Update test examples and script to be more in line with other LAMMPS examples

examples/amoeba/Compare.sh

@@ -1,52 +0,0 @@
-# compare test runs to original runs
-
-# dimer
-
-kdiff.py log.water_dimer.amoeba.1 log.water_dimer.amoeba.1.test
-kdiff.py dump.water_dimer.amoeba.1 dump.water_dimer.amoeba.1.test
-
-kdiff.py log.water_dimer.amoeba.4 log.water_dimer.amoeba.4.test
-kdiff.py dump.water_dimer.amoeba.4 dump.water_dimer.amoeba.4.test
-
-kdiff.py log.water_dimer.hippo.1 log.water_dimer.hippo.1.test
-kdiff.py dump.water_dimer.hippo.1 dump.water_dimer.hippo.1.test
-
-kdiff.py log.water_dimer.hippo.4 log.water_dimer.hippo.4.test
-kdiff.py dump.water_dimer.hippo.4 dump.water_dimer.hippo.4.test
-
-# hexamer
-
-kdiff.py log.water_hexamer.amoeba.1 log.water_hexamer.amoeba.1.test
-kdiff.py dump.water_hexamer.amoeba.1 dump.water_hexamer.amoeba.1.test
-
-kdiff.py log.water_hexamer.amoeba.4 log.water_hexamer.amoeba.4.test
-kdiff.py dump.water_hexamer.amoeba.4 dump.water_hexamer.amoeba.4.test
-
-kdiff.py log.water_hexamer.hippo.1 log.water_hexamer.hippo.1.test
-kdiff.py dump.water_hexamer.hippo.1 dump.water_hexamer.hippo.1.test
-
-kdiff.py log.water_hexamer.hippo.4 log.water_hexamer.hippo.4.test
-kdiff.py dump.water_hexamer.hippo.4 dump.water_hexamer.hippo.4.test
-
-# water box
-
-kdiff.py log.water_box.amoeba.1 log.water_box.amoeba.1.test
-kdiff.py dump.water_box.amoeba.1 dump.water_box.amoeba.1.test
-
-kdiff.py log.water_box.amoeba.32 log.water_box.amoeba.32.test
-kdiff.py dump.water_box.amoeba.32 dump.water_box.amoeba.32.test
-
-kdiff.py log.water_box.hippo.1 log.water_box.hippo.1.test
-kdiff.py dump.water_box.hippo.1 dump.water_box.hippo.1.test
-
-kdiff.py log.water_box.hippo.32 log.water_box.hippo.32.test
-kdiff.py dump.water_box.hippo.32 dump.water_box.hippo.32.test
-
-# ubiquitin
-
-kdiff.py log.ubiquitin.1 log.ubiquitin.1.test
-kdiff.py dump.ubiquitin.1 dump.ubiquitin.1.test
-
-kdiff.py log.ubiquitin.32 log.ubiquitin.32.test
-kdiff.py dump.ubiquitin.32 dump.ubiquitin.32.test
-

examples/amoeba/Test.sh

@@ -1,66 +1,34 @@
-# run test problems
+#!/bin/sh
+# run test problems.
+EXE=${1-../../src/lmp_mpi}
+DATE=$(date +%1d%b%y)
 
 # dimer
 
-../../src/lmp_mpi < in.water_dimer.amoeba.test
+${EXE} -in in.water_dimer.amoeba -log log.${DATE}.water_dimer.amoeba.g++.1
-mv log.lammps log.water_dimer.amoeba.1.test
+mpirun -np 4 ${EXE} -in in.water_dimer.amoeba -log log.${DATE}.water_dimer.amoeba.g++.4
-mv dump.water_dimer dump.water_dimer.amoeba.1.test
 
-mpirun -np 4 ../../src/lmp_mpi < in.water_dimer.amoeba.test
+${EXE} -in in.water_dimer.hippo -log log.${DATE}.water_dimer.hippo.g++.1
-mv log.lammps log.water_dimer.amoeba.4.test
+mpirun -np 4 ${EXE} -in in.water_dimer.hippo -log log.${DATE}.water_dimer.hippo.g++.4
-mv dump.water_dimer dump.water_dimer.amoeba.4.test
-
-../../src/lmp_mpi < in.water_dimer.hippo.test
-mv log.lammps log.water_dimer.hippo.1.test
-mv dump.water_dimer dump.water_dimer.hippo.1.test
-
-mpirun -np 4 ../../src/lmp_mpi < in.water_dimer.hippo.test
-mv log.lammps log.water_dimer.hippo.4.test
-mv dump.water_dimer dump.water_dimer.hippo.4.test
 
