +0,0 @@ -LAMMPS (18 Jul 2015) -# 250 butane system for drude polarizability example (Nose-Hoover) - -units real -boundary p p p - -atom_style full -bond_style harmonic -angle_style harmonic -dihedral_style opls -special_bonds lj/coul 0.0 0.0 0.5 - -pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.089 8.0 -pair_modify mix geometric tail yes -kspace_style pppm 1.0e-4 - -read_data data.butane - orthogonal box = (-19.1 -19.0999 -19.1) to (19.1 19.1 19.1) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 4500 atoms - scanning bonds ... - 5 = max bonds/atom - scanning angles ... - 6 = max angles/atom - scanning dihedrals ... - 9 = max dihedrals/atom - reading bonds ... - 4250 bonds - reading angles ... - 6000 angles - reading dihedrals ... - 6750 dihedrals - 5 = max # of 1-2 neighbors - 8 = max # of 1-3 neighbors - 12 = max # of 1-4 neighbors - 17 = max # of special neighbors - -group gBUTANE molecule 1:250 -4500 atoms in group gBUTANE -group gCORES type 1 2 3 -3500 atoms in group gCORES -group gDRUDES type 4 5 -1000 atoms in group gDRUDES - -pair_coeff 1 1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H -pair_coeff 1 2 lj/cut/coul/long 0.065997 3.500000 # C3H C2H -pair_coeff 1 3 lj/cut/coul/long 0.044496 2.958040 # C3H H -pair_coeff 2 2 lj/cut/coul/long 0.065997 3.500000 # C2H C2H -pair_coeff 2 3 lj/cut/coul/long 0.044496 2.958040 # C2H H -pair_coeff 3 3 lj/cut/coul/long 0.029999 2.500000 # H H -pair_coeff * 4*5 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes -pair_coeff 1 * thole 1.368000 -pair_coeff 2 * thole 1.368000 -pair_coeff 4 * thole 1.368000 -pair_coeff 5 * thole 1.368000 - -neighbor 2.0 bin - -variable vTEMP equal 260.0 -variable vTEMP_D equal 1.0 -variable vPRESS equal 1.0 - -velocity gCORES create ${vTEMP} 12345 -velocity gCORES create 260 12345 -velocity gDRUDES create ${vTEMP_D} 12345 -velocity gDRUDES create 1 12345 - -fix fDRUDE all drude C C N D D - -fix fSHAKE gCORES shake 0.0001 20 0 b 2 4 - 0 = # of size 2 clusters - 500 = # of size 3 clusters - 500 = # of size 4 clusters - 0 = # of frozen angles - -comm_modify vel yes -compute cTEMP_CORE gCORES temp/com -compute cTEMP all temp/drude - -fix fDIRECT all drude/transform/direct -fix fNVT1 gCORES nvt temp ${vTEMP} ${vTEMP} 100.0 -fix fNVT1 gCORES nvt temp 260 ${vTEMP} 100.0 -fix fNVT1 gCORES nvt temp 260 260 100.0 -fix fNVT2 gDRUDES nvt temp ${vTEMP_D} ${vTEMP_D} 20.0 -fix fNVT2 gDRUDES nvt temp 1 ${vTEMP_D} 20.0 -fix fNVT2 gDRUDES nvt temp 1 1 20.0 -fix fINVERSE all drude/transform/inverse - -fix fMOMENTUM all momentum 100 linear 1 1 1 - -thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2] -thermo 50 - -timestep 0.5 -run 2000 -PPPM initialization ... - G vector (1/distance) = 0.367867 - grid = 36 36 36 - stencil order = 5 - estimated absolute RMS force accuracy = 0.031354 - estimated relative force accuracy = 9.44215e-05 - using double precision FFTs - 3d grid and FFT values/proc = 79507 46656 -Rebuild special list taking Drude particles into account -Old max number of 1-2 to 1-4 neighbors: 17 -New max number of 1-2 to 1-4 neighbors: 17 (+0) -Neighbor list info ... - 2 neighbor list requests - update every 1 steps, delay 10 steps, check yes - master list distance cutoff = 10 - ghost atom cutoff = 10 -Memory usage per processor = 20.1567 Mbytes -Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume cTEMP[1] cTEMP[2] - 0 0 6535.5187 2714.74 248.45112 3820.7787 3724.3278 140.75328 1.4735401 0 -518.77975 595169.42 -594696.41 -353319.1 55742.797 334.61375 18.435655 - 50 2.8816051 2130.0808 1490.8248 136.43926 639.25601 192.16834 670.26518 115.15685 0 -766.5636 595300.83 -594872.6 2829.5958 55742.797 187.32686 0.60253137 - 100 5.569447 2172.0554 1656.5476 151.60609 515.50773 180.41449 708.03397 165.80788 0 -971.62525 595305.35 -594872.47 1231.388 55742.797 208.34096 0.16151117 - 150 8.2248161 2216.471 1733.4485 158.644 483.02256 136.16281 713.34485 169.62608 0 -964.30363 595300.47 -594872.27 4400.6234 55742.797 218.02975 0.12336382 - 200 10.911476 2271.1314 1750.9955 160.2499 520.13587 190.12953 725.63606 167.04635 0 -987.11203 595295.5 -594871.06 2107.4949 55742.797 220.19714 0.23035017 - 250 13.588019 2333.7822 1793.0252 164.09642 540.75705 153.18169 833.95287 168.1507 0 -1041.2955 595297.2 -594870.43 1165.6922 55742.797 225.18334 1.0339004 - 300 16.26521 2403.6147 1909.3441 174.74185 494.27059 144.27299 803.8452 155.85505 0 -1036.4615 595297.31 -594870.55 2511.3721 55742.797 239.06243 3.0455686 - 350 18.937858 2448.2389 1862.67 170.47027 585.56885 181.70523 821.7917 164.10713 0 -1005.4167 595293.5 -594870.12 2874.0826 55742.797 233.92745 1.0806435 - 400 21.590191 2498.6994 1942.5496 177.7808 556.14976 168.5792 828.99117 182.0756 0 -1050.149 595296.43 -594869.77 485.86761 55742.797 244.23632 0.3882729 - 450 24.247025 2552.9641 1890.0917 172.97989 662.87241 134.42613 957.3361 181.42951 0 -1036.4237 595295.53 -594869.43 66.452669 55742.797 237.65323 0.34464588 - 500 26.850275 2608.55 1970.0729 180.29971 638.4771 187.01392 838.62129 176.10775 0 -985.23355 595290.89 -594868.93 3471.1633 55742.797 247.59402 0.66791252 - 550 29.482354 2667.002 1875.8227 171.67399 791.17931 178.48765 1003.6885 176.78989 0 -991.21705 595292.35 -594868.92 1767.0543 55742.797 235.34039 1.7252619 - 600 32.10773 2715.2399 1883.279 172.35639 831.96094 186.79504 1047.6877 183.04311 0 -1010.5423 595293.27 -594868.29 931.85523 55742.797 236.28437 1.7094253 - 650 34.715398 2754.4497 1970.794 180.3657 783.65568 166.02823 963.09399 184.8464 0 -952.45217 595290.25 -594868.11 2640.017 55742.797 247.67755 0.68709275 - 700 37.337317 2795.9461 1928.2674 176.4737 867.67874 176.09641 1002.4636 186.11483 0 -920.14356 595291.32 -594868.18 664.78904 55742.797 242.41897 0.44316381 - 750 39.927419 2838.2052 2043.2258 186.99461 794.97945 170.34991 941.73148 193.53082 0 -940.49604 595298.1 -594868.23 410.24758 55742.797 256.84035 0.55229077 - 800 42.469991 2881.9788 1945.9722 178.09402 936.00667 197.5203 1021.5571 202.83524 0 -915.18511 595297.49 -594868.21 -716.81442 55742.797 244.35112 1.2303511 - 850 45.05362 2923.3858 2106.5752 192.79231 816.81052 195.94987 886.41681 184.36064 0 -878.10485 595296.29 -594868.1 -1407.5711 55742.797 264.3276 1.8387296 - 900 47.651245 2950.6673 2039.6221 186.6648 911.04515 183.79618 1000.7954 184.49766 0 -890.38965 595299.97 -594867.63 -1085.794 55742.797 256.21167 1.0198208 - 950 50.451391 2976.6436 2006.5932 183.64202 970.05039 228.60059 985.21322 206.18529 0 -881.65815 595299.54 -594867.83 -1851.9703 55742.797 252.23637 0.54012241 - 1000 53.018937 3003.743 2056.8471 188.24122 946.89587 171.73287 976.85675 207.05097 0 -836.24563 595294.95 -594867.45 282.61914 55742.797 258.5658 0.52076804 - 1050 55.532595 3031.3535 2095.4846 191.7773 935.86887 203.54188 945.75569 204.8504 0 -846.10969 595294.45 -594866.62 -376.91112 55742.797 263.27093 0.93584407 - 1100 58.115412 3058.5347 2047.3098 187.36838 1011.2249 211.94076 1001.093 223.66214 0 -855.82424 595297.13 -594866.78 -1381.6531 55742.797 256.93409 1.6724456 - 1150 60.799698 3078.3996 2123.1811 194.31206 955.21855 189.50189 937.18685 224.21465 0 -823.63222 595294.38 -594866.43 524.70113 55742.797 266.5974 1.3568376 - 1200 63.295243 3093.556 2005.8939 183.57802 1087.6621 201.3428 1044.9909 219.39202 0 -805.37122 595293.83 -594866.52 -370.32492 55742.797 252.0829 0.71475597 - 1250 65.797931 3108.5155 2175.8972 199.13661 932.61826 156.6571 969.72254 225.30586 0 -850.00503 595297.25 -594866.31 -1015.3093 55742.797 273.53154 0.55100418 - 1300 68.300441 3122.9792 2090.3719 191.30939 1032.6073 209.92015 984.36624 236.75408 0 -825.27583 595292.92 -594866.08 -798.51816 55742.797 262.69421 0.75855207 - 1350 70.793202 3136.8213 2084.47 190.76925 1052.3513 186.49827 1004.7564 234.55362 0 -798.08335 595290.25 -594865.63 702.53782 55742.797 261.71553 1.3884089 - 1400 73.326733 3144.9028 2180.3659 199.54558 964.53687 170.02484 962.43948 235.07761 0 -829.27156 595291.77 -594865.51 1682.2488 55742.797 273.7286 1.5246324 - 1450 75.821906 3146.3365 2013.3816 184.26329 1132.9549 193.77936 1084.1403 252.3227 0 -821.23045 595288.54 -594864.6 -160.21484 55742.797 252.96375 0.87780357 - 1500 78.325264 3150.6861 2107.4863 192.87569 1043.1998 185.11752 988.72532 245.47682 0 -796.86739 595285.46 -594864.71 2242.3101 55742.797 264.90216 0.61222547 - 1550 80.779931 3156.3483 2074.5953 189.86552 1081.7531 166.52863 1062.4971 238.93518 0 -810.65247 595289.34 -594864.9 2224.9015 55742.797 260.73559 0.68881715 - 1600 83.275807 3163.8714 2000.6756 183.10045 1163.1958 210.70823 1110.4519 256.16493 0 -840.1463 595290.73 -594864.71 -830.17884 55742.797 251.26533 1.1443116 - 1650 85.768304 3169.3489 2056.4309 188.20313 1112.918 214.6419 1021.762 268.00157 0 -815.69477 595289 -594864.8 813.12089 55742.797 258.12835 1.5476743 - 1700 88.261463 3168.7666 2119.4079 193.96675 1049.3587 147.25006 1027.6415 246.49221 0 -797.55007 595290.74 -594865.22 412.59618 55742.797 266.23017 1.0703149 - 1750 90.746918 3168.2304 2066.7675 189.14913 1101.463 224.44009 1005.0052 243.56874 0 -797.83359 595291.25 -594864.96 -858.91314 55742.797 259.74684 0.69942293 - 1800 93.246077 3169.7579 2109.6017 193.06929 1060.1562 204.57678 981.05867 249.37843 0 -801.42006 595291.51 -594864.95 137.05559 55742.797 265.15197 0.65571606 - 1850 95.734661 3174.8532 2133.5052 195.25692 1041.348 175.87566 982.18775 244.55231 0 -786.49546 595290.43 -594865.21 882.03323 55742.797 268.02768 1.006296 - 1900 98.221874 3180.3842 2106.4808 192.78367 1073.9034 207.8879 977.47746 250.68948 0 -788.04039 595290.55 -594864.66 574.40162 55742.797 264.45175 1.4759897 - 1950 100.72148 3182.921 2084.8893 190.80763 1098.0317 207.26976 1007.5583 256.52302 0 -800.37789 595291.76 -594864.71 -981.75066 55742.797 261.81202 1.271779 - 2000 103.20588 3185.2881 2079.8136 190.3431 1105.4745 185.44441 1008.6997 251.0561 0 -766.97142 595292.22 -594864.97 661.65951 55742.797 261.35563 0.78600155 -Loop time of 103.206 on 1 procs for 2000 steps with 4500 atoms - -Pair time (%) = 60.3651 (58.49) -Bond time (%) = 16.8315 (16.3087) -Kspce time (%) = 20.1106 (19.4859) -Neigh time (%) = 1.52801 (1.48054) -Comm time (%) = 0.328804 (0.318591) -Outpt time (%) = 0.00495553 (0.00480159) -Other time (%) = 4.03695 (3.91155) - -Nlocal: 4500 ave 4500 max 4500 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 10060 ave 10060 max 10060 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 774908 ave 774908 max 774908 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 774908 -Ave neighs/atom = 172.202 -Ave special neighs/atom = 13.3333 -Neighbor list builds = 35 -Dangerous builds = 0 diff --git a/examples/USER/drude/butane/log.butane.nh.18Jul15.linux.4 b/examples/USER/drude/butane/log.butane.nh.18Jul15.linux.4 deleted file mode 100644 index 6a310d08dc..0000000000 --- a/examples/USER/drude/butane/log.butane.nh.18Jul15.linux.4 +++ /dev/null @@ -1,177 +0,0 @@ -LAMMPS (18 Jul 2015) -# 250 butane system for drude polarizability example (Nose-Hoover) - -units real -boundary p p p - -atom_style full -bond_style harmonic -angle_style harmonic -dihedral_style opls -special_bonds lj/coul 0.0 0.0 0.5 - -pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.089 8.0 -pair_modify mix geometric tail yes -kspace_style pppm 1.0e-4 - -read_data data.butane - orthogonal box = (-19.1 -19.0999 -19.1) to (19.1 19.1 19.1) - 2 by 1 by 2 MPI processor grid - reading atoms ... - 4500 atoms - scanning bonds ... - 5 = max bonds/atom - scanning angles ... - 6 = max angles/atom - scanning dihedrals ... - 9 = max dihedrals/atom - reading bonds ... - 4250 bonds - reading angles ... - 6000 angles - reading dihedrals ... - 6750 dihedrals - 5 = max # of 1-2 neighbors - 8 = max # of 1-3 neighbors - 12 = max # of 1-4 neighbors - 17 = max # of special neighbors - -group gBUTANE molecule 1:250 -4500 atoms in group gBUTANE -group gCORES type 1 2 3 -3500 atoms in group gCORES -group gDRUDES type 4 5 -1000 atoms in group gDRUDES - -pair_coeff 1 1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H -pair_coeff 1 2 lj/cut/coul/long 0.065997 3.500000 # C3H C2H -pair_coeff 1 3 lj/cut/coul/long 0.044496 2.958040 # C3H H -pair_coeff 2 2 lj/cut/coul/long 0.065997 3.500000 # C2H C2H -pair_coeff 2 3 lj/cut/coul/long 0.044496 2.958040 # C2H H -pair_coeff 3 3 lj/cut/coul/long 0.029999 2.500000 # H H -pair_coeff * 4*5 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes -pair_coeff 1 * thole 1.368000 -pair_coeff 2 * thole 1.368000 -pair_coeff 4 * thole 1.368000 -pair_coeff 5 * thole 1.368000 - -neighbor 2.0 bin - -variable vTEMP equal 260.0 -variable vTEMP_D equal 1.0 -variable vPRESS equal 1.0 - -velocity gCORES create ${vTEMP} 12345 -velocity gCORES create 260 12345 -velocity gDRUDES create ${vTEMP_D} 12345 -velocity gDRUDES create 1 12345 - -fix fDRUDE all drude C C N D D - -fix fSHAKE gCORES shake 0.0001 20 0 b 2 4 - 0 = # of size 2 clusters - 500 = # of size 3 clusters - 500 = # of size 4 clusters - 0 = # of frozen angles - -comm_modify vel yes -compute cTEMP_CORE gCORES temp/com -compute cTEMP all temp/drude - -fix fDIRECT all drude/transform/direct -fix fNVT1 gCORES nvt temp ${vTEMP} ${vTEMP} 100.0 -fix fNVT1 gCORES nvt temp 260 ${vTEMP} 100.0 -fix fNVT1 gCORES nvt temp 260 260 100.0 -fix fNVT2 gDRUDES nvt temp ${vTEMP_D} ${vTEMP_D} 20.0 -fix fNVT2 gDRUDES nvt temp 1 ${vTEMP_D} 20.0 -fix fNVT2 gDRUDES nvt temp 1 1 20.0 -fix fINVERSE all drude/transform/inverse - -fix fMOMENTUM all momentum 100 linear 1 1 1 - -thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2] -thermo 50 - -timestep 0.5 -run 2000 -PPPM initialization ... - G vector (1/distance) = 0.367867 - grid = 36 36 36 - stencil order = 5 - estimated absolute RMS force accuracy = 0.031354 - estimated relative force accuracy = 9.44215e-05 - using double precision FFTs - 3d grid and FFT values/proc = 26875 11664 -Rebuild special list taking Drude particles into account -Old max number of 1-2 to 1-4 neighbors: 17 -New max number of 1-2 to 1-4 neighbors: 17 (+0) -Neighbor list info ... - 2 neighbor list requests - update every 1 steps, delay 10 steps, check yes - master list distance cutoff = 10 - ghost atom cutoff = 10 -Memory usage per processor = 14.7792 Mbytes -Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume cTEMP[1] cTEMP[2] - 0 0 6535.5187 2714.74 248.45112 3820.7787 3724.3278 140.75328 1.4735401 0 -518.77975 595169.42 -594696.41 -353319.1 55742.797 334.61375 18.435655 - 50 1.019057 2130.0808 1490.8248 136.43926 639.25599 192.16834 670.26518 115.15685 0 -766.5636 595300.83 -594872.6 2829.5958 55742.797 187.32686 0.60253137 - 100 2.043848 2172.0553 1656.5476 151.60609 515.50769 180.41449 708.03397 165.80788 0 -971.62525 595305.35 -594872.47 1231.388 55742.797 208.34096 0.16151117 - 150 3.0405529 2216.471 1733.4485 158.644 483.02256 136.16281 713.34485 169.62608 0 -964.30363 595300.47 -594872.27 4400.6233 55742.797 218.02975 0.12336381 - 200 4.0440719 2271.1314 1750.9955 160.2499 520.13584 190.12953 725.63606 167.04635 0 -987.11203 595295.5 -594871.06 2107.495 55742.797 220.19714 0.23035002 - 250 5.0482569 2333.7821 1793.0252 164.09642 540.75694 153.18169 833.95288 168.1507 0 -1041.2955 595297.2 -594870.43 1165.6922 55742.797 225.18334 1.0339003 - 300 6.044857 2403.6147 1909.3441 174.74185 494.27053 144.273 803.8452 155.85505 0 -1036.4615 595297.31 -594870.55 2511.3723 55742.797 239.06243 3.0455683 - 350 7.0382209 2448.239 1862.67 170.47027 585.56896 181.70522 821.79171 164.10713 0 -1005.4167 595293.5 -594870.12 2874.0826 55742.797 233.92745 1.0806438 - 400 8.025661 2498.6992 1942.5496 177.78079 556.14963 168.5792 828.99116 182.0756 0 -1050.149 595296.43 -594869.77 485.86784 55742.797 244.23632 0.38827289 - 450 9.010309 2552.9639 1890.0917 172.97988 662.87225 134.42613 957.3361 181.42951 0 -1036.4237 595295.53 -594869.43 66.452466 55742.797 237.65323 0.34464586 - 500 9.979717 2608.5501 1970.0729 180.29971 638.47718 187.01392 838.62128 176.10774 0 -985.23355 595290.89 -594868.93 3471.1636 55742.797 247.59402 0.66791289 - 550 10.965174 2667.002 1875.8227 171.674 791.17932 178.48766 1003.6885 176.78987 0 -991.21707 595292.35 -594868.92 1767.0547 55742.797 235.34039 1.7252612 - 600 11.944224 2715.2397 1883.279 172.35639 831.96067 186.79504 1047.6877 183.0431 0 -1010.5423 595293.27 -594868.29 931.85415 55742.797 236.28437 1.7094243 - 650 12.916431 2754.4495 1970.794 180.36571 783.65547 166.02823 963.09393 184.84638 0 -952.45216 595290.25 -594868.11 2640.0169 55742.797 247.67755 0.68709272 - 700 13.889729 2795.9463 1928.2674 176.47369 867.67893 176.09642 1002.4636 186.11482 0 -920.14357 595291.32 -594868.18 664.78857 55742.797 242.41896 0.44316458 - 750 14.849284 2838.2051 2043.2257 186.9946 794.97938 170.34989 941.73149 193.53082 0 -940.49605 595298.1 -594868.23 410.24692 55742.797 256.84034 0.55228895 - 800 15.765569 2881.9786 1945.9721 178.09402 936.00653 197.52035 1021.5571 202.83523 0 -915.18508 595297.49 -594868.21 -716.8133 55742.797 244.35111 1.2303486 - 850 16.62147 2923.386 2106.5752 192.79231 816.81079 195.9499 886.4168 184.36063 0 -878.10486 595296.29 -594868.1 -1407.5716 55742.797 264.3276 1.8387295 - 900 17.476931 2950.6672 2039.6221 186.6648 911.04508 183.7962 1000.7955 184.49765 0 -890.38971 595299.97 -594867.63 -1085.795 55742.797 256.21167 1.0198179 - 950 18.332394 2976.6435 2006.5931 183.64202 970.05037 228.60059 985.21322 206.18531 0 -881.65816 595299.54 -594867.83 -1851.9704 55742.797 252.23636 0.54012295 - 1000 19.192022 3003.7432 2056.8471 188.24122 946.89612 171.73291 976.85679 207.05089 0 -836.24565 595294.95 -594867.45 282.61893 55742.797 258.5658 0.52076763 - 1050 20.070536 3031.3535 2095.4845 191.77729 935.86893 203.54188 945.75571 204.85039 0 -846.10968 595294.45 -594866.62 -376.91144 55742.797 263.27092 0.93584075 - 1100 20.978902 3058.5346 2047.3099 187.36839 1011.2247 211.94079 1001.093 223.66207 0 -855.82432 595297.13 -594866.78 -1381.6546 55742.797 256.93411 1.6724371 - 1150 21.886788 3078.3992 2123.1811 194.31206 955.21814 189.50191 937.18689 224.21463 0 -823.63239 595294.38 -594866.43 524.69914 55742.797 266.59741 1.3568273 - 1200 22.731807 3093.5558 2005.8937 183.57801 1087.6621 201.34278 1044.991 219.39206 0 -805.37129 595293.83 -594866.52 -370.32731 55742.797 252.08289 0.71475598 - 1250 23.577332 3108.5154 2175.8971 199.1366 932.61825 156.65715 969.72264 225.30585 0 -850.00508 595297.25 -594866.31 -1015.3099 55742.797 273.53152 0.55101046 - 1300 24.41954 3122.979 2090.3725 191.30944 1032.6065 209.92008 984.36627 236.75348 0 -825.27575 595292.92 -594866.08 -798.51517 55742.797 262.69428 0.75855174 - 1350 25.260247 3136.8213 2084.4701 190.76926 1052.3512 186.49846 1004.7564 234.55382 0 -798.08358 595290.25 -594865.63 702.53502 55742.797 261.71554 1.3884097 - 1400 26.111855 3144.9027 2180.3656 199.54555 964.53705 170.02479 962.43949 235.07796 0 -829.2718 595291.77 -594865.51 1682.2458 55742.797 273.72857 1.5246347 - 1450 26.950639 3146.3362 2013.3813 184.26326 1132.955 193.77936 1084.1402 252.32287 0 -821.23025 595288.54 -594864.6 -160.21134 55742.797 252.96371 0.87779957 - 1500 27.790502 3150.6919 2107.4861 192.87567 1043.2058 185.11758 988.72513 245.47693 0 -796.86696 595285.47 -594864.71 2242.3607 55742.797 264.90213 0.61222945 - 1550 28.619789 3156.3482 2074.5978 189.86575 1081.7504 166.52858 1062.4966 238.93331 0 -810.65249 595289.34 -594864.9 2224.9023 55742.797 260.7359 0.68881915 - 1600 29.460929 3163.8714 2000.6737 183.10027 1163.1978 210.70797 1110.4522 256.16659 0 -840.14623 595290.73 -594864.71 -830.17835 55742.797 251.26509 1.1443132 - 1650 30.299437 3169.3484 2056.4317 188.20321 1112.9167 214.64223 1021.7623 268.00145 0 -815.6963 595289 -594864.8 813.10459 55742.797 258.12846 1.5476742 - 1700 31.139599 3168.7665 2119.4084 193.96679 1049.3581 147.25025 1027.6419 246.49323 0 -797.55219 595290.74 -594865.22 412.56019 55742.797 266.23023 1.0703144 - 1750 31.982883 3168.2311 2066.7649 189.14889 1101.4662 224.43981 1005.0038 243.56888 0 -797.82899 595291.25 -594864.96 -858.8853 55742.797 259.74652 0.69941609 - 1800 32.826623 3169.7582 2109.6043 193.06952 1060.154 204.57671 981.05578 249.38028 0 -801.42264 595291.51 -594864.95 137.07377 55742.797 265.1523 0.65571522 - 1850 33.670608 3174.8602 2133.4946 195.25594 1041.3657 175.87741 982.18471 244.56078 0 -786.49062 595290.44 -594865.21 882.07943 55742.797 268.02634 1.0063027 - 1900 34.515605 3180.392 2106.493 192.78478 1073.8991 207.88481 977.47602 250.68433 0 -788.04013 595290.55 -594864.66 574.47687 55742.797 264.45328 1.4759962 - 1950 35.361549 3182.9198 2084.8984 190.80846 1098.0214 207.26715 1007.5534 256.52264 0 -800.37486 595291.76 -594864.71 -981.72234 55742.797 261.81317 1.2717649 - 2000 36.208456 3185.292 2079.8093 190.34271 1105.4827 185.44479 1008.7001 251.06381 0 -766.97114 595292.22 -594864.97 661.65731 55742.797 261.3551 0.78598984 -Loop time of 36.2086 on 4 procs for 2000 steps with 4500 atoms - -Pair time (%) = 15.6569 (43.2408) -Bond time (%) = 4.33273 (11.966) -Kspce time (%) = 10.271 (28.3662) -Neigh time (%) = 0.435532 (1.20284) -Comm time (%) = 0.83936 (2.31813) -Outpt time (%) = 0.00456434 (0.0126057) -Other time (%) = 4.66849 (12.8933) - -Nlocal: 1125 ave 1165 max 1096 min -Histogram: 2 0 0 0 0 0 1 0 0 1 -Nghost: 5854.5 ave 5931 max 5788 min -Histogram: 2 0 0 0 0 0 0 0 1 1 -Neighs: 193727 ave 200966 max 187020 min -Histogram: 2 0 0 0 0 0 0 0 0 2 - -Total # of neighbors = 774908 -Ave neighs/atom = 172.202 -Ave special neighs/atom = 13.3333 -Neighbor list builds = 35 -Dangerous builds = 0 diff --git a/examples/USER/drude/ethanol/log.27Nov18.ethanol.lang.g++.1 b/examples/USER/drude/ethanol/log.27Nov18.ethanol.lang.g++.1 new file mode 100644 index 0000000000..127d859702 --- /dev/null +++ b/examples/USER/drude/ethanol/log.27Nov18.ethanol.lang.g++.1 @@ -0,0 +1,277 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +units real +boundary p p p + +atom_style full +bond_style harmonic +angle_style harmonic +dihedral_style opls +special_bonds lj/coul 0.0 0.0 0.5 + +pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.600 8.0 +kspace_style pppm 1.0e-4 + +comm_modify vel yes +read_data data.ethanol + orthogonal box = (-14.0138 -14.0278 -14.0189) to (14.0169 14.0177 14.0857) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 3000 atoms + scanning bonds ... + 5 = max bonds/atom + scanning angles ... + 6 = max angles/atom + scanning dihedrals ... + 9 = max dihedrals/atom + reading bonds ... + 2750 bonds + reading angles ... + 3250 angles + reading dihedrals ... + 3000 dihedrals + 5 = max # of 1-2 neighbors + 6 = max # of 1-3 neighbors + 10 = max # of 1-4 neighbors + 11 = max # of special neighbors + +pair_coeff 1 1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H +pair_coeff 1 2 lj/cut/coul/long 0.065997 3.500000 # C3H CTO +pair_coeff 1 3 lj/cut/coul/long 0.044496 2.958040 # C3H H +pair_coeff 1 4 lj/cut/coul/long 0.105921 3.304542 # C3H OH +pair_coeff 1 5 lj/cut/coul/long 0.000000 0.000000 # C3H HO +pair_coeff 2 2 lj/cut/coul/long 0.065997 3.500000 # CTO CTO +pair_coeff 2 3 lj/cut/coul/long 0.044496 2.958040 # CTO H +pair_coeff 2 4 lj/cut/coul/long 0.105921 3.304542 # CTO OH +pair_coeff 2 5 lj/cut/coul/long 0.000000 0.000000 # CTO HO +pair_coeff 3 3 lj/cut/coul/long 0.029999 2.500000 # H H +pair_coeff 3 4 lj/cut/coul/long 0.071413 2.792848 # H OH +pair_coeff 3 5 lj/cut/coul/long 0.000000 0.000000 # H HO +pair_coeff 4 4 lj/cut/coul/long 0.169996 3.120000 # OH OH +pair_coeff 4 5 lj/cut/coul/long 0.000000 0.000000 # OH HO +pair_coeff 5 5 lj/cut/coul/long 0.000000 0.000000 # HO HO +pair_coeff * 6*8 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes +pair_coeff 1 1 thole 2.051000 +pair_coeff 1 2 thole 1.580265 +pair_coeff 1 4 thole 1.416087 +pair_coeff 1 6 thole 2.051000 +pair_coeff 1 7 thole 1.580265 +pair_coeff 1 8 thole 1.416087 +pair_coeff 2 2 thole 1.217570 +pair_coeff 2 4 thole 1.091074 +pair_coeff 2 6 thole 1.580265 +pair_coeff 2 7 thole 1.217570 +pair_coeff 2 8 thole 1.091074 +pair_coeff 4 4 thole 0.977720 +pair_coeff 4 6 thole 1.416087 +pair_coeff 4 7 thole 1.091074 +pair_coeff 4 8 thole 0.977720 +pair_coeff 6 6 thole 2.051000 +pair_coeff 6 7 thole 1.580265 +pair_coeff 6 8 thole 1.416087 +pair_coeff 7 7 thole 1.217570 +pair_coeff 7 8 thole 1.091074 +pair_coeff 8 8 thole 0.977720 + +group gETHANOL molecule 1:250 +3000 atoms in group gETHANOL +group gATOMS type 1 2 3 4 5 +2250 atoms in group gATOMS +group gDRUDES type 6 7 8 +750 atoms in group gDRUDES + +neighbor 2.0 bin + +variable vTEMP equal 300.0 +variable vTEMP_D equal 1.0 +variable vPRESS equal 1.0 + +velocity gATOMS create ${vTEMP} 12345 +velocity gATOMS create 300 12345 +velocity gDRUDES create ${vTEMP_D} 12345 +velocity gDRUDES create 1 12345 + +fix fDRUDE all drude C C N C N D D D + +fix fSHAKE gATOMS shake 0.0001 20 0 b 2 3 5 + 250 = # of size 2 clusters + 250 = # of size 3 clusters + 250 = # of size 4 clusters + 0 = # of frozen angles + +fix fLANG all langevin/drude ${vTEMP} 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes +fix fLANG all langevin/drude 300 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes +fix fLANG all langevin/drude 300 100.0 200611 1 20.0 260514 zero yes +fix fNPH all nph iso ${vPRESS} ${vPRESS} 500.0 +fix fNPH all nph iso 1 ${vPRESS} 500.0 +fix fNPH all nph iso 1 1 500.0 + +compute cTEMP all temp/drude + +thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2] +thermo 20 + +timestep 0.5 +run 2000 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) + G vector (1/distance) = 0.379738 + grid = 30 30 30 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0289979 + estimated relative force accuracy = 8.73262e-05 + using double precision FFTs + 3d grid and FFT values/proc = 50653 27000 +Rebuild special list taking Drude particles into account +Old max number of 1-2 to 1-4 neighbors: 11 +New max number of 1-2 to 1-4 neighbors: 11 (+0) +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10 + ghost atom cutoff = 10 + binsize = 5, bins = 6 6 6 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) pair thole, perpetual, skip from (1) + attributes: half, newton on + pair build: skip + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 22.48 | 22.48 | 22.48 Mbytes +Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2] + 0 0 13868.828 2013.3852 270.28772 11855.443 3145.896 51.880809 0.00019113234 0 8481.5109 514734.14 -514557.98 170210.19 22094.109 381.62759 10.134301 + 20 0.81254506 10970.11 5646.659 758.03805 5323.451 2059.6082 2216.9981 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1.2739114 +Loop time of 70.805 on 1 procs for 2000 steps with 3000 atoms + +Performance: 1.220 ns/day, 19.668 hours/ns, 28.247 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 | 46.358 | 46.358 | 46.358 | 0.0 | 65.47 +Bond | 1.8097 | 1.8097 | 1.8097 | 0.0 | 2.56 +Kspace | 10.643 | 10.643 | 10.643 | 0.0 | 15.03 +Neigh | 1.8814 | 1.8814 | 1.8814 | 0.0 | 2.66 +Comm | 0.38412 | 0.38412 | 0.38412 | 0.0 | 0.54 +Output | 0.008601 | 0.008601 | 0.008601 | 0.0 | 0.01 +Modify | 9.6728 | 9.6728 | 9.6728 | 0.0 | 13.66 +Other | | 0.04689 | | | 0.07 + +Nlocal: 3000 ave 3000 max 3000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 10022 ave 10022 max 10022 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 721937 ave 721937 max 721937 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 721937 +Ave neighs/atom = 240.646 +Ave special neighs/atom = 10.5 +Neighbor list builds = 49 +Dangerous builds = 0 +Total wall time: 0:01:10 diff --git a/examples/USER/drude/ethanol/log.27Nov18.ethanol.lang.g++.4 b/examples/USER/drude/ethanol/log.27Nov18.ethanol.lang.g++.4 new file mode 100644 index 0000000000..a0f886795b --- /dev/null +++ b/examples/USER/drude/ethanol/log.27Nov18.ethanol.lang.g++.4 @@ -0,0 +1,277 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +units real +boundary p p p + +atom_style full +bond_style harmonic +angle_style harmonic +dihedral_style opls +special_bonds lj/coul 0.0 0.0 0.5 + +pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.600 8.0 +kspace_style pppm 1.0e-4 + +comm_modify vel yes +read_data data.ethanol + orthogonal box = (-14.0138 -14.0278 -14.0189) to (14.0169 14.0177 14.0857) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 3000 atoms + scanning bonds ... + 5 = max bonds/atom + scanning angles ... + 6 = max angles/atom + scanning dihedrals ... + 9 = max dihedrals/atom + reading bonds ... + 2750 bonds + reading angles ... + 3250 angles + reading dihedrals ... + 3000 dihedrals + 5 = max # of 1-2 neighbors + 6 = max # of 1-3 neighbors + 10 = max # of 1-4 neighbors + 11 = max # of special neighbors + +pair_coeff 1 1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H +pair_coeff 1 2 lj/cut/coul/long 0.065997 3.500000 # C3H CTO +pair_coeff 1 3 lj/cut/coul/long 0.044496 2.958040 # C3H H +pair_coeff 1 4 lj/cut/coul/long 0.105921 3.304542 # C3H OH +pair_coeff 1 5 lj/cut/coul/long 0.000000 0.000000 # C3H HO +pair_coeff 2 2 lj/cut/coul/long 0.065997 3.500000 # CTO CTO +pair_coeff 2 3 lj/cut/coul/long 0.044496 2.958040 # CTO H +pair_coeff 2 4 lj/cut/coul/long 0.105921 3.304542 # CTO OH +pair_coeff 2 5 lj/cut/coul/long 0.000000 0.000000 # CTO HO +pair_coeff 3 3 lj/cut/coul/long 0.029999 2.500000 # H H +pair_coeff 3 4 lj/cut/coul/long 0.071413 2.792848 # H OH +pair_coeff 3 5 lj/cut/coul/long 0.000000 0.000000 # H HO +pair_coeff 4 4 lj/cut/coul/long 0.169996 3.120000 # OH OH +pair_coeff 4 5 lj/cut/coul/long 0.000000 0.000000 # OH HO +pair_coeff 5 5 lj/cut/coul/long 0.000000 0.000000 # HO HO +pair_coeff * 6*8 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes +pair_coeff 1 1 thole 2.051000 +pair_coeff 1 2 thole 1.580265 +pair_coeff 1 4 thole 1.416087 +pair_coeff 1 6 thole 2.051000 +pair_coeff 1 7 thole 1.580265 +pair_coeff 1 8 thole 1.416087 +pair_coeff 2 2 thole 1.217570 +pair_coeff 2 4 thole 1.091074 +pair_coeff 2 6 thole 1.580265 +pair_coeff 2 7 thole 1.217570 +pair_coeff 2 8 thole 1.091074 +pair_coeff 4 4 thole 0.977720 +pair_coeff 4 6 thole 1.416087 +pair_coeff 4 7 thole 1.091074 +pair_coeff 4 8 thole 0.977720 +pair_coeff 6 6 thole 2.051000 +pair_coeff 6 7 thole 1.580265 +pair_coeff 6 8 thole 1.416087 +pair_coeff 7 7 thole 1.217570 +pair_coeff 7 8 thole 1.091074 +pair_coeff 8 8 thole 0.977720 + +group gETHANOL molecule 1:250 +3000 atoms in group gETHANOL +group gATOMS type 1 2 3 4 5 +2250 atoms in group gATOMS +group gDRUDES type 6 7 8 +750 atoms in group gDRUDES + +neighbor 2.0 bin + +variable vTEMP equal 300.0 +variable vTEMP_D equal 1.0 +variable vPRESS equal 1.0 + +velocity gATOMS create ${vTEMP} 12345 +velocity gATOMS create 300 12345 +velocity gDRUDES create ${vTEMP_D} 12345 +velocity gDRUDES create 1 12345 + +fix fDRUDE all drude C C N C N D D D + +fix fSHAKE gATOMS shake 0.0001 20 0 b 2 3 5 + 250 = # of size 2 clusters + 250 = # of size 3 clusters + 250 = # of size 4 clusters + 0 = # of frozen angles + +fix fLANG all langevin/drude ${vTEMP} 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes +fix fLANG all langevin/drude 300 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes +fix fLANG all langevin/drude 300 100.0 200611 1 20.0 260514 zero yes +fix fNPH all nph iso ${vPRESS} ${vPRESS} 500.0 +fix fNPH all nph iso 1 ${vPRESS} 500.0 +fix fNPH all nph iso 1 1 500.0 + +compute cTEMP all temp/drude + +thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2] +thermo 20 + +timestep 0.5 +run 2000 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) + G vector (1/distance) = 0.379738 + grid = 30 30 30 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0289979 + estimated relative force accuracy = 8.73262e-05 + using double precision FFTs + 3d grid and FFT values/proc = 17908 7200 +Rebuild special list taking Drude particles into account +Old max number of 1-2 to 1-4 neighbors: 11 +New max number of 1-2 to 1-4 neighbors: 11 (+0) +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10 + ghost atom cutoff = 10 + binsize = 5, bins = 6 6 6 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) pair thole, perpetual, skip from (1) + attributes: half, newton on + pair build: skip + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 15.7 | 15.72 | 15.75 Mbytes +Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2] + 0 0 13868.828 2013.3852 270.28772 11855.443 3145.896 51.880809 0.00019113234 0 8481.5109 514734.14 -514557.98 170210.19 22094.109 381.62759 10.134301 + 20 0.24885726 10977.523 5649.4234 758.40916 5328.0995 2062.3542 2228.2406 127.20787 0 1716.2655 514097.62 -514903.59 75540.788 22441.711 900.66455 425.71754 + 40 0.52037597 8971.222 5307.0197 712.44303 3664.2023 1468.3101 1727.552 263.87374 0 1220.3688 513944.03 -514959.93 46704.125 23047.094 909.55742 251.59686 + 60 0.7807281 7598.3479 4774.3053 640.92856 2824.0427 1194.6424 1771.6653 314.85756 0 553.7151 513952.94 -514963.78 37329.2 23513.994 850.78607 150.29302 + 80 1.1572349 6500.0058 4632.0732 621.83456 1867.9325 914.32396 1444.2432 317.24546 0 213.11185 513930.12 -514951.11 33256.762 23919.646 847.27963 94.966975 + 100 1.4178512 5591.472 4319.1968 579.83234 1272.2752 772.47756 1235.8385 306.35435 0 -56.189361 513990.32 -514976.52 21842.59 24315.598 802.33641 59.89227 + 120 1.6625795 4952.7621 3881.7096 521.1017 1071.0525 630.88446 1260.1912 299.84296 0 -147.16305 514014.9 -514987.6 17191.638 24657.729 728.78527 35.811873 + 140 1.8984792 4373.9331 3440.7548 461.90553 933.1783 670.28429 1238.1308 300.44834 0 -260.57044 513963.56 -514978.68 17252.83 24939.26 649.60264 23.329745 + 160 2.1378865 3923.229 3251.2581 436.46647 671.97091 632.15143 1144.4146 307.32283 0 -436.68046 514014.07 -514989.31 17845.825 25185.451 617.37678 13.751529 + 180 2.3720722 3558.1557 3060.4382 410.84977 497.71755 621.70998 1085.8204 297.1556 0 -495.34468 513968.54 -514980.16 9885.361 25415.428 582.93783 8.7536435 + 200 2.6049569 3228.4936 2864.4301 384.53659 364.06344 591.33636 1077.5366 257.50944 0 -521.78289 513950.34 -514990.87 5925.7217 25605.563 546.61818 5.8335105 + 220 2.8426785 2922.7424 2668.2075 358.19461 254.5349 552.38924 1045.2135 238.94168 0 -548.4004 513955.45 -514989.06 7136.0052 25761.984 509.82785 3.9098309 + 240 3.1155882 2721.0612 2574.2915 345.58681 146.76969 547.99652 1035.0606 226.51837 0 -609.21222 513928.45 -514982.05 6971.5001 25907.597 492.18737 3.0535008 + 260 3.3265111 2525.7518 2460.9077 330.36557 64.844061 536.78625 1022.3311 211.32544 0 -633.92783 513919.8 -514991.47 4534.5804 26040.845 470.74694 2.3688839 + 280 3.5478129 2338.039 2324.3983 312.03981 13.640708 519.09042 970.16233 197.76897 0 -621.27548 513937.32 -514989.43 2909.3322 26151.714 444.74626 1.9753672 + 300 3.7687361 2194.851 2189.0474 293.86956 5.8036062 530.74509 982.33557 190.99311 0 -652.24555 513946.83 -514992.86 4224.0345 26246.212 418.93917 1.6487718 + 320 3.9801922 2045.4487 2132.0617 286.21949 -86.613049 531.53518 935.90803 188.46605 0 -683.41226 513935.36 -514994.47 1710.734 26338.321 408.05555 1.5540687 + 340 4.1992741 1929.4058 2083.452 279.69387 -154.04619 509.02677 906.15126 186.62933 0 -668.19644 513908.44 -514996.09 2736.2098 26423.379 398.77795 1.4580758 + 360 4.4171088 1853.7062 1992.5995 267.49733 -138.89334 525.34864 891.90355 178.21101 0 -654.64078 513920.99 -515000.71 3816.7092 26502.12 381.4127 1.3381612 + 380 4.6217661 1760.9358 1947.0158 261.37793 -186.07997 516.89889 919.58404 172.53796 0 -676.7004 513879.46 -514997.86 2960.1316 26580.115 372.6985 1.2814406 + 400 4.8376818 1687.8988 1905.9227 255.86137 -218.0239 535.53769 922.01769 176.20545 0 -684.03744 513833.88 -515001.63 1297.7806 26648.895 364.81828 1.2874209 + 420 5.0580292 1605.7787 1889.0825 253.60065 -283.30381 517.08427 857.72563 180.14818 0 -663.15367 513826.27 -515001.38 2609.7387 26710.911 361.58795 1.2934789 + 440 5.2613502 1518.1412 1794.5719 240.91304 -276.43077 531.12246 893.04683 188.1283 0 -667.41934 513778.75 -515000.06 1448.9344 26771.955 343.49864 1.2323194 + 460 5.474973 1455.6369 1796.1847 241.12955 -340.54775 527.17043 846.65061 188.73693 0 -650.46422 513749.2 -515001.84 161.63078 26825.587 343.80003 1.2432983 + 480 5.6766918 1423.3951 1780.4686 239.01974 -357.07349 555.37302 861.62016 179.25213 0 -642.3686 513685.22 -514996.17 1728.4109 26870.018 340.77367 1.2753301 + 500 5.8963647 1414.5107 1792.5124 240.63656 -378.00171 562.06965 865.1732 172.51081 0 -638.43613 513657.38 -514996.7 2852.5688 26914.25 343.08652 1.2642269 + 520 6.1024427 1359.8646 1801.0839 241.78725 -441.21931 573.29268 804.68005 169.59419 0 -635.98014 513644.06 -514996.86 917.97283 26965.499 344.72952 1.264948 + 540 6.3182905 1320.129 1763.768 236.77776 -443.63898 564.54015 851.18104 169.65891 0 -632.69528 513601.13 -514997.45 393.78094 27008.775 337.59196 1.2311182 + 560 6.5340965 1288.8769 1741.0597 233.72927 -452.18283 588.80641 843.7906 164.29947 0 -639.61003 513594.25 -515003.72 2022.6586 27046.802 333.24957 1.2004945 + 580 6.738924 1250.8612 1701.7462 228.45162 -450.88502 575.95012 877.76059 153.10544 0 -632.21312 513575.06 -515000.54 319.43567 27087.59 325.68988 1.258461 + 600 6.9839265 1237.7875 1721.861 231.15193 -484.0735 586.2774 851.82884 147.45104 0 -635.34134 513566.1 -515000.39 -1495.8007 27125.397 329.56435 1.2147693 + 620 7.1886187 1255.6883 1741.6598 233.80983 -485.97147 593.81316 838.06474 152.61844 0 -618.48814 513546.09 -514998.07 -239.76675 27153.275 333.35756 1.2207133 + 640 7.403686 1231.453 1734.6085 232.86323 -503.15553 592.94732 847.14537 157.31902 0 -622.72191 513517.06 -514994.9 1262.739 27174.105 331.96914 1.3100227 + 660 7.6087363 1205.9453 1720.7921 231.00844 -514.84686 605.97637 844.61854 156.72343 0 -608.38182 513480.7 -514994.48 541.26917 27199.495 329.34901 1.2412012 + 680 7.8241618 1168.82 1693.3809 227.32862 -524.5609 610.91696 859.82389 152.3176 0 -616.40743 513464.95 -514996.17 -529.37821 27221.433 324.05587 1.3283313 + 700 8.0318077 1139.7968 1686.9214 226.46146 -547.12461 600.49589 835.94756 154.05863 0 -606.7429 513467.63 -514998.52 679.06473 27236.703 322.81056 1.3423643 + 720 8.2363923 1092.9537 1676.7232 225.09239 -583.76953 599.79941 810.70949 154.32485 0 -586.40642 513433.08 -514995.27 -585.69662 27255.925 320.84689 1.3625931 + 740 8.4505181 1128.5561 1686.198 226.36434 -557.64189 608.39888 814.40376 148.31341 0 -576.35219 513440.47 -514992.87 1244.5446 27274.826 322.70284 1.2739521 + 760 8.6553326 1117.7278 1739.2464 233.48585 -621.51863 612.4462 767.55338 143.8046 0 -557.71655 513408.23 -514995.84 1093.5729 27295.505 332.85864 1.3081834 + 780 8.8741109 1106.8963 1694.5955 227.49166 -587.69917 621.94129 814.60472 148.54444 0 -544.5269 513368.24 -514996.5 1020.894 27319.829 324.31438 1.2670368 + 800 9.0792463 1119.8416 1718.8899 230.75307 -599.04828 615.79521 822.09893 150.20192 0 -544.21016 513354.51 -514997.44 -145.29684 27346.503 328.96744 1.27833 + 820 9.2923503 1100.7099 1661.8207 223.0918 -561.11086 634.74953 843.11877 146.78045 0 -554.19608 513367.17 -514998.73 1869.737 27372.705 318.03624 1.2563109 + 840 9.4957469 1050.0874 1692.7796 227.24789 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-514999.31 303.67371 27653.716 316.81728 1.223067 + 1100 12.213108 898.91261 1623.3761 217.93078 -724.46344 664.01917 828.5969 133.99752 0 -516.0614 513164.69 -514999.71 -222.62542 27666.941 310.68427 1.2153994 + 1120 12.41604 853.75082 1604.1305 215.34715 -750.37966 641.42123 819.9451 135.53827 0 -522.84677 513174.17 -514998.61 -712.60931 27680.156 306.99082 1.2247886 + 1140 12.609285 856.11685 1597.8188 214.49984 -741.70197 667.36627 802.82977 138.4139 0 -519.32453 513168.41 -514999.4 -102.39627 27691.615 305.78084 1.224836 + 1160 12.804644 841.06502 1588.8444 213.29507 -747.7794 639.48731 820.18846 145.23411 0 -514.61341 513163.68 -515001.76 -1183.509 27699.206 304.05355 1.2408942 + 1180 13.054664 860.51613 1621.2063 217.6395 -760.69016 641.94901 812.05607 135.63519 0 -518.65348 513173.02 -515004.7 281.47746 27701.81 310.24087 1.2817118 + 1200 13.250304 837.02718 1605.8013 215.57145 -768.77412 647.08878 819.62137 134.70383 0 -535.25329 513169.92 -515004.85 -741.61789 27704.108 307.27044 1.3202509 + 1220 13.454972 847.88424 1630.4606 218.88185 -782.57635 632.73877 814.55949 134.45986 0 -543.58866 513187.28 -515008.03 301.16905 27705.337 312.02884 1.2480776 + 1240 13.650697 847.8463 1613.1526 216.55833 -765.3063 657.26308 817.09263 131.44411 0 -533.77746 513168.85 -515006.17 -1738.246 27705.837 308.69599 1.2825009 + 1260 13.848417 864.10938 1604.3359 215.37473 -740.22655 654.64386 830.80471 136.50167 0 -518.80899 513162.82 -515006.19 -457.58037 27701.516 306.99469 1.3056189 + 1280 14.058141 892.58539 1622.354 217.79358 -729.76865 654.56025 853.72132 146.37045 0 -502.50853 513124.64 -515006.56 1617.9621 27698.218 310.47185 1.2538957 + 1300 14.25655 910.15714 1649.6144 221.45317 -739.4573 669.55948 824.60696 152.88156 0 -495.91044 513118.29 -515008.89 -947.37179 27701.819 315.68715 1.2786016 + 1320 14.462712 881.86464 1653.5515 221.98169 -771.68682 667.15825 811.67934 146.31009 0 -501.83979 513113.06 -515008.06 -836.07194 27703.296 316.44487 1.2716419 + 1340 14.66221 870.89257 1685.0409 226.20901 -814.14836 639.83879 820.7611 137.05399 0 -502.59799 513100.73 -515009.93 1322.9199 27705.806 322.51431 1.1950205 + 1360 14.876581 853.37228 1650.3504 221.55197 -796.97814 646.59807 828.89771 128.53685 0 -518.68585 513127.01 -515009.33 -685.77178 27711.07 315.84173 1.2552323 + 1380 15.07645 846.05537 1652.3957 221.82654 -806.34037 655.80177 845.42057 123.99858 0 -508.17399 513084.95 -515008.34 -1611.4393 27715.739 316.20591 1.3081133 + 1400 15.290876 845.61911 1643.3419 220.6111 -797.72277 681.7704 794.40988 122.51167 0 -491.96431 513103.8 -515008.25 1340.3832 27715.764 314.49703 1.249787 + 1420 15.489104 803.39863 1630.1296 218.83742 -826.73099 671.35628 807.63619 122.01003 0 -484.93762 513065.22 -515008.01 1599.9415 27715.83 311.97673 1.2205741 + 1440 15.695448 798.11794 1586.2583 212.94789 -788.14035 691.5246 832.65594 120.76201 0 -465.82995 513043.17 -515010.42 693.27083 27722.616 303.53977 1.2829192 + 1460 15.91282 786.25408 1614.9027 216.79327 -828.64859 657.62541 813.69119 123.75957 0 -476.8708 513064.69 -515011.54 411.32225 27731.39 309.03286 1.2785029 + 1480 16.12012 763.25782 1608.2178 215.89585 -844.95995 668.25992 798.0135 125.60791 0 -501.0795 513074.18 -515009.94 -210.6788 27739.429 307.75344 1.2722038 + 1500 16.31711 742.2781 1642.6489 220.51807 -900.3708 642.57755 747.85628 128.7751 0 -506.59888 513093.85 -515006.83 657.03263 27745.692 314.34071 1.3056262 + 1520 16.523088 729.1993 1560.7352 209.52153 -831.53586 684.2385 779.3475 135.75119 0 -498.45899 513072.79 -515005.21 64.426284 27753.859 298.64905 1.276366 + 1540 16.719949 744.18971 1581.6321 212.32685 -837.44244 684.68705 806.72314 139.08406 0 -507.07664 513045.21 -515006.07 -1592.594 27760.726 302.65236 1.2826649 + 1560 16.955894 732.25034 1589.2114 213.34434 -856.96111 671.90468 790.0602 135.77523 0 -516.63197 513069.7 -515007.77 -483.90212 27760.814 304.08818 1.324249 + 1580 17.152081 767.01867 1612.3153 216.44593 -845.29663 682.6108 787.28261 132.5621 0 -507.32097 513069.61 -515010.04 -555.1036 27759.537 308.50615 1.3501402 + 1600 17.357651 765.40129 1608.2406 215.89892 -842.8393 685.49537 792.49876 133.14916 0 -503.66586 513056.44 -515006.76 205.34219 27753.467 307.76245 1.2628065 + 1620 17.55409 772.17408 1631.4594 219.01594 -859.28536 668.94991 789.22477 139.7312 0 -488.80931 513038.28 -515006.66 869.15057 27745.263 312.19213 1.312809 + 1640 17.750204 790.00313 1585.8898 212.89842 -795.88666 698.581 834.90324 141.30234 0 -480.2032 513014.32 -515004.79 425.63098 27741.564 303.48802 1.2388328 + 1660 17.9655 747.54165 1583.9657 212.64013 -836.4241 681.84949 818.22116 144.32659 0 -480.9488 513005 -515004.87 393.07342 27741.508 303.09446 1.2953283 + 1680 18.160659 733.30069 1561.2237 209.58711 -827.92298 700.21145 825.04894 140.46392 0 -471.32136 512986.07 -515008.4 358.86819 27742.435 298.74386 1.2734665 + 1700 18.356133 711.44468 1578.4996 211.90632 -867.05487 695.93174 805.45219 136.97231 0 -472.62368 512976.67 -515009.46 536.5943 27744.152 302.06506 1.2553362 + 1720 18.560144 721.96636 1575.331 211.48095 -853.36463 702.17681 830.22534 135.88637 0 -477.83518 512966.99 -515010.81 -645.91282 27748.165 301.45254 1.2652763 + 1740 18.756074 711.63956 1586.0957 212.92606 -874.45612 689.4748 798.79974 136.08847 0 -473.58719 512984.43 -515009.66 -1624.8445 27748.356 303.52048 1.2551975 + 1760 18.958437 724.24881 1594.573 214.0641 -870.32418 693.92297 821.07919 134.86949 0 -499.044 512991.53 -515012.68 -67.704697 27743.489 305.14895 1.2473787 + 1780 19.161341 715.10685 1646.5039 221.03559 -931.39709 696.96446 758.9442 137.66678 0 -506.22154 512995.87 -515014.62 -40.253747 27743.38 315.10841 1.2414332 + 1800 19.355029 729.61134 1620.3158 217.51995 -890.70444 705.93766 795.61246 140.68696 0 -489.30347 512967.54 -515011.18 -766.11724 27742.605 310.0618 1.2972844 + 1820 19.55902 729.31305 1608.8589 215.98192 -879.54588 679.10327 811.20714 148.4305 0 -487.995 512981.33 -515011.62 -171.78807 27733.221 307.90957 1.1975335 + 1840 19.753109 755.00585 1604.0683 215.33881 -849.06248 704.5529 836.72831 145.47772 0 -486.71807 512964.36 -515013.46 214.63499 27724.953 306.97134 1.2429474 + 1860 19.967638 750.425 1611.9697 216.39953 -861.54467 681.08979 817.41958 140.85922 0 -481.23461 512994.18 -515013.86 458.39691 27723.378 308.4884 1.2369562 + 1880 20.162438 731.26375 1599.4322 214.71642 -868.16842 699.34308 809.01864 139.89206 0 -501.58244 512999.06 -515013.9 -1549.9632 27725.425 306.09592 1.211311 + 1900 20.356956 708.62541 1610.6874 216.22739 -902.06199 683.06943 810.51769 134.55613 0 -508.02851 512990.33 -515012.5 675.39868 27720.583 308.23181 1.2620963 + 1920 20.560648 703.81181 1586.8847 213.03199 -883.0729 690.93049 825.78591 131.84894 0 -498.42445 512977.68 -515010.9 367.15667 27713.888 303.69961 1.1917227 + 1940 20.754765 701.93422 1590.5107 213.51875 -888.57645 687.55932 818.62417 128.12087 0 -485.00453 512971.02 -515008.9 1457.2723 27711.175 304.3668 1.2586653 + 1960 20.966151 702.58467 1615.2174 216.83553 -912.63277 695.227 811.79161 131.25635 0 -468.08028 512925.61 -515008.44 812.93978 27708.617 309.10899 1.2402714 + 1980 21.169778 704.12312 1614.6957 216.76549 -910.5726 710.51045 811.95687 140.34792 0 -452.87904 512887.51 -515008.02 -604.37886 27705.003 309.00871 1.242271 + 2000 21.363046 700.52702 1604.4991 215.39664 -903.9721 726.08016 810.67383 139.90807 0 -443.00664 512870.59 -515008.22 148.09738 27699.21 307.02152 1.3180547 +Loop time of 21.3631 on 4 procs for 2000 steps with 3000 atoms + +Performance: 4.044 ns/day, 5.934 hours/ns, 93.619 timesteps/s +97.5% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 10.835 | 11.289 | 12.258 | 17.2 | 52.85 +Bond | 0.4537 | 0.48285 | 0.50792 | 3.1 | 2.26 +Kspace | 4.2572 | 5.2354 | 5.6853 | 25.4 | 24.51 +Neigh | 0.54701 | 0.5472 | 0.54747 | 0.0 | 2.56 +Comm | 0.60596 | 0.64067 | 0.67884 | 3.8 | 3.00 +Output | 0.0058618 | 0.0073152 | 0.011671 | 2.9 | 0.03 +Modify | 2.769 | 2.9549 | 3.1306 | 8.9 | 13.83 +Other | | 0.2055 | | | 0.96 + +Nlocal: 750 ave 757 max 742 min +Histogram: 1 0 1 0 0 0 0 0 0 2 +Nghost: 5838 ave 5894 max 5784 min +Histogram: 1 0 1 0 0 0 0 1 0 1 +Neighs: 175398 ave 186533 max 165750 min +Histogram: 1 0 1 0 0 0 1 0 0 1 + +Total # of neighbors = 701594 +Ave neighs/atom = 233.865 +Ave special neighs/atom = 10.5 +Neighbor list builds = 53 +Dangerous builds = 0 +Total wall time: 0:00:21 diff --git a/examples/USER/drude/ethanol/log.27Nov18.ethanol.nh.g++.1 b/examples/USER/drude/ethanol/log.27Nov18.ethanol.nh.g++.1 new file mode 100644 index 0000000000..f6d4d7452e --- /dev/null +++ b/examples/USER/drude/ethanol/log.27Nov18.ethanol.nh.g++.1 @@ -0,0 +1,286 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +units real +boundary p p p + +atom_style full +bond_style harmonic +angle_style harmonic +dihedral_style opls +special_bonds lj/coul 0.0 0.0 0.5 + +pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.600 8.0 +kspace_style pppm 1.0e-4 + +read_data data.ethanol + orthogonal box = (-14.0138 -14.0278 -14.0189) to (14.0169 14.0177 14.0857) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 3000 atoms + scanning bonds ... + 5 = max bonds/atom + scanning angles ... + 6 = max angles/atom + scanning dihedrals ... + 9 = max dihedrals/atom + reading bonds ... + 2750 bonds + reading angles ... + 3250 angles + reading dihedrals ... + 3000 dihedrals + 5 = max # of 1-2 neighbors + 6 = max # of 1-3 neighbors + 10 = max # of 1-4 neighbors + 11 = max # of special neighbors + + +pair_coeff 1 1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H +pair_coeff 1 2 lj/cut/coul/long 0.065997 3.500000 # C3H CTO +pair_coeff 1 3 lj/cut/coul/long 0.044496 2.958040 # C3H H +pair_coeff 1 4 lj/cut/coul/long 0.105921 3.304542 # C3H OH +pair_coeff 1 5 lj/cut/coul/long 0.000000 0.000000 # C3H HO +pair_coeff 2 2 lj/cut/coul/long 0.065997 3.500000 # CTO CTO +pair_coeff 2 3 lj/cut/coul/long 0.044496 2.958040 # CTO H +pair_coeff 2 4 lj/cut/coul/long 0.105921 3.304542 # CTO OH +pair_coeff 2 5 lj/cut/coul/long 0.000000 0.000000 # CTO HO +pair_coeff 3 3 lj/cut/coul/long 0.029999 2.500000 # H H +pair_coeff 3 4 lj/cut/coul/long 0.071413 2.792848 # H OH +pair_coeff 3 5 lj/cut/coul/long 0.000000 0.000000 # H HO +pair_coeff 4 4 lj/cut/coul/long 0.169996 3.120000 # OH OH +pair_coeff 4 5 lj/cut/coul/long 0.000000 0.000000 # OH HO +pair_coeff 5 5 lj/cut/coul/long 0.000000 0.000000 # HO HO +pair_coeff * 6*8 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes +pair_coeff 1 1 thole 2.051000 +pair_coeff 1 2 thole 1.580265 +pair_coeff 1 4 thole 1.416087 +pair_coeff 1 6 thole 2.051000 +pair_coeff 1 7 thole 1.580265 +pair_coeff 1 8 thole 1.416087 +pair_coeff 2 2 thole 1.217570 +pair_coeff 2 4 thole 1.091074 +pair_coeff 2 6 thole 1.580265 +pair_coeff 2 7 thole 1.217570 +pair_coeff 2 8 thole 1.091074 +pair_coeff 4 4 thole 0.977720 +pair_coeff 4 6 thole 1.416087 +pair_coeff 4 7 thole 1.091074 +pair_coeff 4 8 thole 0.977720 +pair_coeff 6 6 thole 2.051000 +pair_coeff 6 7 thole 1.580265 +pair_coeff 6 8 thole 1.416087 +pair_coeff 7 7 thole 1.217570 +pair_coeff 7 8 thole 1.091074 +pair_coeff 8 8 thole 0.977720 + +group gETHANOL molecule 1:250 +3000 atoms in group gETHANOL +group gATOMS type 1 2 3 4 5 +2250 atoms in group gATOMS +group gDRUDES type 6 7 8 +750 atoms in group gDRUDES + + +neighbor 2.0 bin + +variable vTEMP equal 300.0 +variable vTEMP_D equal 1.0 +variable vPRESS equal 1.0 + +velocity gATOMS create ${vTEMP} 12345 +velocity gATOMS create 300 12345 +velocity gDRUDES create ${vTEMP_D} 12345 +velocity gDRUDES create 1 12345 + +fix fDRUDE all drude C C N C N D D D + +fix fSHAKE gATOMS shake 0.0001 20 0 b 2 3 5 + 250 = # of size 2 clusters + 250 = # of size 3 clusters + 250 = # of size 4 clusters + 0 = # of frozen angles + +comm_modify vel yes +compute cTEMP_ATOM gATOMS temp +compute cTEMP all temp/drude + +fix fDTDIR all drude/transform/direct +fix fNPT gATOMS npt temp ${vTEMP} ${vTEMP} 100 iso ${vPRESS} ${vPRESS} 500 +fix fNPT gATOMS npt temp 300 ${vTEMP} 100 iso ${vPRESS} ${vPRESS} 500 +fix fNPT gATOMS npt temp 300 300 100 iso ${vPRESS} ${vPRESS} 500 +fix fNPT gATOMS npt temp 300 300 100 iso 1 ${vPRESS} 500 +fix fNPT gATOMS npt temp 300 300 100 iso 1 1 500 +fix_modify fNPT temp cTEMP_ATOM press thermo_press +WARNING: Temperature for fix modify is not for group all (src/fix_nh.cpp:1404) +fix fNVT gDRUDES nvt temp ${vTEMP_D} ${vTEMP_D} 100.0 +fix fNVT gDRUDES nvt temp 1 ${vTEMP_D} 100.0 +fix fNVT gDRUDES nvt temp 1 1 100.0 +fix fDTINV all drude/transform/inverse + +thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2] +thermo 20 + +timestep 0.5 +run 2000 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) + G vector (1/distance) = 0.379738 + grid = 30 30 30 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0289979 + estimated relative force accuracy = 8.73262e-05 + using double precision FFTs + 3d grid and FFT values/proc = 50653 27000 +Rebuild special list taking Drude particles into account +Old max number of 1-2 to 1-4 neighbors: 11 +New max number of 1-2 to 1-4 neighbors: 11 (+0) +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10 + ghost atom cutoff = 10 + binsize = 5, bins = 6 6 6 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) pair thole, perpetual, skip from (1) + attributes: half, newton on + pair build: skip + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 22.48 | 22.48 | 22.48 Mbytes +Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2] + 0 0 13868.828 2013.3852 270.28772 11855.443 3145.896 51.880809 0.00019113234 0 8481.5109 514734.14 -514557.98 170210.19 22094.109 381.62759 10.134301 + 20 0.82186079 11385.283 5995.2608 804.83624 5390.0219 2039.7455 2312.5467 131.6964 0 1710.3725 514098.33 -514902.67 75869.034 22408.215 975.27381 406.07545 + 40 1.7293625 9812.345 6009.1868 806.70574 3803.1582 1442.3552 1826.1503 275.19417 0 1288.22 513934.99 -514963.75 48672.13 22980.211 1057.0198 221.56388 + 60 2.5726278 8857.8006 5779.5918 775.88366 3078.2088 1190.8886 1938.5953 328.68401 0 619.17987 513971 -514970.14 39706.347 23441.277 1050.8999 133.14459 + 80 3.4535189 8115.6222 5997.8743 805.18709 2117.7479 901.83124 1587.5299 325.40736 0 288.22238 513957.46 -514942.7 37586.493 23835.221 1111.6406 89.055348 + 100 4.2757752 7496.057 5770.3042 774.63685 1725.7528 829.61731 1420.6409 325.39973 0 62.226626 514051.66 -514963.79 27290.384 24226.433 1080.2534 60.498681 + 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305.87197 1.2204936 + 1860 65.687176 791.36821 1585.9825 212.91087 -794.61429 619.37616 661.00216 170.47785 0 -410.28902 513156.18 -514991.36 -22.140042 28417.059 303.51149 1.2255437 + 1880 66.353485 791.94788 1630.1749 218.8435 -838.22706 591.52981 652.79092 178.67552 0 -433.7293 513160.08 -514987.57 -35.653011 28444.349 312.01504 1.151451 + 1900 67.051143 791.5025 1611.2186 216.2987 -819.71613 604.66631 614.52658 185.27138 0 -426.58089 513192.07 -514989.67 1492.9051 28470.603 308.39205 1.1258287 + 1920 67.749766 789.33745 1638.8687 220.0106 -849.53124 604.75057 634.21383 186.54046 0 -427.33715 513139.73 -514987.43 863.10157 28504.605 313.697 1.1156351 + 1940 68.417711 786.91982 1566.7995 210.33564 -779.87972 606.00187 648.68271 182.72186 0 -430.75201 513205.37 -514991.9 -1132.9713 28541.397 299.9167 1.0327394 + 1960 69.114583 784.25672 1592.2094 213.7468 -807.95267 595.81907 669.03472 172.75782 0 -436.10776 513181.4 -514990.86 78.431195 28569.12 304.79729 1.0106551 + 1980 69.778898 780.04995 1637.1409 219.77865 -857.09092 606.44426 629.01991 163.80784 0 -440.75819 513180.63 -514996.23 1330.6593 28595.247 313.42473 0.97808647 + 2000 70.476083 774.653 1633.3807 219.27386 -858.72771 607.3352 611.62149 162.37854 0 -449.5387 513203.88 -514994.4 -192.50999 28627.445 312.71969 0.94122657 +Loop time of 70.4761 on 1 procs for 2000 steps with 3000 atoms + +Performance: 1.226 ns/day, 19.577 hours/ns, 28.378 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 | 43.881 | 43.881 | 43.881 | 0.0 | 62.26 +Bond | 1.8093 | 1.8093 | 1.8093 | 0.0 | 2.57 +Kspace | 10.585 | 10.585 | 10.585 | 0.0 | 15.02 +Neigh | 2.3196 | 2.3196 | 2.3196 | 0.0 | 3.29 +Comm | 0.38965 | 0.38965 | 0.38965 | 0.0 | 0.55 +Output | 0.0086887 | 0.0086887 | 0.0086887 | 0.0 | 0.01 +Modify | 11.438 | 11.438 | 11.438 | 0.0 | 16.23 +Other | | 0.04561 | | | 0.06 + +Nlocal: 3000 ave 3000 max 3000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 10476 ave 10476 max 10476 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 658684 ave 658684 max 658684 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 658684 +Ave neighs/atom = 219.561 +Ave special neighs/atom = 10.5 +Neighbor list builds = 65 +Dangerous builds = 0 +Total wall time: 0:01:10 diff --git a/examples/USER/drude/ethanol/log.27Nov18.ethanol.nh.g++.4 b/examples/USER/drude/ethanol/log.27Nov18.ethanol.nh.g++.4 new file mode 100644 index 0000000000..593ed8c982 --- /dev/null +++ b/examples/USER/drude/ethanol/log.27Nov18.ethanol.nh.g++.4 @@ -0,0 +1,286 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +units real +boundary p p p + +atom_style full +bond_style harmonic +angle_style harmonic +dihedral_style opls +special_bonds lj/coul 0.0 0.0 0.5 + +pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.600 8.0 +kspace_style pppm 1.0e-4 + +read_data data.ethanol + orthogonal box = (-14.0138 -14.0278 -14.0189) to (14.0169 14.0177 14.0857) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 3000 atoms + scanning bonds ... + 5 = max bonds/atom + scanning angles ... + 6 = max angles/atom + scanning dihedrals ... + 9 = max dihedrals/atom + reading bonds ... + 2750 bonds + reading angles ... + 3250 angles + reading dihedrals ... + 3000 dihedrals + 5 = max # of 1-2 neighbors + 6 = max # of 1-3 neighbors + 10 = max # of 1-4 neighbors + 11 = max # of special neighbors + + +pair_coeff 1 1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H +pair_coeff 1 2 lj/cut/coul/long 0.065997 3.500000 # C3H CTO +pair_coeff 1 3 lj/cut/coul/long 0.044496 2.958040 # C3H H +pair_coeff 1 4 lj/cut/coul/long 0.105921 3.304542 # C3H OH +pair_coeff 1 5 lj/cut/coul/long 0.000000 0.000000 # C3H HO +pair_coeff 2 2 lj/cut/coul/long 0.065997 3.500000 # CTO CTO +pair_coeff 2 3 lj/cut/coul/long 0.044496 2.958040 # CTO H +pair_coeff 2 4 lj/cut/coul/long 0.105921 3.304542 # CTO OH +pair_coeff 2 5 lj/cut/coul/long 0.000000 0.000000 # CTO HO +pair_coeff 3 3 lj/cut/coul/long 0.029999 2.500000 # H H +pair_coeff 3 4 lj/cut/coul/long 0.071413 2.792848 # H OH +pair_coeff 3 5 lj/cut/coul/long 0.000000 0.000000 # H HO +pair_coeff 4 4 lj/cut/coul/long 0.169996 3.120000 # OH OH +pair_coeff 4 5 lj/cut/coul/long 0.000000 0.000000 # OH HO +pair_coeff 5 5 lj/cut/coul/long 0.000000 0.000000 # HO HO +pair_coeff * 6*8 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes +pair_coeff 1 1 thole 2.051000 +pair_coeff 1 2 thole 1.580265 +pair_coeff 1 4 thole 1.416087 +pair_coeff 1 6 thole 2.051000 +pair_coeff 1 7 thole 1.580265 +pair_coeff 1 8 thole 1.416087 +pair_coeff 2 2 thole 1.217570 +pair_coeff 2 4 thole 1.091074 +pair_coeff 2 6 thole 1.580265 +pair_coeff 2 7 thole 1.217570 +pair_coeff 2 8 thole 1.091074 +pair_coeff 4 4 thole 0.977720 +pair_coeff 4 6 thole 1.416087 +pair_coeff 4 7 thole 1.091074 +pair_coeff 4 8 thole 0.977720 +pair_coeff 6 6 thole 2.051000 +pair_coeff 6 7 thole 1.580265 +pair_coeff 6 8 thole 1.416087 +pair_coeff 7 7 thole 1.217570 +pair_coeff 7 8 thole 1.091074 +pair_coeff 8 8 thole 0.977720 + +group gETHANOL molecule 1:250 +3000 atoms in group gETHANOL +group gATOMS type 1 2 3 4 5 +2250 atoms in group gATOMS +group gDRUDES type 6 7 8 +750 atoms in group gDRUDES + + +neighbor 2.0 bin + +variable vTEMP equal 300.0 +variable vTEMP_D equal 1.0 +variable vPRESS equal 1.0 + +velocity gATOMS create ${vTEMP} 12345 +velocity gATOMS create 300 12345 +velocity gDRUDES create ${vTEMP_D} 12345 +velocity gDRUDES create 1 12345 + +fix fDRUDE all drude C C N C N D D D + +fix fSHAKE gATOMS shake 0.0001 20 0 b 2 3 5 + 250 = # of size 2 clusters + 250 = # of size 3 clusters + 250 = # of size 4 clusters + 0 = # of frozen angles + +comm_modify vel yes +compute cTEMP_ATOM gATOMS temp +compute cTEMP all temp/drude + +fix fDTDIR all drude/transform/direct +fix fNPT gATOMS npt temp ${vTEMP} ${vTEMP} 100 iso ${vPRESS} ${vPRESS} 500 +fix fNPT gATOMS npt temp 300 ${vTEMP} 100 iso ${vPRESS} ${vPRESS} 500 +fix fNPT gATOMS npt temp 300 300 100 iso ${vPRESS} ${vPRESS} 500 +fix fNPT gATOMS npt temp 300 300 100 iso 1 ${vPRESS} 500 +fix fNPT gATOMS npt temp 300 300 100 iso 1 1 500 +fix_modify fNPT temp cTEMP_ATOM press thermo_press +WARNING: Temperature for fix modify is not for group all (src/fix_nh.cpp:1404) +fix fNVT gDRUDES nvt temp ${vTEMP_D} ${vTEMP_D} 100.0 +fix fNVT gDRUDES nvt temp 1 ${vTEMP_D} 100.0 +fix fNVT gDRUDES nvt temp 1 1 100.0 +fix fDTINV all drude/transform/inverse + +thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2] +thermo 20 + +timestep 0.5 +run 2000 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) + G vector (1/distance) = 0.379738 + grid = 30 30 30 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0289979 + estimated relative force accuracy = 8.73262e-05 + using double precision FFTs + 3d grid and FFT values/proc = 17908 7200 +Rebuild special list taking Drude particles into account +Old max number of 1-2 to 1-4 neighbors: 11 +New max number of 1-2 to 1-4 neighbors: 11 (+0) +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10 + ghost atom cutoff = 10 + binsize = 5, bins = 6 6 6 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) pair thole, perpetual, skip from (1) + attributes: half, newton on + pair build: skip + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 15.7 | 15.72 | 15.75 Mbytes +Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2] + 0 0 13868.828 2013.3852 270.28772 11855.443 3145.896 51.880809 0.00019113234 0 8481.5109 514734.14 -514557.98 170210.19 22094.109 381.62759 10.134301 + 20 0.26940155 11385.283 5995.2608 804.83624 5390.0219 2039.7455 2312.5467 131.6964 0 1710.3725 514098.33 -514902.67 75869.034 22408.215 975.27381 406.07545 + 40 0.56039548 9812.345 6009.1868 806.70574 3803.1582 1442.3552 1826.1503 275.19417 0 1288.22 513934.99 -514963.75 48672.13 22980.211 1057.0198 221.56388 + 60 0.88414049 8857.8007 5779.5918 775.88366 3078.2089 1190.8886 1938.5954 328.68401 0 619.17987 513971 -514970.14 39706.347 23441.277 1050.8999 133.14459 + 80 1.1696272 8115.6221 5997.8743 805.18709 2117.7478 901.83126 1587.5299 325.40736 0 288.22238 513957.46 -514942.7 37586.493 23835.221 1111.6406 89.055345 + 100 1.4401748 7496.0571 5770.3042 774.63685 1725.7529 829.6173 1420.6409 325.39973 0 62.226624 514051.66 -514963.79 27290.384 24226.433 1080.2534 60.498679 + 120 1.7223158 6986.3333 5396.8053 724.49634 1589.528 678.23214 1535.5139 325.88286 0 -9.8121501 514027.1 -514967.39 21714.378 24578.965 1016.2738 42.716172 + 140 1.9845128 6548.697 5126.4765 688.20593 1422.2205 724.92774 1477.7367 315.11557 0 -99.615085 513960.65 -514956.6 19741.55 24878.09 969.48208 30.977306 + 160 2.2419188 6130.9704 5000.2242 671.25714 1130.7463 703.21482 1302.0806 314.9338 0 -258.62211 514042.38 -514973.24 23045.181 25144.056 948.68855 23.022185 + 180 2.4937162 5749.5572 4700.6896 631.046 1048.8675 674.90328 1301.3631 310.04329 0 -326.92492 514044.37 -514954.88 14218.696 25401.78 893.70987 17.322259 + 200 2.7779307 5429.1755 4392.2849 589.64408 1036.8906 611.96667 1296.169 303.15487 0 -300.55349 514093.83 -514967.68 10827.18 25624.937 836.11247 13.764988 + 220 3.0248075 5133.4101 4290.3608 575.96124 843.04929 572.47215 1261.7692 289.97559 0 -383.86544 514078.49 -514975.79 12503.299 25816.637 817.71346 11.104783 + 240 3.2623236 4849.9512 4119.9045 553.07826 730.04673 553.72776 1263.639 278.92307 0 -487.89902 514091.57 -514969.91 10886.301 25998.932 785.78405 9.3606436 + 260 3.4997547 4583.5434 3910.7331 524.99797 672.81028 541.41985 1175.0582 273.43967 0 -475.41047 514139.92 -514981.62 8078.6153 26172.119 746.49788 7.4648392 + 280 3.7359712 4348.8096 3691.9428 495.62637 656.86681 598.77221 1148.0372 278.86509 0 -444.28193 514045.6 -514970.12 5115.867 26326.635 704.97778 6.478926 + 300 3.9722769 4128.4892 3579.1998 480.49114 549.28936 583.98039 1089.487 267.65383 0 -457.0616 514043.78 -514978.55 8341.4601 26460.833 683.88483 5.2652305 + 320 4.1924908 3913.3825 3456.6177 464.03505 456.76481 556.22097 1103.342 263.77912 0 -485.6864 514000.55 -514981.44 9109.6369 26597.284 660.68387 4.569117 + 340 4.4220572 3712.2735 3258.0794 437.3822 454.19406 533.60886 1068.9435 271.82625 0 -454.64506 514002.17 -514967.71 7179.0608 26741.746 622.91875 3.8804079 + 360 4.651022 3532.9576 3023.6802 405.91518 509.27748 522.48821 1104.2686 276.28277 0 -456.22485 514036.79 -514974.33 4545.2157 26882.126 578.2315 3.3025369 + 380 4.8867376 3366.7464 2970.763 398.8113 395.98341 508.12225 1059.1562 257.91185 0 -499.7941 514032.85 -514962.26 5636.5327 27008.105 568.28964 2.8300765 + 400 5.1070464 3204.509 2873.4151 385.74278 331.09386 543.77873 1018.7946 231.10847 0 -519.43554 514029.65 -514972.81 7243.9777 27130.53 549.73389 2.582555 + 420 5.3353672 3050.3029 2775.7676 372.63405 274.53536 517.37318 953.14843 225.86866 0 -505.67104 514057.59 -514973.77 4018.2518 27257.578 531.12044 2.3356247 + 440 5.5616498 2915.9614 2639.1925 354.29947 276.76893 507.07348 983.90798 236.07196 0 -534.7174 514060.31 -514975.87 1699.7058 27372.134 505.04911 2.0779123 + 460 5.7944629 2787.2801 2609.7652 350.34899 177.51494 485.49336 933.65567 234.4359 0 -560.632 514070.07 -514985.51 3390.2812 27466.685 499.52306 1.8090438 + 480 6.0186839 2662.2225 2514.1129 337.50812 148.10954 464.53577 928.19233 239.15956 0 -570.39024 514071.12 -514984.5 5075.4176 27556.806 481.25539 1.6478044 + 500 6.2357466 2540.259 2432.8587 326.60011 107.40032 473.20958 888.84591 239.12382 0 -565.53821 514057.83 -514986.07 3129.6111 27653.186 465.74794 1.4863829 + 520 6.462676 2431.9888 2374.7256 318.79601 57.263157 460.05319 838.76524 228.73041 0 -579.04849 514094.39 -514985.63 462.28097 27743.092 454.65004 1.3782188 + 540 6.6893921 2328.6141 2274.6316 305.35885 53.982526 473.12143 875.45686 220.60764 0 -604.15443 514076.11 -514987.16 2622.3509 27815.745 435.4755 1.3461673 + 560 6.915879 2228.4408 2278.108 305.82554 -49.667226 455.45527 820.9654 214.46985 0 -604.66926 514053.07 -514988.96 3774.7446 27887.17 436.23196 1.1361161 + 580 7.129838 2134.2136 2127.7972 285.64701 6.4164029 480.53569 836.9992 218.2561 0 -563.43996 514020.11 -514986.04 1347.8991 27963.805 407.42665 1.1136548 + 600 7.3513916 2048.334 2102.8555 282.2987 -54.521528 486.17968 795.85755 224.19382 0 -574.58522 514004 -514990.17 -100.56264 28031.415 402.67851 1.0360672 + 620 7.571908 1967.2653 2050.2743 275.23991 -83.008964 477.31341 785.52964 222.26773 0 -570.58461 513998.54 -514996.08 1809.6139 28084.448 392.60377 1.023916 + 640 7.822695 1887.8873 1984.0468 266.34918 -96.159502 482.78324 800.4011 220.19183 0 -557.48586 513952.64 -514994.69 3804.7387 28138.319 379.94969 0.92618308 + 660 8.0473323 1812.5849 1960.7275 263.21866 -148.14251 497.48053 750.6579 215.15723 0 -556.35642 513938.64 -514993.72 1173.0782 28202.964 375.50053 0.87666213 + 680 8.2574785 1744.229 1912.3049 256.71816 -168.07594 497.12359 725.28373 210.75068 0 -554.76517 513943.75 -514990.22 81.483029 28262.329 366.2483 0.80553356 + 700 8.4756997 1677.5494 1912.8562 256.79217 -235.30682 490.36725 720.72028 204.81842 0 -570.32326 513908.12 -514989.01 2139.1574 28311.757 366.37944 0.74614771 + 720 8.6941352 1611.7137 1859.3792 249.61312 -247.66551 499.4419 727.86911 195.529 0 -552.65432 513871.24 -514989.09 3009.9813 28365.384 356.12774 0.74621707 + 740 8.9091365 1549.6852 1790.3521 240.34656 -240.66693 496.25202 737.75393 180.00372 0 -548.11093 513879.92 -514986.49 718.57423 28427.108 342.91382 0.70248974 + 760 9.1269078 1492.9984 1801.2402 241.80823 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170.02534 0 -554.71869 513740.96 -514982.08 1233.144 28693.074 319.91853 0.57749627 + 900 10.636871 1153.5523 1643.4571 220.62657 -489.90477 500.29822 640.14056 177.40242 0 -558.06881 513735.19 -514984.87 -525.65607 28722.392 314.8151 0.5591483 + 920 10.892932 1114.609 1618.9439 217.33579 -504.33488 511.75888 633.60856 175.1138 0 -554.17472 513720.72 -514991.36 -1519.4599 28743.136 310.10438 0.58594249 + 940 11.111583 1076.5388 1629.6394 218.77161 -553.10061 510.90787 619.76339 167.7895 0 -557.43647 513695.72 -514989.85 296.67789 28751.217 312.16803 0.5549268 + 960 11.321271 1040.3467 1609.1144 216.01622 -568.76774 511.14781 602.93181 166.00661 0 -548.6701 513692.97 -514993.16 742.31157 28759.398 308.22272 0.57970476 + 980 11.542122 1006.0767 1560.5644 209.4986 -554.48764 516.02585 629.21936 171.81429 0 -544.97384 513663.64 -514990.21 -1243.6779 28769.841 298.93237 0.54048524 + 1000 11.766886 974.24702 1558.0041 209.15489 -583.75705 506.64122 601.93463 165.12035 0 -553.064 513688.11 -514992.5 -1282.0718 28770.754 298.4357 0.55413455 + 1020 11.970261 943.47512 1567.4558 210.42375 -623.98071 507.76272 618.07613 152.14193 0 -569.64333 513661.22 -514993.54 -185.99703 28762.511 300.24196 0.56735077 + 1040 12.182541 913.49183 1599.9518 214.78618 -686.45996 487.4406 574.26298 153.41685 0 -593.34617 513684.82 -514993.05 479.3652 28754.257 306.47736 0.55370848 + 1060 12.385323 884.5384 1558.1791 209.17839 -673.64068 500.22922 593.70741 157.65505 0 -604.58403 513672.33 -514992.98 -2207.1147 28748.016 298.45318 0.59162923 + 1080 12.597323 857.28841 1538.9194 206.59286 -681.63097 503.67593 574.77226 165.12151 0 -584.10752 513643 -514984.09 -1836.8716 28728.353 294.7583 0.59804385 + 1100 12.806903 832.2002 1479.2217 198.57873 -647.02154 514.11416 608.92484 165.24735 0 -569.63674 513616.86 -514982.53 -27.131764 28698.73 283.30662 0.61552981 + 1120 13.021407 809.16206 1516.8721 203.63312 -707.71008 513.30089 567.99641 169.86685 0 -560.80062 513584.24 -514982.32 -372.41029 28671.488 290.52701 0.60920306 + 1140 13.226424 787.50897 1484.3443 199.26641 -696.83535 526.29673 582.76992 167.79235 0 -550.76364 513559.47 -514982.41 -1728.2731 28644.54 284.27985 0.6360204 + 1160 13.439471 767.42267 1497.5383 201.03765 -730.11567 515.96405 580.5165 159.12444 0 -534.97892 513529.33 -514980.08 -1872.3497 28608.958 286.79856 0.66079274 + 1180 13.643181 750.19166 1492.1028 200.30795 -741.9111 532.36765 570.69633 154.43336 0 -512.25199 513492.9 -514980.06 926.80786 28566.842 285.72289 0.73932156 + 1200 13.878355 735.34196 1504.4584 201.96663 -769.11641 536.29872 594.4765 155.773 0 -514.98695 513442.46 -514983.13 34.590808 28534.508 288.09313 0.73549598 + 1220 14.095265 720.75191 1495.8784 200.81481 -775.12649 558.18322 561.11868 159.16072 0 -503.00794 513434.4 -514984.98 -986.83251 28506.707 286.44694 0.73874965 + 1240 14.302587 707.62702 1486.8261 199.59958 -779.19911 564.76327 574.98748 160.18253 0 -467.67421 513371.66 -514983.12 38.339148 28476.761 284.68236 0.80695809 + 1260 14.5169 696.93229 1495.1997 200.7237 -798.26742 576.84276 565.66929 154.59183 0 -456.04034 513344.28 -514983.61 859.97875 28450.881 286.26551 0.85851389 + 1280 14.723275 687.92791 1485.1331 199.3723 -797.20519 581.04737 593.2454 150.87332 0 -447.80111 513310.98 -514985.55 747.71864 28434.188 284.33268 0.86557314 + 1300 14.940926 680.08292 1479.193 198.57487 -799.11011 585.53803 589.87487 148.01029 0 -422.72639 513283.11 -514982.92 -525.51472 28424.13 283.16208 0.93995449 + 1320 15.146466 673.56377 1476.0598 198.15425 -802.496 572.76673 595.29767 147.53133 0 -424.76316 513287.72 -514981.04 109.20091 28412.937 282.56994 0.92008603 + 1340 15.360807 668.74056 1484.8781 199.33807 -816.13759 582.36447 588.33732 153.88508 0 -434.18175 513270.79 -514977.34 733.42094 28403.872 284.22277 1.0080038 + 1360 15.565801 665.56738 1519.4405 203.97791 -853.8731 575.96075 554.2097 159.14168 0 -458.4083 513293.33 -514978.1 423.26533 28400.693 290.82823 1.0551985 + 1380 15.785992 663.88904 1467.7833 197.04317 -803.89424 578.34934 592.76078 156.17583 0 -458.96296 513308.25 -514980.47 -202.88792 28400.724 280.90163 1.1107077 + 1400 16.000381 663.53838 1516.5314 203.58738 -852.99304 571.11885 580.68736 146.25518 0 -462.81788 513294.24 -514982.47 -449.44011 28399.391 290.22677 1.1573629 + 1420 16.208723 664.23926 1499.3076 201.27517 -835.06836 566.43752 603.59629 148.52977 0 -471.69399 513300.52 -514982.46 261.17724 28395.582 286.90991 1.1923832 + 1440 16.424351 665.87924 1504.925 202.02927 -839.04575 568.21243 588.179 157.65461 0 -462.88044 513294.99 -514985.2 684.75502 28394.09 287.99547 1.1721041 + 1460 16.630685 668.71536 1501.3751 201.55271 -832.6597 581.26842 579.88403 157.98256 0 -456.9524 513291.74 -514986.58 -272.14551 28396.923 287.26686 1.284286 + 1480 16.851607 672.94191 1510.1794 202.73465 -837.23749 577.53887 567.63332 162.86706 0 -467.21952 513308.9 -514986.95 -937.06962 28397.511 288.94723 1.3016431 + 1500 17.060401 678.34496 1516.5383 203.58831 -838.19335 568.9071 592.24094 169.15958 0 -495.91214 513315.52 -514988.11 85.894805 28392.343 290.14127 1.359925 + 1520 17.280722 684.91448 1526.955 204.9867 -842.04054 557.53201 581.42008 168.46993 0 -496.76555 513336.83 -514989.52 513.1704 28387.948 292.13159 1.3753055 + 1540 17.489951 692.4859 1536.0578 206.20871 -843.5719 552.11665 584.87851 156.09211 0 -473.22273 513327.75 -514991.18 -267.31574 28386.929 293.85398 1.4281354 + 1560 17.713041 700.59595 1541.593 206.95178 -840.99701 551.44763 612.32187 152.35924 0 -499.17884 513335.07 -514993.01 -882.17955 28383.721 294.92477 1.4055318 + 1580 17.929113 708.77379 1550.3407 208.12612 -841.56691 556.60852 582.39053 162.12325 0 -515.10224 513365.77 -514993.35 322.32831 28375.626 296.59534 1.4204419 + 1600 18.144745 717.39964 1559.9665 209.41835 -842.56689 549.07216 592.74611 171.9088 0 -494.99998 513331.85 -514993.14 267.08424 28369.799 298.42556 1.4556193 + 1620 18.363554 726.25369 1544.67 207.36486 -818.41631 564.24547 620.11593 171.47239 0 -481.42668 513299.67 -514992.5 -929.2129 28365.483 295.50817 1.4206365 + 1640 18.578192 735.20307 1599.669 214.74822 -864.46597 559.44554 584.31101 166.36248 0 -485.25281 513300.68 -514990.01 -400.32794 28355.927 306.03975 1.4483397 + 1660 18.788682 744.13508 1567.4804 210.42705 -823.34534 567.22939 620.98009 160.76689 0 -485.86239 513302.82 -514989.28 275.23727 28344.229 299.86144 1.466234 + 1680 19.002967 752.73626 1613.0757 216.548 -860.33939 567.6576 617.82475 157.94412 0 -474.89518 513259.71 -514988.58 145.60417 28335.257 308.62904 1.4035192 + 1700 19.208987 760.45858 1575.0294 211.44047 -814.57086 588.97206 634.68664 166.27782 0 -441.79702 513226.22 -514988.93 -455.69419 28327.746 301.33081 1.4144311 + 1720 19.424031 767.76378 1634.9553 219.48525 -867.19156 594.28118 613.97792 169.57851 0 -435.89528 513178.39 -514987.52 624.6147 28318.833 312.83371 1.3795127 + 1740 19.630425 774.0707 1607.3304 215.77673 -833.25975 612.27366 635.89702 170.90768 0 -425.06946 513156.42 -514983.69 1245.2476 28314.962 307.54418 1.3649994 + 1760 19.88556 778.94063 1606.5499 215.67195 -827.60929 602.10334 636.54708 169.93908 0 -409.46967 513160.13 -514986.86 900.23197 28320.117 307.40099 1.3499664 + 1780 20.156405 783.13015 1582.8925 212.49605 -799.76233 635.8022 637.81662 173.60641 0 -395.27083 513136.4 -514988.12 303.67422 28331.437 302.86049 1.3623691 + 1800 20.394003 786.8472 1629.8795 218.80383 -843.03226 626.87797 613.50519 171.66383 0 -388.22631 513124.5 -514991.35 452.45767 28344.488 311.88054 1.3331104 + 1820 20.604631 789.49317 1623.8201 217.99039 -834.32693 632.3375 629.50791 165.54164 0 -402.81199 513130.95 -514989.85 1435.9558 28360.845 310.74273 1.2776203 + 1840 20.882926 790.84026 1595.8459 214.23498 -805.0056 593.44998 654.04584 168.32988 0 -408.05005 513177.2 -514989.98 869.17595 28385.701 305.40649 1.2158021 + 1860 21.104003 791.82787 1587.2175 213.07667 -795.38968 618.69585 660.77302 168.60246 0 -408.77525 513157.18 -514991.87 14.63364 28414.975 303.75155 1.217843 + 1880 21.318712 792.39264 1628.8097 218.66022 -836.41704 590.23683 653.83304 177.71688 0 -432.28625 513162.12 -514988.04 -17.001449 28442.457 311.75357 1.1508692 + 1900 21.52406 792.00166 1611.7686 216.37254 -819.76695 604.55866 613.59005 183.84763 0 -425.02508 513192.41 -514989.15 1501.7473 28469.05 308.49923 1.1217532 + 1920 21.740008 789.87504 1640.0559 220.16997 -850.18086 603.67271 634.84308 183.31253 0 -426.75252 513142.08 -514987.34 889.51113 28503.487 313.92438 1.1161317 + 1940 21.949681 787.46267 1570.9429 210.89187 -783.48022 605.27114 651.32573 181.65051 0 -435.56723 513206.5 -514992.66 -1213.4071 28540.767 300.71188 1.0306517 + 1960 22.16336 784.79852 1591.8755 213.70197 -807.07695 594.43439 669.69922 174.81078 0 -440.94269 513185.58 -514990.66 -9.1610879 28568.421 304.73308 1.0111234 + 1980 22.368034 780.57674 1632.8138 219.19775 -852.23704 605.41038 630.06225 169.19473 0 -441.49651 513181.33 -514996.74 1265.2908 28593.818 312.59942 0.96826781 + 2000 22.581326 775.20404 1636.2577 219.66008 -861.05366 609.0993 612.37884 163.97498 0 -448.27188 513197.01 -514995.24 -167.85231 28624.885 313.26825 0.94815628 +Loop time of 22.5814 on 4 procs for 2000 steps with 3000 atoms + +Performance: 3.826 ns/day, 6.273 hours/ns, 88.568 timesteps/s +97.4% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 10.479 | 10.867 | 11.348 | 9.5 | 48.12 +Bond | 0.47013 | 0.48392 | 0.50035 | 1.7 | 2.14 +Kspace | 4.4559 | 4.9538 | 5.3493 | 14.5 | 21.94 +Neigh | 0.65502 | 0.65523 | 0.65539 | 0.0 | 2.90 +Comm | 0.47358 | 0.47448 | 0.47606 | 0.1 | 2.10 +Output | 0.0062618 | 0.0089129 | 0.014062 | 3.2 | 0.04 +Modify | 5.0877 | 5.0948 | 5.1016 | 0.3 | 22.56 +Other | | 0.04382 | | | 0.19 + +Nlocal: 750 ave 769 max 722 min +Histogram: 1 0 0 0 0 1 0 0 1 1 +Nghost: 5829.25 ave 5873 max 5791 min +Histogram: 1 0 1 0 0 0 1 0 0 1 +Neighs: 164687 ave 168810 max 157995 min +Histogram: 1 0 0 0 0 0 1 0 1 1 + +Total # of neighbors = 658749 +Ave neighs/atom = 219.583 +Ave special neighs/atom = 10.5 +Neighbor list builds = 65 +Dangerous builds = 0 +Total wall time: 0:00:22 diff --git a/examples/USER/drude/ethanol/log.ethanol.lang.8Jul15.linux.1 b/examples/USER/drude/ethanol/log.ethanol.lang.8Jul15.linux.1 deleted file mode 100644 index 5509458f14..0000000000 --- a/examples/USER/drude/ethanol/log.ethanol.lang.8Jul15.linux.1 +++ /dev/null @@ -1,254 +0,0 @@ -LAMMPS (8 Jul 2015) -units real -boundary p p p - -atom_style full -bond_style harmonic -angle_style harmonic -dihedral_style opls -special_bonds lj/coul 0.0 0.0 0.5 - -pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.600 8.0 -kspace_style pppm 1.0e-4 - -comm_modify vel yes -read_data data.ethanol - orthogonal box = (-14.0138 -14.0278 -14.0189) to (14.0169 14.0177 14.0857) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 3000 atoms - scanning bonds ... - 5 = max bonds/atom - scanning angles ... - 6 = max angles/atom - scanning dihedrals ... - 9 = max dihedrals/atom - reading bonds ... - 2750 bonds - reading angles ... - 3250 angles - reading dihedrals ... - 3000 dihedrals - 5 = max # of 1-2 neighbors - 6 = max # of 1-3 neighbors - 10 = max # of 1-4 neighbors - 11 = max # of special neighbors - -pair_coeff 1 1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H -pair_coeff 1 2 lj/cut/coul/long 0.065997 3.500000 # C3H CTO -pair_coeff 1 3 lj/cut/coul/long 0.044496 2.958040 # C3H H -pair_coeff 1 4 lj/cut/coul/long 0.105921 3.304542 # C3H OH -pair_coeff 1 5 lj/cut/coul/long 0.000000 0.000000 # C3H HO -pair_coeff 2 2 lj/cut/coul/long 0.065997 3.500000 # CTO CTO -pair_coeff 2 3 lj/cut/coul/long 0.044496 2.958040 # CTO H -pair_coeff 2 4 lj/cut/coul/long 0.105921 3.304542 # CTO OH -pair_coeff 2 5 lj/cut/coul/long 0.000000 0.000000 # CTO HO -pair_coeff 3 3 lj/cut/coul/long 0.029999 2.500000 # H H -pair_coeff 3 4 lj/cut/coul/long 0.071413 2.792848 # H OH -pair_coeff 3 5 lj/cut/coul/long 0.000000 0.000000 # H HO -pair_coeff 4 4 lj/cut/coul/long 0.169996 3.120000 # OH OH -pair_coeff 4 5 lj/cut/coul/long 0.000000 0.000000 # OH HO -pair_coeff 5 5 lj/cut/coul/long 0.000000 0.000000 # HO HO -pair_coeff * 6*8 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes -pair_coeff 1 1 thole 2.051000 -pair_coeff 1 2 thole 1.580265 -pair_coeff 1 4 thole 1.416087 -pair_coeff 1 6 thole 2.051000 -pair_coeff 1 7 thole 1.580265 -pair_coeff 1 8 thole 1.416087 -pair_coeff 2 2 thole 1.217570 -pair_coeff 2 4 thole 1.091074 -pair_coeff 2 6 thole 1.580265 -pair_coeff 2 7 thole 1.217570 -pair_coeff 2 8 thole 1.091074 -pair_coeff 4 4 thole 0.977720 -pair_coeff 4 6 thole 1.416087 -pair_coeff 4 7 thole 1.091074 -pair_coeff 4 8 thole 0.977720 -pair_coeff 6 6 thole 2.051000 -pair_coeff 6 7 thole 1.580265 -pair_coeff 6 8 thole 1.416087 -pair_coeff 7 7 thole 1.217570 -pair_coeff 7 8 thole 1.091074 -pair_coeff 8 8 thole 0.977720 - -group gETHANOL molecule 1:250 -3000 atoms in group gETHANOL -group gATOMS type 1 2 3 4 5 -2250 atoms in group gATOMS -group gDRUDES type 6 7 8 -750 atoms in group gDRUDES - -neighbor 2.0 bin - -variable vTEMP equal 300.0 -variable vTEMP_D equal 1.0 -variable vPRESS equal 1.0 - -velocity gATOMS create ${vTEMP} 12345 -velocity gATOMS create 300 12345 -velocity gDRUDES create ${vTEMP_D} 12345 -velocity gDRUDES create 1 12345 - -fix fDRUDE all drude C C N C N D D D - -fix fSHAKE gATOMS shake 0.0001 20 0 b 2 3 5 - 250 = # of size 2 clusters - 250 = # of size 3 clusters - 250 = # of size 4 clusters - 0 = # of frozen angles - -fix fLANG all langevin/drude ${vTEMP} 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes -fix fLANG all langevin/drude 300 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes -fix fLANG all langevin/drude 300 100.0 200611 1 20.0 260514 zero yes -fix fNPH all nph iso ${vPRESS} ${vPRESS} 500.0 -fix fNPH all nph iso 1 ${vPRESS} 500.0 -fix fNPH all nph iso 1 1 500.0 - -compute cTEMP all temp/drude - -thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2] -thermo 20 - -timestep 0.5 -run 2000 -PPPM initialization ... - G vector (1/distance) = 0.379738 - grid = 30 30 30 - stencil order = 5 - estimated absolute RMS force accuracy = 0.0289979 - estimated relative force accuracy = 8.73262e-05 - using double precision FFTs - 3d grid and FFT values/proc = 50653 27000 -Rebuild special list taking Drude particles into account -Old max number of 1-2 to 1-4 neighbors: 11 -New max number of 1-2 to 1-4 neighbors: 11 (+0) -Neighbor list info ... - 2 neighbor list requests - update every 1 steps, delay 10 steps, check yes - master list distance cutoff = 10 -Memory usage per processor = 17.0416 Mbytes -Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume cTEMP[1] cTEMP[2] - 0 0 13868.828 2013.3852 270.28772 11855.443 3145.896 51.880809 0.00019113234 0 8481.5109 514734.14 -514557.98 170217.61 22094.109 381.62759 10.134301 - 20 1.385576 10970.012 5646.6301 758.03417 5323.3819 2059.5936 2216.9884 125.92554 0 1728.6053 514096.92 -514904.65 75436.064 22442.45 899.51659 426.89782 - 40 2.8551838 8946.3004 5328.0205 715.26229 3618.2799 1462.1369 1696.2859 256.70292 0 1227.1291 513938.28 -514962.25 46638.926 23048.183 913.15135 252.56746 - 60 4.256644 7510.9138 4723.1153 634.05655 2787.7985 1200.8153 1745.4103 301.30777 0 557.91727 513950.17 -514967.82 37797.472 23517.111 840.69781 151.04819 - 80 5.6700039 6349.0396 4602.1226 617.81383 1746.917 881.77472 1380.8268 300.54011 0 204.13917 513929.54 -514949.9 33853.354 23924.249 841.20585 95.742025 - 100 7.1165569 5485.3222 4144.7402 556.41234 1340.582 784.84009 1301.8671 289.61557 0 -77.062714 514016.28 -514974.95 23857.465 24318.637 768.91722 59.825738 - 120 8.510273 4862.0053 3777.3363 507.09006 1084.669 621.87069 1297.2363 283.15963 0 -165.00092 514030.24 -514982.84 17467.301 24661.1 708.90876 35.503627 - 140 9.89271 4340.9652 3447.5936 462.82361 893.3716 643.1449 1248.6314 275.36087 0 -264.51028 513962.87 -514972.13 14982.178 24941.74 650.92753 23.297372 - 160 11.266981 3926.9368 3280.8104 440.43373 646.12637 590.77624 1125.7232 275.3221 0 -402.26335 514039.99 -514983.43 17555.529 25182.215 623.03896 13.767615 - 180 12.636709 3510.3411 3034.5182 407.37013 475.82289 580.88726 1065.7063 271.62555 0 -478.17514 514008.07 -514972.29 9901.7384 25408.806 577.95511 8.7953435 - 200 13.951961 3233.2057 2804.8754 376.54165 428.33026 560.57334 1096.7788 268.56938 0 -524.79217 514009.74 -514982.54 8543.4492 25602.16 535.31334 5.5723047 - 220 15.315 3020.0557 2679.3857 359.69523 340.66996 534.37676 1086.1078 252.72365 0 -554.44877 514000.87 -514978.96 7630.6161 25763.835 511.8744 4.1309201 - 240 16.66608 2817.6362 2557.8968 343.3859 259.73947 533.53125 1096.7513 235.23483 0 -594.78212 513968.14 -514979.14 6067.9397 25911.192 489.07601 2.9844639 - 260 18.020921 2631.1316 2460.4934 330.30994 170.63824 520.23801 1043.849 228.55335 0 -637.15729 514004.04 -514988.88 5635.1903 26047.493 470.67196 2.358136 - 280 19.327414 2462.7215 2379.403 319.42393 83.318543 525.36331 972.01762 226.26993 0 -624.36335 513966.76 -514982.73 4763.2439 26167.845 455.32938 1.8853017 - 300 20.664073 2314.007 2233.3945 299.82295 80.612529 521.07514 985.58156 216.6623 0 -622.92535 513969.51 -514989.29 3501.9257 26271.903 427.41388 1.7110326 - 320 21.998284 2171.6005 2216.0458 297.49398 -44.445373 513.1225 926.87268 206.39293 0 -647.39127 513946.45 -514989.89 3556.0249 26368.557 424.16134 1.5401544 - 340 23.295565 2048.7645 2103.0412 282.32362 -54.276671 517.24017 972.17593 198.86832 0 -648.49462 513890.61 -514984.68 3723.4258 26461.822 402.56097 1.3933654 - 360 24.639426 1940.255 2045.2119 274.5603 -104.95688 499.1817 932.32957 187.5616 0 -652.16846 513915.39 -514987.25 2301.433 26551.361 391.50737 1.3177372 - 380 25.919177 1826.4337 1933.9251 259.62057 -107.49138 518.5733 919.38362 182.08763 0 -651.72644 513909.35 -514985.16 2618.7931 26632.025 370.16974 1.3263382 - 400 27.23436 1760.0079 1974.3468 265.04699 -214.33884 494.88766 905.27809 184.94874 0 -673.15814 513861.2 -514987.5 2096.731 26707.742 377.93896 1.2790015 - 420 28.50932 1674.2459 1875.0429 251.7159 -200.79701 494.32791 919.1307 191.42967 0 -660.09631 513843.82 -514989.41 358.06627 26778.924 358.8831 1.3234648 - 440 29.823068 1636.3668 1886.8736 253.30412 -250.50682 501.37304 885.96911 179.94725 0 -646.55634 513813.44 -514984.68 465.97294 26842.197 361.1633 1.2949713 - 460 31.092765 1593.0934 1860.7484 249.79693 -267.65503 491.39115 906.9344 174.33035 0 -666.38274 513814.92 -514988.85 126.16052 26894.743 356.1632 1.2759204 - 480 32.406062 1505.0407 1837.1657 246.63106 -332.12503 509.85902 860.16645 173.43061 0 -651.2259 513765.85 -514990.2 1646.3283 26939.521 351.6473 1.2643358 - 500 33.677199 1442.2558 1798.394 241.42613 -356.13819 522.53768 861.77071 168.42903 0 -655.02572 513738.55 -514992.4 1526.9168 26984.71 344.22043 1.2508825 - 520 34.98888 1429.2148 1796.9298 241.22958 -367.71495 524.55666 871.69773 162.68814 0 -664.81406 513731.94 -514993.79 -680.86121 27027.519 343.9346 1.2628675 - 540 36.290854 1386.5466 1788.8853 240.14964 -402.33868 549.35219 874.93475 154.34652 0 -656.82759 513667.79 -514991.93 -112.10182 27063.585 342.37563 1.3021222 - 560 37.52542 1344.4167 1829.4102 245.58992 -484.99349 543.86102 827.43025 144.96524 0 -643.51447 513638.79 -514996.53 701.10406 27094.487 350.14354 1.3040182 - 580 38.796225 1286.7629 1718.567 230.70973 -431.80414 561.04865 874.04358 152.41827 0 -615.40981 513590.72 -514994.62 826.08615 27125.818 328.91939 1.2462575 - 600 40.032106 1275.3861 1701.9169 228.47454 -426.53082 558.07219 895.26591 163.23964 0 -608.79386 513561.43 -514995.74 284.53547 27152.441 325.68878 1.3366627 - 620 41.297358 1273.8918 1712.1906 229.85372 -438.29876 558.54787 859.08268 175.40704 0 -603.76978 513568.36 -514995.92 -799.98388 27171.09 327.70761 1.2215062 - 640 42.526453 1217.1518 1736.1072 233.06442 -518.95534 572.52862 823.16123 163.5653 0 -606.82177 513521.07 -514992.46 -528.59646 27187.499 332.28172 1.2466277 - 660 43.751388 1139.8934 1675.8281 224.97222 -535.93471 572.5104 829.99341 152.69698 0 -620.77477 513527.1 -514997.46 127.63393 27203.689 320.71564 1.270961 - 680 44.951294 1132.7801 1684.9691 226.19937 -552.18903 579.17897 824.9868 153.95243 0 -613.89121 513497.59 -514994 -375.69988 27217.538 322.46995 1.266406 - 700 46.114508 1123.7259 1689.7673 226.8435 -566.04141 579.34852 817.35591 160.76324 0 -604.95952 513473.67 -514992.22 539.9968 27228.562 323.38291 1.2824201 - 720 47.311101 1109.2452 1679.3944 225.45099 -570.14919 580.49864 815.37954 166.39557 0 -599.53737 513460.9 -514993.78 1379.628 27240.51 321.38269 1.3097525 - 740 48.482072 1103.9038 1664.1003 223.39782 -560.19651 598.28549 826.45607 162.40108 0 -577.67737 513419.55 -514989.21 -688.06905 27252.803 318.47888 1.2441535 - 760 49.66032 1069.6322 1656.8299 222.42181 -587.19776 602.32252 832.89566 153.82032 0 -575.90234 513395.07 -514995.41 40.843646 27264.248 317.07409 1.2699292 - 780 50.861186 1034.9853 1655.3151 222.21845 -620.3298 585.98097 809.14501 152.10567 0 -574.09092 513399.41 -514992.88 -542.13898 27275.872 316.80217 1.2268067 - 800 52.028532 1040.3169 1665.5678 223.59483 -625.25085 605.03042 803.57295 148.68705 0 -581.69335 513396.32 -514997.16 535.8591 27285.478 318.74392 1.2821524 - 820 53.219595 1058.9481 1736.3976 233.1034 -677.4495 598.69968 784.98413 145.24433 0 -598.32684 513390.35 -514998.4 661.30446 27295.669 332.34879 1.2200226 - 840 54.41621 1045.3784 1676.8277 225.10642 -631.4493 612.87881 813.63091 148.70121 0 -579.94856 513372.94 -514999.65 -709.36037 27305.36 320.91078 1.2627849 - 860 55.601647 1020.7309 1672.697 224.55189 -651.96607 601.90752 814.84165 150.80576 0 -580.50172 513365.58 -515004.6 -495.61008 27311.4 320.12878 1.239739 - 880 56.769503 989.87899 1623.5853 217.95888 -633.70636 614.6379 850.57766 146.023 0 -574.97001 513330.69 -515000.67 642.87966 27315.764 310.68993 1.2958041 - 900 57.983504 951.29928 1656.7713 222.41394 -705.47199 612.66694 803.70933 146.11306 0 -578.97014 513313.84 -515002.83 -24.66438 27323.702 317.06441 1.2662666 - 920 59.146542 990.23712 1682.9256 225.92504 -692.68849 625.49291 805.11902 145.39781 0 -566.50947 513298.1 -515000.28 -197.4677 27331.656 322.09842 1.2192545 - 940 60.311439 975.32007 1655.1496 222.19623 -679.82952 644.56888 830.44185 142.39994 0 -571.05582 513274.28 -515000.46 -57.36251 27336.591 316.75027 1.2738836 - 960 61.537265 970.70957 1646.9748 221.0988 -676.26523 621.55653 860.81553 137.50196 0 -570.35847 513277.66 -515003.44 356.66027 27339.657 315.18748 1.2637636 - 980 62.841358 922.60821 1622.7907 217.8522 -700.18247 618.71597 851.23286 133.07652 0 -567.79027 513264.96 -515000.37 5.1281321 27344.467 310.55109 1.2643077 - 1000 64.061049 903.52078 1692.943 227.26982 -789.4222 615.63909 786.17473 136.0751 0 -548.92889 513225.82 -515004.21 -1215.8274 27349.08 323.99743 1.2690479 - 1020 65.198298 880.82937 1611.9406 216.39562 -731.11119 641.95133 825.78985 138.47494 0 -548.19881 513212.76 -515001.89 -120.47994 27348.478 308.46852 1.2703282 - 1040 66.338573 859.35882 1637.2347 219.79124 -777.87584 642.91383 781.96671 129.07882 0 -535.68978 513205.22 -515001.36 -128.41699 27349.25 313.3121 1.2828435 - 1060 67.506762 843.6634 1588.9732 213.31236 -745.30982 645.93104 848.24527 128.71177 0 -531.00457 513167.02 -515004.21 111.3449 27352.063 304.04699 1.3138151 - 1080 68.625545 819.34273 1604.5527 215.40383 -785.20997 653.64454 797.74835 132.82208 0 -520.03981 513152.36 -515001.74 -705.09278 27353.042 307.03668 1.306641 - 1100 69.741567 799.10089 1574.7957 211.40909 -775.69478 654.13763 825.37479 142.68152 0 -514.52184 513120.3 -515003.67 1350.915 27353.287 301.3473 1.2713755 - 1120 70.887971 807.77511 1606.5291 215.66916 -798.75403 677.02 802.76738 138.71115 0 -519.19695 513103.61 -515001.67 551.01047 27358.309 307.4238 1.2874498 - 1140 72.009922 822.40019 1605.593 215.54349 -783.19283 664.08656 825.14971 139.5036 0 -525.0726 513119.2 -515006.06 -1500.6927 27365.732 307.25006 1.2741015 - 1160 73.11993 799.60355 1627.1824 218.44176 -827.57881 660.53797 810.61642 135.99659 0 -549.15929 513120.99 -515006.56 -463.83247 27365.87 311.39885 1.2506312 - 1180 74.237157 808.71869 1627.4862 218.48255 -818.76747 671.07453 814.08104 132.68184 0 -536.0374 513101.27 -515001.83 -1497.9686 27360.344 311.48219 1.1920705 - 1200 75.389495 800.76402 1602.0973 215.0742 -801.33325 661.27319 818.56681 137.56688 0 -528.29009 513116.11 -515006.56 727.09082 27352.249 306.62538 1.1680129 - 1220 76.512266 786.90424 1625.6159 218.23148 -838.7117 654.42667 808.06282 144.23638 0 -544.37793 513103.11 -515004.17 -1016.333 27347.251 311.10383 1.2383451 - 1240 77.618425 784.43915 1618.0202 217.21178 -833.58101 652.75565 810.84854 144.21786 0 -538.55907 513104.01 -515006.86 -1688.0609 27338.945 309.66351 1.2014646 - 1260 78.767789 792.64493 1616.6996 217.03449 -824.05464 659.33158 832.96211 136.95679 0 -535.25333 513087.8 -515005.85 -240.86746 27324.585 309.38787 1.2538953 - 1280 79.890153 772.02964 1579.0067 211.9744 -806.97707 680.62465 825.10068 128.65485 0 -522.39638 513085.1 -515004.06 1026.3484 27308.077 302.15133 1.2789362 - 1300 81.045542 794.71268 1640.9493 220.28991 -846.23661 653.48559 809.8286 126.57126 0 -529.35975 513101 -515007.77 -222.24259 27295.577 314.02093 1.2904787 - 1320 82.165808 784.00371 1619.7825 217.44836 -835.77876 666.10367 843.1839 129.04786 0 -537.48412 513064.75 -515001.38 -904.29245 27284.448 309.98624 1.2367093 - 1340 83.287128 768.52183 1621.7783 217.71629 -853.25649 658.65554 797.98287 135.92558 0 -517.31157 513072.35 -515000.86 556.43774 27269.699 310.3284 1.3310985 - 1360 84.450531 750.55548 1561.8653 209.67325 -811.30983 659.33682 849.22159 146.12076 0 -514.99584 513050.84 -515001.83 156.64838 27254.169 298.83628 1.3466087 - 1380 85.572197 744.55824 1600.9118 214.91506 -856.35357 669.28688 822.92318 135.57716 0 -509.75984 513027.33 -515001.71 395.88113 27246.862 306.32946 1.3282506 - 1400 86.727889 740.37698 