 # hexamer
 
-../../src/lmp_mpi < in.water_hexamer.amoeba.test
+${EXE} -in in.water_hexamer.amoeba -log log.${DATE}.water_hexamer.amoeba.g++.1
-mv log.lammps log.water_hexamer.amoeba.1.test
+mpirun -np 4 ${EXE} -in in.water_hexamer.amoeba -log log.${DATE}.water_hexamer.amoeba.g++.4
-mv dump.water_hexamer dump.water_hexamer.amoeba.1.test
 
-mpirun -np 4 ../../src/lmp_mpi < in.water_hexamer.amoeba.test
+${EXE} -in in.water_hexamer.hippo -log log.${DATE}.water_hexamer.hippo.g++.1
-mv log.lammps log.water_hexamer.amoeba.4.test
+mpirun -np 4 ${EXE} -in in.water_hexamer.hippo -log log.${DATE}.water_hexamer.hippo.g++.4
-mv dump.water_hexamer dump.water_hexamer.amoeba.4.test
-
-../../src/lmp_mpi < in.water_hexamer.hippo.test
-mv log.lammps log.water_hexamer.hippo.1.test
-mv dump.water_hexamer dump.water_hexamer.hippo.1.test
-
-mpirun -np 4 ../../src/lmp_mpi < in.water_hexamer.hippo.test
-mv log.lammps log.water_hexamer.hippo.4.test
-mv dump.water_hexamer dump.water_hexamer.hippo.4.test
 
 # water box
 
-../../src/lmp_mpi < in.water_box.amoeba.test
+${EXE} -in in.water_box.amoeba -log log.${DATE}.water_box.amoeba.g++.1
-mv log.lammps log.water_box.amoeba.1.test
+mpirun -np 4 ${EXE} -in in.water_box.amoeba -log log.${DATE}.water_box.amoeba.g++.4
-mv dump.water_box dump.water_box.amoeba.1.test
 
-mpirun -np 32 ../../src/lmp_mpi < in.water_box.amoeba.test
+${EXE} -in in.water_box.hippo -log log.${DATE}.water_box.hippo.g++.1
-mv log.lammps log.water_box.amoeba.32.test
+mpirun -np 4 ${EXE} -in in.water_box.hippo -log log.${DATE}.water_box.hippo.g++.4
-mv dump.water_box dump.water_box.amoeba.32.test
-
-../../src/lmp_mpi < in.water_box.hippo.test
-mv log.lammps log.water_box.hippo.1.test
-mv dump.water_box dump.water_box.hippo.1.test
-
-mpirun -np 32 ../../src/lmp_mpi < in.water_box.hippo.test
-mv log.lammps log.water_box.hippo.32.test
-mv dump.water_box dump.water_box.hippo.32.test
 
 # ubiquitin
 
-../../src/lmp_mpi < in.ubiquitin.test
+${EXE} -in in.ubiquitin -log log.${DATE}.ubiquitin.g++.1
-mv log.lammps log.ubiquitin.1.test
+mpirun -np 4 ${EXE} -in in.ubiquitin -log log.${DATE}.ubiquitin.g++.4
-mv dump.ubiquitin dump.ubiquitin.1.test
-
-mpirun -np 32 ../../src/lmp_mpi < in.ubiquitin.test
-mv log.lammps log.ubiquitin.32.test
-mv dump.ubiquitin dump.ubiquitin.32.test
 