1618.0191 217.21163 -877.6421 680.34192 804.16104 122.37614 0 -510.05578 513028.7 -515003.17 -1778.0909 27242.463 309.60983 1.3262175 - 1420 87.853329 707.95242 1606.2301 215.62901 -898.27766 681.75825 834.81666 117.56052 0 -511.14444 512980.84 -515002.11 132.87977 27231.78 307.36642 1.2875563 - 1440 88.999557 701.0459 1631.5857 219.03289 -930.53982 689.29026 778.55166 121.13791 0 -503.03703 512986.74 -515003.22 502.08629 27220.348 312.26072 1.2092436 - 1460 90.173845 691.9965 1611.7145 216.36527 -919.71797 691.89285 800.91685 123.97376 0 -504.76462 512970.72 -515002.46 530.64797 27214.26 308.41315 1.2983911 - 1480 91.318457 691.7249 1594.0369 213.99213 -902.31197 688.47809 838.61898 125.21502 0 -504.16566 512953.09 -515003.55 -1094.2326 27210.327 305.01536 1.3192889 - 1500 92.483926 665.64633 1571.5229 210.96973 -905.87653 681.91529 823.02708 127.30163 0 -506.25486 512973.62 -515005.48 -1022.5661 27200.233 300.72872 1.2507982 - 1520 93.612424 675.29951 1631.0635 218.96279 -955.76401 670.77264 825.29942 133.56984 0 -531.08736 512951.49 -515005.81 -389.61365 27187.165 312.13799 1.2620465 - 1540 94.741199 653.89323 1632.9694 219.21864 -979.07615 678.96106 792.69599 132.07987 0 -515.25022 512939.14 -515006.7 -1030.2457 27174.091 312.51532 1.234099 - 1560 95.9062 636.91726 1590.0999 213.46361 -953.18262 687.04134 809.44011 127.54619 0 -523.45302 512956.52 -515010.28 -951.93121 27155.942 304.27362 1.288966 - 1580 97.028125 627.56968 1601.8646 215.04297 -974.29496 686.96797 803.53231 128.08068 0 -517.28126 512935.11 -515010.71 -1043.2395 27131.362 306.54052 1.2619672 - 1600 98.159189 639.59673 1591.5973 213.66464 -952.00062 695.73225 820.03411 126.92265 0 -523.57295 512936.97 -515008.08 -516.36154 27101.901 304.53745 1.3431812 - 1620 99.322595 631.83759 1582.6681 212.46592 -950.83047 708.36138 817.50888 123.99588 0 -518.92537 512930.72 -515012.49 -2198.9765 27071.135 302.85679 1.2706043 - 1640 100.45901 621.88183 1569.4451 210.6908 -947.56326 703.57599 823.87187 132.80048 0 -497.70649 512900.32 -515010.43 -1335.78 27038.969 300.32548 1.2622751 - 1660 101.60839 642.07332 1595.5476 214.19493 -953.47423 705.46998 794.82235 141.09052 0 -484.29874 512898.11 -515008.66 -403.23344 27004.83 305.30235 1.3253687 - 1680 102.77636 620.05889 1604.721 215.42642 -984.66208 704.63874 808.2235 139.26176 0 -475.937 512849.25 -515010.1 -336.0674 26974.635 307.06907 1.3063348 - 1700 103.9216 625.14905 1627.936 218.54293 -1002.7869 700.41444 790.63143 141.47429 0 -472.95296 512847.83 -515010.18 432.43074 26948.842 311.5388 1.2611748 - 1720 105.07527 635.67026 1585.5068 212.84701 -949.83654 711.22133 826.38676 138.90157 0 -470.74615 512857.96 -515013.56 -927.08791 26927.403 303.39054 1.2949652 - 1740 106.19526 622.55036 1629.9419 218.81221 -1007.3915 701.72972 807.03841 133.88234 0 -462.62233 512821.73 -515009.15 60.724835 26906.734 311.91698 1.2759906 - 1760 107.3157 601.07861 1563.031 209.82973 -961.95237 721.05163 813.03641 135.83107 0 -472.1521 512852.13 -515011.85 1071.0762 26889.11 299.11764 1.211508 - 1780 108.47195 615.76689 1612.7311 216.50175 -996.96425 712.00335 812.2101 135.93651 0 -469.54632 512821.55 -515009.11 -1171.9908 26876.291 308.62781 1.2522701 - 1800 109.60652 590.39061 1576.6095 211.65259 -986.21891 706.7567 822.39219 137.15671 0 -470.15251 512825.84 -515008.21 -1051.5297 26860.1 301.6752 1.3176335 - 1820 110.78553 603.65994 1596.51 214.32414 -992.85007 711.49043 808.94991 132.38543 0 -461.89866 512827.37 -515011.15 180.50052 26844.34 305.50815 1.2756752 - 1840 111.93685 591.93917 1596.2013 214.2827 -1004.2621 720.41618 814.51338 137.96161 0 -460.4745 512793.12 -515009.8 605.10058 26833.73 305.47844 1.2069138 - 1860 113.12134 609.8248 1577.7772 211.80934 -967.95236 716.21723 808.30329 144.61624 0 -461.04538 512833.46 -515009.51 -1143.3982 26826.019 301.93343 1.2373879 - 1880 114.2602 614.25513 1599.756 214.7599 -985.50088 748.39555 792.89735 140.36606 0 -460.16996 512800.85 -515007.84 -261.10141 26816.306 306.15319 1.2225442 - 1900 115.40316 615.77501 1599.1853 214.68329 -983.41029 729.35936 798.81735 146.34452 0 -492.16069 512844.21 -515009.98 493.95161 26806.893 306.01603 1.2873103 - 1920 116.55442 628.99417 1652.3184 221.81616 -1023.3242 715.08536 813.8821 147.49091 0 -508.7856 512818.33 -515009.33 -2250.9701 26803.895 316.19125 1.3118467 - 1940 117.73809 613.28705 1595.717 214.21768 -982.42996 719.54904 821.80704 150.0739 0 -493.66309 512828.25 -515008.45 -2187.7221 26796.819 305.33907 1.3154875 - 1960 118.91834 594.22322 1584.9306 212.76966 -990.7074 717.75467 820.27772 151.35897 0 -491.90915 512819.49 -515007.68 -736.31063 26780.283 303.29276 1.2654066 - 1980 120.06148 614.4096 1572.4353 211.09222 -958.02568 732.31342 826.01815 154.79578 0 -487.35165 512824.93 -515008.73 39.731855 26764.092 300.89417 1.2728833 - 2000 121.20194 604.51985 1580.7247 212.20504 -976.20489 716.50209 820.59198 155.66948 0 -482.48478 512823.08 -515009.56 -465.82593 26752.509 302.47674 1.2881296 -Loop time of 121.202 on 1 procs for 2000 steps with 3000 atoms - -Pair time (%) = 58.9106 (48.6053) -Bond time (%) = 7.9266 (6.53999) -Kspce time (%) = 14.2366 (11.7462) -Neigh time (%) = 1.79608 (1.48189) -Comm time (%) = 0.562635 (0.464213) -Outpt time (%) = 0.0137095 (0.0113113) -Other time (%) = 37.7558 (31.1511) - -Nlocal: 3000 ave 3000 max 3000 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 10007 ave 10007 max 10007 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 720894 ave 720894 max 720894 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 720894 -Ave neighs/atom = 240.298 -Ave special neighs/atom = 10.5 -Neighbor list builds = 49 -Dangerous builds = 0 diff --git a/examples/USER/drude/ethanol/log.ethanol.lang.8Jul15.linux.4 b/examples/USER/drude/ethanol/log.ethanol.lang.8Jul15.linux.4 deleted file mode 100644 index 245a37c6d0..0000000000 --- a/examples/USER/drude/ethanol/log.ethanol.lang.8Jul15.linux.4 +++ /dev/null @@ -1,254 +0,0 @@ -LAMMPS (8 Jul 2015) -units real -boundary p p p - -atom_style full -bond_style harmonic -angle_style harmonic -dihedral_style opls -special_bonds lj/coul 0.0 0.0 0.5 - -pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.600 8.0 -kspace_style pppm 1.0e-4 - -comm_modify vel yes -read_data data.ethanol - orthogonal box = (-14.0138 -14.0278 -14.0189) to (14.0169 14.0177 14.0857) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 3000 atoms - scanning bonds ... - 5 = max bonds/atom - scanning angles ... - 6 = max angles/atom - scanning dihedrals ... - 9 = max dihedrals/atom - reading bonds ... - 2750 bonds - reading angles ... - 3250 angles - reading dihedrals ... - 3000 dihedrals - 5 = max # of 1-2 neighbors - 6 = max # of 1-3 neighbors - 10 = max # of 1-4 neighbors - 11 = max # of special neighbors - -pair_coeff 1 1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H -pair_coeff 1 2 lj/cut/coul/long 0.065997 3.500000 # C3H CTO -pair_coeff 1 3 lj/cut/coul/long 0.044496 2.958040 # C3H H -pair_coeff 1 4 lj/cut/coul/long 0.105921 3.304542 # C3H OH -pair_coeff 1 5 lj/cut/coul/long 0.000000 0.000000 # C3H HO -pair_coeff 2 2 lj/cut/coul/long 0.065997 3.500000 # CTO CTO -pair_coeff 2 3 lj/cut/coul/long 0.044496 2.958040 # CTO H -pair_coeff 2 4 lj/cut/coul/long 0.105921 3.304542 # CTO OH -pair_coeff 2 5 lj/cut/coul/long 0.000000 0.000000 # CTO HO -pair_coeff 3 3 lj/cut/coul/long 0.029999 2.500000 # H H -pair_coeff 3 4 lj/cut/coul/long 0.071413 2.792848 # H OH -pair_coeff 3 5 lj/cut/coul/long 0.000000 0.000000 # H HO -pair_coeff 4 4 lj/cut/coul/long 0.169996 3.120000 # OH OH -pair_coeff 4 5 lj/cut/coul/long 0.000000 0.000000 # OH HO -pair_coeff 5 5 lj/cut/coul/long 0.000000 0.000000 # HO HO -pair_coeff * 6*8 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes -pair_coeff 1 1 thole 2.051000 -pair_coeff 1 2 thole 1.580265 -pair_coeff 1 4 thole 1.416087 -pair_coeff 1 6 thole 2.051000 -pair_coeff 1 7 thole 1.580265 -pair_coeff 1 8 thole 1.416087 -pair_coeff 2 2 thole 1.217570 -pair_coeff 2 4 thole 1.091074 -pair_coeff 2 6 thole 1.580265 -pair_coeff 2 7 thole 1.217570 -pair_coeff 2 8 thole 1.091074 -pair_coeff 4 4 thole 0.977720 -pair_coeff 4 6 thole 1.416087 -pair_coeff 4 7 thole 1.091074 -pair_coeff 4 8 thole 0.977720 -pair_coeff 6 6 thole 2.051000 -pair_coeff 6 7 thole 1.580265 -pair_coeff 6 8 thole 1.416087 -pair_coeff 7 7 thole 1.217570 -pair_coeff 7 8 thole 1.091074 -pair_coeff 8 8 thole 0.977720 - -group gETHANOL molecule 1:250 -3000 atoms in group gETHANOL -group gATOMS type 1 2 3 4 5 -2250 atoms in group gATOMS -group gDRUDES type 6 7 8 -750 atoms in group gDRUDES - -neighbor 2.0 bin - -variable vTEMP equal 300.0 -variable vTEMP_D equal 1.0 -variable vPRESS equal 1.0 - -velocity gATOMS create ${vTEMP} 12345 -velocity gATOMS create 300 12345 -velocity gDRUDES create ${vTEMP_D} 12345 -velocity gDRUDES create 1 12345 - -fix fDRUDE all drude C C N C N D D D - -fix fSHAKE gATOMS shake 0.0001 20 0 b 2 3 5 - 250 = # of size 2 clusters - 250 = # of size 3 clusters - 250 = # of size 4 clusters - 0 = # of frozen angles - -fix fLANG all langevin/drude ${vTEMP} 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes -fix fLANG all langevin/drude 300 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes -fix fLANG all langevin/drude 300 100.0 200611 1 20.0 260514 zero yes -fix fNPH all nph iso ${vPRESS} ${vPRESS} 500.0 -fix fNPH all nph iso 1 ${vPRESS} 500.0 -fix fNPH all nph iso 1 1 500.0 - -compute cTEMP all temp/drude - -thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2] -thermo 20 - -timestep 0.5 -run 2000 -PPPM initialization ... - G vector (1/distance) = 0.379738 - grid = 30 30 30 - stencil order = 5 - estimated absolute RMS force accuracy = 0.0289979 - estimated relative force accuracy = 8.73262e-05 - using double precision FFTs - 3d grid and FFT values/proc = 17908 7200 -Rebuild special list taking Drude particles into account -Old max number of 1-2 to 1-4 neighbors: 11 -New max number of 1-2 to 1-4 neighbors: 11 (+0) -Neighbor list info ... - 2 neighbor list requests - update every 1 steps, delay 10 steps, check yes - master list distance cutoff = 10 -Memory usage per processor = 13.7041 Mbytes -Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume cTEMP[1] cTEMP[2] - 0 0 13868.828 2013.3852 270.28772 11855.443 3145.896 51.880809 0.00019113234 0 8481.5109 514734.14 -514557.98 170217.61 22094.109 381.62759 10.134301 - 20 0.44569397 10977.424 5649.3945 758.40528 5328.0296 2062.3394 2228.2308 127.20754 0 1716.2152 514097.63 -514903.59 75539.256 22441.778 900.65907 425.71739 - 40 0.90527296 8971.2482 5307.0059 712.44118 3664.2423 1468.3059 1727.5451 263.87315 0 1220.4282 513944.02 -514959.93 46706.836 23047.009 909.55477 251.59684 - 60 1.361037 7598.4556 4774.303 640.92826 2824.1526 1194.6529 1771.6791 314.85714 0 553.82536 513952.92 -514963.78 37332.483 23513.741 850.78562 150.29304 - 80 1.7987111 6500.1249 4632.1069 621.83909 1868.0179 914.33309 1444.251 317.2453 0 213.21366 513930.08 -514951.11 33258.709 23919.334 847.28599 94.967207 - 100 2.243571 5591.6251 4319.2496 579.83942 1272.3755 772.49711 1235.8559 306.35507 0 -56.084846 513990.28 -514976.52 21846.137 24315.14 802.34652 59.892261 - 120 2.672169 4952.948 3881.7989 521.11369 1071.1491 630.90018 1260.1994 299.84546 0 -147.02839 514014.84 -514987.6 17197.209 24657.008 728.80233 35.812029 - 140 3.0969729 4374.1711 3440.8515 461.91852 933.31957 670.31509 1238.1527 300.45294 0 -260.41129 513963.49 -514978.68 17258.201 24938.237 649.62114 23.329848 - 160 3.522228 3923.495 3251.4038 436.48603 672.0912 632.18705 1144.4394 307.33026 0 -436.52375 514013.97 -514989.32 17850.515 25184.125 617.40474 13.751472 - 180 3.939676 3558.426 3060.6065 410.87237 497.81946 621.75343 1085.8467 297.16091 0 -495.18434 513968.41 -514980.17 9891.4148 25413.786 582.97006 8.7537197 - 200 4.3550711 3228.7597 2864.5929 384.55845 364.16674 591.37767 1077.5669 257.51603 0 -521.62174 513950.21 -514990.89 5932.7994 25603.593 546.64932 5.8336845 - 220 4.781127 2922.9928 2668.3732 358.21686 254.61956 552.45115 1045.2477 238.95571 0 -548.2597 513955.3 -514989.07 7141.8585 25759.687 509.85961 3.9098706 - 240 5.195529 2721.2831 2574.4897 345.61343 146.79339 548.06208 1035.0795 226.53387 0 -609.08183 513928.26 -514982.06 6976.8028 25904.957 492.22535 3.0535597 - 260 5.5978601 2525.9513 2461.0955 330.39077 64.855761 536.85769 1022.3488 211.33422 0 -633.79065 513919.59 -514991.49 4541.0707 26037.832 470.78293 2.3688827 - 280 6.0106721 2338.1989 2324.5678 312.06255 13.63115 519.14801 970.18634 197.76634 0 -621.14257 513937.12 -514989.44 2916.5572 26148.311 444.7787 1.975451 - 300 6.4294651 2194.9975 2189.2141 293.89194 5.7833943 530.82824 982.37216 190.98549 0 -652.12498 513946.6 -514992.88 4231.0047 26242.419 418.97109 1.6488796 - 320 6.825505 2045.5803 2132.2428 286.24381 -86.66256 531.61575 935.95137 188.46723 0 -683.29899 513935.09 -514994.49 1717.7425 26334.126 408.09021 1.554221 - 340 7.23614 1929.4862 2083.5954 279.71312 -154.10925 509.11673 906.18183 186.63991 0 -668.08147 513908.15 -514996.11 2743.5013 26418.758 398.8054 1.4581893 - 360 7.6401701 1853.7734 1992.7639 267.5194 -138.99054 525.44894 891.90785 178.2228 0 -654.5178 513920.68 -515000.73 3824.9512 26497.054 381.4442 1.3381947 - 380 8.035013 1760.9758 1947.1807 261.40007 -186.20493 517.02356 919.61194 172.55666 0 -676.58938 513879.08 -514997.89 2968.2379 26574.581 372.73009 1.2814975 - 400 8.439594 1687.9145 1906.019 255.8743 -218.10451 535.676 922.06535 176.24936 0 -683.92633 513833.49 -515001.66 1305.3348 26642.871 364.83666 1.2876267 - 420 8.849108 1605.8081 1889.1783 253.61351 -283.37015 517.23187 857.77943 180.22369 0 -663.03698 513825.85 -515001.41 2618.2332 26704.387 361.60626 1.2936035 - 440 9.2419581 1518.1322 1794.7348 240.93491 -276.60265 531.28729 893.06522 188.20612 0 -667.29018 513778.24 -515000.11 1458.8151 26764.917 343.52984 1.2323667 - 460 9.6461852 1455.546 1796.4 241.15845 -340.85398 527.34366 846.65226 188.77031 0 -650.31889 513748.59 -515001.89 169.77154 26818.027 343.8413 1.2433195 - 480 10.037471 1423.2564 1780.6643 239.04601 -357.40797 555.56132 861.65053 179.25353 0 -642.23744 513684.59 -514996.23 1737.2169 26861.945 340.81112 1.2754844 - 500 10.442603 1414.4159 1792.7736 240.67163 -378.35771 562.25347 865.25285 172.51254 0 -638.36916 513656.76 -514996.77 2862.5086 26905.68 343.13664 1.264128 - 520 10.840656 1359.8057 1801.5592 241.85105 -441.75349 573.49082 804.76936 169.51784 0 -635.89324 513643.32 -514996.96 927.77773 26956.407 344.82065 1.2649106 - 540 11.24422 1319.969 1763.9685 236.80467 -443.9995 564.76203 851.23442 169.85422 0 -632.66442 513600.38 -514997.57 402.68456 26999.135 337.63034 1.2312338 - 560 11.656965 1288.5175 1741.1847 233.74605 -452.66718 589.0843 843.68941 164.33111 0 -639.59483 513593.61 -515003.78 2031.8562 27036.616 333.27376 1.1999696 - 580 12.050085 1250.4981 1701.8135 228.46065 -451.3154 576.17535 877.82925 152.94556 0 -632.24298 513574.54 -515000.56 328.36451 27076.846 325.70282 1.2583556 - 600 12.463133 1212.0751 1699.8202 228.19306 -487.74513 586.11242 850.6289 146.9891 0 -635.87543 513564.76 -515000.36 -593.07635 27114.131 325.34702 1.1966401 - 620 12.857609 1202.6969 1724.5891 231.51816 -521.8922 586.546 815.3615 149.33058 0 -627.92161 513553.83 -514999.04 -16.881985 27141.295 330.08328 1.2224592 - 640 13.267988 1180.7392 1717.1928 230.52525 -536.45363 595.45079 837.47314 150.14341 0 -635.92342 513512.84 -514996.44 1253.4658 27161.366 328.61164 1.3535393 - 660 13.661833 1146.6245 1693.9969 227.4113 -547.37231 603.66965 823.99031 147.75109 0 -616.07296 513489.44 -514996.15 -632.85642 27186.187 324.23124 1.1905446 - 680 14.057714 1112.6845 1649.8772 221.48844 -537.19275 594.76928 869.75332 148.3474 0 -610.67856 513459.02 -514998.41 -656.86895 27208.556 315.75904 1.2280206 - 700 14.46045 1080.853 1662.6225 223.19944 -581.76952 607.13692 800.72097 155.37025 0 -590.53466 513444.43 -514998.9 1478.4986 27230.38 318.17518 1.2929123 - 720 14.858115 1074.1453 1681.4035 225.7207 -607.2582 602.55649 804.73664 155.69335 0 -578.62035 513406.54 -514998.16 -312.12065 27255.88 321.76305 1.3178416 - 740 15.262165 1057.2173 1626.1913 218.30872 -568.97405 614.54113 851.40449 158.65878 0 -585.61227 513391.12 -514999.09 -252.45558 27276.192 311.20516 1.2592718 - 760 15.664885 1062.4809 1661.9166 223.10468 -599.4357 613.01783 805.30824 157.10102 0 -572.92999 513401.46 -515003.4 8.2424603 27294.015 318.05423 1.2582564 - 780 16.067218 1054.4338 1611.1036 216.28327 -556.66986 619.88711 869.25572 154.03862 0 -563.00792 513365.76 -515002.61 -325.5131 27313.202 308.30577 1.2766112 - 800 16.469454 1045.3661 1667.4808 223.85165 -622.11476 607.72536 819.84304 154.6324 0 -551.0017 513351.46 -515004.78 -711.73517 27333.225 319.1255 1.2459692 - 820 16.874566 1025.6074 1655.4437 222.23572 -629.83638 617.12876 822.09062 147.69173 0 -566.57998 513354.87 -515005.04 399.28085 27347.385 316.79906 1.2953686 - 840 17.272044 995.37917 1669.6204 224.13888 -674.24128 600.79611 821.7655 140.46192 0 -568.05887 513337.46 -515006.66 583.69527 27361.364 319.5132 1.2991152 - 860 17.673279 971.05977 1639.0518 220.03518 -667.99202 608.93496 824.23202 133.94234 0 -564.33929 513334.29 -515005.05 -413.73876 27378.37 313.69629 1.2004828 - 880 18.080302 944.37506 1628.7217 218.64842 -684.34669 617.46083 825.05882 135.40531 0 -569.6048 513312.82 -515005.49 512.87669 27389.533 311.69643 1.2448601 - 900 18.477336 949.5982 1677.4393 225.18853 -727.84115 624.49844 772.75351 136.94704 0 -549.4139 513292.05 -515004.67 271.20937 27400.579 321.05001 1.211493 - 920 18.873705 932.25995 1610.381 216.18626 -678.12109 623.29028 843.94403 144.55915 0 -557.17786 513270.07 -515002.81 1097.4299 27412.447 308.17027 1.2686712 - 940 19.284093 916.57919 1640.5258 220.23305 -723.94658 619.65583 814.76133 144.02609 0 -552.83588 513253.39 -515002.95 -342.60513 27424.209 313.98093 1.1943711 - 960 19.678839 941.9627 1630.8148 218.9294 -688.85213 647.73279 836.44195 147.48183 0 -533.27218 513217.4 -515004.64 -291.64501 27431.009 312.08648 1.2709839 - 980 20.091488 888.07492 1615.6407 216.89235 -727.56578 644.39061 818.66717 151.18945 0 -530.05167 513198.49 -515010.26 835.04931 27433.771 309.19916 1.2205907 - 1000 20.484026 903.45687 1626.7477 218.38341 -723.29085 660.33039 814.13089 154.52432 0 -517.32081 513174.16 -515009.12 -597.08083 27441.855 311.29984 1.2872278 - 1020 20.884939 884.61313 1628.0576 218.55926 -743.44446 659.18164 792.2445 148.42138 0 -501.95147 513167.72 -515009.06 -227.27612 27447.478 311.54441 1.3024911 - 1040 21.279846 852.14085 1593.0292 213.85686 -740.88834 648.79571 822.31823 141.59479 0 -492.90372 513148.22 -515008.91 1544.7468 27454.311 304.83469 1.2878493 - 1060 21.655111 848.20594 1615.8134 216.91553 -767.60742 629.3671 795.01871 137.79728 0 -487.7332 513167.91 -515009.96 818.90975 27467.219 309.21127 1.2684583 - 1080 22.037992 831.86637 1618.7361 217.30789 -786.86971 636.48473 828.1039 138.80398 0 -531.02117 513152.33 -515011.57 -796.09024 27482.281 309.76171 1.2933978 - 1100 22.412974 796.80267 1592.7483 213.81915 -795.94567 625.90981 798.78644 146.80857 0 -536.96836 513184.36 -515014.85 -84.200922 27491.353 304.78282 1.2860228 - 1120 22.801171 772.10069 1567.5834 210.44088 -795.48274 658.82509 788.14264 148.88807 0 -539.176 513162.6 -515014.76 867.66407 27496.215 299.95125 1.3027473 - 1140 23.17888 770.63813 1565.9379 210.21998 -795.2998 640.7064 799.36864 147.80124 0 -535.9357 513166.65 -515013.89 -1183.537 27499.574 299.64709 1.2856405 - 1160 23.563832 764.75496 1564.5598 210.03497 -799.80482 647.22053 811.27899 146.29888 0 -543.29534 513150.92 -515012.23 -1228.125 27500.914 299.39235 1.2526237 - 1180 23.941609 764.17598 1617.4255 217.13195 -853.24954 659.94837 768.65464 144.94873 0 -529.07191 513110.91 -515008.64 107.09246 27498.487 309.51287 1.287252 - 1200 24.317012 762.98696 1589.6792 213.40714 -826.69227 651.88091 816.19739 145.19502 0 -517.91574 513088.48 -515010.53 -1052.4085 27492.624 304.22381 1.2172354 - 1220 24.706198 764.88104 1566.9504 210.3559 -802.06936 679.17803 822.8538 134.80594 0 -509.18914 513076.83 -515006.55 694.03102 27483.433 299.85098 1.253554 - 1240 25.083107 767.93518 1615.6009 216.887 -847.66571 671.38696 801.01511 123.2586 0 -498.24308 513061.33 -515006.42 -367.46541 27476.952 309.13859 1.3441052 - 1260 25.461219 769.84629 1597.441 214.44912 -827.59471 670.93506 820.00134 122.64096 0 -489.27375 513053.94 -515005.84 -58.54717 27470.667 305.70834 1.2250043 - 1280 25.850924 761.02257 1637.0908 219.77192 -876.06819 685.99978 801.7347 121.99508 0 -498.90642 513022.12 -515009.01 667.72097 27460.84 313.30874 1.2269128 - 1300 26.230407 725.15653 1614.5991 216.75252 -889.44257 676.06266 795.73111 129.44616 0 -500.04123 513019.86 -515010.51 346.28961 27453.003 309.01166 1.1958813 - 1320 26.616651 690.04147 1555.4057 208.80608 -865.36428 674.77824 814.17441 138.30234 0 -503.84683 513024.03 -515012.8 -953.72011 27450.174 297.64076 1.2471902 - 1340 26.997168 731.37012 1629.8044 218.79375 -898.43423 672.50861 814.71248 139.58285 0 -509.67436 512995.22 -515010.78 -1831.2948 27443.855 311.896 1.2621742 - 1360 27.377617 745.65434 1610.5181 216.20467 -864.8638 691.11602 810.45797 140.60405 0 -508.77522 513011.95 -515010.21 -479.36536 27427.931 308.19958 1.2616878 - 1380 27.768431 746.41678 1674.6182 224.8098 -928.2014 661.11056 795.29365 134.53957 0 -512.17435 513003.03 -515010 726.71849 27412.674 320.49072 1.2545772 - 1400 28.151466 706.81871 1607.416 215.78822 -900.5973 709.47611 804.4224 129.7539 0 -509.52634 512973.57 -515008.29 -712.21584 27401.879 307.61219 1.2445794 - 1420 28.544365 667.95202 1582.3831 212.42766 -914.43103 664.88892 801.83372 136.47795 0 -514.32654 513008.75 -515012.06 -674.60825 27385.407 302.81863 1.2330197 - 1440 28.92417 662.21363 1572.2132 211.0624 -909.99957 695.6883 812.01519 141.73013 0 -511.80853 512960.55 -515008.18 -73.453766 27362.02 300.86905 1.233181 - 1460 29.303746 673.3058 1590.356 213.49799 -917.05016 660.8122 809.16185 137.34151 0 -506.78651 512991.4 -515008.98 487.20204 27337.657 304.34864 1.2293292 - 1480 29.683979 690.74904 1599.4915 214.72439 -908.74246 688.89665 819.23241 129.49598 0 -495.16925 512954.44 -515005.64 487.60757 27316.061 306.12959 1.159563 - 1500 30.073856 696.13426 1627.5685 218.49359 -931.4342 677.25983 808.26514 125.60011 0 -489.59764 512955.4 -515008.36 519.17541 27293.341 311.4741 1.2480919 - 1520 30.451939 716.4485 1613.3483 216.5846 -896.89978 696.36687 820.98027 134.70464 0 -469.43851 512929.25 -515008.76 544.98379 27271.903 308.73614 1.2765559 - 1540 30.839949 711.84578 1602.4823 215.1259 -890.63656 708.76314 793.80104 146.48285 0 -451.73842 512918.02 -515005.96 454.52189 27257.543 306.63893 1.3081885 - 1560 31.255883 702.95447 1604.1384 215.34821 -901.1839 701.09472 795.80519 150.09855 0 -450.00841 512908.1 -515006.27 -175.16964 27248.208 306.99599 1.217717 - 1580 31.634972 666.16399 1593.9574 213.98146 -927.79341 709.48317 798.22341 141.85062 0 -483.91855 512915.54 -515008.98 -174.37068 27241.403 305.02798 1.2549165 - 1600 32.013681 688.42678 1613.6536 216.62559 -925.22683 708.7011 810.24587 137.18807 0 -474.54073 512902.73 -515009.55 175.74764 27236.695 308.81599 1.2269417 - 1620 32.377997 686.38631 1599.6555 214.7464 -913.26914 723.55612 796.07516 144.8931 0 -474.73319 512907.37 -515010.43 33.582792 27234.316 306.09396 1.3145429 - 1640 32.739099 705.79223 1615.3667 216.85556 -909.57442 705.06325 806.35123 150.08668 0 -479.53397 512919.18 -515010.72 -276.47112 27230.877 309.12408 1.2740414 - 1660 33.111364 701.27726 1607.2688 215.76845 -905.99149 721.97907 787.92231 144.01692 0 -463.68107 512916.64 -515012.87 929.51954 27224.725 307.57382 1.2682264 - 1680 33.474256 700.51394 1604.7821 215.43463 -904.2682 712.18636 816.32021 135.23856 0 -471.34583 512915.88 -515012.55 169.46579 27223.825 307.07661 1.316103 - 1700 33.847599 653.51775 1574.3177 211.34492 -920.79992 708.22805 829.01689 135.77013 0 -456.72703 512872.35 -515009.44 -1331.9277 27225.869 301.24451 1.2944188 - 1720 34.210801 646.19978 1583.018 212.5129 -936.81823 721.83771 788.24431 140.19453 0 -469.87575 512893.23 -515010.45 722.29697 27224.305 302.91185 1.3016769 - 1740 34.57351 650.08331 1600.9298 214.91747 -950.84647 709.99119 789.79721 138.23225 0 -460.97413 512880.98 -515008.87 1102.6045 27225.414 306.34618 1.3045986 - 1760 34.947762 647.44786 1591.6127 213.6667 -944.16484 703.25888 831.27698 133.1631 0 -463.47718 512860.59 -515008.98 1152.8885 27230.97 304.56068 1.2966664 - 1780 35.311829 634.92036 1581.508 212.31019 -946.58767 707.7771 807.97758 140.70709 0 -473.2579 512882.95 -515012.74 229.64632 27235.632 302.63254 1.2770484 - 1800 35.686407 609.58199 1563.2412 209.85795 -953.65919 706.83652 811.29431 136.56443 0 -482.58705 512887.2 -515012.97 -1428.3239 27239.537 299.14762 1.235579 - 1820 36.050632 615.78755 1553.6653 208.57243 -937.87771 721.32849 827.06658 126.75248 0 -476.19143 512873.72 -515010.55 -1558.7353 27240.307 297.30295 1.2564383 - 1840 36.425851 595.24691 1623.2931 217.91965 -1028.0462 715.62813 759.44377 125.14223 0 -486.38933 512873.86 -515015.73 -393.40048 27233.914 310.63049 1.3037899 - 1860 36.791862 584.14833 1580.8506 212.22194 -996.70229 725.49209 786.41557 129.34385 0 -497.01606 512871.73 -515012.67 -445.7964 27227.234 302.53512 1.2082224 - 1880 37.159068 571.94192 1587.3128 213.08945 -1015.3709 727.21492 776.53831 128.97058 0 -472.95741 512835.25 -515010.39 -2430.0222 27217.82 303.74009 1.2871788 - 1900 37.534434 588.18296 1575.532 211.50794 -987.34908 735.18962 822.01431 121.27343 0 -474.15326 512820.83 -515012.5 -1004.9937 27200.966 301.48221 1.2875721 - 1920 37.899018 595.6429 1593.2862 213.89136 -997.64331 728.16052 813.67464 116.25522 0 -474.41478 512829.4 -515010.72 56.20061 27185.033 304.87735 1.3063391 - 1940 38.263855 552.10655 1586.7384 213.01234 -1034.6318 727.69915 794.08444 116.66262 0 -474.42985 512811.77 -515010.42 229.42949 27173.976 303.61874 1.3140118 - 1960 38.637106 571.50083 1614.8554 216.78693 -1043.3546 729.51741 761.23804 128.23909 0 -464.44507 512811.41 -515009.31 -496.32744 27162.867 309.02606 1.2732453 - 1980 38.999486 554.31018 1603.5237 215.26569 -1049.2135 738.87358 785.7371 126.13553 0 -468.044 512779.36 -515011.27 467.45037 27149.813 306.82565 1.3387674 - 2000 39.362048 570.16479 1585.0529 212.78608 -1014.8882 754.53304 813.00379 125.06015 0 -448.86583 512751.21 -515009.83 -257.98779 27141.691 303.29539 1.313977 -Loop time of 39.3621 on 4 procs for 2000 steps with 3000 atoms - -Pair time (%) = 15.1636 (38.5233) -Bond time (%) = 2.04281 (5.18978) -Kspce time (%) = 8.76608 (22.2704) -Neigh time (%) = 0.513343 (1.30415) -Comm time (%) = 1.60174 (4.06924) -Outpt time (%) = 0.00888807 (0.0225803) -Other time (%) = 11.2657 (28.6206) - -Nlocal: 750 ave 771 max 713 min -Histogram: 1 0 0 0 0 0 1 0 1 1 -Nghost: 5881.75 ave 5954 max 5826 min -Histogram: 2 0 0 0 0 0 1 0 0 1 -Neighs: 178004 ave 198102 max 168052 min -Histogram: 1 2 0 0 0 0 0 0 0 1 - -Total # of neighbors = 712018 -Ave neighs/atom = 237.339 -Ave special neighs/atom = 10.5 -Neighbor list builds = 50 -Dangerous builds = 0 diff --git a/examples/USER/drude/ethanol/log.ethanol.nh.8Jul15.linux.1 b/examples/USER/drude/ethanol/log.ethanol.nh.8Jul15.linux.1 deleted file mode 100644 index d8b8fb07f7..0000000000 --- a/examples/USER/drude/ethanol/log.ethanol.nh.8Jul15.linux.1 +++ /dev/null @@ -1,263 +0,0 @@ -LAMMPS (8 Jul 2015) -units real -boundary p p p - -atom_style full -bond_style harmonic -angle_style harmonic -dihedral_style opls -special_bonds lj/coul 0.0 0.0 0.5 - -pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.600 8.0 -kspace_style pppm 1.0e-4 - -read_data data.ethanol - orthogonal box = (-14.0138 -14.0278 -14.0189) to (14.0169 14.0177 14.0857) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 3000 atoms - scanning bonds ... - 5 = max bonds/atom - scanning angles ... - 6 = max angles/atom - scanning dihedrals ... - 9 = max dihedrals/atom - reading bonds ... - 2750 bonds - reading angles ... - 3250 angles - reading dihedrals ... - 3000 dihedrals - 5 = max # of 1-2 neighbors - 6 = max # of 1-3 neighbors - 10 = max # of 1-4 neighbors - 11 = max # of special neighbors - - -pair_coeff 1 1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H -pair_coeff 1 2 lj/cut/coul/long 0.065997 3.500000 # C3H CTO -pair_coeff 1 3 lj/cut/coul/long 0.044496 2.958040 # C3H H -pair_coeff 1 4 lj/cut/coul/long 0.105921 3.304542 # C3H OH -pair_coeff 1 5 lj/cut/coul/long 0.000000 0.000000 # C3H HO -pair_coeff 2 2 lj/cut/coul/long 0.065997 3.500000 # CTO CTO -pair_coeff 2 3 lj/cut/coul/long 0.044496 2.958040 # CTO H -pair_coeff 2 4 lj/cut/coul/long 0.105921 3.304542 # CTO OH -pair_coeff 2 5 lj/cut/coul/long 0.000000 0.000000 # CTO HO -pair_coeff 3 3 lj/cut/coul/long 0.029999 2.500000 # H H -pair_coeff 3 4 lj/cut/coul/long 0.071413 2.792848 # H OH -pair_coeff 3 5 lj/cut/coul/long 0.000000 0.000000 # H HO -pair_coeff 4 4 lj/cut/coul/long 0.169996 3.120000 # OH OH -pair_coeff 4 5 lj/cut/coul/long 0.000000 0.000000 # OH HO -pair_coeff 5 5 lj/cut/coul/long 0.000000 0.000000 # HO HO -pair_coeff * 6*8 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes -pair_coeff 1 1 thole 2.051000 -pair_coeff 1 2 thole 1.580265 -pair_coeff 1 4 thole 1.416087 -pair_coeff 1 6 thole 2.051000 -pair_coeff 1 7 thole 1.580265 -pair_coeff 1 8 thole 1.416087 -pair_coeff 2 2 thole 1.217570 -pair_coeff 2 4 thole 1.091074 -pair_coeff 2 6 thole 1.580265 -pair_coeff 2 7 thole 1.217570 -pair_coeff 2 8 thole 1.091074 -pair_coeff 4 4 thole 0.977720 -pair_coeff 4 6 thole 1.416087 -pair_coeff 4 7 thole 1.091074 -pair_coeff 4 8 thole 0.977720 -pair_coeff 6 6 thole 2.051000 -pair_coeff 6 7 thole 1.580265 -pair_coeff 6 8 thole 1.416087 -pair_coeff 7 7 thole 1.217570 -pair_coeff 7 8 thole 1.091074 -pair_coeff 8 8 thole 0.977720 - -group gETHANOL molecule 1:250 -3000 atoms in group gETHANOL -group gATOMS type 1 2 3 4 5 -2250 atoms in group gATOMS -group gDRUDES type 6 7 8 -750 atoms in group gDRUDES - - -neighbor 2.0 bin - -variable vTEMP equal 300.0 -variable vTEMP_D equal 1.0 -variable vPRESS equal 1.0 - -velocity gATOMS create ${vTEMP} 12345 -velocity gATOMS create 300 12345 -velocity gDRUDES create ${vTEMP_D} 12345 -velocity gDRUDES create 1 12345 - -fix fDRUDE all drude C C N C N D D D - -fix fSHAKE gATOMS shake 0.0001 20 0 b 2 3 5 - 250 = # of size 2 clusters - 250 = # of size 3 clusters - 250 = # of size 4 clusters - 0 = # of frozen angles - -comm_modify vel yes -compute cTEMP_ATOM gATOMS temp -compute cTEMP all temp/drude - -fix fDTDIR all drude/transform/direct -fix fNPT gATOMS npt temp ${vTEMP} ${vTEMP} 100 iso ${vPRESS} ${vPRESS} 500 -fix fNPT gATOMS npt temp 300 ${vTEMP} 100 iso ${vPRESS} ${vPRESS} 500 -fix fNPT gATOMS npt temp 300 300 100 iso ${vPRESS} ${vPRESS} 500 -fix fNPT gATOMS npt temp 300 300 100 iso 1 ${vPRESS} 500 -fix fNPT gATOMS npt temp 300 300 100 iso 1 1 500 -fix_modify fNPT temp cTEMP_ATOM press thermo_press -WARNING: Temperature for fix modify is not for group all (../fix_nh.cpp:1349) -fix fNVT gDRUDES nvt temp ${vTEMP_D} ${vTEMP_D} 100.0 -fix fNVT gDRUDES nvt temp 1 ${vTEMP_D} 100.0 -fix fNVT gDRUDES nvt temp 1 1 100.0 -fix fDTINV all drude/transform/inverse - -thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2] -thermo 20 - -timestep 0.5 -run 2000 -PPPM initialization ... - G vector (1/distance) = 0.379738 - grid = 30 30 30 - stencil order = 5 - estimated absolute RMS force accuracy = 0.0289979 - estimated relative force accuracy = 8.73262e-05 - using double precision FFTs - 3d grid and FFT values/proc = 50653 27000 -Rebuild special list taking Drude particles into account -Old max number of 1-2 to 1-4 neighbors: 11 -New max number of 1-2 to 1-4 neighbors: 11 (+0) -Neighbor list info ... - 2 neighbor list requests - update every 1 steps, delay 10 steps, check yes - master list distance cutoff = 10 -Memory usage per processor = 17.0416 Mbytes -Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume cTEMP[1] cTEMP[2] - 0 0 13868.828 2013.3852 270.28772 11855.443 3145.896 51.880809 0.00019113234 0 8481.5109 514734.14 -514557.98 170217.61 22094.109 381.62759 10.134301 - 20 1.485518 11385.192 5995.2334 804.83256 5389.9589 2039.7325 2312.5375 131.6961 0 1710.3266 514098.34 -514902.67 75867.639 22408.275 975.26848 406.07565 - 40 2.9579411 9812.3728 6009.1747 806.70411 3803.1981 1442.3489 1826.1439 275.19367 0 1288.2864 513934.98 -514963.76 48675.043 22980.115 1057.0176 221.56359 - 60 4.3728549 8857.9452 5779.5973 775.8844 3078.348 1190.8978 1938.6134 328.6837 0 619.31805 513970.98 -514970.15 39710.61 23440.966 1050.9011 133.14424 - 80 5.817939 8115.7843 5997.9225 805.19356 2117.8618 901.84106 1587.5472 325.40763 0 288.34562 513957.43 -514942.71 37588.951 23834.833 1111.65 89.054921 - 100 7.207612 7496.2553 5770.3833 774.64747 1725.872 829.63908 1420.6659 325.4016 0 62.343574 514051.62 -514963.79 27294.064 24225.918 1080.2687 60.498472 - 120 8.656971 6986.593 5396.9479 724.51547 1589.6452 678.24993 1535.5197 325.88462 0 -9.6649617 514027.05 -514967.4 21720.902 24578.195 1016.3014 42.715636 - 140 10.075453 6549.0006 5126.6341 688.22709 1422.3665 724.95472 1477.7714 315.11964 0 -99.456486 513960.58 -514956.6 19747.307 24877.008 969.51239 30.977085 - 160 11.492728 6131.3317 5000.4421 671.2864 1130.8896 703.24858 1302.1192 314.93994 0 -258.4539 514042.29 -514973.25 23050.008 25142.654 948.73049 23.021806 - 180 12.899685 5749.9765 4700.9451 631.0803 1049.0314 674.94525 1301.4114 310.04938 0 -326.73679 514044.26 -514954.9 14225.485 25400.048 893.75893 17.322076 - 200 14.301162 5429.601 4392.5738 589.68286 1037.0272 612.00108 1296.2432 303.16019 0 -300.38658 514093.7 -514967.69 10835.073 25622.866 836.16806 13.764486 - 220 15.696118 5133.8318 4290.7369 576.01173 843.09487 572.51989 1261.8055 289.99072 0 -383.71584 514078.3 -514975.81 12509.826 25814.229 817.78562 11.104636 - 240 17.080213 4850.3856 4120.3632 553.13985 730.0224 553.79224 1263.6533 278.92142 0 -487.76523 514091.35 -514969.93 10891.878 25996.167 785.87194 9.360776 - 260 18.465174 4583.9875 3911.0361 525.03865 672.95138 541.52251 1175.1552 273.43365 0 -475.23638 514139.68 -514981.61 8086.1512 26168.96 746.55574 7.4653786 - 280 19.852883 4349.224 3692.2792 495.67153 656.9448 598.81912 1148.0997 278.8781 0 -444.09603 514045.38 -514970.13 5124.6373 26323.056 705.04252 6.4783461 - 300 21.231065 4128.9017 3579.5067 480.53234 549.39506 584.06591 1089.5131 267.69425 0 -456.87099 514043.55 -514978.56 8350.7757 26456.831 683.9437 5.2650983 - 320 22.561911 3913.7712 3456.9151 464.07498 456.85609 556.31985 1103.3901 263.88855 0 -485.54294 514000.27 -514981.47 9117.6459 26592.844 660.74075 4.5694113 - 340 23.929412 3712.7166 3258.4133 437.42702 454.30336 533.72419 1069.0448 271.85689 0 -454.53939 514001.97 -514967.75 7187.6779 26736.819 622.98237 3.8812919 - 360 25.298241 3533.3834 3024.1004 405.9716 509.283 522.55431 1104.3208 276.30858 0 -456.06655 514036.53 -514974.36 4554.9866 26876.658 578.31181 3.3031408 - 380 26.653809 3367.1792 2971.2716 398.87957 395.9076 508.27241 1059.2248 257.85685 0 -499.68496 514032.55 -514962.31 5645.8914 27002.069 568.38695 2.8305175 - 400 27.984353 3204.91 2874.2403 385.85357 330.6697 543.88404 1018.8809 231.0702 0 -519.33317 514029.07 -514972.9 7250.7332 27123.905 549.89179 2.5832582 - 420 29.327209 3050.6948 2776.6044 372.74639 274.09045 517.42853 953.07587 226.06727 0 -505.60565 514057.02 -514973.9 4026.2599 27250.314 531.28066 2.3360848 - 440 30.659683 2916.2839 2640.2361 354.43958 276.04784 507.06292 983.97321 236.01275 0 -534.64355 514059.65 -514976.01 1708.709 27364.195 505.24974 2.0766005 - 460 31.992583 2787.525 2609.5902 350.32551 177.93474 485.64363 933.57925 234.95003 0 -560.61762 514069.83 -514985.45 3400.5279 27458.081 499.48923 1.8097259 - 480 33.31755 2662.4984 2514.178 337.51686 148.32032 464.67048 928.26208 239.37956 0 -570.38407 514070.86 -514984.47 5084.8141 27547.559 481.26944 1.6441427 - 500 34.613889 2540.5549 2433.5506 326.693 107.00428 473.2945 888.73268 239.40601 0 -565.68704 514057.33 -514986.07 3134.3501 27643.279 465.87942 1.4891047 - 520 35.938482 2432.2066 2375.3401 318.8785 56.866542 460.28751 838.60926 229.00792 0 -579.13212 514093.74 -514985.64 468.2133 27732.471 454.76753 1.3789356 - 540 37.265891 2328.8169 2275.0595 305.41629 53.757389 473.08203 875.54175 220.60944 0 -604.11384 514075.79 -514987.16 2632.7788 27804.408 435.55773 1.3457265 - 560 38.585909 2228.615 2278.3234 305.85446 -49.708475 455.58479 820.87878 215.10334 0 -604.72924 514052.45 -514989 3784.1482 27875.141 436.2741 1.1341618 - 580 39.864162 2134.4158 2127.9962 285.67372 6.4195621 480.68268 836.80009 219.13915 0 -563.30768 514019.28 -514986.18 1359.5813 27951.068 407.46382 1.1159366 - 600 41.132397 2048.4786 2102.9549 282.31205 -54.476369 486.301 796.4297 225.04029 0 -574.89865 514003.04 -514990.39 -91.415091 28017.963 402.69767 1.0358319 - 620 42.405012 1967.4398 2048.4364 274.99318 -80.996617 477.38045 786.20744 223.98682 0 -570.14553 513997.93 -514996.35 1828.8595 28070.312 392.2521 1.022392 - 640 43.643353 1888.1318 1981.566 266.01614 -93.434276 482.74658 801.17689 222.6863 0 -557.43781 513952.32 -514994.92 3812.5364 28123.574 379.47296 0.92888928 - 660 44.915581 1813.0614 1959.0105 262.98817 -145.94913 498.25019 750.64037 217.17325 0 -556.66234 513938.55 -514993.9 1151.2432 28187.531 375.17108 0.87739869 - 680 46.131009 1744.832 1911.6741 256.63347 -166.84215 497.042 725.1867 211.01897 0 -553.89849 513944.3 -514990.49 108.93436 28245.999 366.12859 0.80270448 - 700 47.378681 1678.1626 1915.3894 257.13223 -237.22675 490.51486 719.69339 202.0347 0 -569.53306 513909.13 -514989.07 2213.2126 28294.676 366.86703 0.7415387 - 720 48.690897 1612.159 1862.0857 249.97645 -249.92665 500.42275 728.44427 190.27551 0 -551.64449 513871.72 -514989.15 3052.5203 28347.921 356.64837 0.74199709 - 740 49.934569 1549.9154 1792.3586 240.61591 -242.44316 497.29161 738.6029 175.53735 0 -547.70029 513880.64 -514986.81 738.07583 28409.346 343.29748 0.7047584 - 760 51.094031 1493.142 1799.8956 241.62772 -306.75355 503.57846 709.28495 169.315 0 -559.17689 513862.16 -514991.92 -783.63021 28463.359 344.75885 0.66625263 - 780 52.252971 1437.0347 1824.9884 244.99631 -387.95371 510.42774 661.31982 170.22096 0 -556.6031 513818.26 -514991.58 1267.2418 28503.342 349.56302 0.68065177 - 800 53.379442 1382.5833 1736.7991 233.1573 -354.21576 514.27927 697.39594 172.11416 0 -554.93314 513805.74 -514988.82 1744.7887 28543.483 332.6636 0.66505935 - 820 54.535354 1332.0444 1690.9869 227.00722 -358.94246 509.37721 686.56084 172.95747 0 -552.9503 513815.42 -514990.31 -146.04973 28586.706 323.91193 0.59356881 - 840 55.662329 1285.5292 1685.7755 226.30763 -400.2463 507.19453 662.75433 170.55434 0 -559.51859 513807.26 -514988.49 -690.17907 28621.308 322.91069 0.59874377 - 860 56.818479 1239.7941 1704.701 228.84829 -464.90694 495.88426 658.89439 170.35 0 -574.82793 513772.87 -514988.08 747.19844 28645.708 326.53594 0.60530564 - 880 57.943864 1195.2063 1673.557 224.66734 -478.35068 498.99876 648.88199 170.51747 0 -557.50857 513743.81 -514983.05 1172.7738 28670.551 320.58027 0.57096305 - 900 59.0976 1153.211 1639.9315 220.15327 -486.72046 502.47627 643.51354 178.69816 0 -556.38628 513730.32 -514985.34 -511.45034 28697.8 314.13849 0.56088797 - 920 60.220959 1114.1597 1616.0109 216.94205 -501.85117 514.79499 630.19604 179.36393 0 -549.5453 513714.55 -514991.21 -1422.3991 28716.8 309.54311 0.58363424 - 940 61.375362 1076.2186 1627.0408 218.42275 -550.82218 512.57892 621.31041 171.65194 0 -553.00757 513686.04 -514989.39 298.61672 28723.941 311.6754 0.54200743 - 960 62.499341 1040.0389 1613.5611 216.61317 -573.52223 511.50602 601.98148 170.02159 0 -546.21393 513682.82 -514993.64 795.9161 28731.421 309.07527 0.57946382 - 980 63.655075 1005.556 1568.0264 210.50035 -562.47043 514.81982 629.32987 175.28567 0 -544.55487 513654.62 -514991.97 -1246.9263 28741.462 300.35589 0.55675479 - 1000 64.806202 973.43261 1565.2247 210.12423 -591.79208 505.29272 600.76239 165.17131 0 -554.93533 513685.36 -514993.44 -1299.5982 28742.028 299.81847 0.55749205 - 1020 65.904504 942.29451 1571.0425 210.90525 -628.74802 506.25414 614.54444 152.41332 0 -569.19989 513660.6 -514993.36 -197.56562 28733.474 300.93111 0.56370125 - 1040 67.002294 912.00673 1595.282 214.15928 -683.27525 489.63949 569.70488 159.39981 0 -590.61096 513680.38 -514991.79 467.80409 28724.916 305.58073 0.55701412 - 1060 68.131496 883.21094 1542.2424 207.03896 -659.03142 503.00762 589.40955 165.92561 0 -599.75208 513674.64 -514992.26 -2147.8302 28718.434 295.39729 0.59345978 - 1080 69.232333 856.19557 1533.4133 205.85369 -677.21769 507.87992 576.5184 168.18594 0 -578.48413 513634.34 -514985.66 -1762.0347 28699.147 293.70385 0.59551254 - 1100 70.364775 831.37376 1484.1452 199.23968 -652.77147 514.07523 608.66719 163.10107 0 -567.48676 513613.52 -514984.65 33.310994 28670.682 284.25195 0.61206838 - 1120 71.467535 808.52739 1521.0421 204.19292 -712.51473 513.69276 561.64386 163.23813 0 -559.45919 513591.61 -514983.24 -310.61111 28645.19 291.32265 0.61797603 - 1140 72.601129 786.87835 1489.4671 199.95412 -702.58878 523.98829 584.70722 162.29577 0 -549.08561 513559.92 -514984.41 -1685.4255 28620.437 285.26086 0.63846185 - 1160 73.705792 766.63847 1508.1762 202.46573 -741.53775 514.32182 584.88936 152.54558 0 -535.15913 513525.59 -514983.73 -1902.1776 28587.352 288.83351 0.67096701 - 1180 74.841457 749.02843 1510.9898 202.84344 -761.96133 536.04857 571.2202 147.21017 0 -519.34217 513485.23 -514982.33 867.83936 28547.617 289.35403 0.71492747 - 1200 75.948637 733.34578 1503.6833 201.86257 -770.33748 533.86604 589.40444 152.04389 0 -519.58392 513457.87 -514983.94 16.285861 28517.381 287.94489 0.73468233 - 1220 77.086539 718.25616 1498.0744 201.1096 -779.81819 559.89022 564.22113 156.14265 0 -507.10566 513432.51 -514985.47 -1279.2454 28491.203 286.86449 0.74672427 - 1240 78.196455 704.4456 1488.8421 199.87022 -784.3965 566.03391 579.8182 161.3278 0 -468.50406 513361.56 -514984.64 -54.414997 28461.145 285.0822 0.7757678 - 1260 79.336046 693.03071 1494.0932 200.57516 -801.06253 573.59408 573.29809 158.50778 0 -453.3769 513333.73 -514986.81 977.78497 28434.874 286.06644 0.82806578 - 1280 80.450187 683.34372 1478.8974 198.53519 -795.55372 580.51573 596.90975 153.51449 0 -437.44107 513297.84 -514986.89 809.72996 28418.785 283.14058 0.85789606 - 1300 81.562086 675.21003 1490.4096 200.08064 -815.19955 586.94949 575.877 144.63393 0 -412.94901 513274.99 -514984.7 -448.50658 28409.979 285.3107 0.94374006 - 1320 82.704837 668.21879 1489.4584 199.95295 -821.23962 576.22292 605.97557 140.59647 0 -423.93742 513262.85 -514982.94 -41.054413 28400.286 285.13719 0.9231239 - 1340 83.820401 662.582 1506.0415 202.17916 -843.45952 580.69502 578.24319 144.89986 0 -430.94868 513260.2 -514976.55 977.60126 28392.044 288.28069 1.0060194 - 1360 84.965785 658.24059 1527.9683 205.12273 -869.7277 577.91541 570.19843 152.39114 0 -451.12207 513259.47 -514978.58 371.63239 28390.774 292.47304 1.0318294 - 1380 86.080907 654.92452 1486.6437 199.57509 -831.71915 580.08964 585.152 157.63831 0 -437.00747 513263.59 -514981.18 -247.9673 28392.439 284.5256 1.0911219 - 1400 87.195704 652.93764 1510.6586 202.79899 -857.721 568.92903 573.37125 151.89337 0 -426.43036 513257.39 -514982.88 -51.617883 28392.618 289.11402 1.1268379 - 1420 88.34689 651.93794 1494.4977 200.62946 -842.55979 571.38046 600.63765 145.50987 0 -443.12588 513270.14 -514987.1 743.13616 28392.861 285.98783 1.1924311 - 1440 89.493044 651.84231 1520.3977 204.10641 -868.55537 569.30886 591.50444 144.87083 0 -452.53315 513268.23 -514989.93 461.56063 28397.854 290.94803 1.2038182 - 1460 90.608597 652.79726 1538.7134 206.56522 -885.91619 576.98896 569.0177 144.49629 0 -461.96923 513277.97 -514992.42 -706.12558 28404.942 294.4277 1.2773313 - 1480 91.757208 654.35279 1560.3813 209.47403 -906.02856 573.31257 551.02062 151.79154 0 -471.83285 513285.31 -514995.63 -636.13512 28406.735 298.57005 1.3040147 - 1500 92.886091 656.18474 1535.2238 206.09675 -879.03909 565.77757 581.30733 155.02848 0 -493.04533 513302.18 -514990.29 143.11549 28404.04 293.73748 1.3269254 - 1520 94.042872 658.68485 1540.4536 206.79882 -881.76871 562.4227 566.55678 153.51217 0 -481.25224 513306.12 -514989.13 320.11741 28402.365 294.71422 1.3871403 - 1540 95.163877 662.00561 1525.2953 204.7639 -863.28974 547.96338 591.50659 150.34534 0 -461.18073 513297.4 -514989.32 -131.34055 28402.834 291.79671 1.4143192 - 1560 96.312922 666.1124 1506.6675 202.2632 -840.55513 559.7266 593.99441 157.20165 0 -475.77029 513317.32 -514993.02 -361.762 28402.279 288.23662 1.3888658 - 1580 97.430754 670.56531 1535.7659 206.16953 -865.20063 562.32491 577.33497 164.90914 0 -495.18787 513321.56 -514996.14 281.32907 28399.686 293.815 1.3885206 - 1600 98.548553 676.03467 1559.0361 209.29344 -883.00142 570.63265 568.63747 171.76131 0 -497.53636 513299.62 -514996.12 -83.071675 28398.615 298.25471 1.4380743 - 1620 99.69614 681.61565 1551.6098 208.29649 -869.99417 572.80627 589.25676 175.66645 0 -486.29635 513275.79 -514997.22 -1208.1908 28396.28 296.81124 1.4843702 - 1640 100.81368 687.56466 1565.2232 210.12403 -877.65855 578.7743 586.81939 173.9181 0 -490.97778 513266.56 -514992.76 -587.86248 28386.365 299.44244 1.4342399 - 1660 101.96336 693.76095 1558.3222 209.1976 -864.56124 583.58497 605.24119 171.44101 0 -488.52963 513255.46 -514991.76 335.92415 28373.356 298.0981 1.4841753 - 1680 103.08285 699.76249 1608.1314 215.88426 -908.36892 585.35458 590.64567 171.79357 0 -478.93732 513211.41 -514988.64 91.212095 28363.527 307.67509 1.4177962 - 1700 104.23343 705.16423 1586.5697 212.9897 -881.40546 609.44211 582.01973 172.76356 0 -457.12517 513197.39 -514985.89 -662.76266 28354.912 303.56619 1.3605633 - 1720 105.38429 709.98606 1609.0843 216.01219 -899.09829 612.02708 597.82638 167.68834 0 -444.72348 513153.41 -514985.33 -92.038463 28343.124 307.84128 1.4562833 - 1740 106.50511 714.51622 1579.8945 212.09359 -865.37833 624.49924 619.60972 166.03466 0 -425.9731 513136.37 -514985.92 1173.1099 28332.574 302.27863 1.3790325 - 1760 107.65668 718.07347 1624.056 218.02206 -905.9825 608.96798 597.96224 154.72096 0 -409.37211 513132.37 -514990.63 786.32681 28330.712 310.74964 1.3669913 - 1780 108.77729 720.46707 1606.3817 215.64937 -885.91465 639.71765 615.06161 152.57928 0 -394.48439 513088.38 -514987.17 -271.86201 28334.236 307.3761 1.3327989 - 1800 109.92899 721.98649 1608.1038 215.88055 -886.11732 621.68949 602.68633 163.61329 0 -397.09967 513111.57 -514988.58 587.45646 28336.693 307.73281 1.2707867 - 1820 111.05093 722.92155 1567.2948 210.40212 -844.3732 657.9717 609.80843 174.58395 0 -387.74403 513087.19 -514986.18 1657.5204 28343.522 299.9292 1.2250789 - 1840 112.17289 723.61458 1561.6308 209.64177 -838.01626 621.38222 638.008 181.56394 0 -392.76804 513100.91 -514987.12 951.04423 28360.92 298.8574 1.192447 - 1860 113.32517 724.57888 1559.5079 209.35678 -834.92903 648.61916 621.88348 182.62731 0 -413.59874 513115.13 -514989.59 -474.05956 28382.975 298.4495 1.1946089 - 1880 114.44655 725.74322 1588.6378 213.26733 -862.89459 616.10137 598.6142 185.03327 0 -431.03949 513153.5 -514985.11 326.23753 28401.004 304.06324 1.1258592 - 1900 115.60092 726.63642 1552.6045 208.43002 -825.96805 615.20719 632.90186 175.31959 0 -439.29325 513177.07 -514987.17 1080.7061 28419.738 297.15171 1.1348451 - 1920 116.72882 727.57597 1579.3221 212.01674 -851.74611 606.50987 618.17792 169.75157 0 -442.63284 513179.83 -514983.38 -43.794187 28443.345 302.3028 1.0665772 - 1940 117.88137 728.52961 1573.1141 211.18335 -844.58454 624.72383 626.3057 166.98593 0 -453.41808 513175.12 -514984.3 -900.58801 28464.403 301.13166 1.0223996 - 1960 119.003 728.94698 1626.2629 218.31833 -897.31596 599.28223 602.89095 166.05528 0 -470.08979 513190.07 -514985.52 -260.33773 28477.732 311.33029 0.99933978 - 1980 120.15553 728.20483 1628.3695 218.60113 -900.16467 612.33461 601.10447 163.81406 0 -448.48915 513155.61 -514984.54 821.49207 28488.285 311.74795 0.96708127 - 2000 121.27853 726.32991 1617.7225 217.17182 -891.39259 608.69121 604.99032 169.22497 0 -445.16887 513154.27 -514983.4 -472.67394 28502.073 309.74198 0.88520672 -Loop time of 121.279 on 1 procs for 2000 steps with 3000 atoms - -Pair time (%) = 55.4018 (45.6815) -Bond time (%) = 7.86978 (6.48901) -Kspce time (%) = 13.9231 (11.4803) -Neigh time (%) = 2.17099 (1.79008) -Comm time (%) = 0.43024 (0.354754) -Outpt time (%) = 0.0126977 (0.0104699) -Other time (%) = 41.4699 (34.194) - -Nlocal: 3000 ave 3000 max 3000 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 10468 ave 10468 max 10468 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 662422 ave 662422 max 662422 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 662422 -Ave neighs/atom = 220.807 -Ave special neighs/atom = 10.5 -Neighbor list builds = 63 -Dangerous builds = 0 diff --git a/examples/USER/drude/ethanol/log.ethanol.nh.8Jul15.linux.4 b/examples/USER/drude/ethanol/log.ethanol.nh.8Jul15.linux.4 deleted file mode 100644 index 893c889b8b..0000000000 --- a/examples/USER/drude/ethanol/log.ethanol.nh.8Jul15.linux.4 +++ /dev/null @@ -1,263 +0,0 @@ -LAMMPS (8 Jul 2015) -units real -boundary p p p - -atom_style full -bond_style harmonic -angle_style harmonic -dihedral_style opls -special_bonds lj/coul 0.0 0.0 0.5 - -pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.600 8.0 -kspace_style pppm 1.0e-4 - -read_data data.ethanol - orthogonal box = (-14.0138 -14.0278 -14.0189) to (14.0169 14.0177 14.0857) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 3000 atoms - scanning bonds ... - 5 = max bonds/atom - scanning angles ... - 6 = max angles/atom - scanning dihedrals ... - 9 = max dihedrals/atom - reading bonds ... - 2750 bonds - reading angles ... - 3250 angles - reading dihedrals ... - 3000 dihedrals - 5 = max # of 1-2 neighbors - 6 = max # of 1-3 neighbors - 10 = max # of 1-4 neighbors - 11 = max # of special neighbors - - -pair_coeff 1 1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H -pair_coeff 1 2 lj/cut/coul/long 0.065997 3.500000 # C3H CTO -pair_coeff 1 3 lj/cut/coul/long 0.044496 2.958040 # C3H H -pair_coeff 1 4 lj/cut/coul/long 0.105921 3.304542 # C3H OH -pair_coeff 1 5 lj/cut/coul/long 0.000000 0.000000 # C3H HO -pair_coeff 2 2 lj/cut/coul/long 0.065997 3.500000 # CTO CTO -pair_coeff 2 3 lj/cut/coul/long 0.044496 2.958040 # CTO H -pair_coeff 2 4 lj/cut/coul/long 0.105921 3.304542 # CTO OH -pair_coeff 2 5 lj/cut/coul/long 0.000000 0.000000 # CTO HO -pair_coeff 3 3 lj/cut/coul/long 0.029999 2.500000 # H H -pair_coeff 3 4 lj/cut/coul/long 0.071413 2.792848 # H OH -pair_coeff 3 5 lj/cut/coul/long 0.000000 0.000000 # H HO -pair_coeff 4 4 lj/cut/coul/long 0.169996 3.120000 # OH OH -pair_coeff 4 5 lj/cut/coul/long 0.000000 0.000000 # OH HO -pair_coeff 5 5 lj/cut/coul/long 0.000000 0.000000 # HO HO -pair_coeff * 6*8 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes -pair_coeff 1 1 thole 2.051000 -pair_coeff 1 2 thole 1.580265 -pair_coeff 1 4 thole 1.416087 -pair_coeff 1 6 thole 2.051000 -pair_coeff 1 7 thole 1.580265 -pair_coeff 1 8 thole 1.416087 -pair_coeff 2 2 thole 1.217570 -pair_coeff 2 4 thole 1.091074 -pair_coeff 2 6 thole 1.580265 -pair_coeff 2 7 thole 1.217570 -pair_coeff 2 8 thole 1.091074 -pair_coeff 4 4 thole 0.977720 -pair_coeff 4 6 thole 1.416087 -pair_coeff 4 7 thole 1.091074 -pair_coeff 4 8 thole 0.977720 -pair_coeff 6 6 thole 2.051000 -pair_coeff 6 7 thole 1.580265 -pair_coeff 6 8 thole 1.416087 -pair_coeff 7 7 thole 1.217570 -pair_coeff 7 8 thole 1.091074 -pair_coeff 8 8 thole 0.977720 - -group gETHANOL molecule 1:250 -3000 atoms in group gETHANOL -group gATOMS type 1 2 3 4 5 -2250 atoms in group gATOMS -group gDRUDES type 6 7 8 -750 atoms in group gDRUDES - - -neighbor 2.0 bin - -variable vTEMP equal 300.0 -variable vTEMP_D equal 1.0 -variable vPRESS equal 1.0 - -velocity gATOMS create ${vTEMP} 12345 -velocity gATOMS create 300 12345 -velocity gDRUDES create ${vTEMP_D} 12345 -velocity gDRUDES create 1 12345 - -fix fDRUDE all drude C C N C N D D D - -fix fSHAKE gATOMS shake 0.0001 20 0 b 2 3 5 - 250 = # of size 2 clusters - 250 = # of size 3 clusters - 250 = # of size 4 clusters - 0 = # of frozen angles - -comm_modify vel yes -compute cTEMP_ATOM gATOMS temp -compute cTEMP all temp/drude - -fix fDTDIR all drude/transform/direct -fix fNPT gATOMS npt temp ${vTEMP} ${vTEMP} 100 iso ${vPRESS} ${vPRESS} 500 -fix fNPT gATOMS npt temp 300 ${vTEMP} 100 iso ${vPRESS} ${vPRESS} 500 -fix fNPT gATOMS npt temp 300 300 100 iso ${vPRESS} ${vPRESS} 500 -fix fNPT gATOMS npt temp 300 300 100 iso 1 ${vPRESS} 500 -fix fNPT gATOMS npt temp 300 300 100 iso 1 1 500 -fix_modify fNPT temp cTEMP_ATOM press thermo_press -WARNING: Temperature for fix modify is not for group all (../fix_nh.cpp:1349) -fix fNVT gDRUDES nvt temp ${vTEMP_D} ${vTEMP_D} 100.0 -fix fNVT gDRUDES nvt temp 1 ${vTEMP_D} 100.0 -fix fNVT gDRUDES nvt temp 1 1 100.0 -fix fDTINV all drude/transform/inverse - -thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2] -thermo 20 - -timestep 0.5 -run 2000 -PPPM initialization ... - G vector (1/distance) = 0.379738 - grid = 30 30 30 - stencil order = 5 - estimated absolute RMS force accuracy = 0.0289979 - estimated relative force accuracy = 8.73262e-05 - using double precision FFTs - 3d grid and FFT values/proc = 17908 7200 -Rebuild special list taking Drude particles into account -Old max number of 1-2 to 1-4 neighbors: 11 -New max number of 1-2 to 1-4 neighbors: 11 (+0) -Neighbor list info ... - 2 neighbor list requests - update every 1 steps, delay 10 steps, check yes - master list distance cutoff = 10 -Memory usage per processor = 13.7041 Mbytes -Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume cTEMP[1] cTEMP[2] - 0 0 13868.828 2013.3852 270.28772 11855.443 3145.896 51.880809 0.00019113234 0 8481.5109 514734.14 -514557.98 170217.61 22094.109 381.62759 10.134301 - 20 0.48582006 11385.192 5995.2334 804.83256 5389.9589 2039.7325 2312.5375 131.6961 0 1710.3266 514098.34 -514902.67 75867.639 22408.275 975.26848 406.07565 - 40 0.99611902 9812.3727 6009.1747 806.70411 3803.198 1442.3489 1826.1439 275.19367 0 1288.2864 513934.98 -514963.76 48675.043 22980.115 1057.0177 221.56359 - 60 1.4878449 8857.9452 5779.5973 775.8844 3078.348 1190.8978 1938.6134 328.6837 0 619.31805 513970.98 -514970.15 39710.611 23440.966 1050.9011 133.14424 - 80 1.9926319 8115.7842 5997.9225 805.19356 2117.8617 901.84105 1587.5472 325.40763 0 288.34562 513957.43 -514942.71 37588.95 23834.833 1111.65 89.05492 - 100 2.476769 7496.2555 5770.3833 774.64747 1725.8722 829.63908 1420.6659 325.4016 0 62.343573 514051.62 -514963.79 27294.064 24225.918 1080.2687 60.498473 - 120 2.9719281 6986.5933 5396.9479 724.51547 1589.6454 678.24993 1535.5197 325.88462 0 -9.6649715 514027.05 -514967.4 21720.902 24578.195 1016.3014 42.715633 - 140 3.4472849 6549.0004 5126.6341 688.22709 1422.3663 724.95473 1477.7714 315.11964 0 -99.456489 513960.58 -514956.6 19747.305 24877.008 969.51239 30.977084 - 160 3.8980451 6131.3313 5000.4421 671.2864 1130.8892 703.24856 1302.1192 314.93994 0 -258.4539 514042.28 -514973.25 23050.008 25142.654 948.73049 23.021804 - 180 4.3219371 5749.9765 4700.9451 631.0803 1049.0314 674.94524 1301.4114 310.04938 0 -326.73679 514044.26 -514954.9 14225.484 25400.048 893.75892 17.322075 - 200 4.740237 5429.6012 4392.5738 589.68286 1037.0274 612.00109 1296.2432 303.16019 0 -300.38659 514093.7 -514967.69 10835.073 25622.866 836.16806 13.764486 - 220 5.15255 5133.8314 4290.7369 576.01173 843.09448 572.5199 1261.8055 289.99074 0 -383.71584 514078.3 -514975.81 12509.825 25814.229 817.78562 11.104636 - 240 5.5619049 4850.3859 4120.3634 553.13987 730.0225 553.79223 1263.6533 278.92141 0 -487.76524 514091.35 -514969.93 10891.878 25996.167 785.87197 9.3607763 - 260 5.9694359 4583.988 3911.0361 525.03865 672.95183 541.52258 1175.1553 273.43363 0 -475.23639 514139.68 -514981.61 8086.1508 26168.96 746.55574 7.4653781 - 280 6.3831999 4349.2238 3692.2792 495.67153 656.94461 598.81909 1148.0997 278.87809 0 -444.09603 514045.38 -514970.13 5124.6371 26323.056 705.04252 6.4783461 - 300 6.8002019 4128.9011 3579.5067 480.53234 549.39444 584.0659 1089.513 267.69426 0 -456.87099 514043.55 -514978.56 8350.7748 26456.831 683.94371 5.2650989 - 320 7.2020841 3913.7715 3456.9151 464.07498 456.85644 556.31985 1103.3901 263.8886 0 -485.54294 514000.27 -514981.47 9117.645 26592.844 660.74075 4.5694128 - 340 7.614501 3712.7165 3258.4132 437.42702 454.30329 533.72422 1069.0449 271.85681 0 -454.53938 514001.97 -514967.75 7187.6789 26736.819 622.98237 3.8812925 - 360 8.0251679 3533.3831 3024.1004 405.97159 509.28269 522.55432 1104.3208 276.30864 0 -456.06652 514036.53 -514974.36 4554.9866 26876.658 578.3118 3.3031414 - 380 8.4368989 3367.1791 2971.2717 398.87959 395.90735 508.27248 1059.2247 257.85692 0 -499.68504 514032.55 -514962.31 5645.8885 27002.069 568.38697 2.8305185 - 400 8.841274 3204.9102 2874.2407 385.85361 330.66952 543.884 1018.8809 231.07032 0 -519.33317 514029.07 -514972.9 7250.7314 27123.905 549.89185 2.58326 - 420 9.2528131 3050.6946 2776.6047 372.74643 274.08991 517.42853 953.07588 226.06762 0 -505.60561 514057.02 -514973.9 4026.258 27250.314 531.28072 2.3360857 - 440 9.6643951 2916.2842 2640.2367 354.43965 276.04748 507.06285 983.97334 236.01271 0 -534.64347 514059.65 -514976.01 1708.7076 27364.195 505.24986 2.0765971 - 460 10.070477 2787.525 2609.5902 350.3255 177.93484 485.64382 933.57906 234.95019 0 -560.61753 514069.83 -514985.45 3400.5283 27458.081 499.48921 1.8097272 - 480 10.475857 2662.4983 2514.1778 337.51682 148.3205 464.67048 928.2622 239.37954 0 -570.38391 514070.86 -514984.47 5084.8137 27547.559 481.26939 1.6441432 - 500 10.904204 2540.5544 2433.5504 326.69297 107.00399 473.29419 888.73276 239.40578 0 -565.68691 514057.33 -514986.07 3134.3575 27643.279 465.87938 1.4891037 - 520 11.343421 2432.2068 2375.3395 318.87842 56.867315 460.28707 838.60936 229.00812 0 -579.13202 514093.74 -514985.64 468.2212 27732.471 454.76741 1.3789343 - 540 11.792302 2328.8171 2275.0598 305.41633 53.757301 473.0817 875.54202 220.60952 0 -604.11383 514075.79 -514987.16 2632.7729 27804.408 435.55777 1.3457292 - 560 12.22888 2228.6146 2278.324 305.85454 -49.709377 455.5848 820.87873 215.10398 0 -604.72916 514052.45 -514989 3784.1433 27875.141 436.27421 1.1341637 - 580 12.654423 2134.4153 2127.9966 285.67378 6.418699 480.68271 836.79983 219.13997 0 -563.30761 514019.28 -514986.18 1359.5795 27951.068 407.46389 1.1159357 - 600 13.083667 2048.478 2102.9555 282.31212 -54.477504 486.30135 796.43014 225.04094 0 -574.89912 514003.04 -514990.39 -91.420338 28017.963 402.69778 1.0358317 - 620 13.5203 1967.44 2048.4369 274.99325 -80.99691 477.38009 786.20772 223.98767 0 -570.14552 513997.92 -514996.35 1828.852 28070.312 392.2522 1.022388 - 640 13.946543 1888.1309 1981.5653 266.01604 -93.434406 482.74621 801.17707 222.68721 0 -557.43764 513952.32 -514994.92 3812.5405 28123.574 379.47281 0.92888841 - 660 14.383896 1813.0614 1959.0076 262.98777 -145.94621 498.24936 750.64093 217.17501 0 -556.66175 513938.55 -514993.9 1151.2704 28187.531 375.17051 0.8773937 - 680 14.80455 1744.8321 1911.6727 256.63328 -166.84059 497.04089 725.18698 211.02114 0 -553.89822 513944.3 -514990.49 108.9445 28245.999 366.1283 0.80270876 - 700 15.246875 1678.1628 1915.389 257.13218 -237.22624 490.51443 719.69473 202.03683 0 -569.53274 513909.13 -514989.07 2213.2168 28294.676 366.86695 0.74153849 - 720 15.683303 1612.159 1862.0857 249.97646 -249.9267 500.42186 728.44302 190.2785 0 -551.64436 513871.73 -514989.15 3052.5153 28347.921 356.64838 0.74199104 - 740 16.103407 1549.912 1792.3564 240.61562 -242.44438 497.29156 738.60345 175.54129 0 -547.7015 513880.63 -514986.81 737.97658 28409.346 343.29706 0.70477013 - 760 16.533572 1493.1418 1799.8951 241.62766 -306.75333 503.57865 709.28516 169.31508 0 -559.17797 513862.16 -514991.92 -783.64904 28463.359 344.75876 0.66625709 - 780 16.963103 1437.0356 1824.9946 244.99715 -387.959 510.43018 661.31998 170.2197 0 -556.60498 513818.25 -514991.58 1267.2099 28503.341 349.56422 0.68065257 - 800 17.384911 1382.5837 1736.8044 233.15801 -354.22065 514.28158 697.39733 172.11237 0 -554.93413 513805.74 -514988.82 1744.7575 28543.482 332.66462 0.66506284 - 820 17.818295 1332.0449 1690.9863 227.00714 -358.94137 509.37962 686.56323 172.95557 0 -552.94994 513815.42 -514990.31 -146.04099 28586.704 323.91181 0.59356692 - 840 18.239769 1285.5293 1685.7656 226.30629 -400.23625 507.19659 662.75791 170.55111 0 -559.5183 513807.26 -514988.49 -690.12588 28621.306 322.90879 0.59871543 - 860 18.672279 1239.7943 1704.6913 228.84697 -464.89697 495.88249 658.89516 170.34465 0 -574.82534 513772.88 -514988.07 747.30519 28645.706 326.53407 0.60529545 - 880 19.094243 1195.2074 1673.5516 224.66662 -478.34417 498.99767 648.88222 170.51909 0 -557.50585 513743.81 -514983.05 1172.8191 28670.55 320.57923 0.57095732 - 900 19.530344 1153.213 1639.9317 220.1533 -486.71872 502.48114 643.51414 178.70544 0 -556.38218 513730.3 -514985.34 -511.40662 28697.799 314.13852 0.56091919 - 920 19.954644 1114.1622 1615.9735 216.93702 -501.81127 514.7973 630.19712 179.3982 0 -549.54237 513714.55 -514991.21 -1422.316 28716.8 309.53594 0.58362776 - 940 20.390261 1076.2212 1626.9734 218.41371 -550.75226 512.58732 621.31396 171.70796 0 -553.00677 513686.03 -514989.39 298.59388 28723.942 311.66248 0.54203006 - 960 20.813949 1040.0451 1613.5266 216.60854 -573.48149 511.51922 601.98585 170.02867 0 -546.21382 513682.83 -514993.63 795.90454 28731.424 309.06864 0.57947773 - 980 21.252467 1005.5683 1568.0671 210.50581 -562.49882 514.83412 629.32638 175.23649 0 -544.55558 513654.63 -514991.97 -1246.8402 28741.467 300.36369 0.55676445 - 1000 21.687328 973.43654 1565.2947 210.13362 -591.85814 505.31069 600.76156 165.13032 0 -554.93709 513685.33 -514993.45 -1299.6769 28742.033 299.8319 0.55747244 - 1020 22.104826 942.30585 1571.1252 210.91634 -628.81931 506.25625 614.52982 152.39206 0 -569.20109 513660.58 -514993.37 -197.40138 28733.481 300.94692 0.5637722 - 1040 22.524452 912.01118 1595.3373 214.16671 -683.32616 489.65166 569.71087 159.37841 0 -590.61264 513680.34 -514991.8 467.8096 28724.925 305.59134 0.55703469 - 1060 22.949422 883.20635 1542.2363 207.03814 -659.02996 503.02658 589.43979 165.92415 0 -599.75711 513674.6 -514992.27 -2148.0784 28718.444 295.39616 0.59339691 - 1080 23.371693 856.19688 1533.476 205.86212 -677.27914 507.92146 576.49892 168.14482 0 -578.48635 513634.3 -514985.66 -1762.3643 28699.157 293.71591 0.59543987 - 1100 23.796874 831.36718 1484.0494 199.22681 -652.68218 514.09435 608.64804 163.13622 0 -567.49464 513613.56 -514984.63 33.441222 28670.69 284.23352 0.61219688 - 1120 24.215957 808.52756 1520.8457 204.16656 -712.31817 513.70662 561.61909 163.36198 0 -559.46566 513591.68 -514983.22 -310.69178 28645.197 291.28494 0.61812087 - 1140 24.641242 786.87445 1489.3947 199.9444 -702.52028 523.97711 584.65081 162.32286 0 -549.07998 513560 -514984.39 -1685.574 28620.442 285.24697 0.63849523 - 1160 25.055568 766.64827 1508.2693 202.47822 -741.62101 514.35266 584.91055 152.45332 0 -535.165 513525.54 -514983.72 -1901.0493 28587.357 288.85135 0.67096559 - 1180 25.482658 749.02928 1511.1172 202.86054 -762.08788 536.05747 571.22043 147.19144 0 -519.37083 513485.14 -514982.32 866.88063 28547.627 289.37844 0.71496578 - 1200 25.894749 733.35099 1503.6268 201.85499 -770.27581 533.87098 589.37041 152.16808 0 -519.57804 513457.84 -514983.94 14.805399 28517.39 287.93411 0.73458768 - 1220 26.325628 718.27504 1498.0867 201.11126 -779.81165 559.91487 564.18647 156.27378 0 -507.13199 513432.42 -514985.48 -1279.1075 28491.202 286.86673 0.74700594 - 1240 26.738918 704.4507 1488.7649 199.85985 -784.31417 566.05166 579.79847 161.35046 0 -468.44357 513361.55 -514984.62 -53.3159 28461.135 285.06732 0.77592838 - 1260 27.171522 693.03769 1494.1149 200.57807 -801.07721 573.62194 573.3094 158.43371 0 -453.27917 513333.62 -514986.78 977.9179 28434.863 286.07064 0.82794452 - 1280 27.586875 683.35215 1479.0049 198.54962 -795.65277 580.54264 596.95031 153.53994 0 -437.44286 513297.62 -514986.86 808.24663 28418.774 283.16101 0.85830865 - 1300 28.005456 675.21985 1490.3973 200.079 -815.1775 586.97926 575.85031 144.74048 0 -412.9591 513274.88 -514984.67 -448.16581 28409.96 285.30833 0.9437975 - 1320 28.436763 668.22782 1489.1302 199.90889 -820.90236 576.19343 605.89694 140.779 0 -423.95547 513263.1 -514982.91 -40.766531 28400.261 285.0744 0.92283057 - 1340 28.854671 662.60827 1506.0283 202.17738 -843.42002 580.70797 578.1842 144.8341 0 -430.96333 513260.37 -514976.56 977.60336 28392.015 288.27815 1.0060347 - 1360 29.284718 658.23752 1527.6526 205.08035 -869.41511 577.91716 570.16602 152.14574 0 -451.11548 513260.04 -514978.56 374.82603 28390.744 292.41271 1.031412 - 1380 29.707547 654.96847 1486.4979 199.55551 -831.52939 580.08595 585.05597 157.33942 0 -437.07207 513264.24 -514981.18 -245.84993 28392.431 284.49746 1.0915693 - 1400 30.132399 652.9829 1510.7519 202.81151 -857.76902 568.8718 573.40304 151.53282 0 -426.40132 513257.71 -514982.89 -48.059208 28392.645 289.13172 1.1272637 - 1420 30.56509 652.00089 1494.6519 200.65015 -842.65097 571.38637 600.46686 145.25854 0 -443.09809 513270.44 -514987.1 744.84418 28392.941 286.01743 1.1922923 - 1440 30.993519 651.93656 1520.3356 204.09807 -868.39904 569.20772 591.53184 144.73613 0 -452.45231 513268.58 -514990 462.47894 28397.996 290.93612 1.2038241 - 1460 31.413554 652.8797 1538.7905 206.57555 -885.91076 576.968 569.3361 144.29397 0 -461.95958 513278 -514992.55 -703.88926 28405.143 294.44272 1.2767432 - 1480 31.854234 654.43984 1560.998 209.55681 -906.55813 573.32119 550.83703 151.55603 0 -471.87704 513285.3 -514995.69 -634.5939 28407.003 298.6883 1.3039308 - 1500 32.258767 656.25668 1535.2085 206.0947 -878.95186 565.7821 581.34544 155.11099 0 -493.26681 513302.34 -514990.27 141.09795 28404.376 293.73526 1.3252685 - 1520 32.667376 658.76245 1540.1255 206.75478 -881.36305 562.28162 566.2439 153.62339 0 -481.21787 513306.74 -514989.04 320.45957 28402.754 294.65144 1.3869014 - 1540 33.067487 662.13708 1524.8473 204.70375 -862.71024 547.98628 591.76817 150.15973 0 -460.97843 513297.6 -514989.25 -130.86158 28403.27 291.71099 1.413931 - 1560 33.480413 666.19858 1506.8716 202.29059 -840.67298 559.57219 594.04584 156.75269 0 -475.69342 513317.61 -514992.96 -357.4244 28402.761 288.27566 1.3890257 - 1580 33.881172 670.71346 1535.3958 206.11984 -864.68236 562.04024 577.64202 164.82634 0 -495.24757 513322.21 -514996.15 278.58466 28400.233 293.74325 1.3903967 - 1600 34.282713 676.13061 1559.338 209.33397 -883.20743 570.25038 568.59163 172.20015 0 -497.5923 513299.59 -514996.24 -86.394917 28399.201 298.31271 1.4378209 - 1620 34.693053 681.80099 1552.6868 208.44108 -870.88582 572.69475 589.3952 176.11924 0 -485.89655 513274.18 -514997.38 -1204.2981 28396.883 297.01677 1.4865321 - 1640 35.094327 687.72244 1565.9114 210.21642 -878.189 578.48421 587.25138 174.28163 0 -490.691 513265.29 -514992.8 -581.44816 28387.006 299.57429 1.4344443 - 1660 35.50466 693.90688 1558.2867 209.19283 -864.37979 583.51938 605.39763 171.58103 0 -488.26355 513255.15 -514991.76 341.26177 28374.079 298.09208 1.4823162 - 1680 35.905614 699.81947 1608.5571 215.9414 -908.73759 585.45342 590.42357 171.65094 0 -478.75081 513211.28 -514988.8 77.131096 28364.346 307.75695 1.4172031 - 1700 36.320681 705.27021 1587.164 213.06948 -881.89376 609.44479 581.8672 172.3033 0 -457.17018 513197.71 -514986.05 -666.39751 28355.734 303.6806 1.3594258 - 1720 36.728727 710.00906 1608.1379 215.88513 -898.12885 612.49125 598.01777 167.03198 0 -445.09105 513154.85 -514985.42 -87.720392 28343.913 307.66062 1.454487 - 1740 37.130271 714.53567 1580.0753 212.11786 -865.53967 624.57295 619.34825 165.15138 0 -426.77348 513138.14 -514985.98 1176.8164 28333.357 302.31339 1.3787996 - 1760 37.542675 718.03805 1624.8218 218.12487 -906.78379 608.77029 596.31671 153.7484 0 -409.62158 513134.59 -514990.59 800.3654 28331.535 310.89569 1.3688034 - 1780 37.943518 720.37511 1609.0275 216.00455 -888.65236 640.15257 613.63079 151.83793 0 -394.53333 513087.34 -514987.08 -257.84624 28335.192 307.88341 1.3325434 - 1800 38.353172 721.7956 1606.901 215.71908 -885.1054 621.86791 602.54827 163.37359 0 -396.5738 513111.86 -514988.19 600.83028 28337.874 307.50221 1.2708112 - 1820 38.755103 722.6791 1563.6639 209.9147 -840.98481 658.28036 609.55302 175.97253 0 -386.62661 513087.76 -514985.92 1673.6509 28345.014 299.23272 1.2261086 - 1840 39.156883 723.36526 1560.0643 209.43147 -836.69905 621.56238 639.2919 183.25684 0 -391.12333 513097.3 -514986.98 948.98786 28362.795 298.55837 1.1894608 - 1860 39.568864 724.34062 1560.3485 209.46963 -836.00792 648.95076 621.00344 183.45409 0 -412.61997 513112.89 -514989.69 -494.41519 28385.176 298.60946 1.1973936 - 1880 39.96934 725.55016 1589.2514 213.34971 -863.70126 617.1181 598.13412 185.78351 0 -430.81566 513151.32 -514985.25 301.61577 28403.364 304.1812 1.1250834 - 1900 40.379241 726.4494 1555.4145 208.80726 -828.96513 616.25066 631.90687 175.77829 0 -439.44651 513173.5 -514986.96 1079.4893 28422.072 297.69125 1.1328664 - 1920 40.778163 727.328 1577.4105 211.76012 -850.08251 606.30559 616.55697 170.46944 0 -442.17245 513181.84 -514983.08 4.4471417 28445.679 301.93699 1.065083 - 1940 41.186491 728.19228 1574.1105 211.3171 -845.91818 625.03022 624.89302 167.86917 0 -451.74938 513172.29 -514984.25 -891.08022 28467.03 301.3211 1.026012 - 1960 41.58233 728.61768 1624.4163 218.07043 -895.79862 599.93561 599.92993 167.38843 0 -465.99755 513188.14 -514985.2 -216.32489 28480.762 310.97645 0.99894847 - 1980 41.996931 727.92162 1627.8345 218.52931 -899.91293 612.92861 601.82319 165.16403 0 -447.59836 513151.59 -514983.82 865.41931 28491.981 311.64212 0.97473559 - 2000 42.398021 726.10625 1615.3704 216.85607 -889.26418 609.59944 604.55036 169.50136 0 -443.24252 513152.61 -514982.28 -436.06261 28506.736 309.2898 0.88821892 -Loop time of 42.3981 on 4 procs for 2000 steps with 3000 atoms - -Pair time (%) = 14.495 (34.1878) -Bond time (%) = 2.06082 (4.86065) -Kspce time (%) = 7.76109 (18.3053) -Neigh time (%) = 0.634993 (1.49769) -Comm time (%) = 1.07386 (2.53281) -Outpt time (%) = 0.0100121 (0.0236145) -Other time (%) = 16.3623 (38.5921) - -Nlocal: 750 ave 774 max 711 min -Histogram: 1 0 0 0 0 0 1 0 1 1 -Nghost: 5796.5 ave 5864 max 5731 min -Histogram: 1 0 0 1 0 0 1 0 0 1 -Neighs: 165579 ave 169096 max 157793 min -Histogram: 1 0 0 0 0 0 0 0 1 2 - -Total # of neighbors = 662315 -Ave neighs/atom = 220.772 -Ave special neighs/atom = 10.5 -Neighbor list builds = 63 -Dangerous builds = 0 diff --git a/examples/USER/drude/swm4-ndp/log.27Nov18.swm4-ndp.lang.g++.1 b/examples/USER/drude/swm4-ndp/log.27Nov18.swm4-ndp.lang.g++.1 new file mode 100644 index 0000000000..f68de51a79 --- /dev/null +++ b/examples/USER/drude/swm4-ndp/log.27Nov18.swm4-ndp.lang.g++.1 @@ -0,0 +1,246 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +units real +boundary p p p + +atom_style full +bond_style harmonic +angle_style harmonic +special_bonds lj/coul 0.0 0.0 0.5 + +pair_style lj/cut/coul/long 12.0 12.0 +kspace_style pppm 1.0e-3 + +comm_modify vel yes +read_data data.swm4-ndp + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 2500 atoms + scanning bonds ... + 1 = max bonds/atom + scanning angles ... + 1 = max angles/atom + reading bonds ... + 2000 bonds + reading angles ... + 500 angles + 4 = max # of 1-2 neighbors + 3 = max # of 1-3 neighbors + 3 = max # of 1-4 neighbors + 4 = max # of special neighbors + +pair_coeff 1 1 0.210939 3.183950 # ODw ODw +pair_coeff * 2* 0.000000 0.0 + +group ATOMS type 1:3 +2000 atoms in group ATOMS +group CORES type 1 +500 atoms in group CORES +group DRUDES type 4 +500 atoms in group DRUDES + +variable TK equal 300.0 +variable TDK equal 1.0 +variable PBAR equal 1.0 + +neighbor 2.0 bin + +timestep 1.0 + +fix DRUDE all drude C N N D + +velocity ATOMS create ${TK} 12345 +velocity ATOMS create 300 12345 +velocity DRUDES create ${TDK} 12345 +velocity DRUDES create 1 12345 + +delete_bonds ATOMS multi +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) + G vector (1/distance) = 0.217457 + grid = 10 10 10 + stencil order = 5 + estimated absolute RMS force accuracy = 0.197288 + estimated relative force accuracy = 0.000594128 + using double precision FFTs + 3d grid and FFT values/proc = 3375 1000 +Rebuild special list taking Drude particles into account +Old max number of 1-2 to 1-4 neighbors: 4 +New max number of 1-2 to 1-4 neighbors: 4 (+0) +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 4 4 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + 2000 total bonds, 500 turned on, 1500 turned off + 500 total angles, 0 turned on, 500 turned off + 0 total dihedrals, 0 turned on, 0 turned off + 0 total impropers, 0 turned on, 0 turned off + +fix TEMP all langevin/drude ${TK} 100. 1256 ${TDK} 20. 13977 zero yes +fix TEMP all langevin/drude 300 100. 1256 ${TDK} 20. 13977 zero yes +fix TEMP all langevin/drude 300 100. 1256 1 20. 13977 zero yes +fix NPH ATOMS rigid/nph/small molecule iso ${PBAR} ${PBAR} 500. +fix NPH ATOMS rigid/nph/small molecule iso 1 ${PBAR} 500. +fix NPH ATOMS rigid/nph/small molecule iso 1 1 500. +500 rigid bodies with 2000 atoms + 0.832099 = max distance from body owner to body atom +fix NVE DRUDES nve + +compute TEMP all temp/drude + +thermo_style custom step cpu etotal ke pe ebond eangle evdwl ecoul elong press vol temp c_TEMP[1] c_TEMP[2] +thermo 20 + +run 2000 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) + G vector (1/distance) = 0.217457 + grid = 10 10 10 + stencil order = 5 + estimated absolute RMS force accuracy = 0.197288 + estimated relative force accuracy = 0.000594128 + using double precision FFTs + 3d grid and FFT values/proc = 3375 1000 +Per MPI rank memory allocation (min/avg/max) = 36.15 | 36.15 | 36.15 Mbytes +Step CPU TotEng KinEng PotEng E_bond E_angle E_vdwl E_coul E_long Press Volume Temp c_TEMP[1] c_TEMP[2] + 0 0 4568.0415 903.41148 3664.63 623.46454 0 2890.2449 157955.66 -157804.74 244591.08 13824 202.18534 295.64644 14.858785 + 20 1.2941742 2882.4586 4527.8074 -1645.3488 561.72856 0 600.34616 155114.77 -157922.19 27167.701 14058.741 1013.3326 1438.6699 160.63128 + 40 2.6812835 1331.3822 3348.9313 -2017.5492 681.52311 0 553.09465 154668.62 -157920.79 17925.928 14484.215 749.4977 1105.2032 36.587791 + 60 4.0337768 297.35951 2604.4137 -2307.0542 583.99973 0 409.03992 154634.74 -157934.83 13017.752 15026.564 582.87312 864.55899 18.335647 + 80 5.3483341 -374.31059 2263.3247 -2637.6353 534.80336 0 212.27979 154543.18 -157927.9 6155.9233 15645.855 506.53672 755.45209 7.6929097 + 100 6.6217718 -905.58895 1911.7191 -2817.308 532.30402 0 87.570164 154497.48 -157934.66 2149.3102 16288.797 427.84665 639.27768 4.1289095 + 120 7.8588221 -1233.6892 1675.0884 -2908.7776 544.76423 0 59.500422 154422.72 -157935.76 233.49801 16915.818 374.88821 560.54178 2.8313109 + 140 8.9570706 -1463.4914 1468.7447 -2932.2361 539.69696 0 41.083518 154424.91 -157937.93 -1492.9875 17509.345 328.70809 491.66367 2.1395091 + 160 10.032995 -1695.7544 1385.9606 -3081.7149 552.9156 0 30.022825 154274.72 -157939.37 -3010.5044 18061.925 310.18082 463.9681 1.9858861 + 180 11.181687 -1818.1852 1253.1677 -3071.3529 559.57415 0 20.017285 154289.69 -157940.63 -3354.2207 18564.877 280.4615 419.5755 1.6725842 + 200 12.212811 -1949.6488 1210.0648 -3159.7136 570.0554 0 16.320167 154195.04 -157941.13 -4117.951 19014.456 270.81499 405.06855 1.7662371 + 220 13.224296 -2031.6068 1148.1459 -3179.7527 598.02848 0 30.832907 154127.13 -157935.75 -4514.6121 19406.767 256.95741 384.33718 1.6839577 + 240 14.315843 -2118.6272 1120.0031 -3238.6303 613.29235 0 59.889003 154030.6 -157942.41 -4415.1885 19738.97 250.659 374.93927 1.5971322 + 260 15.300218 -2203.4151 1065.8468 -3269.2619 614.19212 0 77.618884 153980.71 -157941.79 -4563.8872 20011.077 238.53871 356.80712 1.5248251 + 280 16.273073 -2317.9388 1033.2702 -3351.2091 650.51355 0 126.14935 153811.62 -157939.49 -4722.8063 20224.149 231.248 345.84878 1.5839508 + 300 17.240341 -2377.6039 992.48386 -3370.0878 688.02302 0 179.7828 153701.2 -157939.1 -4125.8573 20378.438 222.11992 332.08746 1.7406198 + 320 18.20275 -2419.6151 1023.0261 -3442.6412 720.31006 0 227.7006 153549.39 -157940.04 -4083.286 20479.24 228.95535 342.33558 1.7369708 + 340 19.161978 -2456.7614 1048.823 -3505.5844 754.12989 0 264.46876 153415.73 -157939.91 -3894.4573 20529.72 234.72874 351.04481 1.6271431 + 360 20.2149 -2504.7183 1041.9917 -3546.71 785.42914 0 335.38633 153271.5 -157939.03 -3464.0342 20531.324 233.19988 348.66948 1.7942822 + 380 21.17402 -2596.3611 1000.1227 -3596.4839 825.3161 0 390.15783 153129.43 -157941.39 -3357.8641 20490.649 223.82952 334.61582 1.8092697 + 400 22.139238 -2666.6886 1006.4834 -3673.172 866.01231 0 422.49717 152978.53 -157940.22 -3329.7321 20411.001 225.25305 336.79329 1.7220591 + 420 23.107117 -2676.0182 1036.9614 -3712.9796 909.17035 0 490.73558 152826 -157938.88 -2909.4385 20294.307 232.07409 346.93054 1.8970578 + 440 24.079176 -2731.6451 1054.3541 -3785.9992 935.99044 0 530.99271 152684.71 -157937.69 -2566.5271 20147.069 235.96661 352.81301 1.8018782 + 460 25.058476 -2808.7306 996.20963 -3804.9403 986.66566 0 582.2501 152565.84 -157939.7 -2490.6211 19973.642 222.95376 333.32458 1.7662208 + 480 26.045001 -2862.5602 1012.8284 -3875.3886 1005.2147 0 610.1273 152450.46 -157941.19 -2032.2463 19777.578 226.67307 338.84478 1.876307 + 500 27.043275 -2935.1165 989.42859 -3924.5451 1019.8833 0 633.91479 152362.53 -157940.87 -2210.2423 19561.788 221.43615 331.0551 1.7553824 + 520 28.052607 -2989.5984 969.48801 -3959.0864 1057.825 0 655.88112 152268.64 -157941.44 -2303.725 19328.454 216.97341 324.39473 1.6968168 + 540 29.169729 -3036.3745 1016.2059 -4052.5804 1091.3747 0 658.52433 152140.18 -157942.65 -2235.4034 19080.73 227.42896 340.04854 1.7349328 + 560 30.202366 -3093.8922 946.57093 -4040.4631 1140.9835 0 764.01213 151997.25 -157942.71 -1159.9486 18819.788 211.84452 316.62558 1.85871 + 580 31.245469 -3165.5156 988.32907 -4153.8446 1198.6661 0 795.79314 151795.81 -157944.12 -1299.7687 18555.467 221.19007 330.67963 1.7685771 + 600 32.305233 -3193.4945 981.48315 -4174.9776 1207.1636 0 842.25251 151717.63 -157942.02 -845.49527 18290.083 219.65794 328.37122 1.7920774 + 620 33.378728 -3254.0556 966.92094 -4220.9766 1219.0239 0 848.81235 151653.93 -157942.75 -633.10425 18027.72 216.39889 323.4395 1.8848743 + 640 34.465769 -3267.9659 1003.5996 -4271.5655 1273.644 0 929.19275 151468.58 -157942.99 146.55456 17770.457 224.60765 335.70351 1.9667214 + 660 35.565967 -3292.3649 1001.1012 -4293.4661 1299.7838 0 957.48532 151393.06 -157943.79 252.79622 17523.772 224.0485 334.86273 1.9719336 + 680 36.678817 -3311.7859 1008.4763 -4320.2622 1356.4829 0 987.54908 151279.12 -157943.41 715.95691 17290.15 225.69907 337.35795 1.9299071 + 700 37.804361 -3384.7539 970.95734 -4355.7113 1376.9176 0 1003.218 151209.28 -157945.12 602.03837 17070.444 217.30224 324.76399 1.9441468 + 720 38.944631 -3389.983 1003.4282 -4393.4112 1388.0708 0 1009.042 151153.78 -157944.31 799.15462 16864.409 224.5693 335.74485 1.7690575 + 740 40.095444 -3390.8892 1011.8969 -4402.786 1395.7801 0 1060.0508 151084.65 -157943.27 1475.2637 16672.377 226.4646 338.45322 2.034426 + 760 41.257411 -3430.7027 1037.7609 -4468.4636 1415.8714 0 1069.0374 150989.87 -157943.24 1304.5866 16496.661 232.25301 347.18143 1.9316673 + 780 42.432308 -3457.167 1031.0329 -4488.1999 1428.7433 0 1114.4772 150912.91 -157944.33 1885.5157 16338.236 230.74728 344.90463 1.9710957 + 800 43.614638 -3510.8663 985.5619 -4496.4282 1454.853 0 1136.1159 150858.74 -157946.14 1646.2494 16199.542 220.57078 329.56096 2.1492639 + 820 44.806214 -3561.3122 954.7588 -4516.071 1480.1009 0 1122.7071 150826.81 -157945.69 1635.0446 16080.49 213.67698 319.29136 2.0208705 + 840 46.008772 -3574.3488 957.87693 -4532.2258 1470.2766 0 1075.5497 150865.51 -157943.56 1501.6257 15978.031 214.37482 320.32468 2.0463654 + 860 47.215247 -3579.685 964.25763 -4543.9426 1434.0326 0 1038.1021 150929.67 -157945.75 1011.7367 15888.91 215.80284 322.50392 1.9690629 + 880 48.426587 -3621.2356 959.70408 -4580.9397 1439.8947 0 1036.0768 150886.22 -157943.13 506.78826 15810.176 214.78374 320.9264 2.0688639 + 900 49.644699 -3666.1303 946.8746 -4613.0049 1466.4484 0 1064.2478 150801.81 -157945.51 1109.1589 15739.244 211.91248 316.66479 1.9840376 + 920 50.870043 -3689.2489 931.40538 -4620.6543 1504.5475 0 1112.6525 150708.42 -157946.28 1403.0057 15677.776 208.45044 311.4521 2.0302083 + 940 52.10243 -3721.3501 909.43101 -4630.7811 1542.2534 0 1138.863 150634.25 -157946.14 1347.0651 15627.828 203.53253 304.13886 1.9127999 + 960 53.227722 -3765.0247 879.73583 -4644.7606 1542.4842 0 1151.7551 150607.39 -157946.39 1704.8479 15589.06 196.88668 294.16244 1.9413966 + 980 54.463265 -3768.795 907.84469 -4676.6397 1541.4855 0 1133.986 150593.62 -157945.73 1307.1066 15561.731 203.1775 303.56604 1.9940794 + 1000 55.701727 -3785.8075 880.81809 -4666.6256 1521.7209 0 1096.2695 150662.35 -157946.97 970.21043 15543.592 197.1289 294.56486 1.8627129 + 1020 56.889708 -3802.4725 921.96298 -4724.4355 1530.0248 0 1066.8927 150623.76 -157945.11 4.0693062 15531.676 206.33721 308.27171 2.0555342 + 1040 58.073551 -3805.5983 892.97259 -4698.5709 1517.1505 0 1090.904 150638.66 -157945.28 814.78747 15522.075 199.8491 298.65131 1.8449766 + 1060 59.268992 -3814.9754 904.37152 -4719.3469 1516.0462 0 1073.1076 150635.42 -157943.93 352.09813 15517.26 202.4002 302.40986 1.9760806 + 1080 60.368197 -3799.7772 900.93602 -4700.7132 1525.3102 0 1076.0639 150645.06 -157947.15 399.96911 15516.854 201.63133 301.25571 1.9793146 + 1100 61.57456 -3802.9637 891.80847 -4694.7721 1493.3846 0 1048.571 150708.35 -157945.08 296.41566 15520.259 199.58857 298.21614 1.9342423 + 1120 62.780309 -3783.7153 915.24553 -4698.9609 1504.5486 0 1057.5171 150684.14 -157945.17 489.89871 15526.377 204.83383 306.05465 1.9825112 + 1140 63.986179 -3799.4039 915.28328 -4714.6872 1498.182 0 1037.3595 150696.49 -157946.72 -57.392244 15535.825 204.84228 306.06136 1.9944283 + 1160 65.193113 -3821.1813 889.41687 -4710.5981 1485.5696 0 1035.222 150714.63 -157946.02 -132.88199 15546.599 199.05332 297.34747 2.0669157 + 1180 66.295017 -3815.3668 883.81796 -4699.1847 1475.1971 0 1029.0735 150742.62 -157946.07 -12.015088 15557.826 197.80027 295.60821 1.7888039 + 1200 67.501339 -3799.2243 924.83203 -4724.0563 1503.6728 0 1039.8081 150676.17 -157943.71 -279.42673 15568.706 206.97931 309.25452 2.0149166 + 1220 68.70749 -3793.2571 918.16669 -4711.4238 1500.7028 0 1072.1543 150660.33 -157944.61 396.95956 15579.039 205.48759 307.10011 1.8515828 + 1240 69.913097 -3807.1761 903.62796 -4710.804 1518.0566 0 1098.727 150617.61 -157945.19 571.77344 15592.05 202.23379 302.09539 2.1061249 + 1260 71.120192 -3813.0785 928.88909 -4741.9676 1522.8082 0 1080.2068 150602.14 -157947.12 143.45803 15608.285 207.88729 310.67334 1.8994019 + 1280 72.221799 -3825.0477 896.43989 -4721.4876 1498.3409 0 1057.1098 150667.73 -157944.67 -469.23041 15626.738 200.62509 299.78768 1.8986521 + 1300 73.424948 -3846.2307 907.67631 -4753.907 1477.8354 0 1013.4733 150700.69 -157945.9 -661.19665 15644.394 203.13982 303.56549 1.8822105 + 1320 74.627469 -3829.941 882.93628 -4712.8773 1476.7417 0 1016.2042 150741.02 -157946.85 -14.196904 15658.043 197.60295 295.24326 1.9271172 + 1340 75.833837 -3851.5034 857.32804 -4708.8314 1465.5881 0 1021.2072 150749.47 -157945.1 -96.242387 15669.364 191.87178 286.7037 1.8241831 + 1360 76.936204 -3860.3024 888.18647 -4748.4888 1464.1796 0 984.93111 150747.8 -157945.4 -974.33424 15678.357 198.77795 297.0089 1.9185093 + 1380 78.140865 -3836.5819 880.98802 -4717.5699 1461.9764 0 985.01748 150781.29 -157945.85 -872.9259 15682.263 197.16693 294.58145 1.9435476 + 1400 79.344863 -3828.5386 906.27947 -4734.8181 1482.8705 0 991.46422 150736.59 -157945.74 -1233.9461 15680.599 202.82721 303.0834 1.909166 + 1420 80.548134 -3814.3258 902.48807 -4716.8139 1475.6502 0 1014.0056 150738.18 -157944.65 -555.01708 15672.591 201.97868 301.83062 1.8708541 + 1440 81.755274 -3856.0851 862.48793 -4718.573 1498.2382 0 1065.2356 150663.3 -157945.35 32.56482 15661.106 193.02657 288.38598 1.9216938 + 1460 82.860741 -3844.5162 901.31045 -4745.8266 1509.4529 0 1079.4605 150610.73 -157945.47 187.59843 15650.274 201.71513 301.41292 1.9161214 + 1480 84.068614 -3830.9341 924.4504 -4755.3845 1492.3743 0 1043.7244 150654.84 -157946.33 -493.49005 15640.167 206.8939 309.17217 1.9235617 + 1500 85.277247 -3837.3277 905.31407 -4742.6418 1493.7224 0 1030.5512 150679.62 -157946.53 -614.09435 15628.452 202.61115 302.74791 1.9324006 + 1520 86.48688 -3826.0085 909.05297 -4735.0615 1484.1418 0 1034.4558 150691.85 -157945.51 -146.17552 15614.976 203.44792 304.03751 1.8618391 + 1540 87.592599 -3841.6696 938.60068 -4780.2703 1507.974 0 1041.0705 150616.87 -157946.18 -507.85898 15599.499 210.06076 313.85613 2.0498944 + 1560 88.805017 -3826.9957 909.65333 -4736.649 1544.8227 0 1126.866 150538.2 -157946.54 606.26354 15581.816 203.58228 304.19548 1.9487298 + 1580 90.020651 -3832.1768 912.93266 -4745.1095 1574.5895 0 1176.6062 150449.01 -157945.31 1282.9622 15569.746 204.3162 305.24469 2.0505914 + 1600 91.237675 -3854.9438 913.45738 -4768.4012 1573.5937 0 1137.9072 150465.94 -157945.85 833.4472 15566.901 204.43364 305.43089 2.0302658 + 1620 92.456385 -3858.2579 926.48289 -4784.7408 1547.7966 0 1104.6836 150506.72 -157943.94 175.66142 15569.538 207.34877 309.84283 1.9459647 + 1640 93.67173 -3891.1815 918.17278 -4809.3543 1552.442 0 1100.5019 150484.4 -157946.7 -21.914006 15574.644 205.48895 307.0691 1.9176872 + 1660 94.887992 -3919.3626 865.63387 -4784.9964 1520.4861 0 1071.2498 150569.18 -157945.91 76.169452 15580.674 193.73064 289.45503 1.8943961 + 1680 96.104407 -3895.1048 904.57852 -4799.6834 1528.5992 0 1025.321 150591.92 -157945.52 -806.96969 15586.13 202.44653 302.49383 1.9470391 + 1700 97.217725 -3867.858 892.51088 -4760.3689 1529.7738 0 1070.8486 150584.86 -157945.86 140.65618 15587.548 199.74577 298.38679 2.0642365 + 1720 98.434344 -3893.3744 901.29331 -4794.6677 1574.0498 0 1116.4639 150460.62 -157945.8 58.347282 15588.502 201.71129 301.37785 1.974756 + 1740 99.650283 -3863.7002 920.58199 -4784.2822 1591.6512 0 1158.7562 150411.66 -157946.35 690.62331 15590.533 206.02814 307.90557 1.8612258 + 1760 100.86726 -3861.1571 936.31333 -4797.4705 1577.1868 0 1147.145 150425.93 -157947.74 479.33327 15596.819 209.54885 313.12745 1.9725316 + 1780 102.08407 -3902.9055 937.9542 -4840.8597 1574.1479 0 1089.8436 150439.21 -157944.06 -423.26154 15606.503 209.91608 313.72161 1.8851726 + 1800 103.30044 -3924.3367 882.83761 -4807.1743 1548.9296 0 1083.4742 150506.67 -157946.25 -165.30212 15613.782 197.58087 295.18333 1.9807824 + 1820 104.51493 -3933.257 906.13467 -4839.3917 1566.2208 0 1066.4802 150474.1 -157946.19 -704.84936 15618.451 202.7948 303.015 1.948802 + 1840 105.73189 -3925.7774 886.11608 -4811.8935 1541.3194 0 1071.3574 150522.01 -157946.58 -603.17056 15617.998 198.3146 296.30423 1.9386975 + 1860 106.94721 -3888.206 921.52432 -4809.7304 1579.4857 0 1109.6812 150447.64 -157946.54 104.6013 15613.197 206.23903 308.2177 1.8692298 + 1880 108.06014 -3916.0862 918.21234 -4834.2985 1583.1417 0 1094.2365 150433.88 -157945.56 -253.01422 15607.47 205.49781 306.96538 2.1516579 + 1900 109.27602 -3899.0882 918.64022 -4817.7285 1556.1431 0 1115.1484 150457.92 -157946.94 -143.94816 15600.312 205.59357 307.17307 2.0233622 + 1920 110.49415 -3920.9798 896.1905 -4817.1703 1548.5569 0 1085.0712 150496.68 -157947.48 -337.28194 15592.107 200.56927 299.64783 2.0110119 + 1940 111.71421 -3968.3536 874.10309 -4842.4567 1572.4606 0 1094.9587 150436.32 -157946.19 -303.02321 15581.696 195.62607 292.28508 1.9167899 + 1960 112.93472 -3934.8475 883.5952 -4818.4427 1591.4146 0 1141.0692 150394.9 -157945.83 393.7304 15568.475 197.75042 295.48636 1.883029 + 1980 114.15483 -3907.4423 937.55746 -4844.9997 1643.691 0 1216.6376 150240.27 -157945.59 815.94743 15556.713 209.82728 313.50122 2.0597469 + 2000 115.37626 -3925.4165 915.08958 -4840.506 1623.4406 0 1190.2236 150292.14 -157946.31 519.99833 15550.966 204.79893 305.95187 2.083444 +Loop time of 115.376 on 1 procs for 2000 steps with 2500 atoms + +Performance: 1.498 ns/day, 16.024 hours/ns, 17.335 timesteps/s +99.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 97.091 | 97.091 | 97.091 | 0.0 | 84.15 +Bond | 0.031897 | 0.031897 | 0.031897 | 0.0 | 0.03 +Kspace | 3.7648 | 3.7648 | 3.7648 | 0.0 | 3.26 +Neigh | 10.041 | 10.041 | 10.041 | 0.0 | 8.70 +Comm | 0.79701 | 0.79701 | 0.79701 | 0.0 | 0.69 +Output | 0.0071344 | 0.0071344 | 0.0071344 | 0.0 | 0.01 +Modify | 3.5966 | 3.5966 | 3.5966 | 0.0 | 3.12 +Other | | 0.0467 | | | 0.04 + +Nlocal: 2500 ave 2500 max 2500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 21222 ave 21222 max 21222 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 2.30826e+06 ave 2.30826e+06 max 2.30826e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 2308257 +Ave neighs/atom = 923.303 +Ave special neighs/atom = 4 +Neighbor list builds = 100 +Dangerous builds = 6 + +Total wall time: 0:01:55 diff --git a/examples/USER/drude/swm4-ndp/log.27Nov18.swm4-ndp.lang.g++.4 b/examples/USER/drude/swm4-ndp/log.27Nov18.swm4-ndp.lang.g++.4 new file mode 100644 index 0000000000..c6a45c4ab5 --- /dev/null +++ b/examples/USER/drude/swm4-ndp/log.27Nov18.swm4-ndp.lang.g++.4 @@ -0,0 +1,246 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +units real +boundary p p p + +atom_style full +bond_style harmonic +angle_style harmonic +special_bonds lj/coul 0.0 0.0 0.5 + +pair_style lj/cut/coul/long 12.0 12.0 +kspace_style pppm 1.0e-3 + +comm_modify vel yes +read_data data.swm4-ndp + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 2500 atoms + scanning bonds ... + 1 = max bonds/atom + scanning angles ... + 1 = max angles/atom + reading bonds ... + 2000 bonds + reading angles ... + 500 angles + 4 = max # of 1-2 neighbors + 3 = max # of 1-3 neighbors + 3 = max # of 1-4 neighbors + 4 = max # of special neighbors + +pair_coeff 1 1 0.210939 3.183950 # ODw ODw +pair_coeff * 2* 0.000000 0.0 + +group ATOMS type 1:3 +2000 atoms in group ATOMS +group CORES type 1 +500 atoms in group CORES +group DRUDES type 4 +500 atoms in group DRUDES + +variable TK equal 300.0 +variable TDK equal 1.0 +variable PBAR equal 1.0 + +neighbor 2.0 bin + +timestep 1.0 + +fix DRUDE all drude C N N D + +velocity ATOMS create ${TK} 12345 +velocity ATOMS create 300 12345 +velocity DRUDES create ${TDK} 12345 +velocity DRUDES create 1 12345 + +delete_bonds ATOMS multi +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) + G vector (1/distance) = 0.217457 + grid = 10 10 10 + stencil order = 5 + estimated absolute RMS force accuracy = 0.197288 + estimated relative force accuracy = 0.000594128 + using double precision FFTs + 3d grid and FFT values/proc = 1500 300 +Rebuild special list taking Drude particles into account +Old max number of 1-2 to 1-4 neighbors: 4 +New max number of 1-2 to 1-4 neighbors: 4 (+0) +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 4 4 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + 2000 total bonds, 500 turned on, 1500 turned off + 500 total angles, 0 turned on, 500 turned off + 0 total dihedrals, 0 turned on, 0 turned off + 0 total impropers, 0 turned on, 0 turned off + +fix TEMP all langevin/drude ${TK} 100. 1256 ${TDK} 20. 13977 zero yes +fix TEMP all langevin/drude 300 100. 1256 ${TDK} 20. 13977 zero yes +fix TEMP all langevin/drude 300 100. 1256 1 20. 