examples/amoeba/dump.water_dimer.amoeba.1

@@ -1,165 +0,0 @@
-ITEM: TIMESTEP
-0
-ITEM: NUMBER OF ATOMS
-6
-ITEM: BOX BOUNDS ss ss ss
--1.4632357229999999e+00 9.3247372299999998e-01
--7.5570026690000003e-01 7.5527126690000002e-01
--8.9995638999999985e-03 2.9352285639000000e+00
-ITEM: ATOMS id type x y z fx fy fz
-1 1 -0.024616 -0.001154 -0.003748 7.94661 0.0143882 11.5654
-2 2 -0.244211 -0.000666 0.933978 -7.05777 -0.00770443 -3.06431
-3 2 0.932234 -0.000406 -0.008705 -0.956334 -0.00629552 -7.87238
-4 1 -0.892721 0.00012 2.77367 -12.7377 -0.00815373 2.78728
-5 2 -1.463 0.75512 2.93387 6.39935 4.06267 -1.71086
-6 2 -1.46181 -0.755549 2.93493 6.40581 -4.05491 -1.70517
-ITEM: TIMESTEP
-10
-ITEM: NUMBER OF ATOMS
-6
-ITEM: BOX BOUNDS ss ss ss
--1.4632357229999999e+00 9.3247372299999998e-01
--7.5570026690000003e-01 7.5527126690000002e-01
--8.9995638999999985e-03 2.9352285639000000e+00
-ITEM: ATOMS id type x y z fx fy fz
-1 1 -0.0210901 -0.00114727 0.00187855 -6.1441 -0.00926688 -6.30688
-2 2 -0.299755 -0.000716119 0.924842 7.69349 0.00623407 0.274054
-3 2 0.933941 -0.000453269 -0.0777281 -1.08824 0.00357639 6.29137
-4 1 -0.89902 0.000115499 2.77431 8.40057 0.0041921 -3.3195
-5 2 -1.41411 0.797948 2.92323 -4.42685 -5.12343 1.53409
-6 2 -1.41285 -0.798315 2.92435 -4.43485 5.1187 1.52687
-ITEM: TIMESTEP
-20
-ITEM: NUMBER OF ATOMS
-6
-ITEM: BOX BOUNDS ss ss ss
--1.4632357229999999e+00 9.3247372299999998e-01
--7.5570026690000003e-01 7.5527126690000002e-01
--8.9995638999999985e-03 2.9352285639000000e+00
-ITEM: ATOMS id type x y z fx fy fz
-1 1 -0.0253162 -0.0011519 9.30621e-06 6.65721 0.0114207 8.7962
-2 2 -0.214112 -0.000636438 0.94263 -7.71284 -0.00678668 -1.03908
-3 2 0.928921 -0.000430955 -0.0404651 0.717191 -0.00462784 -7.37266
-4 1 -0.894334 0.00011596 2.76974 -10.0965 -0.00568803 3.16137
-5 2 -1.45804 0.75449 2.94684 5.21348 5.11475 -1.77652
-6 2 -1.45685 -0.754893 2.9479 5.22149 -5.10907 -1.76931
-ITEM: TIMESTEP
-30
-ITEM: NUMBER OF ATOMS
-6
-ITEM: BOX BOUNDS ss ss ss
--1.4632357229999999e+00 9.3247372299999998e-01
--7.5570026690000003e-01 7.5527126690000002e-01
--8.9995638999999985e-03 2.9352285639000000e+00
-ITEM: ATOMS id type x y z fx fy fz
-1 1 -0.0221554 -0.0011439 0.00783939 -8.36895 -0.0130834 -9.24354
-2 2 -0.25261 -0.000667783 0.941075 6.36112 0.00692164 2.73081