13977 zero yes +fix NPH ATOMS rigid/nph/small molecule iso ${PBAR} ${PBAR} 500. +fix NPH ATOMS rigid/nph/small molecule iso 1 ${PBAR} 500. +fix NPH ATOMS rigid/nph/small molecule iso 1 1 500. +500 rigid bodies with 2000 atoms + 0.832099 = max distance from body owner to body atom +fix NVE DRUDES nve + +compute TEMP all temp/drude + +thermo_style custom step cpu etotal ke pe ebond eangle evdwl ecoul elong press vol temp c_TEMP[1] c_TEMP[2] +thermo 20 + +run 2000 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) + G vector (1/distance) = 0.217457 + grid = 10 10 10 + stencil order = 5 + estimated absolute RMS force accuracy = 0.197288 + estimated relative force accuracy = 0.000594128 + using double precision FFTs + 3d grid and FFT values/proc = 1500 300 +Per MPI rank memory allocation (min/avg/max) = 18.29 | 18.3 | 18.3 Mbytes +Step CPU TotEng KinEng PotEng E_bond E_angle E_vdwl E_coul E_long Press Volume Temp c_TEMP[1] c_TEMP[2] + 0 0 4568.0415 903.41148 3664.63 623.46454 0 2890.2449 157955.66 -157804.74 244591.08 13824 202.18534 295.64644 14.858785 + 20 0.3966074 2915.1579 4579.5774 -1664.4194 561.91893 0 600.76451 155095.13 -157922.23 27379.771 14058.574 1024.9188 1455.9194 160.86778 + 40 0.81358027 1320.1722 3337.6372 -2017.4651 726.83344 0 585.5439 154587.28 -157917.12 18749.425 14485.651 746.97006 1101.4061 36.530914 + 60 1.2173033 284.06793 2671.4324 -2387.3645 575.54155 0 387.8792 154580.74 -157931.53 12104.74 15031.425 597.87206 886.98502 18.450412 + 80 1.6120358 -462.53073 2214.284 -2676.8148 560.36346 0 254.65244 154447.22 -157939.05 6285.2446 15651.216 495.56131 739.13811 7.4024414 + 100 1.9901412 -965.1962 1839.8309 -2805.0271 544.5953 0 115.80813 154469.59 -157935.02 2361.9408 16295.72 411.75794 615.12768 4.1969771 + 120 2.4076366 -1316.6354 1649.5851 -2966.2205 554.66642 0 50.928948 154365.49 -157937.3 -493.85718 16925.293 369.18054 552.03453 2.7331858 + 140 2.7559175 -1590.9197 1440.667 -3031.5867 526.07695 0 -24.440541 154404.35 -157937.57 -2586.3198 17517.285 322.42423 482.1612 2.2975751 + 160 3.1113834 -1742.3406 1326.8813 -3069.2219 539.49038 0 -43.846686 154369.1 -157933.96 -3549.2199 18059.707 296.95875 444.11027 2.0644718 + 180 3.4379854 -1895.133 1224.1815 -3119.3145 555.27915 0 -18.261199 154275.94 -157932.27 -3762.2323 18545.519 273.97433 409.78407 1.8069068 + 200 3.772357 -2004.4681 1176.8827 -3181.3508 565.04401 0 0.21397152 154190.38 -157936.99 -4346.6082 18973.343 263.38877 393.94854 1.740057 + 220 4.0741081 -2094.1886 1098.386 -3192.5745 592.45711 0 36.50232 154113.36 -157934.89 -4135.0776 19341.735 245.82103 367.67719 1.6170754 + 240 4.3758588 -2178.9977 1086.8337 -3265.8313 617.63759 0 96.837785 153957.25 -157937.56 -4121.8002 19651.8 243.23561 363.77451 1.6722528 + 260 4.6875975 -2264.8204 1078.4367 -3343.2571 663.36053 0 167.77029 153763.13 -157937.51 -3799.2337 19907.053 241.35634 360.97449 1.6377088 + 280 4.9870708 -2325.8017 1097.4329 -3423.2346 717.74153 0 235.01385 153562.93 -157938.92 -3696.4866 20111.415 245.60773 367.30986 1.7042226 + 300 5.2866828 -2390.4714 1068.102 -3458.5734 751.64774 0 295.31519 153435.36 -157940.9 -3511.7651 20268.755 239.04342 357.49315 1.6658672 + 320 5.587172 -2455.1882 1041.7365 -3496.9247 765.89806 0 331.14936 153345 -157938.97 -3020.2521 20383.476 233.14276 348.62201 1.7179837 + 340 5.8844874 -2536.9586 1050.7417 -3587.7004 793.64691 0 352.69902 153205.76 -157939.81 -3447.4347 20457.614 235.15816 351.64191 1.7214644 + 360 6.1785333 -2603.5522 966.91828 -3570.4705 819.14562 0 391.00832 153158.88 -157939.51 -3164.7275 20490.766 216.3983 323.52165 1.7255664 + 380 6.475884 -2594.7716 1024.7965 -3619.5682 836.45788 0 434.31956 153047.12 -157937.46 -2902.8144 20485.924 229.35156 342.91613 1.7641391 + 400 6.7656763 -2647.3629 982.4772 -3629.8401 864.60508 0 479.09794 152963.5 -157937.04 -2535.5559 20447.667 219.88041 328.70004 1.8030439 + 420 7.0558476 -2687.5292 1023.0073 -3710.5365 928.03183 0 538.52272 152760.85 -157937.94 -2383.1875 20380.424 228.95113 342.29995 1.8044464 + 440 7.3502834 -2765.1784 999.349 -3764.5274 966.2891 0 577.16135 152631.19 -157939.17 -2390.6308 20286.677 223.65636 334.36519 1.794568 + 460 7.6480289 -2806.7277 1004.2012 -3810.9289 996.86402 0 599.42684 152532.82 -157940.04 -2476.2951 20168.787 224.74229 335.9677 1.8474231 + 480 7.9473393 -2830.1149 1013.7084 -3843.8233 1009.5457 0 624.67244 152464.69 -157942.73 -2208.5836 20027.763 226.87003 339.15378 1.8588625 + 500 8.2545588 -2849.2101 1033.8059 -3883.016 1018.8936 0 665.65423 152373.57 -157941.13 -1864.5049 19866.3 231.36788 345.90443 1.8323172 + 520 8.591975 -2883.363 982.80834 -3866.1713 1046.7496 0 716.08257 152311.55 -157940.55 -1180.4653 19690.017 219.95452 328.79387 1.8393955 + 540 8.9018662 -2922.4604 979.55307 -3902.0135 1068.293 0 739.88796 152230.57 -157940.76 -1048.6961 19504.92 219.22599 327.7909 1.6577051 + 560 9.2518864 -2966.9519 973.53114 -3940.4831 1078.4149 0 742.20771 152177.5 -157938.6 -840.75895 19313.099 217.87827 325.70841 1.7798986 + 580 9.5821679 -3053.0997 924.19412 -3977.2939 1102.7966 0 751.05657 152109.51 -157940.66 -919.12753 19115.431 206.83654 309.16882 1.7634757 + 600 9.9095862 -3062.7056 960.18758 -4022.8932 1105.4131 0 725.33328 152088.02 -157941.66 -1565.9872 18911.303 214.89195 321.19255 1.860965 + 620 10.237109 -3087.2168 1011.0151 -4098.2319 1138.4545 0 715.92859 151990.05 -157942.66 -1858.9668 18697.232 226.26725 338.29838 1.752463 + 640 10.571446 -3104.3903 1013.9671 -4118.3574 1151.4213 0 771.17657 151902.66 -157943.62 -1042.667 18472.317 226.92791 339.23913 1.8477429 + 660 10.904144 -3140.5527 1003.0482 -4143.6009 1209.2262 0 856.88154 151734.42 -157944.13 -209.63558 18243.884 224.48425 335.54573 1.90792 + 680 11.269296 -3178.318 984.55406 -4162.872 1244.5687 0 912.27932 151624.96 -157944.68 342.27035 18019.714 220.34522 329.38006 1.8427138 + 700 11.61204 -3220.4931 991.39835 -4211.8914 1287.1899 0 958.87881 151484.75 -157942.71 561.06968 17805.512 221.87699 331.61354 1.9544592 + 720 11.956387 -3270.5677 968.72596 -4239.2937 1318.9328 0 1005.2488 151379.5 -157942.98 980.32825 17604.484 216.80286 324.06313 1.8724276 + 740 12.307601 -3290.3786 992.65117 -4283.0298 1300.6067 0 994.6404 151364.88 -157943.15 981.03868 17418.67 222.15737 332.13302 1.7636245 + 760 12.709807 -3328.535 955.47413 -4284.0092 1326.3889 0 996.60158 151337.63 -157944.63 1057.2942 17247.311 213.83707 319.58671 1.9099364 + 780 13.073534 -3357.4814 992.18506 -4349.6664 1339.5541 0 988.34064 151267.55 -157945.11 569.82212 17090.619 222.05305 331.88822 1.9447924 + 800 13.464632 -3375.243 920.44154 -4295.6846 1344.9357 0 1033.5805 151270.88 -157945.08 1522.7002 16947.373 205.99671 307.8875 1.8152213 + 820 13.825511 -3384.8564 957.24296 -4342.0994 1353.9907 0 1040.4762 151209.02 -157945.59 1664.2884 16820.422 214.23294 320.13875 1.9919112 + 840 14.161551 -3422.503 978.5056 -4401.0087 1362.0589 0 1015.2074 151166.38 -157944.65 799.30788 16709.133 218.99156 327.32752 1.887971 + 860 14.533048 -3467.9469 967.207 -4435.1539 1359.5363 0 1012.6359 151135.59 -157942.92 781.21407 16610.402 216.46291 323.49791 1.9571626 + 880 14.90632 -3453.3858 998.28194 -4451.6677 1357.904 0 965.66218 151167.88 -157943.11 327.66041 16521.416 223.41755 333.88219 2.0414314 + 900 15.304111 -3462.8392 980.22919 -4443.0684 1356.3167 0 986.69144 151157.82 -157943.9 1027.2464 16438.193 219.37731 327.82432 2.0328217 + 920 15.679265 -3447.1555 973.44396 -4420.5994 1360.7957 0 1016.6188 151146.99 -157945 1288.3873 16362.953 217.85876 325.51992 2.1081109 + 940 16.057773 -3481.2586 989.56656 -4470.8252 1370.2709 0 978.71463 151124.98 -157944.79 462.51008 16297.794 221.46703 330.96437 2.0294765 + 960 16.417333 -3513.0231 967.65653 -4480.6797 1332.0395 0 924.14851 151207.66 -157944.53 130.65949 16238.731 216.56352 323.68471 1.8694768 + 980 16.809043 -3552.9742 930.52856 -4483.5028 1369.5671 0 943.1948 151148.51 -157944.78 162.05947 16182.544 208.2542 311.18346 1.9699974 + 1000 17.204374 -3547.8316 928.6749 -4476.5065 1345.2729 0 939.82999 151183.66 -157945.27 165.47858 16127.801 207.83935 310.6291 1.8515304 + 1020 17.596776 -3544.884 939.68436 -4484.5683 1339.8295 0 954.31534 151165.65 -157944.37 520.88879 16074.311 210.30329 314.30017 1.8816955 + 1040 17.979123 -3574.7347 918.01852 -4492.7532 1348.2798 0 985.63357 151118.04 -157944.71 667.98123 16024.2 205.45443 307.00947 1.9378696 + 1060 18.387169 -3558.0092 961.56557 -4519.5748 1357.9517 0 960.15956 151105.93 -157943.62 125.05193 15979.251 215.20035 321.61047 1.9569155 + 1080 18.773684 -3578.9948 924.98329 -4503.9781 1328.198 0 963.29308 151149.83 -157945.3 446.98896 15936.835 207.01316 309.36635 1.8873208 + 1100 19.16304 -3608.0441 897.53939 -4505.5835 1374.0861 0 1014.8258 151052.01 -157946.5 903.7649 15898.367 200.87116 300.13546 1.9333063 + 1120 19.575293 -3614.8945 952.97919 -4567.8736 1384.5634 0 1021.0735 150973.5 -157947.01 900.30601 15866.787 213.2787 318.78179 1.850125 + 1140 19.971095 -3618.8945 941.15802 -4560.0526 1413.1629 0 1052.0922 150920.8 -157946.1 946.48705 15842.856 210.6331 314.72329 2.0381081 + 1160 20.367334 -3593.6555 965.54035 -4559.1959 1410.1926 0 1056.4577 150917.31 -157943.16 1255.7185 15827.388 216.08991 322.92339 1.9871263 + 1180 20.80204 -3616.5746 928.17105 -4544.7457 1396.8419 0 1016.2295 150986.13 -157943.95 787.12503 15820.166 207.72659 310.40871 1.9519704 + 1200 21.354242 -3640.0065 913.1866 -4553.1931 1389.564 0 1003.0365 150999.43 -157945.23 124.9066 15819.562 204.37304 305.34426 2.0128932 + 1220 21.797356 -3633.6726 951.90864 -4585.5813 1378.6589 0 960.35277 151020.87 -157945.46 18.165228 15822.414 213.03911 318.39602 1.9062762 + 1240 22.183053 -3647.5993 945.94087 -4593.5401 1389.2708 0 951.90886 151011.29 -157946.01 -36.466949 15826.558 211.70351 316.39869 1.8959 + 1260 22.604321 -3652.8431 945.01497 -4597.8581 1429.1559 0 1004.3575 150913.05 -157944.42 362.05633 15830.563 211.49629 316.0745 1.946701 + 1280 22.99465 -3653.7982 950.39456 -4604.1928 1435.3114 0 1049.5949 150856.36 -157945.46 625.62312 15836.724 212.70025 317.85889 1.9726129 + 1300 23.381442 -3629.7936 957.73231 -4587.5259 1443.1612 0 1053.2561 150860.98 -157944.93 702.06174 15846.916 214.34246 320.25498 2.0929604 + 1320 23.76752 -3646.7132 952.84473 -4599.5579 1452.1034 0 1053.24 150842.08 -157946.98 574.37181 15862.45 213.24861 318.70565 1.9106871 + 1340 24.144538 -3671.1813 963.35534 -4634.5366 1444.4873 0 998.25657 150869.14 -157946.42 -322.65814 15883.001 215.6009 322.16079 2.04787 + 1360 24.525885 -3706.8433 911.96869 -4618.812 1408.7597 0 994.56958 150923.67 -157945.81 -57.178556 15902.95 204.10046 304.98731 1.9206183 + 1380 24.900833 -3729.8666 893.54172 -4623.4083 1421.5285 0 989.13168 150911.03 -157945.1 -299.2294 15921.536 199.97647 298.78606 1.9572022 + 1400 25.273009 -3793.6665 896.59455 -4690.261 1407.5033 0 927.03218 150922.27 -157947.07 -1625.2355 15935.372 200.6597 299.82059 1.9326242 + 1420 25.649713 -3798.9041 894.49834 -4693.4024 1387.2314 0 908.98338 150956.58 -157946.2 -1336.2681 15939.126 200.19057 299.08979 1.99336 + 1440 26.019568 -3770.2203 926.96956 -4697.1899 1408.3234 0 930.94218 150909.09 -157945.54 -1479.4839 15931.76 207.45769 309.99863 1.9420101 + 1460 26.391048 -3765.611 925.8388 -4691.4498 1453.7458 0 991.60997 150809.05 -157945.85 -840.19764 15915.083 207.20462 309.58977 2.0206113 + 1480 26.764417 -3775.5533 897.45722 -4673.0106 1448.3682 0 1017.1514 150806.55 -157945.08 -350.56805 15893.71 200.85277 300.10571 1.945031 + 1500 27.13281 -3774.5729 890.65309 -4665.226 1446.7764 0 1001.4176 150830.42 -157943.84 -410.46342 15870.464 199.32999 297.86004 1.8712264 + 1520 27.500265 -3789.599 873.98319 -4663.5822 1442.1868 0 1012.8814 150826.03 -157944.68 24.399796 15844.317 195.59923 292.31265 1.7812003 + 1540 27.868039 -3799.4214 879.9876 -4679.409 1470.7765 0 1043.5857 150751.8 -157945.57 -117.3494 15817.531 196.94303 294.27937 1.8764714 + 1560 28.237804 -3808.5737 884.02221 -4692.5959 1476.2544 0 1031.065 150745.8 -157945.71 -134.38328 15790.497 197.84599 295.60533 1.9624808 + 1580 28.614069 -3810.3826 881.02258 -4691.4052 1494.8044 0 1056.2914 150703.91 -157946.41 143.72796 15761.802 197.17466 294.61532 1.9194335 + 1600 28.98594 -3811.3999 900.38301 -4711.7829 1484.7896 0 1008.1585 150740.82 -157945.55 -606.18902 15732.936 201.50757 301.08426 1.975131 + 1620 29.390152 -3806.3652 923.83116 -4730.1964 1451.5712 0 974.75532 150788.99 -157945.52 -803.66402 15700.793 206.75531 308.94868 1.9548773 + 1640 29.770757 -3780.4823 926.08598 -4706.5682 1473.3966 0 1001.2541 150764.99 -157946.2 -267.61953 15664.228 207.25994 309.69886 1.9804041 + 1660 30.150359 -3781.8554 904.38999 -4686.2453 1480.8669 0 1044.4828 150733.32 -157944.92 334.93631 15626.039 202.40434 302.41882 1.9682532 + 1680 30.535691 -3806.1604 913.1776 -4719.338 1495.1709 0 1047.1796 150684.96 -157946.64 187.42287 15589.003 204.37102 305.37701 1.9489831 + 1700 30.914774 -3833.9683 889.78762 -4723.756 1506.0651 0 1085.1426 150631.7 -157946.67 484.91155 15553.147 199.1363 297.62268 1.7777001 + 1720 31.295628 -3842.1369 894.05081 -4736.1877 1523.554 0 1111.0586 150574.13 -157944.93 644.7439 15520.678 200.09041 298.99568 1.8760829 + 1740 31.688478 -3846.6021 868.65036 -4715.2525 1537.3591 0 1138.8056 150555.14 -157946.56 899.91638 15492.771 194.40573 290.47895 1.8712221 + 1760 32.046871 -3857.9528 883.26637 -4741.2192 1542.993 0 1087.2616 150575.49 -157946.97 551.51344 15470.089 197.67683 295.29782 2.0345443 + 1780 32.474213 -3871.4941 935.07928 -4806.5734 1526.7468 0 1036.0478 150576.57 -157945.93 -636.02229 15449.192 209.27266 312.71251 1.9801693 + 1800 32.86394 -3840.4408 916.271 -4756.7118 1576.9326 0 1100.9058 150511.02 -157945.57 628.83596 15425.726 205.06333 306.41471 1.9480945 + 1820 33.2544 -3863.8057 928.94676 -4792.7524 1566.8662 0 1091.867 150492.97 -157944.46 127.39479 15404.045 207.90019 310.61713 2.0438685 + 1840 33.654639 -3866.4315 882.39729 -4748.8287 1571.1231 0 1116.2191 150510.49 -157946.66 775.21837 15384.034 197.48232 295.08631 1.8701078 + 1860 34.049358 -3854.7362 943.50575 -4798.2419 1598.0765 0 1094.2606 150455.31 -157945.89 -185.76137 15367.771 211.15852 315.55119 1.9664963 + 1880 34.452703 -3862.4907 910.1166 -4772.6073 1551.4788 0 1069.6982 150551.3 -157945.09 75.157314 15353.364 203.68596 304.30419 2.0643731 + 1900 34.820253 -3879.6568 921.99593 -4801.6528 1541.8636 0 1071.1404 150530.01 -157944.67 -243.29034 15340.544 206.34458 308.28647 2.0409636 + 1920 35.24159 -3914.6053 894.91511 -4809.5205 1545.6295 0 1087.8419 150502.25 -157945.24 585.4907 15327.629 200.28384 299.29163 1.8721306 + 1940 35.641894 -3916.7204 893.69522 -4810.4157 1558.0228 0 1078.6893 150498.47 -157945.6 -213.58892 15315.774 200.01082 298.82901 1.9662798 + 1960 36.036489 -3916.4155 889.43523 -4805.8507 1569.5342 0 1087.2216 150483.46 -157946.07 197.26075 15304.142 199.05743 297.4414 1.897782 + 1980 36.439917 -3885.2222 890.76008 -4775.9823 1562.1737 0 1087.3549 150520.37 -157945.88 448.96019 15293.261 199.35393 297.81895 2.0239285 + 2000 36.842032 -3890.9997 883.71903 -4774.7187 1561.3244 0 1092.1688 150517.76 -157945.97 292.74093 15284.861 197.77813 295.50959 1.9186189 +Loop time of 36.8421 on 4 procs for 2000 steps with 2500 atoms + +Performance: 4.690 ns/day, 5.117 hours/ns, 54.286 timesteps/s +97.8% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 24.965 | 26.526 | 28.829 | 27.6 | 72.00 +Bond | 0.011653 | 0.012315 | 0.013344 | 0.6 | 0.03 +Kspace | 1.5367 | 3.8315 | 5.3771 | 72.2 | 10.40 +Neigh | 2.6221 | 2.6225 | 2.6227 | 0.0 | 7.12 +Comm | 1.2339 | 1.2536 | 1.2758 | 1.3 | 3.40 +Output | 0.0057538 | 0.0073775 | 0.012186 | 3.2 | 0.02 +Modify | 2.4848 | 2.5068 | 2.5296 | 1.2 | 6.80 +Other | | 0.08209 | | | 0.22 + +Nlocal: 625 ave 639 max 613 min +Histogram: 1 1 0 0 0 0 1 0 0 1 +Nghost: 13529.2 ave 13635 max 13449 min +Histogram: 1 0 1 0 1 0 0 0 0 1 +Neighs: 587190 ave 645917 max 526348 min +Histogram: 1 0 0 1 0 0 1 0 0 1 + +Total # of neighbors = 2348759 +Ave neighs/atom = 939.504 +Ave special neighs/atom = 4 +Neighbor list builds = 102 +Dangerous builds = 7 + +Total wall time: 0:00:36 diff --git a/examples/USER/drude/swm4-ndp/log.27Nov18.swm4-ndp.nh.g++.1 b/examples/USER/drude/swm4-ndp/log.27Nov18.swm4-ndp.nh.g++.1 new file mode 100644 index 0000000000..54fe5ecb01 --- /dev/null +++ b/examples/USER/drude/swm4-ndp/log.27Nov18.swm4-ndp.nh.g++.1 @@ -0,0 +1,252 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +units real +boundary p p p + +atom_style full +bond_style harmonic +angle_style harmonic +special_bonds lj/coul 0.0 0.0 0.5 + +pair_style lj/cut/coul/long 12.0 12.0 +kspace_style pppm 1.0e-3 + +read_data data.swm4-ndp + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 2500 atoms + scanning bonds ... + 1 = max bonds/atom + scanning angles ... + 1 = max angles/atom + reading bonds ... + 2000 bonds + reading angles ... + 500 angles + 4 = max # of 1-2 neighbors + 3 = max # of 1-3 neighbors + 3 = max # of 1-4 neighbors + 4 = max # of special neighbors + +pair_coeff 1 1 0.210939 3.183950 # ODw ODw +pair_coeff * 2* 0.000000 0.0 + +group ATOMS type 1:3 +2000 atoms in group ATOMS +group CORES type 1 +500 atoms in group CORES +group DRUDES type 4 +500 atoms in group DRUDES + +variable TK equal 300.0 +variable TDK equal 1.0 +variable PBAR equal 1.0 + +neighbor 2.0 bin + +timestep 1.0 + +fix DRUDE all drude C N N D + +velocity ATOMS create ${TK} 12345 +velocity ATOMS create 300 12345 +velocity DRUDES create ${TDK} 12345 +velocity DRUDES create 1 12345 + +delete_bonds ATOMS multi +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) + G vector (1/distance) = 0.217457 + grid = 10 10 10 + stencil order = 5 + estimated absolute RMS force accuracy = 0.197288 + estimated relative force accuracy = 0.000594128 + using double precision FFTs + 3d grid and FFT values/proc = 3375 1000 +Rebuild special list taking Drude particles into account +Old max number of 1-2 to 1-4 neighbors: 4 +New max number of 1-2 to 1-4 neighbors: 4 (+0) +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 4 4 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + 2000 total bonds, 500 turned on, 1500 turned off + 500 total angles, 0 turned on, 500 turned off + 0 total dihedrals, 0 turned on, 0 turned off + 0 total impropers, 0 turned on, 0 turned off + +comm_modify vel yes +compute TATOM ATOMS temp/com +compute TEMP all temp/drude + +fix DTDIR all drude/transform/direct +fix RIGID ATOMS rigid/npt/small molecule temp ${TK} ${TK} 100 iso ${PBAR} ${PBAR} 500 +fix RIGID ATOMS rigid/npt/small molecule temp 300 ${TK} 100 iso ${PBAR} ${PBAR} 500 +fix RIGID ATOMS rigid/npt/small molecule temp 300 300 100 iso ${PBAR} ${PBAR} 500 +fix RIGID ATOMS rigid/npt/small molecule temp 300 300 100 iso 1 ${PBAR} 500 +fix RIGID ATOMS rigid/npt/small molecule temp 300 300 100 iso 1 1 500 +500 rigid bodies with 2000 atoms + 0.832099 = max distance from body owner to body atom +fix_modify RIGID temp TATOM press thermo_press +WARNING: Temperature for fix modify is not for group all (src/RIGID/fix_rigid_nh_small.cpp:1338) +fix NVT DRUDES nvt temp ${TDK} ${TDK} 100.0 +fix NVT DRUDES nvt temp 1 ${TDK} 100.0 +fix NVT DRUDES nvt temp 1 1 100.0 +fix DTINV all drude/transform/inverse + +thermo_style custom step cpu etotal ke pe ebond eangle evdwl ecoul elong press vol temp c_TEMP[1] c_TEMP[2] +thermo 20 + +run 2000 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) + G vector (1/distance) = 0.217457 + grid = 10 10 10 + stencil order = 5 + estimated absolute RMS force accuracy = 0.197288 + estimated relative force accuracy = 0.000594128 + using double precision FFTs + 3d grid and FFT values/proc = 3375 1000 +Per MPI rank memory allocation (min/avg/max) = 36.15 | 36.15 | 36.15 Mbytes +Step CPU TotEng KinEng PotEng E_bond E_angle E_vdwl E_coul E_long Press Volume Temp c_TEMP[1] c_TEMP[2] + 0 0 4568.0415 903.41148 3664.63 623.46454 0 2890.2449 157955.66 -157804.74 244591.08 13824 202.18534 295.64644 14.858785 + 20 1.3635511 3742.6843 5338.7884 -1596.1041 567.30749 0 662.23765 155098.37 -157924.01 31679.425 13979.574 1194.8318 1690.2246 201.65659 + 40 2.8319206 2752.8326 4407.7651 -1654.9326 793.00136 0 870.3308 154593.76 -157912.03 27394.569 14278.56 986.46689 1450.7477 55.932383 + 60 4.2769592 1995.5898 3982.037 -1986.4472 660.67727 0 750.60931 154536.67 -157934.4 22230.525 14691.401 891.18805 1315.7323 40.317105 + 80 5.6864653 1376.4611 3451.5427 -2075.0816 617.739 0 606.36728 154625.69 -157924.88 17342.361 15201.343 772.46234 1147.1933 21.455572 + 100 7.0593393 885.62035 3037.6307 -2152.0103 536.23281 0 448.92338 154793.05 -157930.22 13263.277 15783.251 679.82798 1011.6853 14.753602 + 120 8.3966329 487.59021 2926.9825 -2439.3923 534.45241 0 332.92674 154624.58 -157931.35 8680.1218 16409.225 655.06468 977.01117 9.8615821 + 140 9.6922171 159.94255 2531.0921 -2371.1495 507.26507 0 248.61566 154802.72 -157929.75 6400.0155 17052.819 566.4636 845.55884 7.140197 + 160 10.950651 -100.91956 2408.1664 -2509.0859 490.99483 0 134.36058 154800.6 -157935.04 3836.9925 17698.151 538.95257 805.1915 5.3968131 + 180 12.172047 -313.40678 2221.7371 -2535.1439 469.97826 0 75.806422 154853.24 -157934.17 1959.0003 18334.826 497.22932 743.13919 4.4151403 + 200 13.369177 -490.93825 2067.2564 -2558.1946 455.16083 0 77.543554 154841.16 -157932.06 1193.4025 18956.449 462.65622 691.72198 3.5993868 + 220 14.438093 -642.88359 1962.7222 -2605.6058 481.40176 0 64.823738 154779.31 -157931.14 258.47931 19559.018 439.26127 657.06568 2.7739198 + 240 15.577558 -770.43472 1795.7362 -2566.1709 467.25739 0 68.825446 154830.01 -157932.26 19.605411 20139.418 401.88945 601.23804 2.3884997 + 260 16.688265 -878.62151 1752.9509 -2631.5724 476.39236 0 71.926651 154747.16 -157927.05 -779.07206 20696.166 392.31402 587.06568 2.0260792 + 280 17.682964 -971.81622 1649.6272 -2621.4434 473.84812 0 58.450385 154779.58 -157933.32 -1008.5258 21226.441 369.18995 552.55677 1.7179235 + 300 18.755012 -1057.4737 1581.0153 -2638.4889 480.33302 0 92.047223 154721.85 -157932.72 -1272.4892 21728.979 353.83447 529.64527 1.5051853 + 320 19.774572 -1132.8157 1506.8725 -2639.6882 477.53234 0 107.39639 154707.65 -157932.27 -1097.9626 22203.697 337.24116 504.84512 1.3587573 + 340 20.69206 -1199.489 1494.9584 -2694.4474 479.87519 0 106.49874 154656.38 -157937.2 -1428.8049 22652.416 334.57476 500.90442 1.2462835 + 360 21.652272 -1264.9018 1440.9759 -2705.8778 491.74088 0 107.21802 154624.72 -157929.55 -1585.5815 23073.033 322.49337 482.81675 1.2016239 + 380 22.541014 -1323.4812 1376.8139 -2700.295 497.62389 0 130.73162 154602.95 -157931.6 -1822.4176 23465.34 308.13377 461.36583 1.0533711 + 400 23.429899 -1373.4313 1375.7746 -2749.2059 504.5216 0 124.40122 154554.57 -157932.7 -2024.2519 23828.151 307.90118 461.05182 0.98409512 + 420 24.30185 -1426.2004 1375.0825 -2801.2829 515.4234 0 141.95789 154473.92 -157932.58 -2211.7434 24159.844 307.74628 460.87881 0.86572884 + 440 25.220268 -1475.8906 1324.8476 -2800.7382 535.08125 0 196.94504 154398.6 -157931.36 -1603.3424 24460.372 296.50361 443.98822 0.94139759 + 460 26.069995 -1526.8146 1312.6512 -2839.4658 567.30401 0 263.15706 154263.01 -157932.94 -1446.573 24734.601 293.77403 439.95008 0.83440493 + 480 26.912804 -1575.0902 1310.7022 -2885.7924 595.89933 0 312.71625 154137.37 -157931.78 -1115.9617 24986.067 293.33784 439.29118 0.84448526 + 500 27.750046 -1625.867 1316.9545 -2942.8215 622.71944 0 334.05272 154029.75 -157929.34 -1178.3349 25218.467 294.73713 441.38984 0.84223525 + 520 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-4148.4824 1203.2944 0 877.27308 151711.62 -157940.67 -877.19102 21189.111 243.23747 364.15541 0.91512372 + 1380 64.90951 -3092.7485 1046.5902 -4139.3388 1239.0597 0 915.00432 151646.1 -157939.51 -519.03533 20978.348 234.22904 350.66459 0.8894947 + 1400 65.889121 -3121.488 1051.0689 -4172.5569 1298.7247 0 989.25234 151480.54 -157941.07 -54.596483 20769.447 235.23138 352.15827 0.90714599 + 1420 66.880954 -3149.3299 1046.1867 -4195.5166 1316.5513 0 1013.5453 151416.57 -157942.18 -12.199056 20566.196 234.13872 350.49775 0.95239313 + 1440 67.876446 -3172.8201 1046.5913 -4219.4114 1319.1146 0 989.68846 151410.33 -157938.54 -145.84664 20369.571 234.22928 350.68677 0.84585946 + 1460 68.88107 -3200.8425 1052.2514 -4253.0939 1296.3997 0 914.27128 151478.83 -157942.59 -1047.6067 20177.139 235.49603 352.58952 0.83805114 + 1480 69.894247 -3229.1329 1032.538 -4261.6708 1273.6899 0 884.58641 151521.54 -157941.48 -877.62887 19983.452 231.08411 345.95296 0.88426485 + 1500 71.009717 -3256.5597 1060.231 -4316.7907 1291.1374 0 874.13592 151461.84 -157943.91 -1479.1729 19788.536 237.28186 355.23846 0.89410552 + 1520 72.041054 -3283.4789 1004.9547 -4288.4336 1248.3551 0 849.40507 151555.63 -157941.83 -1210.342 19590.335 224.91093 336.73148 0.81999833 + 1540 73.084395 -3307.2541 1008.328 -4315.5821 1259.4211 0 846.2933 151520.12 -157941.42 -1328.6534 19389.457 225.66587 337.86416 0.81796565 + 1560 74.135646 -3333.4164 1009.8078 -4343.2242 1290.3482 0 843.72954 151464.8 -157942.1 -1492.5376 19185.011 225.99706 338.35783 0.82352496 + 1580 75.198241 -3359.5746 1031.9507 -4391.5253 1301.979 0 907.32598 151341.72 -157942.55 -931.21229 18977.005 230.95268 345.78871 0.81873619 + 1600 76.272058 -3383.7255 977.90216 -4361.6277 1350.9107 0 1005.0889 151225.61 -157943.23 -265.11417 18769.775 218.85651 327.62822 0.87537743 + 1620 77.356282 -3399.3062 994.75129 -4394.0575 1387.4383 0 1059.1407 151101.4 -157942.03 574.54697 18568.615 222.62738 333.25885 0.91918263 + 1640 78.448545 -3415.8361 1023.468 -4439.304 1398.4672 0 1052.931 151054.15 -157944.85 470.27927 18377.301 229.05423 342.8805 0.94357863 + 1660 79.550247 -3434.561 975.54176 -4410.1027 1429.1617 0 1081.052 151023.2 -157943.52 1049.9178 18195.592 218.32825 326.8381 0.87189374 + 1680 80.667191 -3451.4085 987.31735 -4438.7259 1473.5691 0 1116.4474 150914.31 -157943.05 1058.2306 18025.735 220.96365 330.80265 0.84371639 + 1700 81.797154 -3467.686 964.72099 -4432.407 1455.6679 0 1109.6516 150945 -157942.73 1282.6999 17867.835 215.90654 323.18716 0.91347876 + 1720 82.926758 -3484.8522 984.05698 -4468.9092 1459.9348 0 1102.3739 150911.78 -157943 919.74849 17722.037 220.23397 329.6527 0.95604421 + 1740 84.064705 -3497.8606 976.97179 -4474.8324 1401.3809 0 1034.3626 151032.67 -157943.25 535.35483 17586.464 218.64829 327.27748 0.95261024 + 1760 85.25497 -3516.3474 990.65511 -4507.0025 1393.0104 0 1015.5429 151026.85 -157942.4 -45.078457 17457.877 221.71065 331.88315 0.92222263 + 1780 86.432811 -3532.5203 981.67325 -4514.1936 1381.8497 0 1018.8916 151028.12 -157943.05 419.25311 17333.542 219.70049 328.86023 0.94159899 + 1800 87.629265 -3551.0627 978.09831 -4529.161 1409.4225 0 1023.8144 150980.45 -157942.84 -136.21958 17214.117 218.90041 327.67684 0.90973891 + 1820 88.810324 -3566.367 953.86873 -4520.2357 1386.004 0 1027.6913 151009.66 -157943.59 272.29498 17097.552 213.47778 319.53574 0.93491142 + 1840 89.996806 -3581.9401 989.35892 -4571.299 1438.2511 0 1011.4985 150924.05 -157945.1 -277.89182 16984.647 221.42056 331.39393 1.0309706 + 1860 91.192728 -3597.0855 939.72505 -4536.8105 1424.7503 0 1045.0751 150938.2 -157944.83 769.1418 16874.282 210.31239 314.73818 1.0402053 + 1880 92.395072 -3609.1452 988.80243 -4597.9477 1452.2757 0 1054.8324 150839.43 -157944.48 448.42199 16769.952 221.29601 331.17499 1.095477 + 1900 93.599308 -3623.9274 981.88757 -4605.815 1467.8981 0 1058.3428 150811.66 -157943.72 440.93441 16671.114 219.74845 328.86095 1.0839713 + 1920 94.800441 -3637.4995 962.46738 -4599.9668 1472.6584 0 1100.9414 150770.55 -157944.12 927.11674 16577.506 215.40217 322.39885 0.97801499 + 1940 96.006696 -3649.8745 932.46317 -4582.3377 1482.9302 0 1127.1576 150751.01 -157943.44 1275.661 16490.871 208.68717 312.30264 1.0388692 + 1960 97.217233 -3660.5717 957.9057 -4618.4774 1471.5387 0 1090.5959 150763.08 -157943.69 926.00133 16412.162 214.38126 320.81698 1.081062 + 1980 98.432616 -3673.974 955.97217 -4629.9462 1448.9016 0 1043.2494 150823.46 -157945.55 585.7993 16339.534 213.94853 320.15896 1.0997884 + 2000 99.651307 -3687.9477 943.17863 -4631.1263 1431.8862 0 1028.9334 150853.1 -157945.05 406.94681 16271.378 211.08531 315.85857 1.1166274 +Loop time of 99.6513 on 1 procs for 2000 steps with 2500 atoms + +Performance: 1.734 ns/day, 13.840 hours/ns, 20.070 timesteps/s +98.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 78.424 | 78.424 | 78.424 | 0.0 | 78.70 +Bond | 0.032606 | 0.032606 | 0.032606 | 0.0 | 0.03 +Kspace | 3.7865 | 3.7865 | 3.7865 | 0.0 | 3.80 +Neigh | 9.511 | 9.511 | 9.511 | 0.0 | 9.54 +Comm | 0.71185 | 0.71185 | 0.71185 | 0.0 | 0.71 +Output | 0.0071998 | 0.0071998 | 0.0071998 | 0.0 | 0.01 +Modify | 7.1361 | 7.1361 | 7.1361 | 0.0 | 7.16 +Other | | 0.04205 | | | 0.04 + +Nlocal: 2500 ave 2500 max 2500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 20897 ave 20897 max 20897 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 2.20428e+06 ave 2.20428e+06 max 2.20428e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 2204275 +Ave neighs/atom = 881.71 +Ave special neighs/atom = 4 +Neighbor list builds = 122 +Dangerous builds = 16 + +Total wall time: 0:01:39 diff --git a/examples/USER/drude/swm4-ndp/log.27Nov18.swm4-ndp.nh.g++.4 b/examples/USER/drude/swm4-ndp/log.27Nov18.swm4-ndp.nh.g++.4 new file mode 100644 index 0000000000..332359e659 --- /dev/null +++ b/examples/USER/drude/swm4-ndp/log.27Nov18.swm4-ndp.nh.g++.4 @@ -0,0 +1,252 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +units real +boundary p p p + +atom_style full +bond_style harmonic +angle_style harmonic +special_bonds lj/coul 0.0 0.0 0.5 + +pair_style lj/cut/coul/long 12.0 12.0 +kspace_style pppm 1.0e-3 + +read_data data.swm4-ndp + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 2500 atoms + scanning bonds ... + 1 = max bonds/atom + scanning angles ... + 1 = max angles/atom + reading bonds ... + 2000 bonds + reading angles ... + 500 angles + 4 = max # of 1-2 neighbors + 3 = max # of 1-3 neighbors + 3 = max # of 1-4 neighbors + 4 = max # of special neighbors + +pair_coeff 1 1 0.210939 3.183950 # ODw ODw +pair_coeff * 2* 0.000000 0.0 + +group ATOMS type 1:3 +2000 atoms in group ATOMS +group CORES type 1 +500 atoms in group CORES +group DRUDES type 4 +500 atoms in group DRUDES + +variable TK equal 300.0 +variable TDK equal 1.0 +variable PBAR equal 1.0 + +neighbor 2.0 bin + +timestep 1.0 + +fix DRUDE all drude C N N D + +velocity ATOMS create ${TK} 12345 +velocity ATOMS create 300 12345 +velocity DRUDES create ${TDK} 12345 +velocity DRUDES create 1 12345 + +delete_bonds ATOMS multi +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) + G vector (1/distance) = 0.217457 + grid = 10 10 10 + stencil order = 5 + estimated absolute RMS force accuracy = 0.197288 + estimated relative force accuracy = 0.000594128 + using double precision FFTs + 3d grid and FFT values/proc = 1500 300 +Rebuild special list taking Drude particles into account +Old max number of 1-2 to 1-4 neighbors: 4 +New max number of 1-2 to 1-4 neighbors: 4 (+0) +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 4 4 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + 2000 total bonds, 500 turned on, 1500 turned off + 500 total angles, 0 turned on, 500 turned off + 0 total dihedrals, 0 turned on, 0 turned off + 0 total impropers, 0 turned on, 0 turned off + +comm_modify vel yes +compute TATOM ATOMS temp/com +compute TEMP all temp/drude + +fix DTDIR all drude/transform/direct +fix RIGID ATOMS rigid/npt/small molecule temp ${TK} ${TK} 100 iso ${PBAR} ${PBAR} 500 +fix RIGID ATOMS rigid/npt/small molecule temp 300 ${TK} 100 iso ${PBAR} ${PBAR} 500 +fix RIGID ATOMS rigid/npt/small molecule temp 300 300 100 iso ${PBAR} ${PBAR} 500 +fix RIGID ATOMS rigid/npt/small molecule temp 300 300 100 iso 1 ${PBAR} 500 +fix RIGID ATOMS rigid/npt/small molecule temp 300 300 100 iso 1 1 500 +500 rigid bodies with 2000 atoms + 0.832099 = max distance from body owner to body atom +fix_modify RIGID temp TATOM press thermo_press +WARNING: Temperature for fix modify is not for group all (src/RIGID/fix_rigid_nh_small.cpp:1338) +fix NVT DRUDES nvt temp ${TDK} ${TDK} 100.0 +fix NVT DRUDES nvt temp 1 ${TDK} 100.0 +fix NVT DRUDES nvt temp 1 1 100.0 +fix DTINV all drude/transform/inverse + +thermo_style custom step cpu etotal ke pe ebond eangle evdwl ecoul elong press vol temp c_TEMP[1] c_TEMP[2] +thermo 20 + +run 2000 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) + G vector (1/distance) = 0.217457 + grid = 10 10 10 + stencil order = 5 + estimated absolute RMS force accuracy = 0.197288 + estimated relative force accuracy = 0.000594128 + using double precision FFTs + 3d grid and FFT values/proc = 1500 300 +Per MPI rank memory allocation (min/avg/max) = 18.29 | 18.3 | 18.3 Mbytes +Step CPU TotEng KinEng PotEng E_bond E_angle E_vdwl E_coul E_long Press Volume Temp c_TEMP[1] c_TEMP[2] + 0 0 4568.0415 903.41148 3664.63 623.46454 0 2890.2449 157955.66 -157804.74 244591.08 13824 202.18534 295.64644 14.858785 + 20 0.45823026 3742.7989 5338.7966 -1595.9977 567.29056 0 662.23349 155098.48 -157924 31679.045 13979.575 1194.8336 1690.2267 201.65776 + 40 0.95719695 2752.9392 4407.9332 -1654.994 792.86724 0 870.27523 154593.92 -157912.06 27392.303 14278.564 986.5045 1450.7624 56.079839 + 60 1.4402499 1995.9776 3980.851 -1984.8734 660.64219 0 750.43211 154538.47 -157934.42 22242.677 14691.413 890.92262 1315.3403 40.305318 + 80 1.9050057 1377.133 3449.7879 -2072.6549 617.64238 0 605.75691 154628.64 -157924.69 17345.359 15201.397 772.06961 1146.6088 21.447181 + 100 2.3745039 886.38999 3038.411 -2152.021 537.89929 0 450.99966 154789.13 -157930.05 13299.226 15783.335 680.00261 1011.6773 15.016235 + 120 2.8589215 488.05512 2928.1336 -2440.0785 536.23142 0 334.886 154620.05 -157931.25 8694.3495 16409.509 655.32232 977.40122 9.853881 + 140 3.2965367 160.14918 2538.5119 -2378.3627 509.19544 0 249.89187 154793.34 -157930.79 6363.0936 17053.486 568.12418 847.92535 7.2744487 + 160 3.7223189 -103.57483 2403.1617 -2506.7365 494.69852 0 144.07166 154790.83 -157936.34 4017.2081 17699.095 537.83252 803.44789 5.3901447 + 180 4.1554348 -315.60495 2216.8001 -2532.405 477.29347 0 80.852028 154842.41 -157932.96 1958.2418 18336.716 496.1244 741.47039 4.4401782 + 200 4.5533779 -490.60343 2058.8989 -2549.5023 470.22934 0 80.797892 154831.65 -157932.18 1260.3909 18960.132 460.78579 688.924 3.5878094 + 220 4.9085493 -644.11131 2001.1202 -2645.2315 494.11411 0 53.067462 154741.64 -157934.05 -16.783051 19564.819 447.8548 669.94702 2.7746354 + 240 5.2955835 -773.77077 1911.0789 -2684.8496 491.56671 0 36.573942 154722.87 -157935.86 -773.28467 20144.754 427.70337 639.97783 2.2990474 + 260 5.7046614 -886.74825 1719.7065 -2606.4547 462.97836 0 47.58745 154814.53 -157931.55 -695.31939 20696.484 384.87384 575.96438 1.9230094 + 280 6.0633757 -983.59043 1659.2126 -2642.803 476.05207 0 65.528 154749.28 -157933.67 -1099.7766 21220.608 371.33519 555.77921 1.7044743 + 300 6.4097662 -1069.381 1531.6365 -2601.0175 487.38768 0 130.0599 154709.01 -157927.47 -548.94313 21717.512 342.78339 513.13082 1.4029607 + 320 6.7455602 -1144.854 1562.925 -2707.779 508.98546 0 127.16624 154591.4 -157935.34 -1515.6429 22190.677 349.78582 523.6096 1.414493 + 340 7.0504746 -1216.4848 1511.8539 -2728.3386 518.41635 0 144.67031 154541.86 -157933.28 -1346.5299 22636.537 338.356 506.57907 1.2331509 + 360 7.3652327 -1279.8842 1434.5465 -2714.4306 524.92137 0 153.81139 154537.16 -157930.32 -1445.625 23056.451 321.05444 480.69079 1.1396531 + 380 7.6638732 -1340.1922 1391.8227 -2732.0149 537.12747 0 180.48607 154482.89 -157932.52 -1316.0441 23450.122 311.49278 466.4254 1.0045437 + 400 7.9763258 -1398.97 1401.3049 -2800.275 547.10484 0 190.74701 154394.07 -157932.19 -1697.8502 23818.202 313.61492 469.64586 0.92579849 + 420 8.2703266 -1450.483 1357.937 -2808.4199 555.88824 0 178.22829 154390.11 -157932.65 -1958.9883 24158.533 303.90908 455.10587 0.90768013 + 440 8.5902264 -1501.4161 1341.5516 -2842.9677 573.14949 0 195.16753 154320.41 -157931.7 -1876.025 24469.636 300.24201 449.65628 0.81297929 + 460 8.8937869 -1551.3256 1326.1262 -2877.4518 581.25352 0 206.82716 154267.73 -157933.26 -2033.2771 24752.01 296.78977 444.48443 0.8068672 + 480 9.1780484 -1598.4261 1289.0614 -2887.4875 599.31424 0 250.55266 154195.32 -157932.67 -1734.9907 25004.733 288.4946 432.05986 0.78706924 + 500 9.4627533 -1647.1265 1310.6504 -2957.7768 620.75343 0 278.84436 154075.73 -157933.11 -1819.9564 25230.755 293.32624 439.2975 0.79707067 + 520 9.744127 -1694.4448 1256.1824 -2950.6272 640.46082 0 300.05753 154043.8 -157934.95 -1676.1925 25430.395 281.13621 421.05228 0.74177674 + 540 10.022904 -1741.636 1235.1581 -2976.794 663.79651 0 343.79844 153947.6 -157931.99 -1450.0194 25605.442 276.43091 414.00136 0.73713962 + 560 10.317977 -1784.6341 1213.4226 -2998.0567 667.043 0 361.93171 153904.04 -157931.07 -1633.3649 25757.73 271.56648 406.71944 0.71740617 + 580 10.599227 -1824.7401 1203.2527 -3027.9928 695.49991 0 399.21355 153809.37 -157932.08 -1210.3391 25887.112 269.29042 403.29611 0.74045254 + 600 10.872629 -1865.8971 1201.7743 -3067.6714 714.59075 0 432.45767 153718.17 -157932.89 -1199.4783 25998.228 268.95956 402.78195 0.77684613 + 620 11.144566 -1905.4349 1175.2733 -3080.7082 746.97979 0 456.14057 153649.58 -157933.41 -952.82994 26092.511 263.02858 393.89597 0.76773558 + 640 11.426686 -1943.5065 1165.9307 -3109.4372 755.41374 0 483.29607 153585.09 -157933.23 -984.52156 26172.87 260.93768 390.78613 0.7189019 + 660 11.699499 -1980.6601 1149.4782 -3130.1383 744.34638 0 460.44858 153597.74 -157932.67 -1312.9908 26238.692 257.25559 385.23533 0.78159645 + 680 12.011345 -2017.8555 1159.1341 -3176.9896 734.22636 0 422.37481 153599.86 -157933.45 -1747.0103 26285.639 259.41659 388.49552 0.73989774 + 700 12.310963 -2054.4791 1156.1376 -3210.6166 733.10466 0 423.00212 153565.55 -157932.27 -1636.1386 26309.504 258.74596 387.47025 0.77987596 + 720 12.582198 -2091.6681 1174.8015 -3266.4696 739.49203 0 428.4236 153500.55 -157934.93 -1696.6642 26311.163 262.923 393.72409 0.79497316 + 740 12.970993 -2130.5966 1159.8063 -3290.403 749.2778 0 449.89501 153443.16 -157932.74 -1820.153 26290.013 259.56704 388.70043 0.78112554 + 760 13.328577 -2169.5713 1138.8137 -3308.385 783.90384 0 538.06269 153303 -157933.35 -1011.1163 26246.385 254.86884 381.62657 0.84363887 + 780 13.701648 -2205.5168 1142.2259 -3347.7427 832.2034 0 585.43846 153169.83 -157935.21 -877.81856 26188.431 255.63251 382.73539 0.91548041 + 800 14.064343 -2244.3113 1142.1063 -3386.4176 846.00692 0 618.31624 153083.94 -157934.68 -661.72264 26119.157 255.60573 382.69013 0.92572469 + 820 14.33644 -2280.7153 1109.9081 -3390.6234 858.49264 0 654.04808 153031.02 -157934.18 -465.91138 26042.068 248.39971 371.86079 0.98075233 + 840 14.635953 -2313.2679 1104.4689 -3417.7368 870.71302 0 653.66264 152993.54 -157935.66 -613.02846 25959.467 247.1824 370.05309 0.94666727 + 860 14.907509 -2345.7077 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0 819.37794 152214.82 -157936.33 -419.50711 23686.912 238.40502 356.77133 1.1955971 + 1160 19.294018 -2799.8843 1046.0072 -3845.8914 1068.2773 0 805.55181 152215.61 -157935.33 -627.01178 23494.818 234.09856 350.34221 1.1430413 + 1180 19.649965 -2828.7115 1062.1027 -3890.8142 1081.854 0 768.64664 152195.11 -157936.43 -1113.3883 23300.677 237.70076 355.77198 1.0829394 + 1200 19.96859 -2856.704 1046.499 -3903.203 1081.2546 0 753.81059 152196.72 -157934.99 -1184.6559 23100.615 234.20861 350.52914 1.0991524 + 1220 20.326653 -2886.057 1023.9211 -3909.9781 1088.5712 0 740.41133 152197.78 -157936.75 -1477.5653 22893.4 229.15565 343.00067 1.0072919 + 1240 20.659779 -2913.7708 995.31097 -3909.0818 1069.874 0 758.11146 152202.13 -157939.2 -1090.4758 22677.17 222.75264 333.41163 0.98913753 + 1260 20.982659 -2936.9388 1011.886 -3948.8248 1101.8407 0 796.10406 152091.56 -157938.33 -917.17194 22454.903 226.46216 338.97372 0.98612749 + 1280 21.296781 -2960.7771 994.15899 -3954.9361 1129.3448 0 823.90727 152029.43 -157937.61 -820.42886 22229.299 222.49482 333.04692 0.94562797 + 1300 21.610997 -2984.3569 1049.8825 -4034.2394 1141.808 0 815.97434 151946.6 -157938.63 -777.81536 22002.292 234.96586 351.7259 0.97584665 + 1320 21.939147 -3010.5287 1015.4181 -4025.9468 1162.122 0 814.19766 151933.87 -157936.14 -896.97771 21774.771 227.25266 340.00602 1.1005558 + 1340 22.290971 -3038.0553 985.5931 -4023.6484 1161.8588 0 834.2486 151919.16 -157938.92 -776.69761 21546.055 220.57776 330.09107 1.0139801 + 1360 22.647999 -3060.107 995.10747 -4055.2145 1155.9364 0 823.15336 151904.81 -157939.11 -1060.7954 21316.783 222.70709 333.36443 0.91659915 + 1380 23.10948 -3084.6301 1045.0151 -4129.6452 1182.7352 0 811.15693 151815.78 -157939.31 -1245.9569 21085.59 233.87652 350.01917 1.0453875 + 1400 23.508905 -3109.9777 987.57375 -4097.5514 1174.5153 0 826.73317 151839.75 -157938.55 -936.38803 20851.737 221.02103 330.8031 0.91405623 + 1420 23.906708 -3133.4897 996.08018 -4129.5698 1204.428 0 883.9796 151722.31 -157940.29 -279.27606 20617.831 222.92479 333.68351 0.93320818 + 1440 24.340815 -3156.6284 1002.5391 -4159.1675 1256.8861 0 938.67074 151584.42 -157939.15 -252.37357 20388.73 224.3703 335.78661 1.0353205 + 1460 24.814756 -3174.2482 1025.2447 -4199.493 1219.0264 0 890.12474 151633.42 -157942.07 -472.20532 20165.369 229.45188 343.47039 0.91379457 + 1480 25.194546 -3199.1381 1019.3011 -4218.4392 1263.6197 0 907.8062 151551.73 -157941.59 -357.34642 19946.233 228.12168 341.47893 0.95052162 + 1500 25.6163 -3221.8311 999.94752 -4221.7787 1277.1026 0 966.69277 151477.62 -157943.19 163.84163 19732.291 223.79031 334.84833 1.1106364 + 1520 26.062775 -3240.6737 1026.9402 -4267.6139 1307.0169 0 971.17205 151397.27 -157943.07 300.59837 19526.783 229.83132 344.05076 0.92328807 + 1540 26.51185 -3263.1162 1054.1755 -4317.2916 1310.0417 0 972.81145 151342.02 -157942.16 -71.812538 19330.083 235.92663 353.19321 0.92162655 + 1560 26.975349 -3285.1217 1012.3967 -4297.5183 1317.4278 0 1037.4478 151290.29 -157942.68 862.26427 19140.892 226.57645 339.17946 0.91729521 + 1580 27.358741 -3305.5601 989.56962 -4295.1297 1340.9939 0 1081.7847 151223.92 -157941.82 1218.8084 18963.059 221.46771 331.53455 0.89110049 + 1600 27.75085 -3325.3691 1029.8506 -4355.2197 1351.2586 0 1061.6722 151170.95 -157939.1 749.81991 18797.795 230.48267 344.98106 1.0044287 + 1620 28.144375 -3345.1891 1016.654 -4361.8431 1337.3071 0 1043.5237 151199.64 -157942.31 600.76159 18642.93 227.52925 340.61677 0.89914217 + 1640 28.539596 -3364.6709 980.13009 -4344.801 1354.0177 0 1066.4673 151176.84 -157942.13 1010.3991 18496.839 219.35513 328.33786 0.95094445 + 1660 28.935194 -3382.7945 996.82121 -4379.6158 1343.4606 0 1016.5523 151199.22 -157938.85 546.93155 18360.15 223.09063 333.92162 0.96051901 + 1680 29.338179 -3403.1864 976.66081 -4379.8472 1355.1038 0 1029.6963 151176.44 -157941.09 748.54459 18230.922 218.57869 327.20355 0.89183674 + 1700 29.743355 -3417.6904 994.06517 -4411.7556 1368.1157 0 1013.9323 151145.57 -157939.38 351.45668 18109.291 222.47382 332.98346 0.9529814 + 1720 30.14859 -3434.6282 979.89215 -4414.5203 1377.0869 0 1043.321 151104.18 -157939.11 1004.1915 17993.82 219.30187 328.11073 1.0747474 + 1740 30.591568 -3451.0422 966.54361 -4417.5858 1376.9794 0 1050.8109 151097.44 -157942.82 1079.9737 17886.467 216.31444 323.72083 1.0159044 + 1760 31.006144 -3469.3784 980.75469 -4450.1331 1396.5756 0 1015.9581 151078.09 -157940.75 190.14272 17786.919 219.49491 328.49844 0.97971363 + 1780 31.424875 -3485.9292 1008.375 -4494.3041 1373.9658 0 984.95385 151090.2 -157943.42 -155.51723 17691.03 225.67639 337.7992 0.97942677 + 1800 31.849784 -3502.475 976.23102 -4478.706 1385.4591 0 994.63329 151084.94 -157943.74 288.55406 17597.361 218.48251 327.04845 0.91364963 + 1820 32.275504 -3520.5204 971.19507 -4491.7155 1407.4082 0 1049.909 150992.97 -157942.01 526.1499 17507.18 217.35545 325.30923 0.99414761 + 1840 32.701591 -3535.2936 982.97322 -4518.2668 1419.0124 0 1050.2222 150955.57 -157943.08 420.31843 17421.408 219.99142 329.22593 1.0824421 + 1860 33.133267 -3551.8598 947.45359 -4499.3134 1430.136 0 1069.4805 150943.73 -157942.66 669.02599 17340.063 212.04206 317.36556 0.97096264 + 1880 33.56593 -3564.7527 963.54319 -4528.2959 1418.0293 0 1050.1008 150947.78 -157944.21 529.33841 17263.982 215.64294 322.72997 0.96836521 + 1900 34.00203 -3580.0607 963.5239 -4543.5846 1424.6268 0 1048.9836 150925.17 -157942.36 464.00157 17192.083 215.63863 322.69033 1.0695571 + 1920 34.44279 -3593.8573 957.94124 -4551.7986 1437.3475 0 1061.2427 150893.58 -157943.97 400.78058 17123.621 214.38922 320.8512 1.015936 + 1940 34.877758 -3608.3005 951.71962 -4560.0201 1421.2611 0 1059.2678 150903.97 -157944.52 332.6227 17058.096 212.9968 318.72703 1.0660417 + 1960 35.315982 -3623.3562 948.66706 -4572.0233 1438.6049 0 1066.4475 150868.57 -157945.64 448.04656 16995.11 212.31364 317.61154 1.1874864 + 1980 35.79727 -3635.1448 958.32383 -4593.4687 1448.1655 0 1056.2971 150846.27 -157944.2 110.28409 16935.142 214.47484 320.97102 1.0535213 + 2000 36.231822 -3649.7345 959.87855 -4609.6131 1458.7554 0 1080.5488 150796.28 -157945.2 615.27816 16877.582 214.82279 321.49302 1.0526861 +Loop time of 36.2319 on 4 procs for 2000 steps with 2500 atoms + +Performance: 4.769 ns/day, 5.032 hours/ns, 55.200 timesteps/s +96.5% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 19.246 | 21.089 | 23.446 | 32.8 | 58.21 +Bond | 0.012314 | 0.012709 | 0.013402 | 0.4 | 0.04 +Kspace | 2.0259 | 4.3875 | 6.228 | 72.1 | 12.11 +Neigh | 2.6629 | 2.6673 | 2.6718 | 0.3 | 7.36 +Comm | 0.95863 | 0.96795 | 0.97884 | 0.9 | 2.67 +Output | 0.0071304 | 0.0093493 | 0.0142 | 2.9 | 0.03 +Modify | 7.0096 | 7.0134 | 7.0186 | 0.1 | 19.36 +Other | | 0.08472 | | | 0.23 + +Nlocal: 625 ave 683 max 565 min +Histogram: 1 0 0 0 1 0 1 0 0 1 +Nghost: 12687 ave 12923 max 12461 min +Histogram: 1 0 0 1 0 0 1 0 0 1 +Neighs: 531145 ave 625145 max 458041 min +Histogram: 1 0 1 0 1 0 0 0 0 1 + +Total # of neighbors = 2124581 +Ave neighs/atom = 849.832 +Ave special neighs/atom = 4 +Neighbor list builds = 122 +Dangerous builds = 16 + +Total wall time: 0:00:36 diff --git a/examples/USER/drude/swm4-ndp/log.swm4-ndp.lang.8Jul15.linux.1 b/examples/USER/drude/swm4-ndp/log.swm4-ndp.lang.8Jul15.linux.1 deleted file mode 100644 index e66f4c69c2..0000000000 --- a/examples/USER/drude/swm4-ndp/log.swm4-ndp.lang.8Jul15.linux.1 +++ /dev/null @@ -1,230 +0,0 @@ -LAMMPS (8 Jul 2015) -units real -boundary p p p - -atom_style full -bond_style harmonic -angle_style harmonic -special_bonds lj/coul 0.0 0.0 0.5 - -pair_style lj/cut/coul/long 12.0 12.0 -kspace_style pppm 1.0e-3 - -comm_modify vel yes -read_data data.swm4-ndp - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 2500 atoms - scanning bonds ... - 1 = max bonds/atom - scanning angles ... - 1 = max angles/atom - reading bonds ... - 2000 bonds - reading angles ... - 500 angles - 4 = max # of 1-2 neighbors - 3 = max # of 1-3 neighbors - 3 = max # of 1-4 neighbors - 4 = max # of special neighbors - -pair_coeff 1 1 0.210939 3.183950 # ODw ODw -pair_coeff * 2* 0.000000 0.0 - -group ATOMS type 1:3 -2000 atoms in group ATOMS -group CORES type 1 -500 atoms in group CORES -group DRUDES type 4 -500 atoms in group DRUDES - -variable TK equal 300.0 -variable TDK equal 1.0 -variable PBAR equal 1.0 - -neighbor 2.0 bin - -timestep 1.0 - -fix DRUDE all drude C N N D - -velocity ATOMS create ${TK} 12345 -velocity ATOMS create 300 12345 -velocity DRUDES create ${TDK} 12345 -velocity DRUDES create 1 12345 - -delete_bonds ATOMS multi -PPPM initialization ... - G vector (1/distance) = 0.217457 - grid = 10 10 10 - stencil order = 5 - estimated absolute RMS force accuracy = 0.197288 - estimated relative force accuracy = 0.000594128 - using double precision FFTs - 3d grid and FFT values/proc = 3375 1000 -Rebuild special list taking Drude particles into account -Old max number of 1-2 to 1-4 neighbors: 4 -New max number of 1-2 to 1-4 neighbors: 4 (+0) -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 10 steps, check yes - master list distance cutoff = 14 - 2000 total bonds, 500 turned on, 1500 turned off - 500 total angles, 0 turned on, 500 turned off - 0 total dihedrals, 0 turned on, 0 turned off - 0 total impropers, 0 turned on, 0 turned off - -fix TEMP all langevin/drude ${TK} 100. 