-3 2 0.92432 -0.000494304 -0.125343 2.07038 0.00615069 6.42537
-4 1 -0.900866 0.00010992 2.76846 11.0986 0.00640696 -3.42785
-5 2 -1.40977 0.795072 2.93807 -5.57817 -3.04583 1.75974
-6 2 -1.40852 -0.795411 2.93919 -5.58301 3.03943 1.75548
-ITEM: TIMESTEP
-40
-ITEM: NUMBER OF ATOMS
-6
-ITEM: BOX BOUNDS ss ss ss
--1.4632357229999999e+00 9.3247372299999998e-01
--7.5570026690000003e-01 7.5527126690000002e-01
--8.9995638999999985e-03 2.9352285639000000e+00
-ITEM: ATOMS id type x y z fx fy fz
-1 1 -0.0269208 -0.00114842 0.00674288 5.42877 0.00730481 4.31748
-2 2 -0.171607 -0.000594964 0.954009 -8.40692 -0.00484075 2.50346
-3 2 0.92209 -0.000466908 -0.0840066 2.3456 -0.00296432 -6.82561
-4 1 -0.895716 0.000110956 2.76419 -6.18264 -0.00259137 3.07323
-5 2 -1.45218 0.754436 2.95353 3.40261 6.39649 -1.53879
-6 2 -1.45099 -0.75482 2.9546 3.41259 -6.3934 -1.52976
-ITEM: TIMESTEP
-50
-ITEM: NUMBER OF ATOMS
-6
-ITEM: BOX BOUNDS ss ss ss
--1.4632357229999999e+00 9.3247372299999998e-01
--7.5570026690000003e-01 7.5527126690000002e-01
--8.9995638999999985e-03 2.9352285639000000e+00
-ITEM: ATOMS id type x y z fx fy fz
-1 1 -0.0239329 -0.00114175 0.0128926 -8.15007 -0.014184 -11.0504
-2 2 -0.230937 -0.000644481 0.949766 5.72493 0.00756591 4.36142
-3 2 0.91871 -0.000511822 -0.144074 2.40885 0.00639366 6.3907
-4 1 -0.899724 0.000108594 2.76531 11.5106 0.00694105 -3.03119
-5 2 -1.41275 0.792848 2.92798 -5.74551 -2.08247 1.6662
-6 2 -1.41151 -0.793206 2.9291 -5.7488 2.07576 1.66327
-ITEM: TIMESTEP
-60
-ITEM: NUMBER OF ATOMS
-6
-ITEM: BOX BOUNDS ss ss ss
--1.4632357229999999e+00 9.3247372299999998e-01
--7.5570026690000003e-01 7.5527126690000002e-01
--8.9995638999999985e-03 2.9352285639000000e+00
-ITEM: ATOMS id type x y z fx fy fz
-1 1 -0.0287434 -0.0011479 0.00953424 6.82379 0.00862743 4.63675
-2 2 -0.180318 -0.000600308 0.956082 -8.03241 -0.00482631 2.10983
-3 2 0.922397 -0.000459471 -0.0739414 0.782565 -0.00412295 -6.72684
-4 1 -0.892694 0.000113827 2.76489 -6.55004 -0.00361317 2.26756
-5 2 -1.45749 0.757284 2.91975 3.48398 5.14308 -1.14726
-6 2 -1.4563 -0.757724 2.92081 3.49211 -5.13915 -1.14003
-ITEM: TIMESTEP
-70
-ITEM: NUMBER OF ATOMS
-6
-ITEM: BOX BOUNDS ss ss ss
--1.4632357229999999e+00 9.3247372299999998e-01
--7.5570026690000003e-01 7.5527126690000002e-01
--8.9995638999999985e-03 2.9352285639000000e+00
-ITEM: ATOMS id type x y z fx fy fz
-1 1 -0.025848 -0.00114271 0.0136758 -6.10179 -0.0106002 -8.24377
-2 2 -0.259382 -0.000669072 0.94681 6.59121 0.0065405 1.93161
-3 2 0.923692 -0.000484045 -0.110366 -0.0484081 0.00428029 6.1322
-4 1 -0.894893 0.000114175 2.76783 7.43985 0.00424265 -2.1131
-5 2 -1.42416 0.79251 2.88639 -3.9377 -3.53776 1.14903
-6 2 -1.42292 -0.792944 2.88751 -3.94318 3.53329 1.14403
-ITEM: TIMESTEP
-80
-ITEM: NUMBER OF ATOMS
-6
-ITEM: BOX BOUNDS ss ss ss
--1.4632357229999999e+00 9.3247372299999998e-01
--7.5570026690000003e-01 7.5527126690000002e-01
--8.9995638999999985e-03 2.9352285639000000e+00
-ITEM: ATOMS id type x y z fx fy fz
-1 1 -0.030135 -0.00114891 0.00965506 7.41429 0.0123912 9.3266
-2 2 -0.213346 -0.000627628 0.954378 -6.76672 -0.00675668 -2.04974
-3 2 0.924938 -0.000432456 -0.0385785 -0.591495 -0.00546702 -7.10385
-4 1 -0.888796 0.000119275 2.76827 -9.03539 -0.00642914 1.05959
-5 2 -1.46214 0.762697 2.87512 4.48797 2.10983 -0.617778
-6 2 -1.46094 -0.763208 2.87619 4.49133 -2.10357 -0.61482
-ITEM: TIMESTEP
-90
-ITEM: NUMBER OF ATOMS
-6
-ITEM: BOX BOUNDS ss ss ss
--1.4632357229999999e+00 9.3247372299999998e-01
--7.5570026690000003e-01 7.5527126690000002e-01
--8.9995638999999985e-03 2.9352285639000000e+00
-ITEM: ATOMS id type x y z fx fy fz
-1 1 -0.0270206 -0.00114299 0.0145983 -6.11813 -0.00811207 -4.69194
-2 2 -0.274281 -0.000680382 0.947366 7.50569 0.00503125 -1.23144
-3 2 0.92514 -0.000469353 -0.0912836 -0.650877 0.00352314 5.72916
-4 1 -0.891964 0.000116952 2.76852 3.17186 0.0014363 -1.52231
-5 2 -1.43137 0.791127 2.86377 -1.95059 -4.67792 0.861555
-6 2 -1.43013 -0.791605 2.86488 -1.95795 4.67604 0.85497
-ITEM: TIMESTEP
-100
-ITEM: NUMBER OF ATOMS
-6
-ITEM: BOX BOUNDS ss ss ss
--1.4632357229999999e+00 9.3247372299999998e-01
--7.5570026690000003e-01 7.5527126690000002e-01
--8.9995638999999985e-03 2.9352285639000000e+00
-ITEM: ATOMS id type x y z fx fy fz
-1 1 -0.030669 -0.00114759 0.0121427 6.42493 0.0120997 10.0073
-2 2 -0.203569 -0.000615753 0.960107 -6.40597 -0.00736639 -3.30674
-3 2 0.923036 -0.000442107 -0.0503324 -0.0528607 -0.00477186 -6.71539
-4 1 -0.889443 0.000116814 2.76553 -7.7691 -0.0050422 1.37075
-5 2 -1.45671 0.76736 2.88018 3.9012 0.426437 -0.678284
-6 2 -1.4555 -0.767854 2.88126 3.9018 -0.421357 -0.677675