1256 ${TDK} 20. 13977 zero yes -fix TEMP all langevin/drude 300 100. 1256 ${TDK} 20. 13977 zero yes -fix TEMP all langevin/drude 300 100. 1256 1 20. 13977 zero yes -fix NPH ATOMS rigid/nph/small molecule iso ${PBAR} ${PBAR} 500. -fix NPH ATOMS rigid/nph/small molecule iso 1 ${PBAR} 500. -fix NPH ATOMS rigid/nph/small molecule iso 1 1 500. -500 rigid bodies with 2000 atoms - 0.832099 = max distance from body owner to body atom -fix NVE DRUDES nve - -compute TEMP all temp/drude - -thermo_style custom step cpu etotal ke pe ebond eangle evdwl ecoul elong press vol temp c_TEMP[1] c_TEMP[2] -thermo 20 - -run 2000 -PPPM initialization ... - G vector (1/distance) = 0.217457 - grid = 10 10 10 - stencil order = 5 - estimated absolute RMS force accuracy = 0.197288 - estimated relative force accuracy = 0.000594128 - using double precision FFTs - 3d grid and FFT values/proc = 3375 1000 -Rebuild special list taking Drude particles into account -Old max number of 1-2 to 1-4 neighbors: 4 -New max number of 1-2 to 1-4 neighbors: 4 (+0) -Memory usage per processor = 24.8361 Mbytes -Step CPU TotEng KinEng PotEng E_bond E_angle E_vdwl E_coul E_long Press Volume Temp TEMP[1] TEMP[2] - 0 0 4568.0415 903.41148 3664.63 623.46454 0 2890.2449 157955.66 -157804.74 244591.08 13824 202.18534 295.64644 14.858785 - 20 1.529202 2882.459 4527.8074 -1645.3484 561.72857 0 600.34616 155114.77 -157922.19 27167.702 14058.741 1013.3326 1438.6699 160.63128 - 40 3.073256 1331.3826 3348.9313 -2017.5487 681.52309 0 553.09465 154668.62 -157920.79 17925.93 14484.215 749.4977 1105.2032 36.587791 - 60 4.584862 297.35979 2604.4137 -2307.0539 583.99971 0 409.0399 154634.74 -157934.83 13017.752 15026.564 582.87312 864.55899 18.335649 - 80 6.053256 -374.31023 2263.3247 -2637.635 534.80338 0 212.27981 154543.18 -157927.9 6155.9261 15645.855 506.53672 755.45209 7.6929084 - 100 7.4787509 -905.58889 1911.7191 -2817.308 532.30405 0 87.570168 154497.48 -157934.66 2149.3099 16288.797 427.84666 639.27768 4.1289101 - 120 8.8570309 -1233.6894 1675.0881 -2908.7775 544.7643 0 59.500519 154422.72 -157935.76 233.4994 16915.818 374.88816 560.54169 2.8313123 - 140 10.102229 -1463.4927 1468.7443 -2932.237 539.69692 0 41.083584 154424.91 -157937.93 -1492.9865 17509.345 328.70799 491.66353 2.1394958 - 160 11.319324 -1695.7535 1385.9603 -3081.7137 552.91518 0 30.022893 154274.72 -157939.37 -3010.4983 18061.925 310.18075 463.968 1.9858941 - 180 12.62008 -1818.1958 1253.169 -3071.3648 559.57456 0 20.01719 154289.67 -157940.63 -3354.4536 18564.877 280.4618 419.57594 1.6725953 - 200 13.836408 -1949.6497 1210.0669 -3159.7167 570.055 0 16.319449 154195.04 -157941.13 -4118.0013 19014.456 270.81546 405.06925 1.766255 - 220 15.032024 -2031.6125 1148.1454 -3179.7579 598.02981 0 30.833041 154127.13 -157935.75 -4514.7299 19406.767 256.9573 384.33701 1.6839691 - 240 16.302775 -2118.6259 1120.0048 -3238.6307 613.2903 0 59.888138 154030.6 -157942.41 -4415.1944 19738.97 250.65937 374.93983 1.5971234 - 260 17.465169 -2203.4348 1065.8476 -3269.2823 614.19171 0 77.619746 153980.69 -157941.79 -4564.2677 20011.077 238.53887 356.80737 1.5247856 - 280 18.614435 -2317.9282 1033.2676 -3351.1958 650.51218 0 126.14976 153811.64 -157939.49 -4722.7543 20224.149 231.24742 345.8479 1.5839508 - 300 19.757547 -2377.6306 992.4842 -3370.1148 688.02217 0 179.77994 153701.18 -157939.1 -4126.4983 20378.439 222.12 332.08757 1.7406267 - 320 20.888309 -2419.6547 1023.0345 -3442.6892 720.31567 0 227.70007 153549.33 -157940.04 -4083.8776 20479.241 228.95722 342.33844 1.7368676 - 340 22.018005 -2456.7661 1048.83 -3505.5961 754.13021 0 264.44865 153415.74 -157939.91 -3894.7125 20529.721 234.73031 351.04714 1.6271854 - 360 23.241519 -2504.7475 1041.9912 -3546.7386 785.42547 0 335.38743 153271.47 -157939.03 -3464.4465 20531.323 233.19976 348.66924 1.7943874 - 380 24.370763 -2596.2223 1000.109 -3596.3313 825.31479 0 390.18238 153129.56 -157941.39 -3355.5804 20490.646 223.82645 334.61119 1.8093168 - 400 25.499192 -2666.6702 1006.474 -3673.1442 865.9858 0 422.51674 152978.57 -157940.21 -3329.4637 20411.001 225.25095 336.79016 1.7220267 - 420 26.635042 -2675.8885 1036.9567 -3712.8452 909.14044 0 490.71452 152826.18 -157938.88 -2907.7096 20294.317 232.07303 346.92895 1.8970394 - 440 27.774963 -2731.5399 1054.4488 -3785.9886 935.99349 0 530.9675 152684.75 -157937.7 -2566.587 20147.094 235.9878 352.84462 1.8021906 - 460 28.922784 -2808.5929 996.20283 -3804.7957 986.6991 0 582.25374 152565.95 -157939.7 -2489.2912 19973.682 222.95224 333.32237 1.7660757 - 480 30.07189 -2862.64 1012.7035 -3875.3436 1005.1596 0 610.07691 152450.62 -157941.2 -2031.6453 19777.635 226.64513 338.80268 1.8767218 - 500 31.210731 -2935.4679 989.23412 -3924.702 1019.9115 0 633.87354 152362.4 -157940.89 -2214.2821 19561.863 221.39263 330.98935 1.7563884 - 520 32.363073 -2989.4684 968.83888 -3958.3072 1057.5825 0 655.88302 152269.68 -157941.45 -2298.887 19328.548 216.82813 324.17678 1.6971802 - 540 33.631173 -3036.6833 1016.2589 -4052.9421 1091.2498 0 658.37327 152140.1 -157942.67 -2240.561 19080.875 227.44082 340.06628 1.7350202 - 560 34.815099 -3093.7794 947.7515 -4041.5309 1141.2318 0 764.1603 151995.79 -157942.71 -1157.5191 18819.961 212.10873 317.02152 1.858938 - 580 36.012327 -3166.4133 987.9563 -4154.3696 1199.2171 0 796.34125 151794.12 -157944.05 -1304.4967 18555.635 221.10665 330.55449 1.7687509 - 600 37.228579 -3194.8572 979.66264 -4174.5199 1206.8265 0 842.68836 151717.96 -157941.99 -843.16439 18290.222 219.25051 327.76152 1.7899831 - 620 38.457464 -3255.2052 965.87596 -4221.0812 1218.8406 0 849.13897 151653.64 -157942.7 -628.0114 18027.862 216.16502 323.08905 1.8846337 - 640 39.700987 -3269.6729 1003.1309 -4272.8038 1273.0417 0 928.68865 151468.54 -157943.07 117.71698 17770.578 224.50275 335.54575 1.9677468 - 660 40.961165 -3293.6967 1002.4504 -4296.1471 1299.7531 0 955.60765 151392.37 -157943.87 207.76414 17523.763 224.35045 335.3089 1.9848634 - 680 42.237597 -3310.539 1011.7934 -4322.3324 1358.9202 0 986.69345 151275.62 -157943.56 677.05046 17289.864 226.44145 338.46824 1.9349743 - 700 43.530486 -3380.6882 976.5597 -4357.2479 1378.7945 0 1003.8845 151205.15 -157945.07 605.30766 17069.732 218.55607 326.63938 1.9523301 - 720 44.837568 -3385.7377 1005.1302 -4390.8679 1389.9512 0 1012.3035 151151.06 -157944.19 817.35931 16863.381 224.95021 336.31657 1.7675955 - 740 46.162222 -3378.6942 1023.8252 -4402.5194 1400.0688 0 1063.4211 151077.64 -157943.65 1513.5741 16671.518 229.13418 342.45655 2.0311926 - 760 47.500172 -3425.4378 1036.4011 -4461.8389 1408.8321 0 1068.7339 151003.75 -157943.15 1350.0894 16496.502 231.9487 346.7108 1.9605952 - 780 48.851472 -3453.9533 1021.8895 -4475.8428 1425.2091 0 1104.5857 150938.44 -157944.08 1801.2205 16339.019 228.70097 341.83264 1.9802343 - 800 50.2129 -3497.6136 979.31494 -4476.9285 1441.1399 0 1119.8292 150908.27 -157946.17 1649.8638 16200.982 219.17269 327.47284 2.1340593 - 820 51.586885 -3545.7792 969.50276 -4515.282 1479.3831 0 1103.1191 150847.98 -157945.76 1410.2174 16081.771 216.97671 324.23659 2.0229826 - 840 52.968935 -3562.4777 972.83071 -4535.3084 1470.5582 0 1079.9217 150857.46 -157943.25 1608.0813 15977.891 217.72151 325.33963 2.0498221 - 860 54.3603 -3569.1307 987.8631 -4556.9938 1446.8392 0 1055.8137 150885.62 -157945.27 1110.2002 15887.947 221.08579 330.4231 1.9689916 - 880 55.752677 -3612.6783 957.13055 -4569.8088 1435.3619 0 1056.264 150883.35 -157944.78 914.27883 15809.361 214.20778 320.06673 2.0614732 - 900 57.105164 -3660.821 939.51428 -4600.3353 1463.6114 0 1070.121 150812.25 -157946.31 1261.3306 15740.285 210.26522 314.20385 1.967446 - 920 58.464501 -3685.0371 941.21956 -4626.2567 1483.8487 0 1096.8187 150737.38 -157944.31 1236.4144 15680.989 210.64687 314.81024 1.89883 - 940 59.82202 -3719.0907 915.61639 -4634.7071 1515.6474 0 1104.1119 150691.39 -157945.86 1066.5855 15632.292 204.91683 306.20627 1.9280979 - 960 61.189826 -3752.7758 893.54303 -4646.3189 1517.1996 0 1125.6182 150656.81 -157945.94 1449.4275 15593.029 199.97676 298.74917 2.0320058 - 980 62.459059 -3752.1139 925.61635 -4677.7302 1528.3468 0 1137.3575 150600.83 -157944.27 1493.1803 15564.263 207.15484 309.5242 2.0018169 - 1000 63.8395 -3737.7642 905.82477 -4643.589 1505.254 0 1110.1192 150686.75 -157945.72 1296.1084 15546.258 202.72544 302.92529 1.9202879 - 1020 65.169118 -3767.2178 892.14155 -4659.3593 1493.2162 0 1085.8721 150707.12 -157945.57 922.80521 15537.177 199.66311 298.24598 2.0980372 - 1040 66.474103 -3783.5702 891.57404 -4675.1442 1484.1631 0 1076.2171 150710.25 -157945.77 707.15481 15535.102 199.5361 298.15469 1.8998396 - 1060 67.68596 -3816.1219 868.55884 -4684.6807 1478.7568 0 1060.3026 150723.2 -157946.94 638.16846 15538.641 194.38525 290.46937 1.8282435 - 1080 69.003517 -3807.3485 875.34276 -4682.6913 1482.2148 0 1055.6143 150725.66 -157946.19 416.14661 15546.427 195.90351 292.75831 1.802085 - 1100 70.315532 -3814.5517 894.42504 -4708.9768 1492.6318 0 1053.4891 150692.22 -157947.31 341.55654 15557.253 200.17416 299.12904 1.8640462 - 1120 71.62724 -3837.42 886.31149 -4723.7315 1497.9422 0 1047.1133 150677.33 -157946.12 4.9308474 15569.465 198.35833 296.42678 1.8247148 - 1140 72.956868 -3802.3965 899.40687 -4701.8034 1479.6329 0 1020.1254 150744.44 -157946 -142.99064 15582.446 201.2891 300.81318 1.8383791 - 1160 74.274932 -3810.7658 902.84695 -4713.6127 1472.5916 0 1018.8174 150740.5 -157945.52 12.783208 15594.928 202.059 301.90406 1.9647721 - 1180 75.595463 -3786.4338 929.44447 -4715.8783 1477.4053 0 1016.2942 150735.81 -157945.39 -53.70556 15606.416 208.01158 310.85718 1.9043666 - 1200 76.915409 -3800.0338 897.43664 -4697.4705 1483.1401 0 1059.31 150706.14 -157946.06 534.37576 15617.028 200.84816 300.11638 1.9100302 - 1220 78.119883 -3799.6824 882.65153 -4682.3339 1488.5302 0 1036.1696 150739.15 -157946.19 155.57627 15628.242 197.53922 295.16257 1.8974641 - 1240 79.419663 -3800.7533 911.18613 -4711.9394 1475.5968 0 1005.3229 150752.61 -157945.47 -457.64009 15638.953 203.92533 304.69739 1.9733514 - 1260 80.721954 -3763.5149 950.12041 -4713.6353 1441.6787 0 964.69517 150825.9 -157945.91 -604.24646 15647.017 212.6389 317.74138 2.0086447 - 1280 82.018768 -3770.742 937.09634 -4707.8384 1445.4659 0 949.37244 150842.61 -157945.28 -993.94783 15650.702 209.72409 313.39122 1.9703726 - 1300 83.314893 -3777.4899 904.34062 -4681.8306 1435.5873 0 967.49755 150860.85 -157945.76 -640.04936 15648.293 202.39329 302.46077 1.8535337 - 1320 84.617907 -3766.6204 885.81908 -4652.4395 1416.0678 0 971.89494 150906.86 -157947.27 -366.46049 15641.654 198.24813 296.26647 1.8149522 - 1340 85.931152 -3774.8032 919.58694 -4694.3901 1425.1776 0 939.16654 150887.07 -157945.81 -950.33698 15631.589 205.80544 307.5014 2.0019282 - 1360 87.242691 -3787.4243 922.65238 -4710.0767 1430.1028 0 964.01827 150842.71 -157946.91 -767.13405 15614.998 206.4915 308.53756 1.9863831 - 1380 88.556261 -3792.754 900.77391 -4693.5279 1420.8035 0 953.09514 150878.52 -157945.95 -1072.9667 15593.378 201.59505 301.19366 1.9946415 - 1400 89.868914 -3772.1032 910.85489 -4682.9581 1401.9732 0 959.20659 150901.09 -157945.23 -640.48972 15566.828 203.85119 304.58411 1.9776581 - 1420 91.085535 -3782.5246 898.64718 -4681.1718 1436.1885 0 1010.9254 150817.16 -157945.45 -21.80524 15536.721 201.11908 300.5555 1.8440133 - 1440 92.406331 -3775.4206 919.73488 -4695.1554 1446.1057 0 1018.1835 150785.23 -157944.68 46.810177 15507.157 205.83855 307.4904 2.123189 - 1460 93.732761 -3757.7457 938.91361 -4696.6593 1451.5945 0 1008.6517 150787.38 -157944.28 -175.88589 15478.297 210.13079 313.97065 2.030827 - 1480 95.057074 -3776.8625 933.4271 -4710.2896 1469.7064 0 1033.8521 150731.34 -157945.19 171.44717 15450.004 208.9029 312.19981 1.8912834 - 1500 96.391192 -3764.5196 945.12068 -4709.6403 1483.0898 0 1052.3029 150699.59 -157944.62 431.18844 15423.716 211.51995 316.14058 1.85565 - 1520 97.721669 -3760.514 960.29952 -4720.8136 1507.6965 0 1068.2902 150648.96 -157945.76 714.27148 15402.108 214.917 321.14587 2.0294443 - 1540 99.056402 -3787.9932 950.73472 -4738.728 1514.4781 0 1058.2368 150635.29 -157946.73 547.92963 15384.955 212.77638 318.01984 1.8639142 - 1560 100.30064 -3822.5612 921.12091 -4743.6821 1519.8628 0 1084.8337 150596.5 -157944.88 479.4088 15370.571 206.14875 308.02344 1.987069 - 1580 101.63827 -3832.4207 936.50822 -4768.9289 1562.5808 0 1124.0034 150490.87 -157946.38 833.06708 15360.019 209.59246 313.15266 2.0528778 - 1600 102.98354 -3862.3688 922.42346 -4784.7923 1571.2038 0 1110.9988 150479.2 -157946.19 674.29885 15354.399 206.44026 308.48417 1.9395764 - 1620 104.32562 -3863.8731 946.37539 -4810.2485 1562.9498 0 1094.323 150478.98 -157946.5 -224.35579 15352.811 211.80075 316.51174 1.9551706 - 1640 105.66368 -3834.5163 952.04367 -4786.5599 1536.5144 0 1078.6783 150544.66 -157946.41 -30.565669 15352.152 213.06933 318.41145 1.9589345 - 1660 107.00124 -3859.131 892.31028 -4751.4413 1515.0462 0 1076.4059 150603.91 -157946.81 227.01045 15352.058 199.70087 298.41871 1.8658052 - 1680 108.2363 -3858.2995 918.6578 -4776.9573 1533.9319 0 1064.9106 150570.69 -157946.49 335.15388 15352.595 205.5975 307.20976 1.9617869 - 1700 109.5659 -3850.0817 929.25672 -4779.3384 1552.5519 0 1094.2161 150519.21 -157945.31 393.76719 15353.331 207.96956 310.72982 2.0330981 - 1720 110.90017 -3890.603 917.87519 -4808.4781 1566.3302 0 1075.6092 150495.91 -157946.33 -76.371955 15355.997 205.42235 306.92393 2.0083539 - 1740 112.13829 -3891.5259 936.37478 -4827.9007 1568.2195 0 1085.8514 150464.14 -157946.11 0.9297943 15358.36 209.5626 313.09836 2.0719603 - 1760 113.46951 -3881.0244 903.38798 -4784.4124 1524.2547 0 1079.0557 150557.47 -157945.19 192.41461 15360.098 202.18008 302.05776 2.0203699 - 1780 114.81068 -3885.7248 910.74799 -4796.4728 1532.8732 0 1055.4583 150560.36 -157945.17 -530.84683 15362.305 203.82727 304.58876 1.8966227 - 1800 116.14689 -3907.0506 885.50025 -4792.5508 1533.7624 0 1068.2841 150550.77 -157945.37 240.13827 15362.751 198.17677 296.0834 1.9671724 - 1820 117.48197 -3898.1244 894.18625 -4792.3107 1521.378 0 1059.1428 150574.05 -157946.88 34.574046 15361.495 200.12072 298.96924 2.0234207 - 1840 118.82815 -3874.3766 895.94028 -4770.3169 1523.7865 0 1077.7882 150573.72 -157945.61 324.16201 15359.092 200.51327 299.59285 1.9530985 - 1860 120.06522 -3892.2617 891.17198 -4783.4337 1526.1544 0 1091.1167 150543.11 -157943.82 574.32363 15357.261 199.44612 297.92332 2.0928308 - 1880 121.40834 -3906.8943 911.93286 -4818.8271 1552.4086 0 1113.1993 150462.35 -157946.79 279.12422 15356.96 204.09245 304.90059 2.0679776 - 1900 122.76151 -3922.7591 879.82965 -4802.5888 1550.6607 0 1108.3657 150485.77 -157947.38 356.47291 15359.386 196.90768 294.18644 1.9563556 - 1920 124.11267 -3960.2437 869.21003 -4829.4537 1521.5339 0 1036.9974 150558.9 -157946.89 -839.29936 15362.76 194.53099 290.66184 1.8802157 - 1940 125.45713 -3954.661 876.75754 -4831.4186 1506.7448 0 1007.0383 150601.14 -157946.34 -1316.6937 15361.338 196.22014 293.17781 1.9123591 - 1960 126.70769 -3938.7558 876.41976 -4815.1756 1481.7627 0 996.84388 150652.15 -157945.93 -887.63902 15352.095 196.14454 293.08662 1.8680915 - 1980 128.05176 -3911.4383 894.43818 -4805.8765 1516.4382 0 1037.517 150585.32 -157945.15 -176.75144 15336.185 200.1771 299.12472 1.8815139 - 2000 129.4091 -3920.2641 888.06919 -4808.3333 1495.9942 0 1040.703 150601.72 -157946.75 -243.72475 15316.676 198.75171 296.94612 1.9653682 -Loop time of 129.409 on 1 procs for 2000 steps with 2500 atoms - -Pair time (%) = 109.108 (84.3128) -Bond time (%) = 0.0499372 (0.0385887) -Kspce time (%) = 3.30969 (2.55754) -Neigh time (%) = 9.70209 (7.49723) -Comm time (%) = 0.829103 (0.640684) -Outpt time (%) = 0.00999022 (0.00771987) -Other time (%) = 6.39989 (4.94547) - -Nlocal: 2500 ave 2500 max 2500 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 21780 ave 21780 max 21780 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 2.34087e+06 ave 2.34087e+06 max 2.34087e+06 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 2340869 -Ave neighs/atom = 936.348 -Ave special neighs/atom = 4 -Neighbor list builds = 100 -Dangerous builds = 6 - diff --git a/examples/USER/drude/swm4-ndp/log.swm4-ndp.lang.8Jul15.linux.4 b/examples/USER/drude/swm4-ndp/log.swm4-ndp.lang.8Jul15.linux.4 deleted file mode 100644 index b43b75cc35..0000000000 --- a/examples/USER/drude/swm4-ndp/log.swm4-ndp.lang.8Jul15.linux.4 +++ /dev/null @@ -1,230 +0,0 @@ -LAMMPS (8 Jul 2015) -units real -boundary p p p - -atom_style full -bond_style harmonic -angle_style harmonic -special_bonds lj/coul 0.0 0.0 0.5 - -pair_style lj/cut/coul/long 12.0 12.0 -kspace_style pppm 1.0e-3 - -comm_modify vel yes -read_data data.swm4-ndp - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 2500 atoms - scanning bonds ... - 1 = max bonds/atom - scanning angles ... - 1 = max angles/atom - reading bonds ... - 2000 bonds - reading angles ... - 500 angles - 4 = max # of 1-2 neighbors - 3 = max # of 1-3 neighbors - 3 = max # of 1-4 neighbors - 4 = max # of special neighbors - -pair_coeff 1 1 0.210939 3.183950 # ODw ODw -pair_coeff * 2* 0.000000 0.0 - -group ATOMS type 1:3 -2000 atoms in group ATOMS -group CORES type 1 -500 atoms in group CORES -group DRUDES type 4 -500 atoms in group DRUDES - -variable TK equal 300.0 -variable TDK equal 1.0 -variable PBAR equal 1.0 - -neighbor 2.0 bin - -timestep 1.0 - -fix DRUDE all drude C N N D - -velocity ATOMS create ${TK} 12345 -velocity ATOMS create 300 12345 -velocity DRUDES create ${TDK} 12345 -velocity DRUDES create 1 12345 - -delete_bonds ATOMS multi -PPPM initialization ... - G vector (1/distance) = 0.217457 - grid = 10 10 10 - stencil order = 5 - estimated absolute RMS force accuracy = 0.197288 - estimated relative force accuracy = 0.000594128 - using double precision FFTs - 3d grid and FFT values/proc = 1500 300 -Rebuild special list taking Drude particles into account -Old max number of 1-2 to 1-4 neighbors: 4 -New max number of 1-2 to 1-4 neighbors: 4 (+0) -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 10 steps, check yes - master list distance cutoff = 14 - 2000 total bonds, 500 turned on, 1500 turned off - 500 total angles, 0 turned on, 500 turned off - 0 total dihedrals, 0 turned on, 0 turned off - 0 total impropers, 0 turned on, 0 turned off - -fix TEMP all langevin/drude ${TK} 100. 1256 ${TDK} 20. 13977 zero yes -fix TEMP all langevin/drude 300 100. 1256 ${TDK} 20. 13977 zero yes -fix TEMP all langevin/drude 300 100. 1256 1 20. 13977 zero yes -fix NPH ATOMS rigid/nph/small molecule iso ${PBAR} ${PBAR} 500. -fix NPH ATOMS rigid/nph/small molecule iso 1 ${PBAR} 500. -fix NPH ATOMS rigid/nph/small molecule iso 1 1 500. -500 rigid bodies with 2000 atoms - 0.832099 = max distance from body owner to body atom -fix NVE DRUDES nve - -compute TEMP all temp/drude - -thermo_style custom step cpu etotal ke pe ebond eangle evdwl ecoul elong press vol temp c_TEMP[1] c_TEMP[2] -thermo 20 - -run 2000 -PPPM initialization ... - G vector (1/distance) = 0.217457 - grid = 10 10 10 - stencil order = 5 - estimated absolute RMS force accuracy = 0.197288 - estimated relative force accuracy = 0.000594128 - using double precision FFTs - 3d grid and FFT values/proc = 1500 300 -Rebuild special list taking Drude particles into account -Old max number of 1-2 to 1-4 neighbors: 4 -New max number of 1-2 to 1-4 neighbors: 4 (+0) -Memory usage per processor = 15.0906 Mbytes -Step CPU TotEng KinEng PotEng E_bond E_angle E_vdwl E_coul E_long Press Volume Temp TEMP[1] TEMP[2] - 0 0 4568.0415 903.41148 3664.63 623.46454 0 2890.2449 157955.66 -157804.74 244591.08 13824 202.18534 295.64644 14.858785 - 20 0.47649789 2915.1578 4579.5774 -1664.4195 561.91893 0 600.76451 155095.13 -157922.23 27379.77 14058.574 1024.9188 1455.9194 160.86778 - 40 0.97488093 1320.1721 3337.6372 -2017.4651 726.83344 0 585.5439 154587.28 -157917.12 18749.425 14485.651 746.97006 1101.4061 36.530914 - 60 1.4631288 284.06852 2671.4325 -2387.3639 575.54157 0 387.8792 154580.74 -157931.53 12104.741 15031.425 597.87207 886.98502 18.450413 - 80 1.937151 -462.53017 2214.284 -2676.8142 560.36347 0 254.65245 154447.22 -157939.05 6285.2465 15651.216 495.56131 739.13811 7.4024411 - 100 2.3922298 -965.19662 1839.831 -2805.0276 544.59528 0 115.80812 154469.59 -157935.02 2361.9397 16295.72 411.75795 615.12769 4.196977 - 120 2.832803 -1316.6351 1649.585 -2966.2202 554.6664 0 50.928925 154365.49 -157937.3 -493.85523 16925.293 369.18052 552.0345 2.7331855 - 140 3.2340388 -1590.9162 1440.6669 -3031.5831 526.07679 0 -24.44055 154404.35 -157937.57 -2586.2431 17517.285 322.42421 482.16117 2.297578 - 160 3.6521859 -1742.3401 1326.8812 -3069.2213 539.49044 0 -43.846659 154369.1 -157933.96 -3549.2196 18059.707 296.95874 444.11026 2.0644677 - 180 4.033325 -1895.1332 1224.1816 -3119.3148 555.27887 0 -18.261233 154275.94 -157932.27 -3762.2304 18545.518 273.97437 409.78413 1.806893 - 200 4.4333398 -2004.4682 1176.8828 -3181.351 565.0443 0 0.21425471 154190.38 -157936.99 -4346.6036 18973.342 263.38879 393.94856 1.7400558 - 220 4.8055639 -2094.1888 1098.3856 -3192.5744 592.45764 0 36.50238 154113.36 -157934.89 -4135.0794 19341.735 245.82095 367.67707 1.617053 - 240 5.1688328 -2178.9829 1086.8322 -3265.8151 617.63697 0 96.836936 153957.27 -157937.56 -4121.5262 19651.8 243.23528 363.77401 1.6722646 - 260 5.5313618 -2264.8265 1078.4348 -3343.2613 663.35817 0 167.76882 153763.13 -157937.52 -3799.3346 19907.052 241.35592 360.97385 1.6377289 - 280 5.8937738 -2325.7764 1097.4356 -3423.212 717.74089 0 235.0127 153562.96 -157938.92 -3696.0526 20111.414 245.60833 367.31076 1.7042318 - 300 6.254128 -2390.4932 1068.1054 -3458.5986 751.64681 0 295.31516 153435.34 -157940.9 -3512.2095 20268.754 239.04419 357.49427 1.665921 - 320 6.6138928 -2455.1776 1041.7419 -3496.9195 765.8972 0 331.14997 153345 -157938.97 -3020.0674 20383.474 233.14397 348.62385 1.7179273 - 340 6.9748628 -2536.9935 1050.7304 -3587.7239 793.64536 0 352.69908 153205.74 -157939.81 -3447.9127 20457.612 235.15562 351.6381 1.7214573 - 360 7.3319299 -2603.5606 966.90943 -3570.47 819.14306 0 391.00909 153158.89 -157939.51 -3164.629 20490.764 216.39631 323.51872 1.7254892 - 380 7.691319 -2594.787 1024.7927 -3619.5797 836.44816 0 434.32118 153047.12 -157937.47 -2902.9345 20485.923 229.35071 342.91482 1.7641915 - 400 8.044276 -2647.3896 982.46478 -3629.8543 864.59805 0 479.08516 152963.5 -157937.04 -2535.9236 20447.668 219.87764 328.69587 1.8030508 - 420 8.3971269 -2687.5263 1023.0437 -3710.57 928.04551 0 538.49845 152760.83 -157937.94 -2383.6292 20380.427 228.95928 342.31215 1.8044964 - 440 8.753284 -2765.2192 999.28342 -3764.5026 966.26754 0 577.15359 152631.24 -157939.17 -2391.0923 20286.676 223.64168 334.34309 1.7947669 - 460 9.1102748 -2806.7385 1004.2311 -3810.9696 996.86893 0 599.41867 152532.79 -157940.05 -2476.5754 20168.782 224.74899 335.97767 1.8475589 - 480 9.471664 -2830.2582 1013.6925 -3843.9506 1009.5553 0 624.64584 152464.58 -157942.73 -2210.7254 20027.747 226.86645 339.14841 1.8588685 - 500 9.8365009 -2865.4993 1024.473 -3889.9723 1017.2606 0 658.56598 152375.13 -157940.93 -2047.5735 19865.992 229.27916 342.78576 1.8103481 - 520 10.207523 -2918.9299 973.10292 -3892.0328 1049.357 0 699.16951 152300.27 -157940.83 -1453.4121 19688.211 217.78243 325.51403 1.8799495 - 540 10.583098 -2970.1121 925.84385 -3895.956 1077.9578 0 758.25478 152208.67 -157940.84 -821.19447 19499.417 207.20575 309.67486 1.8442683 - 560 10.962813 -3008.9942 954.33133 -3963.3255 1114.7309 0 751.85274 152112.75 -157942.66 -1023.0801 19304.314 213.58131 319.23167 1.8463043 - 580 11.351938 -3069.9822 951.38041 -4021.3626 1127.8186 0 765.20411 152027.82 -157942.2 -954.30565 19101.694 212.92089 318.20155 1.9391088 - 600 11.74351 -3090.3867 973.25557 -4063.6423 1123.3487 0 744.86978 152009.46 -157941.32 -1226.2333 18891.444 217.81659 325.5949 1.8227604 - 620 12.138507 -3114.2347 1002.2136 -4116.4483 1159.4812 0 766.24573 151899.05 -157941.23 -1406.6638 18672.922 224.29746 335.32178 1.8002314 - 640 12.53874 -3160.3172 973.01388 -4133.3311 1181.5814 0 805.79135 151821.94 -157942.65 -1444.0821 18448.163 217.7625 325.51017 1.8464735 - 660 12.945363 -3185.1871 975.57462 -4160.7618 1177.1798 0 795.84414 151809.59 -157943.38 -962.08053 18220.064 218.3356 326.36793 1.8252243 - 680 13.358243 -3226.8034 977.21534 -4204.0187 1215.3088 0 862.3869 151662.05 -157943.76 -538.09214 17991.009 218.7028 326.90984 1.8513045 - 700 13.774714 -3267.0358 979.72611 -4246.7619 1229.2873 0 878.80049 151588.58 -157943.43 -526.4724 17765.058 219.26471 327.74412 1.86738 - 720 14.198356 -3275.0063 987.91851 -4262.9248 1260.2342 0 905.19546 151515.01 -157943.36 -285.51035 17544.004 221.09819 330.48021 1.8901628 - 740 14.624448 -3298.9204 992.679 -4291.5994 1283.7665 0 917.78414 151449.24 -157942.39 351.98558 17329.448 222.1636 332.09658 1.843264 - 760 15.05056 -3316.7113 1010.6458 -4327.3571 1296.6728 0 951.2091 151368.47 -157943.71 419.51796 17123.095 226.18459 338.07068 1.9518407 - 780 15.504961 -3294.5707 1053.9493 -4348.52 1300.722 0 975.60682 151317.15 -157942 1040.7668 16927.715 235.87602 352.49204 2.1793007 - 800 15.933704 -3363.0539 987.22337 -4350.2773 1325.1641 0 1013.664 151255.26 -157944.36 1462.6199 16747.7 220.94262 330.24432 1.8985721 - 820 16.364414 -3437.2117 980.5397 -4417.7514 1350.8684 0 1029.953 151144.46 -157943.03 817.95684 16584.026 219.4468 327.9943 1.9129039 - 840 16.799625 -3465.5868 981.23685 -4446.8236 1388.7125 0 1043.4314 151066.43 -157945.4 1366.0731 16434.707 219.60282 328.17006 2.0308095 - 860 17.241996 -3460.2301 1020.3681 -4480.5981 1418.4709 0 1090.9207 150954.21 -157944.2 1450.0443 16300.524 228.36046 341.31823 2.0218282 - 880 17.688347 -3499.5491 994.43799 -4493.9871 1444.4283 0 1113.276 150893.43 -157945.12 2227.6739 16183.439 222.55726 332.59403 2.0408296 - 900 18.136371 -3526.9176 952.87144 -4479.789 1443.8422 0 1118.5107 150902.72 -157944.87 2220.1643 16085.505 213.25458 318.69359 1.9574553 - 920 18.599828 -3545.2479 976.95271 -4522.2006 1443.4309 0 1118.3924 150859.69 -157943.71 2107.6215 16006.466 218.64402 326.75181 1.9926282 - 940 19.064528 -3560.4406 994.62379 -4555.0644 1431.3624 0 1098.4902 150860.38 -157945.3 1495.9356 15944.46 222.59885 332.62316 2.0953461 - 960 19.529192 -3590.569 964.78915 -4555.3582 1431.9284 0 1092.1793 150866.87 -157946.34 1559.1687 15897.003 215.92179 322.6406 2.0442546 - 980 19.991661 -3599.6592 986.56344 -4586.2227 1435.7543 0 1034.8682 150889.35 -157946.2 679.01087 15862.242 220.79492 330.01359 1.9307016 - 1000 20.427668 -3634.9266 939.78172 -4574.7083 1424.4834 0 1022.664 150924.73 -157946.59 733.04572 15834.345 210.32508 314.30018 1.9584145 - 1020 20.873712 -3669.298 934.76265 -4604.0606 1452.3 0 1016.3445 150873.46 -157946.16 143.60284 15811.749 209.2018 312.55492 2.0808526 - 1040 21.319204 -3682.4175 935.86127 -4618.2788 1447.0344 0 1035.4526 150844.58 -157945.34 515.93558 15792.261 209.44767 312.98247 1.9790896 - 1060 21.766855 -3704.0833 901.03929 -4605.1226 1476.4857 0 1067.779 150794.42 -157943.8 1092.0636 15777.267 201.65444 301.3325 1.8948719 - 1080 22.214459 -3699.4923 921.66268 -4621.155 1475.7351 0 1079.7576 150767.2 -157943.85 1003.4205 15769.569 206.27 308.27973 1.8458618 - 1100 22.662445 -3667.6761 957.47147 -4625.1476 1507.2355 0 1102.9252 150708.15 -157943.46 927.20789 15768.898 214.28408 320.17339 2.0742837 - 1120 23.085055 -3668.1399 935.38917 -4603.5291 1507.3367 0 1080.9826 150753.9 -157945.75 810.87137 15775.175 209.34202 312.79082 2.0279075 - 1140 23.534417 -3710.7149 937.22068 -4647.9356 1499.5413 0 1020.4759 150776.54 -157944.49 -138.27816 15786.277 209.75191 313.34734 2.1346658 - 1160 23.985544 -3711.7493 900.74897 -4612.4983 1430.3269 0 990.84122 150911.11 -157944.78 8.4592568 15798.538 201.58947 301.24561 1.8661211 - 1180 24.439474 -3729.7115 928.82825 -4658.5398 1435.7711 0 937.43508 150913.97 -157945.72 -905.33202 15809.125 207.87367 310.65722 1.8872897 - 1200 24.895124 -3738.2838 909.79315 -4648.077 1436.4199 0 938.10918 150922.8 -157945.41 -1112.9968 15812.511 203.61357 304.28121 1.8714711 - 1220 25.352201 -3757.8302 907.08742 -4664.9176 1424.1514 0 930.13653 150924.86 -157944.06 -1078.0621 15807.893 203.00803 303.40134 1.8521625 - 1240 25.780748 -3778.5355 905.88168 -4684.4171 1453.9568 0 959.37689 150846.21 -157943.96 -975.25032 15795.393 202.73818 303.00695 1.778808 - 1260 26.238145 -3773.7584 879.94641 -4653.7048 1473.5812 0 1002.67 150815.41 -157945.36 -360.58922 15776.466 196.93381 294.2433 1.9174557 - 1280 26.696751 -3755.4956 904.13603 -4659.6316 1493.7103 0 1017.8327 150773.94 -157945.12 -256.88128 15755.525 202.3475 302.35592 1.9294965 - 1300 27.158244 -3754.9246 903.51795 -4658.4425 1498.1329 0 1006.1786 150782.15 -157944.9 -455.2258 15732.436 202.20917 302.19365 1.8353806 - 1320 27.619539 -3758.1232 913.25769 -4671.3808 1500.2049 0 1032.0703 150739.71 -157943.37 -251.62277 15706.775 204.38895 305.38485 1.9968111 - 1340 28.079132 -3784.7481 937.61449 -4722.3626 1505.7439 0 993.46365 150723.27 -157944.84 -853.9871 15680.38 209.84005 313.60153 1.8911101 - 1360 28.514251 -3808.7787 864.89279 -4673.6715 1475.0618 0 1009.2569 150785.65 -157943.64 -331.64382 15650.208 193.56478 289.20988 1.8929896 - 1380 28.975972 -3798.7281 892.2622 -4690.9903 1465.561 0 993.58051 150793.83 -157943.96 -567.64508 15617.156 199.69011 298.39786 1.8757635 - 1400 29.439238 -3807.9228 893.51775 -4701.4406 1459.3875 0 1000.4434 150784.38 -157945.65 -456.80001 15580.856 199.97111 298.79789 1.925086 - 1420 29.904427 -3818.6783 890.66153 -4709.3398 1515.8208 0 1064.6851 150655.36 -157945.21 450.86768 15542.76 199.33188 297.83132 1.927452 - 1440 30.368352 -3822.016 910.79285 -4732.8089 1539.2325 0 1076.0339 150597.99 -157946.07 429.02044 15506.302 203.83731 304.53724 2.0216852 - 1460 30.835555 -3821.2117 931.47963 -4752.6914 1540.1582 0 1089.9477 150561.76 -157944.55 645.54716 15472.89 208.46705 311.56653 1.8487206 - 1480 31.306455 -3838.255 920.25737 -4758.5124 1546.6509 0 1107.4468 150533.86 -157946.47 556.76352 15443.298 205.95549 307.74395 1.9637305 - 1500 31.747528 -3839.4323 942.18813 -4781.6204 1557.1836 0 1105.7209 150502.68 -157947.21 535.34633 15417.723 210.86364 315.07463 2.0384198 - 1520 32.218974 -3827.551 925.42642 -4752.9774 1555.4578 0 1097.174 150540.89 -157946.5 680.16246 15396 207.11233 309.42351 2.0793499 - 1540 32.691924 -3836.1802 885.40721 -4721.5874 1558.3851 0 1144.6478 150521.13 -157945.75 1216.5367 15378.972 198.15595 296.02524 2.015983 - 1560 33.164075 -3830.4342 955.31807 -4785.7523 1574.0464 0 1105.7294 150481.06 -157946.59 169.17645 15369.126 213.80214 319.4694 2.0400237 - 1580 33.636497 -3808.4082 948.31996 -4756.7281 1556.8058 0 1079.1205 150552.4 -157945.06 603.87966 15363.124 212.23595 317.13706 2.0112224 - 1600 34.111529 -3835.9681 925.63461 -4761.6027 1575.0508 0 1091.3896 150517.16 -157945.2 356.94873 15359.871 207.15893 309.60148 1.8514712 - 1620 34.558112 -3865.8357 866.45292 -4732.2886 1577.3357 0 1137.1716 150497.63 -157944.43 945.81112 15359.844 193.91394 289.72922 1.8926829 - 1640 35.029171 -3849.5025 884.49282 -4733.9954 1547.0606 0 1101.4292 150561.92 -157944.41 703.96326 15365.598 197.95131 295.76038 1.913597 - 1660 35.495665 -3861.3162 906.62112 -4767.9373 1547.2773 0 1074.8986 150555.48 -157945.6 46.512723 15375.298 202.90367 303.1667 1.9573677 - 1680 35.959871 -3857.7679 907.8657 -4765.6336 1547.7327 0 1089.3299 150543.52 -157946.22 383.48079 15386.165 203.18221 303.5736 2.0202069 - 1700 36.428885 -3869.0902 891.82145 -4760.9117 1512.1728 0 1012.6239 150658.31 -157944.02 -488.95961 15397.869 199.59147 298.24425 1.8990607 - 1720 36.903833 -3870.4685 893.82411 -4764.2926 1485.7646 0 989.27762 150706.25 -157945.59 -542.70653 15406.338 200.03967 298.80302 2.1113341 - 1740 37.380529 -3847.3408 893.93384 -4741.2746 1509.8117 0 1031.6641 150663.04 -157945.79 -307.1162 15410.521 200.06423 298.90093 2.0090208 - 1760 37.827319 -3840.438 868.84851 -4709.2865 1474.404 0 1018.599 150744.2 -157946.49 -276.44721 15412.838 194.45008 290.51398 1.9203414 - 1780 38.297568 -3842.0322 910.50606 -4752.5383 1494.2187 0 1002.3762 150696.05 -157945.18 -585.57252 15412.983 203.77313 304.47127 1.9624414 - 1800 38.76671 -3861.9431 881.98228 -4743.9254 1471.6721 0 978.01808 150752.55 -157946.17 -711.07254 15409.636 197.38944 294.90206 1.9749925 - 1820 39.233968 -3890.8613 856.10452 -4746.9658 1505.1405 0 991.9875 150701.72 -157945.82 -509.17282 15401.428 191.59795 286.24213 1.9311068 - 1840 39.704207 -3860.2881 907.57785 -4767.866 1492.5264 0 999.80677 150685.45 -157945.65 -697.50098 15387.414 203.11779 303.52338 1.9123566 - 1860 40.174673 -3879.0681 938.58496 -4817.653 1532.9628 0 1046.6919 150550.41 -157947.72 -311.83188 15369.15 210.05724 313.84514 2.0580305 - 1880 40.646746 -3871.1182 925.64972 -4796.7679 1531.6363 0 1064.5321 150553.96 -157946.9 136.0161 15350.638 207.16231 309.48972 2.0957912 - 1900 41.120691 -3868.9005 949.1652 -4818.0657 1593.1686 0 1150.4095 150384.01 -157945.65 753.94006 15333.301 212.42512 317.39691 2.0615952 - 1920 41.59464 -3868.6343 954.03473 -4822.669 1610.5603 0 1192.2159 150320.88 -157946.33 1209.5547 15321.106 213.51493 319.06152 2.011006 - 1940 42.037294 -3884.0548 926.13369 -4810.1885 1595.5448 0 1167.6153 150372.25 -157945.6 1289.8018 15318.433 207.27062 309.70304 1.9619634 - 1960 42.507917 -3889.403 953.52537 -4842.9284 1598.8799 0 1116.9498 150388.89 -157947.65 327.93587 15323.804 213.40093 318.9112 1.9579466 - 1980 42.973861 -3911.0951 911.40927 -4822.5043 1553.4244 0 1085.4519 150485.64 -157947.02 169.14591 15332.113 203.97527 304.77814 1.9637281 - 2000 43.43889 -3892.0279 902.31728 -4794.3452 1534.2125 0 1088.703 150530.25 -157947.51 473.37009 15341.654 201.94046 301.71557 1.9929295 -Loop time of 43.4389 on 4 procs for 2000 steps with 2500 atoms - -Pair time (%) = 30.8131 (70.9343) -Bond time (%) = 0.0167851 (0.0386406) -Kspce time (%) = 2.78529 (6.41196) -Neigh time (%) = 2.7229 (6.26835) -Comm time (%) = 2.36382 (5.4417) -Outpt time (%) = 0.00704503 (0.0162182) -Other time (%) = 4.72998 (10.8888) - -Nlocal: 625 ave 641 max 600 min -Histogram: 1 0 0 0 0 0 0 2 0 1 -Nghost: 13465.2 ave 13518 max 13362 min -Histogram: 1 0 0 0 0 0 1 0 0 2 -Neighs: 585334 ave 608376 max 546210 min -Histogram: 1 0 0 0 0 0 1 0 1 1 - -Total # of neighbors = 2341334 -Ave neighs/atom = 936.534 -Ave special neighs/atom = 4 -Neighbor list builds = 100 -Dangerous builds = 7 - diff --git a/examples/USER/drude/swm4-ndp/log.swm4-ndp.nh.8Jul15.linux.1 b/examples/USER/drude/swm4-ndp/log.swm4-ndp.nh.8Jul15.linux.1 deleted file mode 100644 index 5180a5ff69..0000000000 --- a/examples/USER/drude/swm4-ndp/log.swm4-ndp.nh.8Jul15.linux.1 +++ /dev/null @@ -1,236 +0,0 @@ -LAMMPS (8 Jul 2015) -units real -boundary p p p - -atom_style full -bond_style harmonic -angle_style harmonic -special_bonds lj/coul 0.0 0.0 0.5 - -pair_style lj/cut/coul/long 12.0 12.0 -kspace_style pppm 1.0e-3 - -read_data data.swm4-ndp - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 2500 atoms - scanning bonds ... - 1 = max bonds/atom - scanning angles ... - 1 = max angles/atom - reading bonds ... - 2000 bonds - reading angles ... - 500 angles - 4 = max # of 1-2 neighbors - 3 = max # of 1-3 neighbors - 3 = max # of 1-4 neighbors - 4 = max # of special neighbors - -pair_coeff 1 1 0.210939 3.183950 # ODw ODw -pair_coeff * 2* 0.000000 0.0 - -group ATOMS type 1:3 -2000 atoms in group ATOMS -group CORES type 1 -500 atoms in group CORES -group DRUDES type 4 -500 atoms in group DRUDES - -variable TK equal 300.0 -variable TDK equal 1.0 -variable PBAR equal 1.0 - -neighbor 2.0 bin - -timestep 1.0 - -fix DRUDE all drude C N N D - -velocity ATOMS create ${TK} 12345 -velocity ATOMS create 300 12345 -velocity DRUDES create ${TDK} 12345 -velocity DRUDES create 1 12345 - -delete_bonds ATOMS multi -PPPM initialization ... - G vector (1/distance) = 0.217457 - grid = 10 10 10 - stencil order = 5 - estimated absolute RMS force accuracy = 0.197288 - estimated relative force accuracy = 0.000594128 - using double precision FFTs - 3d grid and FFT values/proc = 3375 1000 -Rebuild special list taking Drude particles into account -Old max number of 1-2 to 1-4 neighbors: 4 -New max number of 1-2 to 1-4 neighbors: 4 (+0) -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 10 steps, check yes - master list distance cutoff = 14 - 2000 total bonds, 500 turned on, 1500 turned off - 500 total angles, 0 turned on, 500 turned off - 0 total dihedrals, 0 turned on, 0 turned off - 0 total impropers, 0 turned on, 0 turned off - -comm_modify vel yes -compute TATOM ATOMS temp/com -compute TEMP all temp/drude - -fix DTDIR all drude/transform/direct -fix RIGID ATOMS rigid/npt/small molecule temp ${TK} ${TK} 100 iso ${PBAR} ${PBAR} 500 -fix RIGID ATOMS rigid/npt/small molecule temp 300 ${TK} 100 iso ${PBAR} ${PBAR} 500 -fix RIGID ATOMS rigid/npt/small molecule temp 300 300 100 iso ${PBAR} ${PBAR} 500 -fix RIGID ATOMS rigid/npt/small molecule temp 300 300 100 iso 1 ${PBAR} 500 -fix RIGID ATOMS rigid/npt/small molecule temp 300 300 100 iso 1 1 500 -500 rigid bodies with 2000 atoms - 0.832099 = max distance from body owner to body atom -fix_modify RIGID temp TATOM press thermo_press -WARNING: Temperature for fix modify is not for group all (../fix_rigid_nh_small.cpp:1395) -fix NVT DRUDES nvt temp ${TDK} ${TDK} 100.0 -fix NVT DRUDES nvt temp 1 ${TDK} 100.0 -fix NVT DRUDES nvt temp 1 1 100.0 -fix DTINV all drude/transform/inverse - -thermo_style custom step cpu etotal ke pe ebond eangle evdwl ecoul elong press vol temp c_TEMP[1] c_TEMP[2] -thermo 20 - -run 2000 -PPPM initialization ... - G vector (1/distance) = 0.217457 - grid = 10 10 10 - stencil order = 5 - estimated absolute RMS force accuracy = 0.197288 - estimated relative force accuracy = 0.000594128 - using double precision FFTs - 3d grid and FFT values/proc = 3375 1000 -Rebuild special list taking Drude particles into account -Old max number of 1-2 to 1-4 neighbors: 4 -New max number of 1-2 to 1-4 neighbors: 4 (+0) -Memory usage per processor = 24.8361 Mbytes -Step CPU TotEng KinEng PotEng E_bond E_angle E_vdwl E_coul E_long Press Volume Temp TEMP[1] TEMP[2] - 0 0 4568.0415 903.41148 3664.63 623.46454 0 2890.2449 157955.66 -157804.74 244591.08 13824 202.18534 295.64644 14.858785 - 20 1.5779378 3742.6839 5338.7884 -1596.1045 567.30749 0 662.23765 155098.36 -157924.01 31679.424 13979.574 1194.8318 1690.2246 201.65659 - 40 3.2595179 2752.8331 4407.7651 -1654.932 793.00135 0 870.33079 154593.76 -157912.03 27394.571 14278.56 986.46688 1450.7477 55.932382 - 60 4.9160559 1995.591 3982.0372 -1986.4462 660.67737 0 750.60932 154536.67 -157934.4 22230.527 14691.401 891.1881 1315.7324 40.317107 - 80 6.5368109 1376.4607 3451.5429 -2075.0822 617.73899 0 606.3673 154625.69 -157924.88 17342.36 15201.343 772.46238 1147.1933 21.455584 - 100 8.1206679 885.61474 3037.6308 -2152.0161 536.23281 0 448.92334 154793.04 -157930.22 13263.15 15783.251 679.82802 1011.6854 14.7536 - 120 9.6622779 487.58833 2926.9844 -2439.396 534.45257 0 332.92672 154624.58 -157931.35 8680.1072 16409.225 655.06511 977.0118 9.8615914 - 140 11.151044 159.92993 2531.0941 -2371.1641 507.26614 0 248.61605 154802.7 -157929.75 6399.7614 17052.819 566.46405 845.55948 7.1402545 - 160 12.594065 -100.92554 2408.1685 -2509.0941 490.99513 0 134.36067 154800.59 -157935.04 3836.8939 17698.15 538.95306 805.19219 5.3968881 - 180 13.99897 -313.40437 2221.7416 -2535.1459 469.97779 0 75.805558 154853.24 -157934.17 1959.0151 18334.826 497.23032 743.14066 4.4151864 - 200 15.366489 -490.94535 2067.2605 -2558.2059 455.16264 0 77.545085 154841.14 -157932.06 1193.2843 18956.449 462.65715 691.7234 3.5993432 - 220 16.600555 -642.90899 1962.7268 -2605.6358 481.409 0 64.82886 154779.27 -157931.14 257.97318 19559.017 439.26229 657.06726 2.7738353 - 240 17.905356 -770.44499 1795.759 -2566.204 467.25833 0 68.82314 154829.98 -157932.26 19.366424 20139.417 401.89456 601.24562 2.3886434 - 260 19.179106 -878.63388 1752.9497 -2631.5836 476.38325 0 71.933328 154747.16 -157927.06 -779.27927 20696.165 392.31375 587.06527 2.0260796 - 280 20.338816 -971.86313 1649.5511 -2621.4143 473.83718 0 58.460942 154779.6 -157933.32 -1008.6839 21226.44 369.17293 552.5314 1.7176302 - 300 21.569212 -1057.5245 1580.9766 -2638.5012 480.33124 0 92.042617 154721.84 -157932.72 -1273.0871 21728.981 353.82581 529.63244 1.5049172 - 320 22.749114 -1132.8131 1507.0527 -2639.8658 477.51281 0 107.39942 154707.48 -157932.26 -1098.1682 22203.702 337.28149 504.90539 1.3591193 - 340 23.866651 -1199.4814 1495.1233 -2694.6047 479.99745 0 106.51864 154656.08 -157937.2 -1429.2857 22652.428 334.61166 500.95977 1.2462004 - 360 25.082959 -1264.8469 1440.8985 -2705.7454 491.71868 0 107.29672 154624.8 -157929.57 -1584.3973 23073.056 322.47604 482.79111 1.2009575 - 380 26.115491 -1323.6479 1376.047 -2699.695 497.4857 0 130.64748 154603.75 -157931.58 -1822.0261 23465.375 307.96215 461.10877 1.0530068 - 400 27.098619 -1373.3921 1374.977 -2748.3691 504.29487 0 124.46131 154555.55 -157932.67 -2021.5919 23828.229 307.72267 460.78429 0.98399317 - 420 28.070089 -1426.0355 1375.3813 -2801.4168 515.478 0 142.00079 154473.71 -157932.61 -2208.8244 24160.02 307.81316 460.97813 0.86759754 - 440 29.088747 -1476.2448 1329.2669 -2805.5117 535.72651 0 196.6858 154393.5 -157931.42 -1618.3009 24460.675 297.49266 445.47247 0.93805929 - 460 30.039555 -1527.7744 1320.4118 -2848.1861 568.66085 0 263.35802 154252.43 -157932.64 -1494.5444 24734.828 295.51087 442.54962 0.84234766 - 480 30.98472 -1576.2009 1300.9323 -2877.1332 594.86236 0 314.31593 154144.87 -157931.19 -1089.6762 24985.934 291.15132 436.02273 0.82622001 - 500 31.921181 -1626.4788 1317.6697 -2944.1486 623.62396 0 334.61944 154026.32 -157928.71 -1168.0859 25218.234 294.89719 441.63818 0.82542904 - 520 32.850868 -1678.487 1262.6568 -2941.1438 633.47682 0 363.44379 153992.91 -157930.98 -1163.3304 25431.978 282.58518 423.21273 0.76490406 - 540 33.831238 -1726.1374 1271.5003 -2997.6376 640.74261 0 345.52688 153948.98 -157932.89 -1537.3705 25626.826 284.56437 426.19842 0.72713952 - 560 34.751061 -1771.2597 1269.233 -3040.4927 644.30805 0 317.8435 153929.28 -157931.92 -1722.5181 25799.253 284.05695 425.41542 0.77189915 - 580 35.665466 -1815.0265 1246.413 -3061.4395 683.24088 0 371.72686 153815.69 -157932.1 -1494.5382 25947.498 278.94979 417.73291 0.82565978 - 600 36.573731 -1858.3541 1196.3137 -3054.6678 696.06741 0 437.52527 153744.09 -157932.35 -954.95797 26075.526 267.73745 400.95599 0.76490653 - 620 37.479106 -1899.6548 1179.8195 -3079.4743 696.68256 0 400.17078 153755.86 -157932.18 -1545.546 26187.542 264.04602 395.42296 0.76404516 - 640 38.439799 -1936.5953 1175.0129 -3111.6082 690.67817 0 392.53009 153736.67 -157931.49 -1651.1722 26278.598 262.97029 393.82361 0.73771389 - 660 39.342719 -1974.4946 1176.582 -3151.0766 687.10898 0 368.78109 153725.56 -157932.53 -1642.1352 26346.954 263.32147 394.35652 0.72471807 - 680 40.233007 -2011.9427 1170.7634 -3182.7062 704.7553 0 376.83243 153670.03 -157934.32 -1891.1355 26391.697 262.01926 392.39338 0.74699214 - 700 41.124436 -2051.0351 1135.0688 -3186.1039 725.49013 0 408.02789 153612.64 -157932.26 -1554.558 26411.443 254.03072 380.39243 0.79925352 - 720 42.014817 -2087.2728 1127.2712 -3214.544 747.73788 0 483.80639 153486.98 -157933.07 -1246.9189 26409.313 252.28561 377.77086 0.81053421 - 740 42.908141 -2122.8783 1145.0602 -3267.9385 791.69089 0 545.96341 153327.46 -157933.05 -1064.8488 26390.224 256.26683 383.71741 0.85313379 - 760 43.799068 -2155.8658 1189.0654 -3344.9312 789.63603 0 492.27945 153309.89 -157936.74 -1502.4138 26356.52 266.11528 398.4847 0.84422302 - 780 44.690825 -2197.1759 1166.0016 -3363.1774 813.89866 0 521.14986 153239.56 -157937.79 -1316.1431 26304.488 260.95354 390.75511 0.82849551 - 800 45.65434 -2236.6034 1147.1342 -3383.7376 858.77647 0 581.50775 153111.46 -157935.49 -1059.9568 26235.547 256.73099 384.3699 0.93971538 - 820 46.655089 -2273.5686 1128.3309 -3401.8996 876.66305 0 635.8842 153020.42 -157934.87 -522.03009 26154.47 252.52277 378.09253 0.87820184 - 840 47.581215 -2310.5392 1107.1453 -3417.6845 906.73 0 663.59923 152946.29 -157934.31 -660.73299 26066.561 247.78139 370.96848 0.9116362 - 860 48.461532 -2342.7319 1130.0857 -3472.8176 942.10066 0 680.8635 152839.09 -157934.87 -541.95751 25971.767 252.91551 378.61448 1.0117334 - 880 49.348792 -2377.0856 1100.1359 -3477.2215 941.37588 0 700.77054 152814.73 -157934.1 -443.18233 25871.504 246.21267 368.56741 1.0107473 - 900 50.240716 -2408.6694 1120.4615 -3529.131 953.77939 0 683.49952 152768.93 -157935.34 -805.27426 25765.603 250.76159 375.35036 1.0825367 - 920 51.130132 -2442.8312 1111.7289 -3554.56 950.77289 0 674.01395 152754.6 -157933.95 -905.29746 25651.192 248.80721 372.46424 0.9955159 - 940 52.02236 -2475.7651 1083.1001 -3558.8652 929.08218 0 652.94438 152792.16 -157933.05 -788.57962 25527.175 242.40003 362.8243 1.0666862 - 960 52.924057 -2508.9913 1065.8755 -3574.8668 958.92048 0 698.81111 152699.64 -157932.24 -628.47136 25394.225 238.54512 356.97396 1.2103698 - 980 53.828788 -2536.4577 1080.5323 -3616.99 965.47688 0 709.51639 152642.64 -157934.62 -711.96055 25254.689 241.82535 361.89287 1.2066617 - 1000 54.736123 -2567.3495 1049.6524 -3617.0019 961.00327 0 711.26219 152645.74 -157935.01 -767.44539 25108.887 234.91437 351.52221 1.2288643 - 1020 55.707224 -2595.1206 1073.4918 -3668.6124 974.79134 0 682.20149 152609.52 -157935.12 -1086.5823 24955.503 240.24966 359.53972 1.1890491 - 1040 56.677394 -2626.5258 1072.5969 -3699.1227 1013.3934 0 711.73335 152511.92 -157936.17 -993.59976 24792.452 240.04939 359.23966 1.1887504 - 1060 57.582305 -2655.4118 1059.0687 -3714.4806 1011.7018 0 747.43846 152460.24 -157933.86 -555.51961 24621.133 237.02176 354.6316 1.3280226 - 1080 58.451085 -2684.3286 1093.9034 -3778.232 1041.5624 0 765.98574 152348.29 -157934.07 -993.29607 24444.559 244.81782 366.39031 1.183205 - 1100 59.320593 -2716.1558 1073.5935 -3789.7493 1046.6309 0 741.4524 152358.32 -157936.15 -1031.9439 24260.537 240.27243 359.559 1.2187426 - 1120 60.197434 -2748.4358 1043.9493 -3792.3851 1050.7685 0 732.61894 152361.65 -157937.42 -1173.2273 24068.431 233.638 349.62448 1.1977845 - 1140 61.088693 -2777.1545 1036.6106 -3813.7651 1060.884 0 757.21086 152307.36 -157939.22 -1043.4335 23867.228 231.99557 347.17994 1.1628589 - 1160 62.010573 -2805.5456 1027.0164 -3832.5621 1057.9262 0 777.84714 152269.56 -157937.89 -729.25379 23659.194 229.84839 343.97766 1.1301417 - 1180 62.973114 -2832.7144 1030.8608 -3863.5752 1084.2376 0 767.80175 152221.94 -157937.56 -1365.8515 23446.354 230.70875 345.24169 1.1814637 - 1200 63.943778 -2860.0062 1032.0824 -3892.0886 1078.2587 0 781.38106 152185.86 -157937.59 -1050.1069 23225.033 230.98216 345.65138 1.1817665 - 1220 64.923382 -2887.3006 1026.4756 -3913.7762 1073.1543 0 809.51178 152141.13 -157937.57 -956.1976 22997.996 229.72734 343.81693 1.0887098 - 1240 65.912183 -2912.0696 1020.0729 -3932.1425 1095.3889 0 826.297 152085.57 -157939.4 -534.84968 22767.897 228.2944 341.63565 1.15531 - 1260 66.908861 -2938.0025 1009.7902 -3947.7927 1120.1948 0 846.76965 152025.28 -157940.04 -581.84084 22538.229 225.99312 338.22714 1.0731061 - 1280 67.970707 -2960.3724 1046.6347 -4007.0071 1144.3297 0 866.43256 151921.62 -157939.39 -368.35961 22310.088 234.239 350.59018 1.0681573 - 1300 68.984941 -2983.8905 1039.0599 -4022.9504 1162.4788 0 878.40157 151876.66 -157940.49 -408.4644 22085.613 232.54373 348.07145 1.0232144 - 1320 70.043952 -3009.5808 969.8918 -3979.4726 1186.5907 0 935.08613 151836.22 -157937.36 431.8242 21865.457 217.06378 324.88371 0.98977725 - 1340 71.117119 -3028.1057 1016.1027 -4044.2084 1215.7197 0 933.65661 151744.63 -157938.22 -118.90908 21653.612 227.40587 340.39676 0.96927182 - 1360 72.19871 -3048.8293 986.21586 -4035.0452 1231.0917 0 974.10814 151697.47 -157937.72 485.3122 21448.458 220.71713 330.39668 0.91660237 - 1380 73.289545 -3067.6975 1046.3647 -4114.0622 1252.358 0 948.20869 151626.66 -157941.29 -131.77945 21251.912 234.17856 350.55699 0.95332826 - 1400 74.389534 -3091.6437 1003.804 -4095.4478 1223.2343 0 914.21639 151708.69 -157941.59 -228.59592 21060.319 224.6534 336.27611 0.95868112 - 1420 75.496459 -3117.9845 1017.2871 -4135.2716 1252.8701 0 934.95412 151617.13 -157940.22 -328.62774 20872.161 227.67095 340.80959 0.93833238 - 1440 76.611495 -3137.2342 990.73612 -4127.9703 1224.5861 0 925.81135 151661.05 -157939.42 -23.294916 20687.614 221.72878 331.93708 0.86871384 - 1460 77.73649 -3159.4947 1040.535 -4200.0297 1218.936 0 881.92261 151636.87 -157937.75 -581.29505 20507.346 232.87387 348.59778 0.96029886 - 1480 78.872562 -3183.8273 1037.9432 -4221.7705 1246.5207 0 908.21966 151561.59 -157938.1 -884.42345 20328.04 232.29381 347.7323 0.95226246 - 1500 80.110645 -3206.5826 1008.5663 -4215.1489 1236.8936 0 929.15034 151558.28 -157939.47 -91.502556 20149.349 225.7192 337.88949 0.92718943 - 1520 81.168804 -3228.1152 994.3422 -4222.4574 1276.2214 0 948.25706 151492.45 -157939.39 -262.49453 19974.554 222.53583 333.16141 0.83959152 - 1540 82.328931 -3248.9878 997.70762 -4246.6954 1273.2453 0 944.04689 151475.31 -157939.3 -310.12487 19802.717 223.28901 334.28865 0.84316615 - 1560 83.500822 -3268.9264 1001.6639 -4270.5903 1283.2174 0 972.25539 151413.47 -157939.53 -368.92162 19633.499 224.17444 335.57814 0.91870789 - 1580 84.681217 -3289.8506 972.05937 -4261.9099 1290.892 0 995.40503 151394.08 -157942.29 309.3174 19467.313 217.54888 325.64947 0.91261747 - 1600 85.872982 -3306.0485 999.0593 -4305.1078 1336.2852 0 1018.2817 151281.27 -157940.94 78.176324 19307.332 223.59152 334.68976 0.94786237 - 1620 87.166941 -3323.911 1023.7518 -4347.6628 1346.5659 0 1012.0297 151235.76 -157942.02 401.58054 19152.885 229.11774 342.98696 0.92107142 - 1640 88.373719 -3346.3201 1013.0953 -4359.4153 1368.3551 0 1038.3633 151174.74 -157940.87 115.49888 19004.339 226.7328 339.39185 0.96123977 - 1660 89.588199 -3366.6764 980.18808 -4346.8645 1385.5623 0 1066.3348 151143.21 -157941.97 785.51107 18860.969 219.3681 328.38652 0.89253119 - 1680 90.812635 -3382.4343 999.75094 -4382.1852 1367.9173 0 1045.8848 151142.33 -157938.32 549.73441 18726.008 223.74631 334.953 0.88544944 - 1700 92.044767 -3400.8462 996.00209 -4396.8483 1351.6629 0 1019.0394 151174.27 -157941.83 32.327852 18598.28 222.90731 333.67893 0.91827006 - 1720 93.284649 -3418.3313 989.38116 -4407.7125 1347.9882 0 1026.3475 151161.41 -157943.46 700.69172 18474.978 221.42553 331.45637 0.92100955 - 1740 94.538928 -3435.1347 964.16624 -4399.301 1357.6456 0 1051.1466 151135.74 -157943.84 477.68306 18358.2 215.78238 322.997 0.92157841 - 1760 95.90276 -3452.4681 996.08241 -4448.5506 1365.9896 0 1001.3994 151128.36 -157944.3 -77.655143 18246.618 222.92529 333.72093 0.88815023 - 1780 97.200704 -3470.0186 947.16368 -4417.1823 1357.1769 0 1006.9477 151162.27 -157943.57 100.19368 18137.3 211.97718 317.3159 0.87577473 - 1800 98.461648 -3484.6818 988.75293 -4473.4348 1367.5971 0 995.1924 151106.14 -157942.36 -208.37477 18030.204 221.28494 331.23294 0.94635825 - 1820 99.729642 -3503.5324 959.4974 -4463.0298 1386.9033 0 1035.1867 151057.26 -157942.38 196.09637 17924.392 214.73749 321.44422 0.89454363 - 1840 101.00392 -3518.4137 985.10207 -4503.5157 1425.227 0 1062.1927 150951.14 -157942.08 189.40933 17821.795 220.46787 330.02248 0.91769756 - 1860 102.28783 -3531.6076 978.71334 -4510.3209 1447.6145 0 1081.8026 150905.2 -157944.94 369.13672 17723.495 219.03805 327.84302 0.99005655 - 1880 103.57975 -3546.6803 982.10151 -4528.7818 1416.6032 0 1040.8725 150959.42 -157945.68 206.83653 17629.384 219.79633 328.97668 0.9960403 - 1900 104.81168 -3563.7438 961.75306 -4525.4969 1426.2883 0 1055.2567 150936.42 -157943.46 223.06115 17537.856 215.24231 322.15829 0.97986655 - 1920 106.04042 -3579.7815 953.8957 -4533.6772 1420.242 0 1053.3469 150938.67 -157945.93 264.48404 17448.909 213.48382 319.52979 0.96489929 - 1940 107.27692 -3592.4628 995.11883 -4587.5816 1434.5738 0 1036.2736 150885.59 -157944.02 -203.71783 17362.885 222.70964 333.32982 1.0238542 - 1960 108.52049 -3607.1225 959.8186 -4566.9411 1454.811 0 1091.6157 150830.59 -157943.96 412.09226 17278.194 214.80937 321.46995 1.0586113 - 1980 109.76987 -3621.5836 950.82575 -4572.4094 1481.3655 0 1148.5036 150742.3 -157944.58 1156.6083 17197.362 212.79675 318.42806 1.1085537 - 2000 111.02457 -3632.4321 939.77229 -4572.2044 1484.3457 0 1154.0077 150733.65 -157944.21 1008.3019 17124.028 210.32297 314.7467 1.0548599 -Loop time of 111.025 on 1 procs for 2000 steps with 2500 atoms - -Pair time (%) = 87.5509 (78.8572) -Bond time (%) = 0.0493031 (0.0444073) -Kspce time (%) = 3.35179 (3.01896) -Neigh time (%) = 9.36055 (8.43106) -Comm time (%) = 0.69479 (0.625798) -Outpt time (%) = 0.0108259 (0.00975088) -Other time (%) = 10.0064 (9.01281) - -Nlocal: 2500 ave 2500 max 2500 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 20348 ave 20348 max 20348 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 2.09326e+06 ave 2.09326e+06 max 2.09326e+06 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 2093261 -Ave neighs/atom = 837.304 -Ave special neighs/atom = 4 -Neighbor list builds = 120 -Dangerous builds = 16 - diff --git a/examples/USER/drude/swm4-ndp/log.swm4-ndp.nh.8Jul15.linux.4 b/examples/USER/drude/swm4-ndp/log.swm4-ndp.nh.8Jul15.linux.4 deleted file mode 100644 index eb91fb883c..0000000000 --- a/examples/USER/drude/swm4-ndp/log.swm4-ndp.nh.8Jul15.linux.4 +++ /dev/null @@ -1,236 +0,0 @@ -LAMMPS (8 Jul 2015) -units real -boundary p p p - -atom_style full -bond_style harmonic -angle_style harmonic -special_bonds lj/coul 0.0 0.0 0.5 - -pair_style lj/cut/coul/long 12.0 12.0 -kspace_style pppm 1.0e-3 - -read_data data.swm4-ndp - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 2500 atoms - scanning bonds ... - 1 = max bonds/atom - scanning angles ... - 1 = max angles/atom - reading bonds ... - 2000 bonds - reading angles ... - 500 angles - 4 = max # of 1-2 neighbors - 3 = max # of 1-3 neighbors - 3 = max # of 1-4 neighbors - 4 = max # of special neighbors - -pair_coeff 1 1 0.210939 3.183950 # ODw ODw -pair_coeff * 2* 0.000000 0.0 - -group ATOMS type 1:3 -2000 atoms in group ATOMS -group CORES type 1 -500 atoms in group CORES -group DRUDES type 4 -500 atoms in group DRUDES - -variable TK equal 300.0 -variable TDK equal 1.0 -variable PBAR equal 1.0 - -neighbor 2.0 bin - -timestep 1.0 - -fix DRUDE all drude C N N D - -velocity ATOMS create ${TK} 12345 -velocity ATOMS create 300 12345 -velocity DRUDES create ${TDK} 12345 -velocity DRUDES create 1 12345 - -delete_bonds ATOMS multi -PPPM initialization ... - G vector (1/distance) = 0.217457 - grid = 10 10 10 - stencil order = 5 - estimated absolute RMS force accuracy = 0.197288 - estimated relative force accuracy = 0.000594128 - using double precision FFTs - 3d grid and FFT values/proc = 1500 300 -Rebuild special list taking Drude particles into account -Old max number of 1-2 to 1-4 neighbors: 4 -New max number of 1-2 to 1-4 neighbors: 4 (+0) -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 10 steps, check yes - master list distance cutoff = 14 - 2000 total bonds, 500 turned on, 1500 turned off - 500 total angles, 0 turned on, 500 turned off - 0 total dihedrals, 0 turned on, 0 turned off - 0 total impropers, 0 turned on, 0 turned off - -comm_modify vel yes -compute TATOM ATOMS temp/com -compute TEMP all temp/drude - -fix DTDIR all drude/transform/direct -fix RIGID ATOMS rigid/npt/small molecule temp ${TK} ${TK} 100 iso ${PBAR} ${PBAR} 500 -fix RIGID ATOMS rigid/npt/small molecule temp 300 ${TK} 100 iso ${PBAR} ${PBAR} 500 -fix RIGID ATOMS rigid/npt/small molecule temp 300 300 100 iso ${PBAR} ${PBAR} 500 -fix RIGID ATOMS rigid/npt/small molecule temp 300 300 100 iso 1 ${PBAR} 500 -fix RIGID ATOMS rigid/npt/small molecule temp 300 300 100 iso 1 1 500 -500 rigid bodies with 2000 atoms - 0.832099 = max distance from body owner to body atom -fix_modify RIGID temp TATOM press thermo_press -WARNING: Temperature for fix modify is not for group all (../fix_rigid_nh_small.cpp:1395) -fix NVT DRUDES nvt temp ${TDK} ${TDK} 100.0 -fix NVT DRUDES nvt temp 1 ${TDK} 100.0 -fix NVT DRUDES nvt temp 1 1 100.0 -fix DTINV all drude/transform/inverse - -thermo_style custom step cpu etotal ke pe ebond eangle evdwl ecoul elong press vol temp c_TEMP[1] c_TEMP[2] -thermo 20 - -run 2000 -PPPM initialization ... - G vector (1/distance) = 0.217457 - grid = 10 10 10 - stencil order = 5 - estimated absolute RMS force accuracy = 0.197288 - estimated relative force accuracy = 0.000594128 - using double precision FFTs - 3d grid and FFT values/proc = 1500 300 -Rebuild special list taking Drude particles into account -Old max number of 1-2 to 1-4 neighbors: 4 -New max number of 1-2 to 1-4 neighbors: 4 (+0) -Memory usage per processor = 15.0906 Mbytes -Step CPU TotEng KinEng PotEng E_bond E_angle E_vdwl E_coul E_long Press Volume Temp TEMP[1] TEMP[2] - 0 0 4568.0415 903.41148 3664.63 623.46454 0 2890.2449 157955.66 -157804.74 244591.08 13824 202.18534 295.64644 14.858785 - 20 0.60629702 3742.7991 5338.7966 -1595.9975 567.29055 0 662.23349 155098.48 -157924 31679.046 13979.575 1194.8336 1690.2267 201.65776 - 40 1.2431891 2752.9388 4407.9332 -1654.9944 792.86725 0 870.27523 154593.92 -157912.06 27392.302 14278.564 986.5045 1450.7624 56.079837 - 60 1.875339 1995.9775 3980.851 -1984.8735 660.64216 0 750.43214 154538.47 -157934.42 22242.676 14691.413 890.92262 1315.3403 40.305321 - 80 2.471236 1377.1261 3449.7879 -2072.6618 617.64243 0 605.75693 154628.63 -157924.69 17345.214 15201.397 772.06962 1146.6088 21.44718 - 100 3.0357449 886.38995 3038.4108 -2152.0208 537.89929 0 450.99962 154789.13 -157930.05 13299.227 15783.335 680.00257 1011.6773 15.016231 - 120 3.585844 488.055 2928.1336 -2440.0786 536.23164 0 334.88597 154620.05 -157931.25 8694.3472 16409.509 655.3223 977.40122 9.8538294 - 140 4.117424 160.14918 2538.5116 -2378.3624 509.19396 0 249.89205 154793.34 -157930.79 6363.1137 17053.486 568.1241 847.92526 7.2744139 - 160 4.6321139 -103.57595 2403.1613 -2506.7372 494.69822 0 144.07174 154790.83 -157936.34 4017.2005 17699.095 537.83243 803.44775 5.3901399 - 180 5.126441 -315.61252 2216.7944 -2532.4069 477.29447 0 80.852363 154842.41 -157932.96 1958.1627 18336.716 496.12314 741.4685 4.440167 - 200 5.6090059 -490.61276 2058.9074 -2549.5202 470.23217 0 80.799455 154831.63 -157932.18 1260.1943 18960.132 460.78771 688.92684 3.5878733 - 220 6.0495639 -644.09355 2001.1189 -2645.2125 494.11524 0 53.071997 154741.65 -157934.05 -16.373549 19564.819 447.85452 669.94663 2.7746068 - 240 6.5042329 -773.76581 1911.0759 -2684.8417 491.56501 0 36.579309 154722.88 -157935.86 -773.18555 20144.755 427.70271 639.97688 2.2989541 - 260 6.9512041 -886.818 1719.7038 -2606.5218 462.97731 0 47.595907 154814.45 -157931.55 -696.23419 20696.487 384.87324 575.96351 1.9229602 - 280 7.3921249 -983.57561 1659.2167 -2642.7923 476.06924 0 65.542713 154749.27 -157933.68 -1099.4208 21220.613 371.3361 555.78067 1.7042918 - 300 7.8054619 -1069.4015 1531.598 -2600.9995 487.38132 0 130.06616 154709.03 -157927.47 -548.86446 21717.521 342.77477 513.11788 1.4030219 - 320 8.2272029 -1144.9139 1562.933 -2707.8469 509.00464 0 127.16899 154591.31 -157935.33 -1516.7077 22190.692 349.78761 523.61225 1.4145866 - 340 8.6145689 -1216.4369 1511.7737 -2728.2106 518.42214 0 144.71934 154541.92 -157933.27 -1345.493 22636.556 338.33806 506.55234 1.2328234 - 360 9.0159991 -1279.8637 1435.4044 -2715.2681 525.01973 0 153.83119 154536.21 -157930.33 -1447.797 23056.471 321.24646 480.9789 1.1390786 - 380 9.4004741 -1340.2241 1391.5909 -2731.815 536.93555 0 180.52081 154483.31 -157932.58 -1315.0222 23450.141 311.4409 466.34776 1.004293 - 400 9.7971771 -1398.7544 1401.1636 -2799.918 547.12264 0 190.99461 154394.23 -157932.27 -1686.7786 23818.238 313.5833 469.59825 0.92621346 - 420 10.175245 -1450.5676 1355.0166 -2805.5842 555.43355 0 178.57277 154392.99 -157932.58 -1948.3006 24158.665 303.2555 454.12588 0.90821389 - 440 10.550016 -1501.2755 1336.6037 -2837.8792 573.29095 0 195.76657 154324.78 -157931.72 -1845.698 24470.004 299.13465 447.99648 0.8127319 - 460 10.93798 -1551.1246 1327.3311 -2878.4557 580.57019 0 206.92238 154267.88 -157933.83 -2059.7154 24752.911 297.05944 444.88976 0.80466605 - 480 11.304226 -1597.9166 1280.274 -2878.1906 596.27629 0 247.5201 154210.94 -157932.93 -1714.1239 25006.108 286.52794 429.10945 0.79188456 - 500 11.66949 -1645.4221 1303.9947 -2949.4168 620.22431 0 275.42964 154086.38 -157931.45 -1833.6239 25232.592 291.83668 437.06941 0.78754301 - 520 12.030775 -1692.7733 1261.2365 -2954.0098 639.32812 0 295.13753 154045.85 -157934.32 -1715.0443 25432.412 282.26732 422.73896 0.75950535 - 540 12.389967 -1739.3602 1247.1301 -2986.4903 666.88476 0 341.37591 153937.16 -157931.91 -1556.9492 25607.225 279.11027 418.00746 0.75767537 - 560 12.765452 -1783.4916 1212.3647 -2995.8563 669.09681 0 366.501 153899.16 -157930.62 -1543.0147 25758.368 271.3297 406.37068 0.70509124 - 580 13.122579 -1824.6061 1200.7205 -3025.3267 699.41498 0 409.47507 153794.95 -157929.16 -1053.8519 25887.592 268.72372 402.43012 0.77346975 - 600 13.47702 -1864.0982 1206.4231 -3070.5213 726.9912 0 439.25863 153695.5 -157932.27 -1130.6737 26000.4 269.99996 404.33899 0.78190692 - 620 13.82937 -1902.6883 1167.061 -3069.7493 741.54351 0 453.21801 153667.95 -157932.46 -921.61026 26097.341 261.19065 391.14672 0.7561126 - 640 14.180362 -1941.2814 1168.4808 -3109.7622 758.6291 0 484.81029 153578.39 -157931.59 -1084.6877 26180.233 261.50841 391.64626 0.70968727 - 660 14.527615 -1977.9114 1159.1979 -3137.1094 746.51288 0 452.2958 153598.59 -157934.51 -1424.6628 26247.07 259.43088 388.52145 0.73088365 - 680 14.875155 -2015.8231 1149.125 -3164.9481 730.41157 0 417.95266 153620.83 -157934.15 -1485.3138 26293.983 257.17653 385.144 0.72723522 - 700 15.22063 -2052.4439 1175.9011 -3228.345 735.43016 0 393.72125 153577.95 -157935.44 -1936.2883 26318.916 263.16908 394.10321 0.77446426 - 720 15.565813 -2092.4868 1137.4051 -3229.892 739.27374 0 431.22089 153537.92 -157938.3 -1669.6367 26318.64 254.5536 381.18868 0.77432854 - 740 15.926298 -2128.2671 1117.2535 -3245.5206 763.39303 0 451.2336 153475.75 -157935.89 -1554.5185 26294.984 250.04362 374.42691 0.77695221 - 760 16.273413 -2164.5578 1132.9117 -3297.4695 791.93983 0 493.17297 153351.43 -157934.01 -1464.3621 26250.086 253.54797 379.63211 0.87260304 - 780 16.620524 -2201.7367 1138.2941 -3340.0308 832.89022 0 542.69718 153217.14 -157932.76 -1185.0268 26186.538 254.75255 381.43046 0.88724559 - 800 16.968419 -2236.9734 1127.0464 -3364.0197 849.94855 0 579.03844 153137.36 -157930.36 -957.1991 26107.922 252.23529 377.65702 0.8873688 - 820 17.320858 -2274.0191 1152.6791 -3426.6982 878.53555 0 605.98285 153020.89 -157932.1 -1004.5494 26016.264 257.97196 386.24526 0.90940959 - 840 17.671788 -2312.5555 1157.6702 -3470.2257 915.53242 0 653.69994 152892.11 -157931.56 -793.45868 25912.528 259.08897 387.88866 0.97141875 - 860 18.021136 -2351.0088 1136.5124 -3487.5212 921.37408 0 665.09396 152857.19 -157931.18 -528.38134 25800.163 254.35382 380.78143 0.98986969 - 880 18.370286 -2387.3364 1155.2826 -3542.619 934.02359 0 660.06761 152795.05 -157931.76 -775.58796 25681.702 258.55463 386.99987 1.1470186 - 900 18.737898 -2425.9324 1151.5543 -3577.4867 936.00838 0 670.95003 152749.78 -157934.22 -883.49007 25555.357 257.72021 385.72656 1.1920669 - 920 19.09607 -2461.264 1119.906 -3581.17 931.8496 0 682.4928 152739.5 -157935.01 -890.93067 25420.635 250.63726 375.12148 1.1675653 - 940 19.45002 -2496.7293 1081.4763 -3578.2056 971.61744 0 731.21429 152653.33 -157934.36 -483.6151 25277.795 242.03662 362.20568 1.2144341 - 960 19.805087 -2527.097 1111.841 -3638.938 964.7058 0 704.68407 152623.89 -157932.22 -841.64397 25129.524 248.8323 372.33505 1.3291216 - 980 20.160533 -2560.1354 1096.9132 -3657.0486 954.19645 0 693.42648 152627.51 -157932.19 -949.1276 24974.275 245.49142 367.3853 1.2126954 - 1000 20.518917 -2592.9079 1053.7186 -3646.6266 959.23242 0 684.31399 152644.74 -157934.91 -869.15319 24811.035 235.8244 352.90011 1.2013298 - 1020 20.849072 -2623.091 1066.4493 -3689.5404 998.09604 0 709.32917 152535.4 -157932.37 -881.38225 24640.265 238.67355 357.17132 1.2006706 - 1040 21.194962 -2652.822 1083.618 -3736.44 1011.32 0 727.70427 152458.99 -157934.45 -815.2175 24461.841 242.51594 362.90994 1.2429114 - 1060 21.530151 -2683.6347 1074.3994 -3758.0341 1029.3659 0 763.93884 152381.4 -157932.73 -616.78933 24277.069 240.45279 359.82116 1.235143 - 1080 21.868091 -2715.2991 1094.3032 -3809.6022 1068.1764 0 785.28284 152272.57 -157935.63 -541.23611 24088.232 244.9073 366.48583 1.2604348 - 1100 22.209137 -2747.0371 1066.1644 -3813.2016 1080.2369 0 833.94072 152208.13 -157935.51 -217.98411 23897.246 238.60979 357.0619 1.2283546 - 1120 22.551618 -2774.9066 1084.3361 -3859.2427 1113.055 0 847.43384 152114.69 -157934.42 -77.787494 23707.475 242.67665 363.13214 1.2803322 - 1140 22.899431 -2803.21 1072.4113 -3875.6213 1090.9217 0 807.02034 152161.17 -157934.73 -668.47773 23520.606 240.00786 359.14316 1.2572349 - 1160 23.252016 -2834.8697 1052.5943 -3887.464 1096.5034 0 789.77107 152162.88 -157936.62 -589.78074 23331.777 235.57277 352.55512 1.1369148 - 1180 23.609597 -2863.7817 1031.8109 -3895.5926 1087.1932 0 789.79657 152165.44 -157938.03 -586.94333 23140.391 230.92139 345.60929 1.0837566 - 1200 23.970129 -2891.3631 1042.111 -3933.4741 1093.7082 0 775.83298 152136.1 -157939.12 -1109.7168 22947.229 233.22659 349.07035 1.0726257 - 1220 24.3333 -2919.3393 1043.3795 -3962.7187 1095.6802 0 760.56643 152121.29 -157940.25 -1189.6331 22748.747 233.51046 349.50414 1.0560945 - 1240 24.699158 -2942.4201 1015.5889 -3958.009 1114.7861 0 821.20595 152042.69 -157936.69 -581.49954 22545.116 227.29088 340.1868 1.0444581 - 1260 25.06694 -2965.9906 1011.5209 -3977.5115 1137.3984 0 850.69736 151972.34 -157937.95 -557.09399 22340.759 226.38045 338.85243 0.98374803 - 1280 25.506043 -2989.5484 1016.7798 -4006.3282 1160.9102 0 882.24024 151890.5 -157939.98 -93.844073 22136.859 227.55742 340.60408 1.0089629 - 1300 25.885481 -3011.5964 1043.7628 -4055.3592 1184.2311 0 891.6381 151808.85 -157940.08 -307.32007 21936.757 233.59626 349.6133 1.0504806 - 1320 26.286564 -3035.1132 1037.5333 -4072.6466 1179.597 0 903.59052 151784.33 -157940.16 -91.53774 21739.794 232.20209 347.62923 0.8833997 - 1340 26.707803 -3061.1043 1034.7198 -4095.8241 1231.5568 0 955.77666 151655.57 -157938.72 53.261099 21546.978 231.57242 346.58931 1.0307605 - 1360 27.133179 -3085.252 983.77833 -4069.0303 1230.971 0 968.86383 151669.63 -157938.5 197.66951 21360.266 220.17161 329.49241 1.002352 - 1380 27.554558 -3101.9696 1037.9918 -4139.9614 1216.6215 0 897.01691 151685.79 -157939.39 -392.64446 21180.32 232.3047 347.61632 1.0380526 - 1400 27.956349 -3124.8379 1003.328 -4128.1659 1199.4883 0 863.54306 151748.07 -157939.27 -548.32584 21003.378 224.54686 336.16828 0.85494391 - 1420 28.361482 -3146.8927 1020.9417 -4167.8344 1210.319 0 850.57584 151710.13 -157938.86 -1093.8532 20825.938 228.48885 342.04449 0.9178739 - 1440 28.768238 -3170.6554 993.33274 -4163.9882 1239.5959 0 893.87046 151642.2 -157939.65 -436.10089 20645.122 222.30991 332.79717 0.88336557 - 1460 29.177687 -3191.0873 980.2106 -4171.2979 1257.3639 0 955.42122 151554.27 -157938.35 -139.1763 20465.429 219.37314 328.30589 0.99602014 - 1480 29.586943 -3208.4185 993.92387 -4202.3424 1243.9183 0 936.28667 151555.9 -157938.45 -261.1948 20289.512 222.4422 333.01034 0.85071989 - 1500 29.995233 -3229.0775 1028.0284 -4257.1059 1272.6443 0 960.80911 151449.75 -157940.31 -307.25416 20116.744 230.07487 344.43881 0.88683413 - 1520 30.435761 -3250.8294 998.11977 -4248.9491 1282.1976 0 990.08774 151419.81 -157941.05 64.772936 19947.298 223.38125 334.38841 0.90320757 - 1540 30.853458 -3268.3168 1004.1599 -4272.4768 1299.4164 0 987.20608 151381.91 -157941.01 -80.22578 19782.738 224.73305 336.30685 1.007422 - 1560 31.279241 -3289.0826 966.08591 -4255.1685 1287.1272 0 982.95309 151416.22 -157941.47 198.4371 19622.918 216.21201 323.54353 0.99939162 - 1580 31.708028 -3306.2125 979.26815 -4285.4807 1288.5111 0 952.23769 151415.68 -157941.91 -206.26434 19467.717 219.16222 328.0518 0.90689318 - 1600 32.140092 -3325.1219 984.21128 -4309.3331 1308.258 0 963.95207 151360.81 -157942.35 -284.04656 19314.766 220.2685 329.66568 0.9610293 - 1620 32.5727 -3340.9024 1013.5306 -4354.433 1318.1025 0 944.3489 151325.17 -157942.05 -653.005 19163.698 226.83023 339.47468 1.0097397 - 1640 32.982791 -3360.2312 974.13546 -4334.3667 1312.594 0 986.63361 151308.68 -157942.28 343.78235 19013.496 218.01352 326.28924 0.99083786 - 1660 33.419277 -3375.6484 982.60503 -4358.2535 1345.3148 0 970.47388 151266.28 -157940.32 -374.81541 18867.836 219.90902 329.06869 1.0301828 - 1680 33.858902 -3394.428 981.74052 -4376.1685 1319.3919 0 955.09161 151289.81 -157940.47 -162.3498 18724.14 219.71554 328.81202 0.99514477 - 1700 34.30191 -3412.8462 973.87976 -4386.7259 1341.294 0 965.41854 151248.54 -157941.98 -351.70824 18582.062 217.95629 326.03525 1.1973975 - 1720 34.776698 -3429.9352 986.76909 -4416.7043 1362.6752 0 1013.2358 151149.58 -157942.2 37.299904 18441.349 220.84095 330.4706 1.0534043 - 1740 35.222457 -3446.5561 971.25044 -4417.8065 1381.6012 0 1046.8608 151096.61 -157942.88 336.29665 18304.289 217.36784 325.28479 1.0839935 - 1760 35.644247 -3463.1798 999.75562 -4462.9354 1395.5442 0 1012.1296 151070.28 -157940.88 -252.71902 18172.322 223.74736 334.82695 1.1205298 - 1780 36.095301 -3481.5453 991.5153 -4473.0606 1403.686 0 1029.7008 151037.13 -157943.57 -108.73918 18043.082 221.90316 332.00846 1.1669904 - 1800 36.548801 -3496.9886 965.33662 -4462.3252 1390.3088 0 1050.6761 151040.12 -157943.43 539.62368 17917.488 216.04432 323.23991 1.1447201 - 1820 37.00671 -3510.113 991.32596 -4501.439 1392.0482 0 1034.7898 151015.68 -157943.96 152.36115 17797.781 221.86078 332.04409 1.050451 - 1840 37.465953 -3528.9352 974.95032 -4503.8855 1387.6457 0 1012.5199 151036.63 -157940.68 -250.11127 17681.765 218.19588 326.4633 1.104675 - 1860 37.926741 -3545.3967 970.46573 -4515.8624 1391.3683 0 1035.1551 151000.11 -157942.49 -218.15781 17567.52 217.19222 325.05524 1.0190724 - 1880 38.391252 -3561.7398 933.83134 -4495.5711 1404.458 0 1032.7156 151010.9 -157943.64 -1.9885562 17454.833 208.99337 312.70412 1.1301542 - 1900 38.856336 -3574.6165 984.6503 -4559.2668 1422.0814 0 1060.3245 150900.79 -157942.46 190.15103 17344.24 220.36676 329.66505 1.2027369 - 1920 39.32352 -3589.0687 963.85062 -4552.9193 1427.8662 0 1075.6986 150887.22 -157943.7 506.81653 17237.394 215.71175 322.81523 1.0733524 - 1940 39.79544 -3604.8214 970.89136 -4575.7128 1416.926 0 1037.9197 150913.56 -157944.12 -60.261935 17135.412 217.28748 325.12481 1.144127 - 1960 40.270815 -3620.548 963.48434 -4584.0323 1401.1546 0 1016.5609 150941.43 -157943.17 -388.03612 17035.264 215.62977 322.67138 1.1152888 - 1980 40.749353 -3638.3971 977.90456 -4616.3017 1415.5473 0 1009.486 150904.71 -157946.04 -640.67547 16934.97 218.85705 327.48198 1.1614525 - 2000 41.229238 -3654.2588 957.08437 -4611.3432 1418.1059 0 1031.2688 150883.23 -157943.95 -595.60403 16834.098 214.19745 320.55039 1.0631632 -Loop time of 41.2293 on 4 procs for 2000 steps with 2500 atoms - -Pair time (%) = 23.5391 (57.0932) -Bond time (%) = 0.0153775 (0.0372976) -Kspce time (%) = 3.17798 (7.70806) -Neigh time (%) = 2.51543 (6.10108) -Comm time (%) = 1.6585 (4.02262) -Outpt time (%) = 0.00876421 (0.0212572) -Other time (%) = 10.3141 (25.0165) - -Nlocal: 625 ave 632 max 619 min -Histogram: 1 0 0 1 0 1 0 0 0 1 -Nghost: 12577 ave 12644 max 12511 min -Histogram: 1 0 0 1 0 0 1 0 0 1 -Neighs: 532752 ave 581561 max 492708 min -Histogram: 1 1 0 0 0 0 1 0 0 1 - -Total # of neighbors = 2131009 -Ave neighs/atom = 852.404 -Ave special neighs/atom = 4 -Neighbor list builds = 120 -Dangerous builds = 16 - diff --git a/examples/USER/drude/toluene/log.27Nov18.toluene.lang.g++.1 b/examples/USER/drude/toluene/log.27Nov18.toluene.lang.g++.1 new file mode 100644 index 0000000000..08cc2f0f5c --- /dev/null +++ b/examples/USER/drude/toluene/log.27Nov18.toluene.lang.g++.1 @@ -0,0 +1,14 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# 250 toluene system for drude polarizability example (Langevin) + +units real +boundary p p p + +atom_style full +bond_style harmonic +angle_style harmonic +dihedral_style opls +improper_style opls +ERROR: Unknown improper style opls (src/force.cpp:634) +Last command: improper_style opls diff --git a/examples/USER/drude/toluene/log.27Nov18.toluene.lang.g++.4 b/examples/USER/drude/toluene/log.27Nov18.toluene.lang.g++.4 new file mode 100644 index 0000000000..08cc2f0f5c --- /dev/null +++ b/examples/USER/drude/toluene/log.27Nov18.toluene.lang.g++.4 @@ -0,0 +1,14 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# 250 toluene system for drude polarizability example (Langevin) + +units real +boundary p p p + +atom_style full +bond_style harmonic +angle_style harmonic +dihedral_style opls +improper_style opls +ERROR: Unknown improper style opls (src/force.cpp:634) +Last command: improper_style opls diff --git a/examples/USER/drude/toluene/log.27Nov18.toluene.nh.g++.1 b/examples/USER/drude/toluene/log.27Nov18.toluene.nh.g++.1 new file mode 100644 index 0000000000..a6807f8ee1 --- /dev/null +++ b/examples/USER/drude/toluene/log.27Nov18.toluene.nh.g++.1 @@ -0,0 +1,14 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# 250 toluene system for drude polarizability example (Nose-Hoover) + +units real +boundary p p p + +atom_style full +bond_style harmonic +angle_style harmonic +dihedral_style opls +improper_style opls +ERROR: Unknown improper style opls (src/force.cpp:634) +Last command: improper_style opls diff --git a/examples/USER/drude/toluene/log.27Nov18.toluene.nh.g++.4 b/examples/USER/drude/toluene/log.27Nov18.toluene.nh.g++.4 new file mode 100644 index 0000000000..a6807f8ee1 --- /dev/null +++ b/examples/USER/drude/toluene/log.27Nov18.toluene.nh.g++.4 @@ -0,0 +1,14 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# 250 toluene system for drude polarizability example (Nose-Hoover) + +units real +boundary p p p + +atom_style full +bond_style harmonic +angle_style harmonic +dihedral_style opls +improper_style opls +ERROR: Unknown improper style opls (src/force.cpp:634) +Last command: improper_style opls diff --git a/examples/USER/drude/toluene/log.toluene.lang.11Aug17.linux.1 b/examples/USER/drude/toluene/log.toluene.lang.11Aug17.linux.1 deleted file mode 100644 index bc51063341..0000000000 --- a/examples/USER/drude/toluene/log.toluene.lang.11Aug17.linux.1 +++ /dev/null @@ -1,251 +0,0 @@ -LAMMPS (11 Aug 2017) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) - using 1 OpenMP thread(s) per MPI task -# 250 toluene system for drude polarizability example (Langevin) - -units real -boundary p p p - -atom_style full -bond_style harmonic -angle_style harmonic -dihedral_style opls -improper_style opls -special_bonds lj/coul 0.0 0.0 0.5 - -pair_style lj/cut/thole/long 2.600 8.0 8.0 -pair_modify mix geometric tail yes -kspace_style pppm 1.0e-4 - -read_data data.toluene extra/special/per/atom 1 - orthogonal box = (-18.2908 -18.1636 -18.223) to (18.3357 18.1621 18.3287) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 5500 atoms - scanning bonds ... - 4 = max bonds/atom - scanning angles ... - 6 = max angles/atom - scanning dihedrals ... - 8 = max dihedrals/atom - scanning impropers ... - 2 = max impropers/atom - reading bonds ... - 5500 bonds - reading angles ... - 6000 angles - reading dihedrals ... - 6000 dihedrals - reading impropers ... - 1500 impropers - 5 = max # of 1-2 neighbors - 10 = max # of 1-3 neighbors - 16 = max # of 1-4 neighbors - 20 = max # of special neighbors - -comm_modify vel yes - -group gTOLUENE molecule 1:250 -5500 atoms in group gTOLUENE -group gCORES type 1 2 3 4 5 6 7 -3750 atoms in group gCORES -group gDRUDES type 8 9 10 11 12 -1750 atoms in group gDRUDES - -pair_coeff 1 1 0.069998 3.550000 1.620000 # CAT CAT -pair_coeff 1 2 0.069998 3.550000 1.620000 # CAT CAO -pair_coeff 1 3 0.069998 3.550000 1.620000 # CAT CAM -pair_coeff 1 4 0.069998 3.550000 1.620000 # CAT CAP -pair_coeff 1 5 0.067968 3.524911 1.620000 # CAT CTT -pair_coeff 1 6 0.045825 2.931041 0.000000 # CAT HAT -pair_coeff 1 7 0.045825 2.931041 0.000000 # CAT HT -pair_coeff 2 2 0.069998 3.550000 1.620000 # CAO CAO -pair_coeff 2 3 0.069998 3.550000 1.620000 # CAO CAM -pair_coeff 2 4 0.069998 3.550000 1.620000 # CAO CAP -pair_coeff 2 5 0.067968 3.524911 1.620000 # CAO CTT -pair_coeff 2 6 0.045825 2.931041 0.000000 # CAO HAT -pair_coeff 2 7 0.045825 2.931041 0.000000 # CAO HT -pair_coeff 3 3 0.069998 3.550000 1.620000 # CAM CAM -pair_coeff 3 4 0.069998 3.550000 1.620000 # CAM CAP -pair_coeff 3 5 0.067968 3.524911 1.620000 # CAM CTT -pair_coeff 3 6 0.045825 2.931041 0.000000 # CAM HAT -pair_coeff 3 7 0.045825 2.931041 0.000000 # CAM HT -pair_coeff 4 4 0.069998 3.550000 1.620000 # CAP CAP -pair_coeff 4 5 0.067968 3.524911 1.620000 # CAP CTT -pair_coeff 4 6 0.045825 2.931041 0.000000 # CAP HAT -pair_coeff 4 7 0.045825 2.931041 0.000000 # CAP HT -pair_coeff 5 5 0.065997 3.500000 1.620000 # CTT CTT -pair_coeff 5 6 0.044496 2.910326 0.000000 # CTT HAT -pair_coeff 5 7 0.044496 2.910326 0.000000 # CTT HT -pair_coeff 6 6 0.029999 2.420000 0.000000 # HAT HAT -pair_coeff 6 7 0.029999 2.420000 0.000000 # HAT HT -pair_coeff 7 7 0.029999 2.420000 0.000000 # HT HT -pair_coeff 1 8 0.000000 0.000000 1.620000 # CAT D_CAT -pair_coeff 1 9 0.000000 0.000000 1.620000 # CAT D_CAO -pair_coeff 1 10 0.000000 0.000000 1.620000 # CAT D_CAM -pair_coeff 1 11 0.000000 0.000000 1.620000 # CAT D_CAP -pair_coeff 1 12 0.000000 0.000000 1.620000 # CAT D_CTT -pair_coeff 2 8 0.000000 0.000000 1.620000 # CAO D_CAT -pair_coeff 2 9 0.000000 0.000000 1.620000 # CAO D_CAO -pair_coeff 2 10 0.000000 0.000000 1.620000 # CAO D_CAM -pair_coeff 2 11 0.000000 0.000000 1.620000 # CAO D_CAP -pair_coeff 2 12 0.000000 0.000000 1.620000 # CAO D_CTT -pair_coeff 3 8 0.000000 0.000000 1.620000 # CAM D_CAT -pair_coeff 3 9 0.000000 0.000000 1.620000 # CAM D_CAO -pair_coeff 3 10 0.000000 0.000000 1.620000 # CAM D_CAM -pair_coeff 3 11 0.000000 0.000000 1.620000 # CAM D_CAP -pair_coeff 3 12 0.000000 0.000000 1.620000 # CAM D_CTT -pair_coeff 4 8 0.000000 0.000000 1.620000 # CAP D_CAT -pair_coeff 4 9 0.000000 0.000000 1.620000 # CAP D_CAO -pair_coeff 4 10 0.000000 0.000000 1.620000 # CAP D_CAM -pair_coeff 4 11 0.000000 0.000000 1.620000 # CAP D_CAP -pair_coeff 4 12 0.000000 0.000000 1.620000 # CAP D_CTT -pair_coeff 5 8 0.000000 0.000000 1.620000 # CTT D_CAT -pair_coeff 5 9 0.000000 0.000000 1.620000 # CTT D_CAO -pair_coeff 5 10 0.000000 0.000000 1.620000 # CTT D_CAM -pair_coeff 5 11 0.000000 0.000000 1.620000 # CTT D_CAP -pair_coeff 5 12 0.000000 0.000000 1.620000 # CTT D_CTT -pair_coeff 8 8 0.000000 0.000000 1.620000 # D_CAT D_CAT -pair_coeff 8 9 0.000000 0.000000 1.620000 # D_CAT D_CAO -pair_coeff 8 10 0.000000 0.000000 1.620000 # D_CAT D_CAM -pair_coeff 8 11 0.000000 0.000000 1.620000 # D_CAT D_CAP -pair_coeff 8 12 0.000000 0.000000 1.620000 # D_CAT D_CTT -pair_coeff 9 9 0.000000 0.000000 1.620000 # D_CAO D_CAO -pair_coeff 9 10 0.000000 0.000000 1.620000 # D_CAO D_CAM -pair_coeff 9 11 0.000000 0.000000 1.620000 # D_CAO D_CAP -pair_coeff 9 12 0.000000 0.000000 1.620000 # D_CAO D_CTT -pair_coeff 10 10 0.000000 0.000000 1.620000 # D_CAM D_CAM -pair_coeff 10 11 0.000000 0.000000 1.620000 # D_CAM D_CAP -pair_coeff 10 12 0.000000 0.000000 1.620000 # D_CAM D_CTT -pair_coeff 11 11 0.000000 0.000000 1.620000 # D_CAP D_CAP -pair_coeff 11 12 0.000000 0.000000 1.620000 # D_CAP D_CTT -pair_coeff 12 12 0.000000 0.000000 1.620000 # D_CTT D_CTT - -neighbor 2.0 bin - -variable vTEMP equal 260.0 -variable vTEMP_D equal 1.0 -variable vPRESS equal 1.0 - -velocity gCORES create ${vTEMP} 12345 -velocity gCORES create 260 12345 -velocity gDRUDES create ${vTEMP_D} 12345 -velocity gDRUDES create 1 12345 - -fix fDRUDE all drude C C C C C N N D D D D D - -fix fSHAKE gCORES shake 0.0001 20 0 b 4 6 7 8 - 1250 = # of size 2 clusters - 0 = # of size 3 clusters - 250 = # of size 4 clusters - 0 = # of frozen angles - -fix fLANG all langevin/drude ${vTEMP} 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes -fix fLANG all langevin/drude 260 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes -fix fLANG all langevin/drude 260 100.0 200611 1 20.0 260514 zero yes -fix fNPH all nve - -compute cTEMP all temp/drude - -thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2] -thermo 50 - -timestep 0.5 -run 2000 -PPPM initialization ... -WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) - G vector (1/distance) = 0.382011 - grid = 40 40 40 - stencil order = 5 - estimated absolute RMS force accuracy = 0.0325934 - estimated relative force accuracy = 9.8154e-05 - using double precision FFTs - 3d grid and FFT values/proc = 103823 64000 -Rebuild special list taking Drude particles into account -Old max number of 1-2 to 1-4 neighbors: 19 -New max number of 1-2 to 1-4 neighbors: 20 (+1) -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 10 - ghost atom cutoff = 10 - binsize = 5, bins = 8 8 8 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut/thole/long, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 42.06 | 42.06 | 42.06 Mbytes -Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2] - 0 0 14386.197 2910.7282 202.07402 11475.469 6565.4851 20.333365 1.0706727e-06 1.3894617e-07 4972.8631 1306116.6 -1306199.8 40273.68 48631.318 314.89553 3.1777821 - 50 4.311986 8083.3901 4729.9995 328.37487 3353.3906 1812.5186 685.40417 646.10358 50.083281 804.80656 1305984.8 -1306630.3 16960.287 48631.318 448.67988 116.22125 - 100 8.756623 6206.7865 3683.944 255.75365 2522.8425 977.52675 777.45439 838.58809 68.086914 471.97862 1306097.1 -1306707.9 15657.142 48631.318 380.53159 35.760643 - 150 13.134938 5386.0219 3582.482 248.70976 1803.5399 752.25928 803.04832 643.43249 49.76684 131.97853 1306139.2 -1306716.2 15140.102 48631.318 383.61303 10.880935 - 200 17.508189 4846.4097 3254.3932 225.93257 1592.0166 700.43329 812.26722 657.52279 51.044716 -64.045174 1306160.5 -1306725.7 13844.277 48631.318 351.90677 3.8489009 - 250 21.871676 4473.215 3091.5333 214.6262 1381.6817 688.24707 842.63267 590.45999 48.22798 -214.02425 1306156.6 -1306730.5 8808.7402 48631.318 335.32872 1.8372171 - 300 26.226064 4191.8834 2883.8468 200.2078 1308.0367 734.36657 856.15482 584.87904 47.590787 -343.44615 1306163.4 -1306734.9 3389.3777 48631.318 313.03581 1.3011826 - 350 30.568716 3972.0739 2756.8392 191.39044 1215.2347 664.4688 866.06348 580.13632 48.515297 -378.8729 1306173.3 -1306738.3 8458.1149 48631.318 299.31146 1.1345329 - 400 34.845648 3838.3528 2731.3975 189.62419 1106.9552 684.0318 870.67752 548.93014 44.038787 -460.1537 1306160.4 -1306741 6697.9188 48631.318 296.54405 1.1332149 - 450 39.17477 3731.18 2607.8585 181.04762 1123.3216 719.57572 894.99915 571.99504 47.625227 -537.60494 1306171.9 -1306745.2 2450.4224 48631.318 283.13713 1.0721818 - 500 43.497489 3607.0055 2565.9469 178.13796 1041.0586 717.36452 841.34375 551.39834 45.985413 -542.47313 1306170.9 -1306743.4 3077.1849 48631.318 278.59462 1.0410963 - 550 47.812038 3513.8132 2548.7259 176.94241 965.08736 673.81272 852.38161 522.99297 44.276434 -552.27379 1306171.2 -1306747.4 4659.7275 48631.318 276.70124 1.0757459 - 600 52.124423 3386.9627 2471.0692 171.55118 915.89348 689.99732 833.61298 517.49343 43.023588 -594.96363 1306170.6 -1306743.8 2159.7328 48631.318 268.27854 1.0287605 - 650 56.370068 3374.3191 2413.6719 167.56644 960.64717 703.32428 874.12028 535.41271 43.256032 -617.25815 1306168.6 -1306746.8 1262.4757 48631.318 261.99584 1.0950976 - 700 60.667476 3342.9467 2412.9563 167.51676 929.99042 683.70355 882.22521 527.03932 43.661355 -616.70117 1306161 -1306751 2950.9009 48631.318 261.92814 1.0771869 - 750 64.964696 3327.7938 2414.3547 167.61385 913.43902 695.12778 863.48248 542.99202 46.408369 -639.60076 1306160.7 -1306755.6 1583.0277 48631.318 262.09771 1.0464936 - 800 69.256916 3391.689 2452.2049 170.24155 939.48407 694.2176 892.61592 557.53726 45.495129 -654.56675 1306155.2 -1306751 1232.1671 48631.318 266.20601 1.0640309 - 850 73.527972 3386.8618 2486.6928 172.63584 900.16902 696.7684 880.27643 545.11446 46.474227 -665.90464 1306154.7 -1306757.3 1129.2062 48631.318 269.97945 1.027015 - 900 77.775993 3368.0724 2416.7145 167.77767 951.35789 718.66654 893.18396 537.79136 46.404626 -641.29596 1306152.9 -1306756.3 1673.0743 48631.318 262.34697 1.0597091 - 950 82.028341 3300.4793 2409.5613 167.28107 890.918 728.06888 890.51193 515.08456 44.36547 -671.13741 1306142.3 -1306758.2 1038.6579 48631.318 261.57036 1.0567234 - 1000 86.189789 3333.2955 2452.2486 170.24458 881.04692 699.8414 915.33862 506.83261 41.77374 -665.68264 1306141.6 -1306758.7 467.42142 48631.318 266.19104 1.0987814 - 1050 90.384168 3303.87 2376.9713 165.01854 926.89875 706.12941 930.65844 524.73304 42.644613 -657.19573 1306139.3 -1306759.4 1737.6624 48631.318 258.00246 1.0954432 - 1100 94.549452 3367.668 2454.9154 170.42973 912.75259 715.68494 935.8363 516.52205 43.261761 -671.86101 1306137.9 -1306764.6 961.79199 48631.318 266.492 1.0797548 - 1150 98.65493 3350.0898 2485.3993 172.54604 864.69051 699.23072 933.76405 510.60424 42.381362 -684.53513 1306127.1 -1306763.8 -272.48178 48631.318 269.82496 1.0512421 - 1200 102.82045 3309.6871 2398.9577 166.54492 910.72944 705.58979 934.53183 531.90967 45.872142 -664.58495 1306126.9 -1306769.5 627.31931 48631.318 260.41866 1.0531639 - 1250 106.9899 3304.504 2491.6998 172.98344 812.80426 710.83366 881.33764 494.90045 41.71618 -672.49264 1306123.8 -1306767.3 136.11723 48631.318 270.51026 1.0516137 - 1300 111.16224 3318.9543 2462.0621 170.92588 856.89219 709.17314 932.87209 503.80373 43.426006 -680.2474 1306121.2 -1306773.3 1276.2503 48631.318 267.28591 1.0510113 - 1350 115.27184 3314.8515 2434.8483 169.03659 880.00316 710.91641 922.28347 540.40795 44.753548 -686.09335 1306124.5 -1306776.7 -438.87694 48631.318 264.31236 1.0731666 - 1400 119.44228 3349.0785 2457.7697 170.62788 891.30875 711.28064 936.58607 516.63511 42.396287 -653.09763 1306113.8 -1306776.3 350.79618 48631.318 266.80555 1.0745043 - 1450 123.61267 3364.1486 2459.8741 170.77397 904.27455 696.57265 946.32098 538.55368 44.69075 -652.75091 1306111 -1306780.1 502.47466 48631.318 267.03201 1.0789056 - 1500 127.72962 3341.9369 2454.3302 170.3891 887.60672 726.46979 903.40815 557.73064 47.536125 -667.65025 1306100.7 -1306780.6 -248.0975 48631.318 266.44821 1.044725 - 1550 131.91041 3270.4282 2437.7916 169.24093 832.63655 691.49462 910.83807 523.17366 44.83093 -654.48655 1306100.5 -1306783.7 490.32965 48631.318 264.63652 1.0662604 - 1600 136.0834 3252.0725 2429.6805 168.67782 822.39196 689.68155 898.22828 535.31963 43.84399 -660.93277 1306100.1 -1306783.9 1729.5956 48631.318 263.74523 1.0817172 - 1650 140.26444 3239.748 2442.6258 169.57653 797.12222 671.1832 907.1659 507.03947 43.048028 -648.14001 1306103.3 -1306786.5 970.43988 48631.318 265.15987 1.0708872 - 1700 144.3855 3202.9157 2410.267 167.33006 792.64869 686.40974 882.40791 527.02899 43.819792 -656.82001 1306096 -1306786.2 -107.50166 48631.318 261.64368 1.062837 - 1750 148.56592 3214.6107 2366.3264 164.27953 848.28434 696.38228 915.58636 538.2236 47.852688 -652.7697 1306093.6 -1306790.6 -164.14366 48631.318 256.84519 1.0937744 - 1800 152.74611 3209.5771 2421.4089 168.10357 788.16819 683.61816 869.45802 532.77927 45.708374 -658.39221 1306103.1 -1306788.1 277.61781 48631.318 262.83282 1.1036154 - 1850 156.86567 3146.3973 2362.3333 164.00232 784.064 697.87032 875.8451 523.54452 43.851379 -665.83106 1306101.5 -1306792.7 497.88657 48631.318 256.42683 1.0654271 - 1900 161.0419 3141.5496 2367.1077 164.33378 774.44186 693.39945 878.97447 515.65653 44.619392 -668.11692 1306103.8 -1306793.9 -1427.3998 48631.318 256.94212 1.0727903 - 1950 165.22235 3134.6473 2295.577 159.36784 839.07025 699.62719 905.76937 519.32307 46.109334 -645.08933 1306104.9 -1306791.6 1744.2846 48631.318 249.19694 1.0064565 - 2000 169.4 3146.866 2361.3821 163.93628 785.48386 682.24124 889.6864 534.94877 46.855983 -678.1614 1306104 -1306794.1 699.8735 48631.318 256.32873 1.0559143 -Loop time of 169.4 on 1 procs for 2000 steps with 5500 atoms - -Performance: 0.510 ns/day, 47.056 hours/ns, 11.806 timesteps/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 | 107.93 | 107.93 | 107.93 | 0.0 | 63.71 -Bond | 19.76 | 19.76 | 19.76 | 0.0 | 11.66 -Kspace | 34.926 | 34.926 | 34.926 | 0.0 | 20.62 -Neigh | 1.9932 | 1.9932 | 1.9932 | 0.0 | 1.18 -Comm | 0.73555 | 0.73555 | 0.73555 | 0.0 | 0.43 -Output | 0.0065863 | 0.0065863 | 0.0065863 | 0.0 | 0.00 -Modify | 3.9135 | 3.9135 | 3.9135 | 0.0 | 2.31 -Other | | 0.133 | | | 0.08 - -Nlocal: 5500 ave 5500 max 5500 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 13219 ave 13219 max 13219 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 1.33739e+06 ave 1.33739e+06 max 1.33739e+06 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 1337388 -Ave neighs/atom = 243.161 -Ave special neighs/atom = 15.6364 -Neighbor list builds = 32 -Dangerous builds = 0 -Total wall time: 0:02:49 diff --git a/examples/USER/drude/toluene/log.toluene.lang.11Aug17.linux.4 b/examples/USER/drude/toluene/log.toluene.lang.11Aug17.linux.4 deleted file mode 100644 index cebe687c11..0000000000 --- a/examples/USER/drude/toluene/log.toluene.lang.11Aug17.linux.4 +++ /dev/null @@ -1,251 +0,0 @@ -LAMMPS (11 Aug 2017) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) - using 1 OpenMP thread(s) per MPI task -# 250 toluene system for drude polarizability example (Langevin) - -units real -boundary p p p - -atom_style full -bond_style harmonic -angle_style harmonic -dihedral_style opls -improper_style opls -special_bonds lj/coul 0.0 0.0 0.5 - -pair_style lj/cut/thole/long 2.600 8.0 8.0 -pair_modify mix geometric tail yes -kspace_style pppm 1.0e-4 - -read_data data.toluene extra/special/per/atom 1 - orthogonal box = (-18.2908 -18.1636 -18.223) to (18.3357 18.1621 18.3287) - 2 by 1 by 2 MPI processor grid - reading atoms ... - 5500 atoms - scanning bonds ... - 4 = max bonds/atom - scanning angles ... - 6 = max angles/atom - scanning dihedrals ... - 8 = max dihedrals/atom - scanning impropers ... - 2 = max impropers/atom - reading bonds ... - 5500 bonds - reading angles ... - 6000 angles - reading dihedrals ... - 6000 dihedrals - reading impropers ... - 1500 impropers - 5 = max # of 1-2 neighbors - 10 = max # of 1-3 neighbors - 16 = max # of 1-4 neighbors - 20 = max # of special neighbors - -comm_modify vel yes - -group gTOLUENE molecule 1:250 -5500 atoms in group gTOLUENE -group gCORES type 1 2 3 4 5 6 7 -3750 atoms in group gCORES -group gDRUDES type 8 9 10 11 12 -1750 atoms in group gDRUDES - -pair_coeff 1 1 0.069998 3.550000 1.620000 # CAT CAT -pair_coeff 1 2 0.069998 3.550000 1.620000 # CAT CAO -pair_coeff 1 3 0.069998 3.550000 1.620000 # CAT CAM -pair_coeff 1 4 0.069998 3.550000 1.620000 # CAT CAP -pair_coeff 1 5 0.067968 3.524911 1.620000 # CAT CTT -pair_coeff 1 6 0.045825 2.931041 0.000000 # CAT HAT -pair_coeff 1 7 0.045825 2.931041 0.000000 # CAT HT -pair_coeff 2 2 0.069998 3.550000 1.620000 # CAO CAO -pair_coeff 2 3 0.069998 3.550000 1.620000 # CAO CAM -pair_coeff 2 4 0.069998 3.550000 1.620000 # CAO CAP -pair_coeff 2 5 0.067968 3.524911 1.620000 # CAO CTT -pair_coeff 2 6 0.045825 2.931041 0.000000 # CAO HAT -pair_coeff 2 7 0.045825 2.931041 0.000000 # CAO HT -pair_coeff 3 3 0.069998 3.550000 1.620000 # CAM CAM -pair_coeff 3 4 0.069998 3.550000 1.620000 # CAM CAP -pair_coeff 3 5 0.067968 3.524911 1.620000 # CAM CTT -pair_coeff 3 6 0.045825 2.931041 0.000000 # CAM HAT -pair_coeff 3 7 0.045825 2.931041 0.000000 # CAM HT -pair_coeff 4 4 0.069998 3.550000 1.620000 # CAP CAP -pair_coeff 4 5 0.067968 3.524911 1.620000 # CAP CTT -pair_coeff 4 6 0.045825 2.931041 0.000000 # CAP HAT -pair_coeff 4 7 0.045825 2.931041 0.000000 # CAP HT -pair_coeff 5 5 0.065997 3.500000 1.620000 # CTT CTT -pair_coeff 5 6 0.044496 2.910326 0.000000 # CTT HAT -pair_coeff 5 7 0.044496 2.910326 0.000000 # CTT HT -pair_coeff 6 6 0.029999 2.420000 0.000000 # HAT HAT -pair_coeff 6 7 0.029999 2.420000 0.000000 # HAT HT -pair_coeff 7 7 0.029999 2.420000 0.000000 # HT HT -pair_coeff 1 8 0.000000 0.000000 1.620000 # CAT D_CAT -pair_coeff 1 9 0.000000 0.000000 1.620000 # CAT D_CAO -pair_coeff 1 10 0.000000 0.000000 1.620000 # CAT D_CAM -pair_coeff 1 11 0.000000 0.000000 1.620000 # CAT D_CAP -pair_coeff 1 12 0.000000 0.000000 1.620000 # CAT D_CTT -pair_coeff 2 8 0.000000 0.000000 1.620000 # CAO D_CAT -pair_coeff 2 9 0.000000 0.000000 1.620000 # CAO D_CAO -pair_coeff 2 10 0.000000 0.000000 1.620000 # CAO D_CAM -pair_coeff 2 11 0.000000 0.000000 1.620000 # CAO D_CAP -pair_coeff 2 12 0.000000 0.000000 1.620000 # CAO D_CTT -pair_coeff 3 8 0.000000 0.000000 1.620000 # CAM D_CAT -pair_coeff 3 9 0.000000 0.000000 1.620000 # CAM D_CAO -pair_coeff 3 10 0.000000 0.000000 1.620000 # CAM D_CAM -pair_coeff 3 11 0.000000 0.000000 1.620000 # CAM D_CAP -pair_coeff 3 12 0.000000 0.000000 1.620000 # CAM D_CTT -pair_coeff 4 8 0.000000 0.000000 1.620000 # CAP D_CAT -pair_coeff 4 9 0.000000 0.000000 1.620000 # CAP D_CAO -pair_coeff 4 10 0.000000 0.000000 1.620000 # CAP D_CAM -pair_coeff 4 11 0.000000 0.000000 1.620000 # CAP D_CAP -pair_coeff 4 12 0.000000 0.000000 1.620000 # CAP D_CTT -pair_coeff 5 8 0.000000 0.000000 1.620000 # CTT D_CAT -pair_coeff 5 9 0.000000 0.000000 1.620000 # CTT D_CAO -pair_coeff 5 10 0.000000 0.000000 1.620000 # CTT D_CAM -pair_coeff 5 11 0.000000 0.000000 1.620000 # CTT D_CAP -pair_coeff 5 12 0.000000 0.000000 1.620000 # CTT D_CTT -pair_coeff 8 8 0.000000 0.000000 1.620000 # D_CAT D_CAT -pair_coeff 8 9 0.000000 0.000000 1.620000 # D_CAT D_CAO -pair_coeff 8 10 0.000000 0.000000 1.620000 # D_CAT D_CAM -pair_coeff 8 11 0.000000 0.000000 1.620000 # D_CAT D_CAP -pair_coeff 8 12 0.000000 0.000000 1.620000 # D_CAT D_CTT -pair_coeff 9 9 0.000000 0.000000 1.620000 # D_CAO D_CAO -pair_coeff 9 10 0.000000 0.000000 1.620000 # D_CAO D_CAM -pair_coeff 9 11 0.000000 0.000000 1.620000 # D_CAO D_CAP -pair_coeff 9 12 0.000000 0.000000 1.620000 # D_CAO D_CTT -pair_coeff 10 10 0.000000 0.000000 1.620000 # D_CAM D_CAM -pair_coeff 10 11 0.000000 0.000000 1.620000 # D_CAM D_CAP -pair_coeff 10 12 0.000000 0.000000 1.620000 # D_CAM D_CTT -pair_coeff 11 11 0.000000 0.000000 1.620000 # D_CAP D_CAP -pair_coeff 11 12 0.000000 0.000000 1.620000 # D_CAP D_CTT -pair_coeff 12 12 0.000000 0.000000 1.620000 # D_CTT D_CTT - -neighbor 2.0 bin - -variable vTEMP equal 260.0 -variable vTEMP_D equal 1.0 -variable vPRESS equal 1.0 - -velocity gCORES create ${vTEMP} 12345 -velocity gCORES create 260 12345 -velocity gDRUDES create ${vTEMP_D} 12345 -velocity gDRUDES create 1 12345 - -fix fDRUDE all drude C C C C C N N D D D D D - -fix fSHAKE gCORES shake 0.0001 20 0 b 4 6 7 8 - 1250 = # of size 2 clusters - 0 = # of size 3 clusters - 250 = # of size 4 clusters - 0 = # of frozen angles - -fix fLANG all langevin/drude ${vTEMP} 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes -fix fLANG all langevin/drude 260 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes -fix fLANG all langevin/drude 260 100.0 200611 1 20.0 260514 zero yes -fix fNPH all nve - -compute cTEMP all temp/drude - -thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2] -thermo 50 - -timestep 0.5 -run 2000 -PPPM initialization ... -WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) - G vector (1/distance) = 0.382011 - grid = 40 40 40 - stencil order = 5 - estimated absolute RMS force accuracy = 0.0325934 - estimated relative force accuracy = 9.8154e-05 - using double precision FFTs - 3d grid and FFT values/proc = 34263 16000 -Rebuild special list taking Drude particles into account -Old max number of 1-2 to 1-4 neighbors: 19 -New max number of 1-2 to 1-4 neighbors: 20 (+1) -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 10 - ghost atom cutoff = 10 - binsize = 5, bins = 8 8 8 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut/thole/long, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 18 | 18 | 18 Mbytes -Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2] - 0 0 14386.197 2910.7282 202.07402 11475.469 6565.4851 20.333365 1.0706727e-06 1.3894617e-07 4972.8631 1306116.6 -1306199.8 40273.68 48631.318 314.89553 3.1777821 - 50 1.0658228 8014.6879 4671.7498 324.33095 3342.9381 1798.7991 670.22837 651.99307 50.352024 819.34616 1305984.9 -1306632.7 17255.952 48631.318 442.52888 116.12397 - 100 2.136163 6185.5007 3697.0414 256.66292 2488.4593 974.42931 774.88353 840.46625 66.896007 427.27085 1306105.5 -1306701 15044.739 48631.318 381.93582 35.802658 - 150 3.202647 5418.0644 3628.2714 251.88864 1789.7929 764.02696 804.61034 641.14915 47.995428 108.05084 1306138.9 -1306714.9 15258.194 48631.318 388.65363 10.777816 - 200 4.2728949 4838.4235 3303.8964 229.36927 1534.5271 702.10438 772.85348 625.99718 52.299187 -63.792745 1306166.5 -1306721.4 13487.722 48631.318 357.35337 3.7423617 - 250 5.3275268 4461.2438 3084.8973 214.16551 1376.3465 693.85145 823.23815 599.85313 48.280277 -230.56822 1306167.8 -1306726.1 8779.0061 48631.318 334.59262 1.8620294 - 300 6.3794398 4179.6462 2885.0738 200.29299 1294.5724 739.337 868.84011 555.04912 44.838819 -354.73738 1306171.3 -1306730 4410.8735 48631.318 313.17473 1.2892347 - 350 7.427706 3934.3968 2756.2421 191.34899 1178.1546 666.16877 877.32996 548.99846 45.087026 -404.32209 1306179 -1306734.1 8477.8828 48631.318 299.22663 1.1698531 - 400 8.4820418 3800.4769 2674.8317 185.69716 1125.6452 693.29433 841.29833 579.61438 48.325361 -470.18802 1306170.5 -1306737.2 6265.7532 48631.318 290.39105 1.1303952 - 450 9.528651 3685.28 2616.9074 181.67583 1068.3726 702.68328 886.66644 555.74511 46.160811 -557.70651 1306176.6 -1306741.7 2701.7737 48631.318 284.11064 1.091646 - 500 10.579133 3582.6591 2517.6443 174.78461 1065.0148 701.82101 894.9429 554.06012 46.074357 -570.49878 1306181.8 -1306743.2 3643.7426 48631.318 273.31525 1.0831346 - 550 11.629649 3542.0402 2527.0386 175.4368 1015.0016 688.73877 916.2381 521.69932 44.014375 -580.05437 1306171 -1306746.6 2928.6632 48631.318 274.34257 1.0740018 - 600 12.684143 3507.0443 2519.9749 174.94641 987.06936 711.58734 894.63276 525.57884 42.944226 -603.24423 1306161.2 -1306745.7 2082.9907 48631.318 273.57124 1.0784841 - 650 13.737965 3416.2001 2445.9361 169.80635 970.26394 706.95207 891.76446 540.90369 45.970985 -626.32832 1306160.2 -1306749.2 1912.8783 48631.318 265.5023 1.1021764 - 700 14.777375 3419.7572 2446.117 169.81891 973.64019 664.17579 936.51992 551.67148 45.696531 -634.70926 1306159.6 -1306749.4 2215.7085 48631.318 265.53614 1.0774684 - 750 15.795347 3418.6537 2449.343 170.04287 969.31069 706.12432 899.61553 553.21874 45.793213 -642.75298 1306158.1 -1306750.8 1022.2516 48631.318 265.89304 1.0681488 - 800 16.835794 3385.2449 2465.4963 171.16429 919.74864 692.34918 888.91243 530.24204 45.132243 -638.54787 1306154.6 -1306753 1601.1391 48631.318 267.64361 1.0797553 - 850 17.87536 3397.1124 2426.3129 168.44403 970.79951 717.48898 878.71057 580.26487 46.675101 -646.96926 1306150.9 -1306756.3 1048.7905 48631.318 263.38063 1.0785255 - 900 18.899639 3324.2064 2447.5004 169.91495 876.70599 683.62339 881.77789 531.98758 43.646731 -648.59248 1306144.4 -1306760.2 2221.5859 48631.318 265.69596 1.0608373 - 950 19.938468 3316.6329 2398.6988 166.52695 917.93405 702.84237 885.96473 540.35376 45.671318 -638.80334 1306144.4 -1306762.5 1955.2237 48631.318 260.38167 1.0687233 - 1000 20.973543 3287.4205 2384.191 165.51976 903.22949 705.56988 889.96387 535.23674 44.902139 -661.28175 1306150.4 -1306761.6 90.200683 48631.318 258.81506 1.0477545 - 1050 21.990961 3297.7806 2392.0372 166.06448 905.74339 697.33157 889.75086 537.2395 46.319713 -636.03286 1306135.9 -1306764.8 1893.8234 48631.318 259.67633 1.0344207 - 1100 23.006456 3240.651 2370.2217 164.54996 870.42931 693.87289 897.0846 526.89184 43.778979 -657.83716 1306132.1 -1306765.5 799.62979 48631.318 257.28711 1.0618941 - 1150 24.014558 3232.457 2377.9797 165.08855 854.47728 692.51558 897.77048 520.3269 43.903959 -657.38369 1306126.9 -1306769.6 178.21408 48631.318 258.13876 1.0479172 - 1200 25.010178 3238.4266 2392.0623 166.06622 846.36427 695.98996 887.237 522.01974 42.355716 -660.92843 1306124.7 -1306765 1006.1877 48631.318 259.66037 1.0698925 - 1250 26.01949 3198.3364 2332.7551 161.94888 865.58134 690.81786 897.35028 524.47996 44.421121 -640.92419 1306116.3 -1306766.8 2073.9672 48631.318 253.227 1.0326937 - 1300 27.026911 3237.6809 2386.3739 165.67131 851.30706 672.11785 901.04813 530.2964 44.020263 -655.33033 1306125.7 -1306766.5 579.46013 48631.318 259.05838 1.0374113 - 1350 28.033721 3285.9536 2371.155 164.61476 914.79862 718.12968 928.41764 524.02349 43.89896 -657.10221 1306127.3 -1306769.9 518.88041 48631.318 257.36737 1.0993197 - 1400 29.026742 3272.2173 2391.4158 166.02134 880.80147 712.59883 896.13616 532.95785 45.989768 -658.37495 1306125.6 -1306774.1 961.2067 48631.318 259.5968 1.0557033 - 1450 30.032566 3244.2627 2356.0955 163.56926 888.16727 714.72692 901.18382 534.59787 45.517573 -655.58258 1306124.5 -1306776.8 596.10558 48631.318 255.75173 1.058657 - 1500 31.03878 3244.8598 2408.5382 167.21004 836.32161 695.63105 867.27743 527.37333 44.496971 -648.96393 1306125.2 -1306774.7 443.71088 48631.318 261.45495 1.0648973 - 1550 32.041435 3239.3658 2367.1336 164.33557 872.23223 704.16965 884.5938 544.41685 46.110791 -654.61963 1306124.1 -1306776.5 -446.5562 48631.318 256.96289 1.0409003 - 1600 33.058977 3221.4258 2334.2656 162.05375 887.1602 713.8296 885.80472 533.86753 45.413663 -633.58824 1306119.6 -1306777.8 1527.9489 48631.318 253.36367 1.0817678 - 1650 34.080875 3224.4472 2385.9055 165.63879 838.54168 681.01628 879.88017 536.75983 43.884394 -643.24788 1306114 -1306773.8 1314.2208 48631.318 258.97106 1.1033457 - 1700 35.095047 3178.6575 2352.4294 163.31475 826.2281 700.79494 854.06687 549.39826 46.155483 -662.57181 1306115.2 -1306776.9 -187.36898 48631.318 255.35015 1.0638209 - 1750 36.093828 3219.473 2371.9421 164.6694 847.53093 699.44953 891.26068 541.91687 45.714235 -679.13432 1306120.3 -1306771.9 -618.32924 48631.318 257.48034 1.0512601 - 1800 37.110101 3202.0094 2371.8909 164.66585 830.11842 698.44522 858.38216 550.82008 46.315893 -667.77838 1306119.2 -1306775.3 -9.4963278 48631.318 257.46873 1.0619052 - 1850 38.121337 3202.0111 2366.6984 164.30536 835.31277 714.69988 849.6778 553.24258 46.502994 -667.44162 1306114.9 -1306776.3 131.11108 48631.318 256.90165 1.0656162 - 1900 39.132607 3228.7805 2365.934 164.25229 862.84648 720.68418 890.65533 554.75943 45.736726 -685.52803 1306115.1 -1306778.5 -82.525994 48631.318 256.81451 1.0726218 - 1950 40.127507 3218.4068 2443.0023 169.60267 775.40452 673.40001 874.63022 529.69964 43.166847 -680.57322 1306115.4 -1306780.3 622.76654 48631.318 265.20173 1.0693092 - 2000 41.138176 3257.463 2375.6246 164.92505 881.83842 677.60747 933.47776 547.01076 46.507189 -665.56273 1306123.7 -1306780.9 1829.3477 48631.318 257.88171 1.0500311 -Loop time of 41.1383 on 4 procs for 2000 steps with 5500 atoms - -Performance: 2.100 ns/day, 11.427 hours/ns, 48.617 timesteps/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 | 21.082 | 22.483 | 24.145 | 26.6 | 54.65 -Bond | 4.9992 | 5.0781 | 5.1544 | 2.7 | 12.34 -Kspace | 9.1202 | 10.806 | 12.272 | 39.7 | 26.27 -Neigh | 0.45045 | 0.45076 | 0.45094 | 0.0 | 1.10 -Comm | 0.85982 | 0.87287 | 0.88725 | 1.2 | 2.12 -Output | 0.0036495 | 0.004005 | 0.0049655 | 0.9 | 0.01 -Modify | 1.4009 | 1.401 | 1.4013 | 0.0 | 3.41 -Other | | 0.04245 | | | 0.10 - -Nlocal: 1375 ave 1398 max 1361 min -Histogram: 1 0 2 0 0 0 0 0 0 1 -Nghost: 7745.75 ave 7788 max 7697 min -Histogram: 1 0 0 1 0 0 0 0 1 1 -Neighs: 334374 ave 348629 max 319495 min -Histogram: 2 0 0 0 0 0 0 0 0 2 - -Total # of neighbors = 1337494 -Ave neighs/atom = 243.181 -Ave special neighs/atom = 15.6364 -Neighbor list builds = 31 -Dangerous builds = 0 -Total wall time: 0:00:41 diff --git a/examples/USER/drude/toluene/log.toluene.nh.11Aug17.linux.1 b/examples/USER/drude/toluene/log.toluene.nh.11Aug17.linux.1 deleted file mode 100644 index 6070b858be..0000000000 --- a/examples/USER/drude/toluene/log.toluene.nh.11Aug17.linux.1 +++ /dev/null @@ -1,259 +0,0 @@ -LAMMPS (11 Aug 2017) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) - using 1 OpenMP thread(s) per MPI task -# 250 toluene system for drude polarizability example (Nose-Hoover) - -units real -boundary p p p - -atom_style full -bond_style harmonic -angle_style harmonic -dihedral_style opls -improper_style opls -special_bonds lj/coul 0.0 0.0 0.5 - -pair_style lj/cut/thole/long 2.600 8.0 8.0 -pair_modify mix geometric tail yes -kspace_style pppm 1.0e-4 - -read_data data.toluene extra/special/per/atom 1 - orthogonal box = (-18.2908 -18.1636 -18.223) to (18.3357 18.1621 18.3287) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 5500 atoms - scanning bonds ... - 4 = max bonds/atom - scanning angles ... - 6 = max angles/atom - scanning dihedrals ... - 8 = max dihedrals/atom - scanning impropers ... - 2 = max impropers/atom - reading bonds ... - 5500 bonds - reading angles ... - 6000 angles - reading dihedrals ... - 6000 dihedrals - reading impropers ... - 1500 impropers - 5 = max # of 1-2 neighbors - 10 = max # of 1-3 neighbors - 16 = max # of 1-4 neighbors - 20 = max # of special neighbors - -comm_modify vel yes - -group gTOLUENE molecule 1:250 -5500 atoms in group gTOLUENE -group gCORES type 1 2 3 4 5 6 7 -3750 atoms in group gCORES -group gDRUDES type 8 9 10 11 12 -1750 atoms in group gDRUDES - -pair_coeff 1 1 0.069998 3.550000 1.620000 # CAT CAT -pair_coeff 1 2 0.069998 3.550000 1.620000 # CAT CAO -pair_coeff 1 3 0.069998 3.550000 1.620000 # CAT CAM -pair_coeff 1 4 0.069998 3.550000 1.620000 # CAT CAP -pair_coeff 1 5 0.067968 3.524911 1.620000 # CAT CTT -pair_coeff 1 6 0.045825 2.931041 0.000000 # CAT HAT -pair_coeff 1 7 0.045825 2.931041 0.000000 # CAT HT -pair_coeff 2 2 0.069998 3.550000 1.620000 # CAO CAO -pair_coeff 2 3 0.069998 3.550000 1.620000 # CAO CAM -pair_coeff 2 4 0.069998 3.550000 1.620000 # CAO CAP -pair_coeff 2 5 0.067968 3.524911 1.620000 # CAO CTT -pair_coeff 2 6 0.045825 2.931041 0.000000 # CAO HAT -pair_coeff 2 7 0.045825 2.931041 0.000000 # CAO HT -pair_coeff 3 3 0.069998 3.550000 1.620000 # CAM CAM -pair_coeff 3 4 0.069998 3.550000 1.620000 # CAM CAP -pair_coeff 3 5 0.067968 3.524911 1.620000 # CAM CTT -pair_coeff 3 6 0.045825 2.931041 0.000000 # CAM HAT -pair_coeff 3 7 0.045825 2.931041 0.000000 # CAM HT -pair_coeff 4 4 0.069998 3.550000 1.620000 # CAP CAP -pair_coeff 4 5 0.067968 3.524911 1.620000 # CAP CTT -pair_coeff 4 6 0.045825 2.931041 0.000000 # CAP HAT -pair_coeff 4 7 0.045825 2.931041 0.000000 # CAP HT -pair_coeff 5 5 0.065997 3.500000 1.620000 # CTT CTT -pair_coeff 5 6 0.044496 2.910326 0.000000 # CTT HAT -pair_coeff 5 7 0.044496 2.910326 0.000000 # CTT HT -pair_coeff 6 6 0.029999 2.420000 0.000000 # HAT HAT -pair_coeff 6 7 0.029999 2.420000 0.000000 # HAT HT -pair_coeff 7 7 0.029999 2.420000 0.000000 # HT HT -pair_coeff 1 8 0.000000 0.000000 1.620000 # CAT D_CAT -pair_coeff 1 9 0.000000 0.000000 1.620000 # CAT D_CAO -pair_coeff 1 10 0.000000 0.000000 1.620000 # CAT D_CAM -pair_coeff 1 11 0.000000 0.000000 1.620000 # CAT D_CAP -pair_coeff 1 12 0.000000 0.000000 1.620000 # CAT D_CTT -pair_coeff 2 8 0.000000 0.000000 1.620000 # CAO D_CAT -pair_coeff 2 9 0.000000 0.000000 1.620000 # CAO D_CAO -pair_coeff 2 10 0.000000 0.000000 1.620000 # CAO D_CAM -pair_coeff 2 11 0.000000 0.000000 1.620000 # CAO D_CAP -pair_coeff 2 12 0.000000 0.000000 1.620000 # CAO D_CTT -pair_coeff 3 8 0.000000 0.000000 1.620000 # CAM D_CAT -pair_coeff 3 9 0.000000 0.000000 1.620000 # CAM D_CAO -pair_coeff 3 10 0.000000 0.000000 1.620000 # CAM D_CAM -pair_coeff 3 11 0.000000 0.000000 1.620000 # CAM D_CAP -pair_coeff 3 12 0.000000 0.000000 1.620000 # CAM D_CTT -pair_coeff 4 8 0.000000 0.000000 1.620000 # CAP D_CAT -pair_coeff 4 9 0.000000 0.000000 1.620000 # CAP D_CAO -pair_coeff 4 10 0.000000 0.000000 1.620000 # CAP D_CAM -pair_coeff 4 11 0.000000 0.000000 1.620000 # CAP D_CAP -pair_coeff 4 12 0.000000 0.000000 1.620000 # CAP D_CTT -pair_coeff 5 8 0.000000 0.000000 1.620000 # CTT D_CAT -pair_coeff 5 9 0.000000 0.000000 1.620000 # CTT D_CAO -pair_coeff 5 10 0.000000 0.000000 1.620000 # CTT D_CAM -pair_coeff 5 11 0.000000 0.000000 1.620000 # CTT D_CAP -pair_coeff 5 12 0.000000 0.000000 1.620000 # CTT D_CTT -pair_coeff 8 8 0.000000 0.000000 1.620000 # D_CAT D_CAT -pair_coeff 8 9 0.000000 0.000000 1.620000 # D_CAT D_CAO -pair_coeff 8 10 0.000000 0.000000 1.620000 # D_CAT D_CAM -pair_coeff 8 11 0.000000 0.000000 1.620000 # D_CAT D_CAP -pair_coeff 8 12 0.000000 0.000000 1.620000 # D_CAT D_CTT -pair_coeff 9 9 0.000000 0.000000 1.620000 # D_CAO D_CAO -pair_coeff 9 10 0.000000 0.000000 1.620000 # D_CAO D_CAM -pair_coeff 9 11 0.000000 0.000000 1.620000 # D_CAO D_CAP -pair_coeff 9 12 0.000000 0.000000 1.620000 # D_CAO D_CTT -pair_coeff 10 10 0.000000 0.000000 1.620000 # D_CAM D_CAM -pair_coeff 10 11 0.000000 0.000000 1.620000 # D_CAM D_CAP -pair_coeff 10 12 0.000000 0.000000 1.620000 # D_CAM D_CTT -pair_coeff 11 11 0.000000 0.000000 1.620000 # D_CAP D_CAP -pair_coeff 11 12 0.000000 0.000000 1.620000 # D_CAP D_CTT -pair_coeff 12 12 0.000000 0.000000 1.620000 # D_CTT D_CTT - - -neighbor 2.0 bin - -variable vTEMP equal 260.0 -variable vTEMP_D equal 1.0 -variable vPRESS equal 1.0 - -velocity gCORES create ${vTEMP} 12345 -velocity gCORES create 260 12345 -velocity gDRUDES create ${vTEMP_D} 12345 -velocity gDRUDES create 1 12345 - -fix fDRUDE all drude C C C C C N N D D D D D - -fix fSHAKE gCORES shake 0.0001 20 0 b 4 6 7 8 - 1250 = # of size 2 clusters - 0 = # of size 3 clusters - 250 = # of size 4 clusters - 0 = # of frozen angles - -compute cTEMP_CORE gCORES temp/com -compute cTEMP all temp/drude - -fix fDIRECT all drude/transform/direct -fix fNVT1 gCORES nvt temp ${vTEMP} ${vTEMP} 100.0 -fix fNVT1 gCORES nvt temp 260 ${vTEMP} 100.0 -fix fNVT1 gCORES nvt temp 260 260 100.0 -fix fNVT2 gDRUDES nvt temp ${vTEMP_D} ${vTEMP_D} 20.0 -fix fNVT2 gDRUDES nvt temp 1 ${vTEMP_D} 20.0 -fix fNVT2 gDRUDES nvt temp 1 1 20.0 -fix fINVERSE all drude/transform/inverse - -fix fMOMENTUM all momentum 100 linear 1 1 1 - -thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2] -thermo 50 - -timestep 0.5 -run 2000 -PPPM initialization ... -WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) - G vector (1/distance) = 0.382011 - grid = 40 40 40 - stencil order = 5 - estimated absolute RMS force accuracy = 0.0325934 - estimated relative force accuracy = 9.8154e-05 - using double precision FFTs - 3d grid and FFT values/proc = 103823 64000 -Rebuild special list taking Drude particles into account -Old max number of 1-2 to 1-4 neighbors: 19 -New max number of 1-2 to 1-4 neighbors: 20 (+1) -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 10 - ghost atom cutoff = 10 - binsize = 5, bins = 8 8 8 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut/thole/long, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 42.06 | 42.06 | 42.06 Mbytes -Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2] - 0 0 14386.197 2910.7282 202.07402 11475.469 6565.4851 20.333365 1.0706727e-06 1.3894617e-07 4972.8631 1306116.6 -1306199.8 40273.68 48631.318 314.89553 3.1777821 - 50 4.462481 6863.642 4633.9267 321.70512 2229.7153 735.2547 604.6946 648.35773 49.039129 824.06033 1306091.3 -1306722.9 17914.827 48631.318 504.18525 0.0086839843 - 100 8.8666639 6628.0722 4376.1868 303.81182 2251.8853 598.11249 651.43051 919.41359 74.216826 589.6504 1306135.1 -1306716 17450.721 48631.318 476.14276 0.0075129702 - 150 13.323556 6336.1884 4726.0692 328.10201 1610.1192 560.01225 621.30109 640.32475 45.531175 288.99128 1306173.9 -1306720 18303.624 48631.318 514.21215 0.0061921467 - 200 17.710109 5997.6194 4565.6288 316.96362 1431.9906 524.2765 591.79843 718.11015 56.374558 88.660843 1306183 -1306730.3 17986.182 48631.318 496.75522 0.00681205 - 250 22.154451 5648.1758 4433.1558 307.76682 1215.02 502.13687 578.85369 665.27326 49.096119 -19.019967 1306179.2 -1306740.5 11771.328 48631.318 482.34141 0.0071619539 - 300 26.524393 5317.8584 4075.2077 282.91669 1242.6506 602.55113 637.40817 647.27074 44.769726 -123.22347 1306183.3 -1306749.5 3571.1867 48631.318 443.3952 0.0071733829 - 350 30.881443 4996.709 3935.7988 273.23838 1060.9102 455.75196 634.36552 638.77826 45.831053 -157.6304 1306198.1 -1306754.3 13525.264 48631.318 428.22739 0.0063722044 - 400 35.218285 4695.9297 3742.6585 259.82983 953.27122 457.49584 620.73047 591.94411 42.495713 -183.91838 1306186.7 -1306762.2 10901.217 48631.318 407.21326 0.005787501 - 450 39.545502 4417.8027 3513.6374 243.9303 904.16528 519.61263 580.76003 624.06933 45.631271 -286.60025 1306184.3 -1306763.6 2956.9012 48631.318 382.29486 0.0057536613 - 500 43.868895 4165.0012 3333.7203 231.43976 831.28089 465.5234 579.36085 580.60005 42.34515 -254.82269 1306183.9 -1306765.6 5818.5565 48631.318 362.71904 0.0059224891 - 550 48.242395 3934.5209 3211.9362 222.98504 722.58462 431.14864 581.46511 517.2025 39.188196 -265.47041 1306182.7 -1306763.6 8537.9404 48631.318 349.46863 0.0055762504 - 600 52.542171 3714.8655 3121.0494 216.67532 593.81611 425.12998 539.89496 490.30508 34.564566 -305.82069 1306175.2 -1306765.5 7402.7677 48631.318 339.57967 0.0057486673 - 650 56.830079 3516.2452 2930.7498 203.46399 585.49537 511.91461 512.48859 521.40636 37.766801 -391.65392 1306163.5 -1306770 381.72879 48631.318 318.87447 0.0054629243 - 700 61.119511 3342.7694 2864.1576 198.8409 478.6118 451.54683 498.82407 489.17207 35.23127 -375.78886 1306153.8 -1306774.2 3691.2716 48631.318 311.62801 0.0071278731 - 750 65.401576 3181.7673 2786.7104 193.46422 395.05691 409.83192 508.19542 454.56182 32.890716 -379.80692 1306149 -1306779.6 7428.3698 48631.318 303.20195 0.006233194 - 800 69.680899 3032.4158 2699.8707 187.43547 332.54509 453.40673 486.16575 441.1235 32.847786 -437.39338 1306144.4 -1306788 1701.7652 48631.318 293.75377 0.0056528223 - 850 73.96463 2898.4928 2563.6959 177.98169 334.7969 463.66637 486.19929 453.38803 34.062233 -455.86062 1306144.2 -1306790.9 -285.03665 48631.318 278.9376 0.0052777781 - 900 78.229548 2780.3555 2528.3241 175.52604 252.03136 396.92692 451.76463 435.59744 33.035257 -413.46176 1306142.9 -1306794.7 3836.4341 48631.318 275.08801 0.0070306435 - 950 82.482848 2679.3417 2456.8817 170.56624 222.45998 385.66656 434.6516 418.37977 32.156722 -387.2201 1306136.9 -1306798.1 5510.2309 48631.318 267.31515 0.0064042654 - 1000 86.722726 2593.4365 2367.4477 164.35738 225.98882 427.8524 453.27435 415.48809 31.097577 -436.62051 1306131.8 -1306796.9 1166.3909 48631.318 257.58464 0.0059160543 - 1050 90.888482 2524.7788 2305.0253 160.02377 219.75349 432.90807 438.86657 412.79356 30.892593 -414.29436 1306119.4 -1306800.8 1698.2687 48631.318 250.79245 0.0065593259 - 1100 95.024656 2471.8176 2311.0953 160.44518 160.72227 378.43572 453.3435 392.48525 29.012472 -409.64374 1306119.6 -1306802.5 4190.91 48631.318 251.45323 0.0059713432 - 1150 99.165724 2433.9279 2279.0766 158.22231 154.8513 395.30434 436.87933 414.39389 31.118973 -428.90902 1306110.2 -1306804.2 3274.8924 48631.318 247.96893 0.0069039065 - 1200 103.31062 2411.3777 2238.4638 155.40282 172.91381 453.61551 460.27693 408.59237 31.237062 -482.78549 1306110.2 -1306808.2 -523.10179 48631.318 243.55012 0.0068754631 - 1250 107.40149 2402.1932 2286.0576 158.70696 116.13565 416.44979 462.75875 391.75373 29.446705 -477.67214 1306102.2 -1306808.8 484.04837 48631.318 248.72579 0.011679749 - 1300 111.55448 2406.5029 2261.2729 156.98631 145.23005 408.68043 437.74725 400.4567 30.448106 -418.44274 1306096.8 -1306810.5 4490.4165 48631.318 245.99228 0.076574936 - 1350 115.71244 2459.1398 2317.5855 160.89575 141.55434 651.84862 447.40877 400.66793 29.060967 -461.45124 1305884.3 -1306810.3 693.59782 48631.318 250.14098 3.5622064 - 1400 119.88515 2479.5991 2285.6701 158.68006 193.929 582.54021 457.54475 430.29254 30.183876 -449.49979 1305955.6 -1306812.8 930.31169 48631.318 247.21826 2.5935077 - 1450 124.05689 2498.3537 2286.4924 158.73715 211.86128 434.79588 477.9598 402.79356 31.070492 -406.60813 1306086.4 -1306814.5 2933.4418 48631.318 248.74646 0.058608522 - 1500 128.29115 2546.66 2423.6257 168.25747 123.03432 392.07474 456.01536 385.97457 29.255586 -417.92459 1306089.9 -1306812.3 3333.3497 48631.318 263.694 0.011243575 - 1550 132.46344 2596.5481 2325.2227 161.42596 271.32542 462.52464 469.53612 461.20308 34.616094 -423.51186 1306080.4 -1306813.4 2155.0566 48631.318 252.98739 0.011191115 - 1600 136.64497 2646.7844 2387.8797 165.77585 258.90469 424.6071 484.95314 449.56642 33.318144 -395.67454 1306077 -1306814.8 1291.5449 48631.318 259.80403 0.012426122 - 1650 140.83234 2700.2847 2387.3033 165.73584 312.98138 431.00741 496.39504 455.52303 32.724808 -357.63815 1306070.3 -1306815.3 5007.2365 48631.318 259.70198 0.081729799 - 1700 145.02103 2777.9556 2386.7756 165.6992 391.18003 636.61544 523.12627 482.84847 35.186128 -391.10505 1305919.7 -1306815.2 2192.7076 48631.318 258.14043 2.7318649 - 1750 149.22218 2829.5998 2559.2796 177.67509 270.32019 684.587 479.93609 446.30457 31.888933 -385.84966 1305832.5 -1306819.1 1683.1471 48631.318 276.95798 2.6465587 - 1800 153.41978 2835.768 2465.6959 171.17815 370.07208 470.05934 508.38934 479.71489 37.826868 -369.0767 1306062.8 -1306819.6 3023.0762 48631.318 268.22249 0.097440318 - 1850 157.62632 2857.7601 2504.3893 173.86439 353.37083 436.06841 516.10132 487.71301 36.514956 -385.43181 1306078.9 -1306816.5 2950.5189 48631.318 272.47825 0.016816883 - 1900 161.8372 2867.791 2528.8957 175.56572 338.89527 446.38065 509.27013 485.03036 37.283587 -402.68445 1306076.6 -1306812.9 3161.5045 48631.318 275.1476 0.011615474 - 1950 166.10858 2861.34 2513.9103 174.52538 347.4297 470.9855 536.84666 467.9604 36.049051 -430.05716 1306079.3 -1306813.6 738.77866 48631.318 273.51233 0.020075246 - 2000 170.32286 2838.0367 2530.4481 175.6735 307.58858 423.18694 516.91384 454.72628 35.048394 -387.67176 1306074.6 -1306809.3 4321.7103 48631.318 275.24492 0.13775419 -Loop time of 170.323 on 1 procs for 2000 steps with 5500 atoms - -Performance: 0.507 ns/day, 47.312 hours/ns, 11.742 timesteps/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 | 105.66 | 105.66 | 105.66 | 0.0 | 62.04 -Bond | 19.802 | 19.802 | 19.802 | 0.0 | 11.63 -Kspace | 35.029 | 35.029 | 35.029 | 0.0 | 20.57 -Neigh | 2.7502 | 2.7502 | 2.7502 | 0.0 | 1.61 -Comm | 0.62654 | 0.62654 | 0.62654 | 0.0 | 0.37 -Output | 0.006705 | 0.006705 | 0.006705 | 0.0 | 0.00 -Modify | 6.3072 | 6.3072 | 6.3072 | 0.0 | 3.70 -Other | | 0.1366 | | | 0.08 - -Nlocal: 5500 ave 5500 max 5500 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 15407 ave 15407 max 15407 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 1.30509e+06 ave 1.30509e+06 max 1.30509e+06 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 1305088 -Ave neighs/atom = 237.289 -Ave special neighs/atom = 15.6364 -Neighbor list builds = 44 -Dangerous builds = 0 -Total wall time: 0:02:50 diff --git a/examples/USER/drude/toluene/log.toluene.nh.11Aug17.linux.4 b/examples/USER/drude/toluene/log.toluene.nh.11Aug17.linux.4 deleted file mode 100644 index 673f867ab4..0000000000 --- a/examples/USER/drude/toluene/log.toluene.nh.11Aug17.linux.4 +++ /dev/null @@ -1,259 +0,0 @@ -LAMMPS (11 Aug 2017) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) - using 1 OpenMP thread(s) per MPI task -# 250 toluene system for drude polarizability example (Nose-Hoover) - -units real -boundary p p p - -atom_style full -bond_style harmonic -angle_style harmonic -dihedral_style opls -improper_style opls -special_bonds lj/coul 0.0 0.0 0.5 - -pair_style lj/cut/thole/long 2.600 8.0 8.0 -pair_modify mix geometric tail yes -kspace_style pppm 1.0e-4 - -read_data data.toluene extra/special/per/atom 1 - orthogonal box = (-18.2908 -18.1636 -18.223) to (18.3357 18.1621 18.3287) - 2 by 1 by 2 MPI processor grid - reading atoms ... - 5500 atoms - scanning bonds ... - 4 = max bonds/atom - scanning angles ... - 6 = max angles/atom - scanning dihedrals ... - 8 = max dihedrals/atom - scanning impropers ... - 2 = max impropers/atom - reading bonds ... - 5500 bonds - reading angles ... - 6000 angles - reading dihedrals ... - 6000 dihedrals - reading impropers ... - 1500 impropers - 5 = max # of 1-2 neighbors - 10 = max # of 1-3 neighbors - 16 = max # of 1-4 neighbors - 20 = max # of special neighbors - -comm_modify vel yes - -group gTOLUENE molecule 1:250 -5500 atoms in group gTOLUENE -group gCORES type 1 2 3 4 5 6 7 -3750 atoms in group gCORES -group gDRUDES type 8 9 10 11 12 -1750 atoms in group gDRUDES - -pair_coeff 1 1 0.069998 3.550000 1.620000 # CAT CAT -pair_coeff 1 2 0.069998 3.550000 1.620000 # CAT CAO -pair_coeff 1 3 0.069998 3.550000 1.620000 # CAT CAM -pair_coeff 1 4 0.069998 3.550000 1.620000 # CAT CAP -pair_coeff 1 5 0.067968 3.524911 1.620000 # CAT CTT -pair_coeff 1 6 0.045825 2.931041 0.000000 # CAT HAT -pair_coeff 1 7 0.045825 2.931041 0.000000 # CAT HT -pair_coeff 2 2 0.069998 3.550000 1.620000 # CAO CAO -pair_coeff 2 3 0.069998 3.550000 1.620000 # CAO CAM -pair_coeff 2 4 0.069998 3.550000 1.620000 # CAO CAP -pair_coeff 2 5 0.067968 3.524911 1.620000 # CAO CTT -pair_coeff 2 6 0.045825 2.931041 0.000000 # CAO HAT -pair_coeff 2 7 0.045825 2.931041 0.000000 # CAO HT -pair_coeff 3 3 0.069998 3.550000 1.620000 # CAM CAM -pair_coeff 3 4 0.069998 3.550000 1.620000 # CAM CAP -pair_coeff 3 5 0.067968 3.524911 1.620000 # CAM CTT -pair_coeff 3 6 0.045825 2.931041 0.000000 # CAM HAT -pair_coeff 3 7 0.045825 2.931041 0.000000 # CAM HT -pair_coeff 4 4 0.069998 3.550000 1.620000 # CAP CAP -pair_coeff 4 5 0.067968 3.524911 1.620000 # CAP CTT -pair_coeff 4 6 0.045825 2.931041 0.000000 # CAP HAT -pair_coeff 4 7 0.045825 2.931041 0.000000 # CAP HT -pair_coeff 5 5 0.065997 3.500000 1.620000 # CTT CTT -pair_coeff 5 6 0.044496 2.910326 0.000000 # CTT HAT -pair_coeff 5 7 0.044496 2.910326 0.000000 # CTT HT -pair_coeff 6 6 0.029999 2.420000 0.000000 # HAT HAT -pair_coeff 6 7 0.029999 2.420000 0.000000 # HAT HT -pair_coeff 7 7 0.029999 2.420000 0.000000 # HT HT -pair_coeff 1 8 0.000000 0.000000 1.620000 # CAT D_CAT -pair_coeff 1 9 0.000000 0.000000 1.620000 # CAT D_CAO -pair_coeff 1 10 0.000000 0.000000 1.620000 # CAT D_CAM -pair_coeff 1 11 0.000000 0.000000 1.620000 # CAT D_CAP -pair_coeff 1 12 0.000000 0.000000 1.620000 # CAT D_CTT -pair_coeff 2 8 0.000000 0.000000 1.620000 # CAO D_CAT -pair_coeff 2 9 0.000000 0.000000 1.620000 # CAO D_CAO -pair_coeff 2 10 0.000000 0.000000 1.620000 # CAO D_CAM -pair_coeff 2 11 0.000000 0.000000 1.620000 # CAO D_CAP -pair_coeff 2 12 0.000000 0.000000 1.620000 # CAO D_CTT -pair_coeff 3 8 0.000000 0.000000 1.620000 # CAM D_CAT -pair_coeff 3 9 0.000000 0.000000 1.620000 # CAM D_CAO -pair_coeff 3 10 0.000000 0.000000 1.620000 # CAM D_CAM -pair_coeff 3 11 0.000000 0.000000 1.620000 # CAM D_CAP -pair_coeff 3 12 0.000000 0.000000 1.620000 # CAM D_CTT -pair_coeff 4 8 0.000000 0.000000 1.620000 # CAP D_CAT -pair_coeff 4 9 0.000000 0.000000 1.620000 # CAP D_CAO -pair_coeff 4 10 0.000000 0.000000 1.620000 # CAP D_CAM -pair_coeff 4 11 0.000000 0.000000 1.620000 # CAP D_CAP -pair_coeff 4 12 0.000000 0.000000 1.620000 # CAP D_CTT -pair_coeff 5 8 0.000000 0.000000 1.620000 # CTT D_CAT -pair_coeff 5 9 0.000000 0.000000 1.620000 # CTT D_CAO -pair_coeff 5 10 0.000000 0.000000 1.620000 # CTT D_CAM -pair_coeff 5 11 0.000000 0.000000 1.620000 # CTT D_CAP -pair_coeff 5 12 0.000000 0.000000 1.620000 # CTT D_CTT -pair_coeff 8 8 0.000000 0.000000 1.620000 # D_CAT D_CAT -pair_coeff 8 9 0.000000 0.000000 1.620000 # D_CAT D_CAO -pair_coeff 8 10 0.000000 0.000000 1.620000 # D_CAT D_CAM -pair_coeff 8 11 0.000000 0.000000 1.620000 # D_CAT D_CAP -pair_coeff 8 12 0.000000 0.000000 1.620000 # D_CAT D_CTT -pair_coeff 9 9 0.000000 0.000000 1.620000 # D_CAO D_CAO -pair_coeff 9 10 0.000000 0.000000 1.620000 # D_CAO D_CAM -pair_coeff 9 11 0.000000 0.000000 1.620000 # D_CAO D_CAP -pair_coeff 9 12 0.000000 0.000000 1.620000 # D_CAO D_CTT -pair_coeff 10 10 0.000000 0.000000 1.620000 # D_CAM D_CAM -pair_coeff 10 11 0.000000 0.000000 1.620000 # D_CAM D_CAP -pair_coeff 10 12 0.000000 0.000000 1.620000 # D_CAM D_CTT -pair_coeff 11 11 0.000000 0.000000 1.620000 # D_CAP D_CAP -pair_coeff 11 12 0.000000 0.000000 1.620000 # D_CAP D_CTT -pair_coeff 12 12 0.000000 0.000000 1.620000 # D_CTT D_CTT - - -neighbor 2.0 bin - -variable vTEMP equal 260.0 -variable vTEMP_D equal 1.0 -variable vPRESS equal 1.0 - -velocity gCORES create ${vTEMP} 12345 -velocity gCORES create 260 12345 -velocity gDRUDES create ${vTEMP_D} 12345 -velocity gDRUDES create 1 12345 - -fix fDRUDE all drude C C C C C N N D D D D D - -fix fSHAKE gCORES shake 0.0001 20 0 b 4 6 7 8 - 1250 = # of size 2 clusters - 0 = # of size 3 clusters - 250 = # of size 4 clusters - 0 = # of frozen angles - -compute cTEMP_CORE gCORES temp/com -compute cTEMP all temp/drude - -fix fDIRECT all drude/transform/direct -fix fNVT1 gCORES nvt temp ${vTEMP} ${vTEMP} 100.0 -fix fNVT1 gCORES nvt temp 260 ${vTEMP} 100.0 -fix fNVT1 gCORES nvt temp 260 260 100.0 -fix fNVT2 gDRUDES nvt temp ${vTEMP_D} ${vTEMP_D} 20.0 -fix fNVT2 gDRUDES nvt temp 1 ${vTEMP_D} 20.0 -fix fNVT2 gDRUDES nvt temp 1 1 20.0 -fix fINVERSE all drude/transform/inverse - -fix fMOMENTUM all momentum 100 linear 1 1 1 - -thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2] -thermo 50 - -timestep 0.5 -run 2000 -PPPM initialization ... -WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) - G vector (1/distance) = 0.382011 - grid = 40 40 40 - stencil order = 5 - estimated absolute RMS force accuracy = 0.0325934 - estimated relative force accuracy = 9.8154e-05 - using double precision FFTs - 3d grid and FFT values/proc = 34263 16000 -Rebuild special list taking Drude particles into account -Old max number of 1-2 to 1-4 neighbors: 19 -New max number of 1-2 to 1-4 neighbors: 20 (+1) -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 10 - ghost atom cutoff = 10 - binsize = 5, bins = 8 8 8 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut/thole/long, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 18 | 18 | 18 Mbytes -Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2] - 0 0 14386.197 2910.7282 202.07402 11475.469 6565.4851 20.333365 1.0706727e-06 1.3894617e-07 4972.8631 1306116.6 -1306199.8 40273.68 48631.318 314.89553 3.1777821 - 50 1.1419601 6863.6417 4633.9267 321.70512 2229.715 735.2547 604.69459 648.35773 49.039129 824.06033 1306091.3 -1306722.9 17914.827 48631.318 504.18525 0.0086839775 - 100 2.3001912 6628.0719 4376.1868 303.81182 2251.8851 598.11248 651.43051 919.41359 74.216825 589.6504 1306135.1 -1306716 17450.721 48631.318 476.14276 0.0075129701 - 150 3.473469 6336.1884 4726.0692 328.10201 1610.1192 560.01225 621.30109 640.32474 45.531174 288.99129 1306173.9 -1306720 18303.624 48631.318 514.21215 0.006192153 - 200 4.6296241 5997.6192 4565.6288 316.96362 1431.9903 524.27651 591.79844 718.11014 56.374557 88.66084 1306183 -1306730.3 17986.183 48631.318 496.75522 0.0068120542 - 250 5.7982912 5648.1756 4433.1557 307.76682 1215.0199 502.13686 578.8537 665.27326 49.096119 -19.019961 1306179.2 -1306740.5 11771.328 48631.318 482.34141 0.0071619522 - 300 6.9468622 5317.8583 4075.2077 282.91669 1242.6505 602.55113 637.40818 647.27073 44.769725 -123.22347 1306183.3 -1306749.5 3571.1872 48631.318 443.3952 0.0071733908 - 350 8.0925181 4996.7094 3935.7988 273.23838 1060.9106 455.75195 634.3655 638.77824 45.831051 -157.63039 1306198.1 -1306754.3 13525.265 48631.318 428.22739 0.0063722017 - 400 9.2309761 4695.9294 3742.6584 259.82983 953.27093 457.49585 620.73048 591.94413 42.495714 -183.91838 1306186.7 -1306762.2 10901.217 48631.318 407.21326 0.0057875 - 450 10.363872 4417.8018 3513.6374 243.9303 904.1644 519.61261 580.76003 624.06933 45.631272 -286.60025 1306184.3 -1306763.6 2956.9021 48631.318 382.29485 0.0057536673 - 500 11.493601 4165.0005 3333.7203 231.43976 831.28022 465.52341 579.36085 580.60004 42.345149 -254.82269 1306183.9 -1306765.6 5818.5549 48631.318 362.71904 0.0059224858 - 550 12.636785 3934.5207 3211.9362 222.98504 722.58446 431.14864 581.46511 517.20249 39.188194 -265.4704 1306182.7 -1306763.6 8537.9415 48631.318 349.46863 0.0055762027 - 600 13.759642 3714.8658 3121.0493 216.67532 593.81649 425.12998 539.89497 490.30506 34.564567 -305.82067 1306175.2 -1306765.5 7402.7688 48631.318 339.57967 0.005748668 - 650 14.880794 3516.2453 2930.7499 203.464 585.49542 511.91457 512.48857 521.40634 37.766798 -391.65394 1306163.5 -1306770 381.72898 48631.318 318.87448 0.0054629381 - 700 15.99791 3342.7693 2864.1576 198.8409 478.61174 451.54685 498.82406 489.17206 35.231269 -375.78888 1306153.8 -1306774.2 3691.2706 48631.318 311.62801 0.0071278792 - 750 17.111346 3181.7665 2786.7104 193.46422 395.05608 409.83191 508.19537 454.56183 32.890719 -379.80694 1306149 -1306779.6 7428.3698 48631.318 303.20196 0.0062331873 - 800 18.219225 3032.4162 2699.8707 187.43547 332.54543 453.40674 486.16573 441.12346 32.847783 -437.39291 1306144.4 -1306788 1701.7675 48631.318 293.75377 0.0056528077 - 850 19.320825 2898.4936 2563.6961 177.9817 334.79757 463.66634 486.19928 453.38802 34.062236 -455.86081 1306144.2 -1306790.9 -285.04073 48631.318 278.93762 0.0052778244 - 900 20.41979 2780.3551 2528.3241 175.52604 252.03099 396.92693 451.7645 435.59756 33.035261 -413.46181 1306142.9 -1306794.7 3836.4347 48631.318 275.08801 0.0070307677 - 950 21.517533 2679.3418 2456.8821 170.56626 222.45967 385.66649 434.6516 418.37957 32.156706 -387.22039 1306136.9 -1306798.1 5510.2277 48631.318 267.31518 0.0064041284 - 1000 22.614275 2593.435 2367.4471 164.35734 225.98798 427.85237 453.27432 415.48822 31.097611 -436.61808 1306131.8 -1306796.9 1166.3709 48631.318 257.58457 0.0059160188 - 1050 23.688642 2524.7784 2305.0257 160.0238 219.75264 432.90797 438.8666 412.79338 30.892595 -414.29467 1306119.4 -1306800.8 1698.2602 48631.318 250.7925 0.0065595368 - 1100 24.750163 2471.818 2311.095 160.44516 160.72297 378.43554 453.3434 392.485 29.012487 -409.64322 1306119.6 -1306802.5 4190.9174 48631.318 251.4532 0.0059713928 - 1150 25.813605 2433.9311 2279.0768 158.22233 154.85433 395.30409 436.87935 414.39367 31.118959 -428.90913 1306110.2 -1306804.2 3274.9237 48631.318 247.96895 0.0069037916 - 1200 26.876952 2411.3772 2238.4639 155.40283 172.91329 453.61525 460.27658 408.59192 31.237007 -482.78468 1306110.2 -1306808.2 -523.10237 48631.318 243.55013 0.0068752641 - 1250 27.929701 2402.1937 2286.0559 158.70685 116.13778 416.44884 462.75935 391.75448 29.446777 -477.6718 1306102.2 -1306808.8 484.0561 48631.318 248.72561 0.011679662 - 1300 29.000999 2406.5014 2261.274 156.98639 145.22737 408.678 437.74824 400.45662 30.448139 -418.44472 1306096.8 -1306810.5 4490.4105 48631.318 245.9924 0.076575975 - 1350 30.07322 2459.141 2317.5852 160.89573 141.55579 651.85736 447.40791 400.66662 29.060882 -461.45016 1305884.3 -1306810.3 693.5247 48631.318 250.14112 3.5619231 - 1400 31.14859 2479.6103 2285.6714 158.68015 193.93893 582.54135 457.54445 430.29301 30.184026 -449.49877 1305955.6 -1306812.8 930.44669 48631.318 247.21806 2.5941109 - 1450 32.226914 2498.357 2286.4857 158.73668 211.87137 434.79636 477.95951 402.79572 31.070593 -406.60139 1306086.4 -1306814.5 2933.5045 48631.318 248.74572 0.058613153 - 1500 33.410717 2546.6608 2423.6247 168.25741 123.03609 392.07322 456.01243 385.97344 29.255562 -417.91413 1306089.9 -1306812.3 3333.391 48631.318 263.6939 0.011242005 - 1550 34.466176 2596.5534 2325.2208 161.42583 271.33259 462.52172 469.54241 461.20405 34.616224 -423.51068 1306080.4 -1306813.4 2155.1194 48631.318 252.98718 0.011190963 - 1600 35.524206 2646.7837 2387.8846 165.77619 258.8991 424.60563 484.95051 449.57767 33.318683 -395.68293 1306077 -1306814.8 1291.42 48631.318 259.80456 0.01242131 - 1650 36.582854 2700.2921 2387.3119 165.73643 312.98026 431.01369 496.39909 455.52591 32.725057 -357.65832 1306070.3 -1306815.3 5006.9348 48631.318 259.70291 0.081728845 - 1700 37.641527 2777.9572 2386.7777 165.69934 391.1795 636.55763 523.11512 482.8483 35.185863 -391.0955 1305919.8 -1306815.2 2192.6733 48631.318 258.1403 2.7324891 - 1750 38.722299 2829.6167 2559.2488 177.67295 270.36793 684.60746 479.95058 446.29664 31.887359 -385.83616 1305832.5 -1306819 1683.6061 48631.318 276.955 2.6459088 - 1800 39.800548 2835.7772 2465.7031 171.17865 370.07414 470.05306 508.38361 479.70121 37.826988 -369.0694 1306062.8 -1306819.6 3022.9801 48631.318 268.22328 0.097437593 - 1850 40.878327 2857.76 2504.4099 173.86582 353.35016 436.05857 516.10495 487.70907 36.514477 -385.43957 1306078.9 -1306816.5 2950.6415 48631.318 272.48049 0.016822774 - 1900 41.9583 2867.7843 2528.8424 175.56202 338.94193 446.38058 509.30719 485.04661 37.284135 -402.67104 1306076.5 -1306812.9 3161.5835 48631.318 275.1418 0.011620333 - 1950 43.058281 2861.3388 2513.8846 174.5236 347.45414 470.99292 536.81741 467.97736 36.047648 -430.00695 1306079.3 -1306813.6 739.25154 48631.318 273.50953 0.020089235 - 2000 44.142059 2838.068 2530.3189 175.66453 307.74914 423.19157 516.85371 454.76945 35.048253 -387.49234 1306074.6 -1306809.3 4324.0966 48631.318 275.23081 0.13784772 -Loop time of 44.1421 on 4 procs for 2000 steps with 5500 atoms - -Performance: 1.957 ns/day, 12.262 hours/ns, 45.308 timesteps/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 | 21.008 | 22.592 | 23.892 | 21.7 | 51.18 -Bond | 4.8951 | 5.1338 | 5.2542 | 6.4 | 11.63 -Kspace | 9.1158 | 10.514 | 12.296 | 35.3 | 23.82 -Neigh | 0.63826 | 0.63849 | 0.63875 | 0.0 | 1.45 -Comm | 0.78008 | 0.80146 | 0.84186 | 2.7 | 1.82 -Output | 0.0036852 | 0.0040929 | 0.0052037 | 1.0 | 0.01 -Modify | 4.3966 | 4.4074 | 4.4147 | 0.3 | 9.98 -Other | | 0.05088 | | | 0.12 - -Nlocal: 1375 ave 1415 max 1340 min -Histogram: 2 0 0 0 0 0 0 0 1 1 -Nghost: 8101 ave 8147 max 8056 min -Histogram: 2 0 0 0 0 0 0 0 1 1 -Neighs: 326274 ave 342552 max 306832 min -Histogram: 1 0 0 0 1 0 1 0 0 1 - -Total # of neighbors = 1305095 -Ave neighs/atom = 237.29 -Ave special neighs/atom = 15.6364 -Neighbor list builds = 44 -Dangerous builds = 0 -Total wall time: 0:00:44 From 7d3caaa1a41c12acdd97e482308833a1bf7de7d3 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 10 Dec 2018 11:24:35 -0500 Subject: [PATCH 5/9] step version date for stable release on wednesday --- doc/src/Manual.txt | 4 ++-- src/version.h | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt index 6fcd5d1f49..bbbc11a1ba 100644 --- a/doc/src/Manual.txt +++ b/doc/src/Manual.txt @@ -1,7 +1,7 @@ LAMMPS Users Manual - + @@ -21,7 +21,7 @@ :line LAMMPS Documentation :c,h1 -7 Dec 2018 version :c,h2 +12 Dec 2018 version :c,h2 "What is a LAMMPS version?"_Manual_version.html diff --git a/src/version.h b/src/version.h index 4bbc739421..9b4a006f86 100644 --- a/src/version.h +++ b/src/version.h @@ -1 +1 @@ -#define LAMMPS_VERSION "7 Dec 2018" +#define LAMMPS_VERSION "12 Dec 2018" From fb08d3ea46e913cb8042adb7261c15bf519760be Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 10 Dec 2018 11:25:24 -0500 Subject: [PATCH 6/9] ignore MSCG build folder more generally --- lib/mscg/.gitignore | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/mscg/.gitignore b/lib/mscg/.gitignore index 7d45bcb60a..6c9a531977 100644 --- a/lib/mscg/.gitignore +++ b/lib/mscg/.gitignore @@ -1,4 +1,4 @@ # files to ignore /liblink /includelink -/MSCG-release-master +/MSCG-release-* From 52a1f257c530acb5036c4309b75d0141b5f58fb2 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 10 Dec 2018 14:19:03 -0500 Subject: [PATCH 7/9] fix typo --- doc/src/Tools.txt | 2 +- doc/utils/sphinx-config/false_positives.txt | 1 - 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/doc/src/Tools.txt b/doc/src/Tools.txt index d2e53d8b77..9204ae992a 100644 --- a/doc/src/Tools.txt +++ b/doc/src/Tools.txt @@ -485,7 +485,7 @@ README for more info on Pizza.py and how to use these scripts. reax tool :h4,link(reax_tool) -The reax sub-directory contains stand-alond codes that can +The reax sub-directory contains stand-alone codes that can post-process the output of the "fix reax/bonds"_fix_reax_bonds.html command from a LAMMPS simulation using "ReaxFF"_pair_reax.html. See the README.txt file for more info. diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index de60206304..08e106f6d7 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -63,7 +63,6 @@ aliceblue allocaters allosws AlO -alond Alonso amap Amatrix From 052828284d48eab2f7ee2ce1cfc586b10623d871 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 10 Dec 2018 14:53:31 -0500 Subject: [PATCH 8/9] fix typo --- doc/src/Build_extras.txt | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/src/Build_extras.txt b/doc/src/Build_extras.txt index 60bb5bbfea..58ae16a372 100644 --- a/doc/src/Build_extras.txt +++ b/doc/src/Build_extras.txt @@ -621,8 +621,8 @@ The USER-ATC package requires the MANYBODY package also be installed. [CMake build]: -No additional settings are needed besides "-D PKG_REAX=yes" and "-D -PKG_MANYBODY=yes". +No additional settings are needed besides "-D PKG_USER-ATC=yes" +and "-D PKG_MANYBODY=yes". [Traditional make]: From 8422bf64fa094e29abead130365d93a3a91aee19 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 10 Dec 2018 17:42:38 -0500 Subject: [PATCH 9/9] prevent configuring -D PKG_USER-ATC=yes with -D LAMMPS_SIZES=bigbig in CMake --- cmake/CMakeLists.txt | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 7ee1b7f521..e950db99c5 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -221,7 +221,7 @@ else() endif() -set(LAMMPS_SIZES "smallbig" CACHE STRING "LAMMPS size limit") +set(LAMMPS_SIZES "smallbig" CACHE STRING "LAMMPS integer sizes (smallsmall: all 32-bit, smallbig: 64-bit #atoms #timesteps, bigbig: also 64-bit imageint, 64-bit atom ids)") set(LAMMPS_SIZES_VALUES smallbig bigbig smallsmall) set_property(CACHE LAMMPS_SIZES PROPERTY STRINGS ${LAMMPS_SIZES_VALUES}) validate_option(LAMMPS_SIZES LAMMPS_SIZES_VALUES) @@ -856,6 +856,9 @@ if(PKG_USER-AWPMD) endif() if(PKG_USER-ATC) + if(LAMMPS_SIZES STREQUAL BIGBIG) + message(FATAL_ERROR "The USER-ATC Package is not compatible with -DLAMMPS_BIGBIG") + endif() target_link_libraries(atc ${LAPACK_LIBRARIES}) endif()