examples/amoeba/dump.water_dimer.amoeba.4

@@ -1,165 +0,0 @@
-ITEM: TIMESTEP
-0
-ITEM: NUMBER OF ATOMS
-6
-ITEM: BOX BOUNDS ss ss ss
--1.4632357229999999e+00 9.3247372299999998e-01
--7.5570026690000003e-01 7.5527126690000002e-01
--8.9995638999999985e-03 2.9352285639000000e+00
-ITEM: ATOMS id type x y z fx fy fz
-1 1 -0.024616 -0.001154 -0.003748 7.94661 0.0143882 11.5654
-2 2 -0.244211 -0.000666 0.933978 -7.05777 -0.00770443 -3.06431
-3 2 0.932234 -0.000406 -0.008705 -0.956334 -0.00629552 -7.87238
-4 1 -0.892721 0.00012 2.77367 -12.7377 -0.00815373 2.78728
-5 2 -1.463 0.75512 2.93387 6.39935 4.06267 -1.71086
-6 2 -1.46181 -0.755549 2.93493 6.40581 -4.05491 -1.70517
-ITEM: TIMESTEP
-10
-ITEM: NUMBER OF ATOMS
-6
-ITEM: BOX BOUNDS ss ss ss
--1.4632357229999999e+00 9.3247372299999998e-01
--7.5570026690000003e-01 7.5527126690000002e-01
--8.9995638999999985e-03 2.9352285639000000e+00
-ITEM: ATOMS id type x y z fx fy fz
-1 1 -0.0210901 -0.00114727 0.00187855 -6.1441 -0.00926688 -6.30688
-2 2 -0.299755 -0.000716119 0.924842 7.69349 0.00623407 0.274054
-3 2 0.933941 -0.000453269 -0.0777281 -1.08824 0.00357639 6.29137
-4 1 -0.89902 0.000115499 2.77431 8.40057 0.0041921 -3.3195
-5 2 -1.41411 0.797948 2.92323 -4.42685 -5.12343 1.53409
-6 2 -1.41285 -0.798315 2.92435 -4.43485 5.1187 1.52687
-ITEM: TIMESTEP
-20
-ITEM: NUMBER OF ATOMS
-6
-ITEM: BOX BOUNDS ss ss ss
--1.4632357229999999e+00 9.3247372299999998e-01
--7.5570026690000003e-01 7.5527126690000002e-01
--8.9995638999999985e-03 2.9352285639000000e+00
-ITEM: ATOMS id type x y z fx fy fz
-1 1 -0.0253162 -0.0011519 9.30621e-06 6.65721 0.0114207 8.7962
-2 2 -0.214112 -0.000636438 0.94263 -7.71284 -0.00678668 -1.03908
-3 2 0.928921 -0.000430955 -0.0404651 0.717191 -0.00462784 -7.37266
-4 1 -0.894334 0.00011596 2.76974 -10.0965 -0.00568803 3.16137
-5 2 -1.45804 0.75449 2.94684 5.21348 5.11475 -1.77652
-6 2 -1.45685 -0.754893 2.9479 5.22149 -5.10907 -1.76931
-ITEM: TIMESTEP
-30
-ITEM: NUMBER OF ATOMS
-6
-ITEM: BOX BOUNDS ss ss ss
--1.4632357229999999e+00 9.3247372299999998e-01
--7.5570026690000003e-01 7.5527126690000002e-01
--8.9995638999999985e-03 2.9352285639000000e+00
-ITEM: ATOMS id type x y z fx fy fz
-1 1 -0.0221554 -0.0011439 0.00783939 -8.36895 -0.0130834 -9.24354
-2 2 -0.25261 -0.000667783 0.941075 6.36112 0.00692164 2.73081
-3 2 0.92432 -0.000494304 -0.125343 2.07038 0.00615069 6.42537
-4 1 -0.900866 0.00010992 2.76846 11.0986 0.00640696 -3.42785
-5 2 -1.40977 0.795072 2.93807 -5.57817 -3.04583 1.75974
-6 2 -1.40852 -0.795411 2.93919 -5.58301 3.03943 1.75548
-ITEM: TIMESTEP
-40
-ITEM: NUMBER OF ATOMS
-6
-ITEM: BOX BOUNDS ss ss ss
--1.4632357229999999e+00 9.3247372299999998e-01
--7.5570026690000003e-01 7.5527126690000002e-01
--8.9995638999999985e-03 2.9352285639000000e+00
-ITEM: ATOMS id type x y z fx fy fz
-1 1 -0.0269208 -0.00114842 0.00674288 5.42877 0.00730481 4.31748
-2 2 -0.171607 -0.000594964 0.954009 -8.40692 -0.00484075 2.50346
-3 2 0.92209 -0.000466908 -0.0840066 2.3456 -0.00296432 -6.82561
-4 1 -0.895716 0.000110956 2.76419 -6.18264 -0.00259137 3.07323
-5 2 -1.45218 0.754436 2.95353 3.40261 6.39649 -1.53879
-6 2 -1.45099 -0.75482 2.9546 3.41259 -6.3934 -1.52976
-ITEM: TIMESTEP
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-ITEM: NUMBER OF ATOMS
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-ITEM: TIMESTEP
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-ITEM: NUMBER OF ATOMS
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-ITEM: BOX BOUNDS ss ss ss
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-ITEM: TIMESTEP
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-ITEM: NUMBER OF ATOMS
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-ITEM: BOX BOUNDS ss ss ss
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-6 2 -1.42292 -0.792944 2.88751 -3.94318 3.53329 1.14403
-ITEM: TIMESTEP
-80
-ITEM: NUMBER OF ATOMS
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-ITEM: BOX BOUNDS ss ss ss
--1.4632357229999999e+00 9.3247372299999998e-01
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-ITEM: TIMESTEP
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-ITEM: NUMBER OF ATOMS
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-ITEM: BOX BOUNDS ss ss ss
--1.4632357229999999e+00 9.3247372299999998e-01
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-2 2 -0.274281 -0.000680382 0.947366 7.50569 0.00503125 -1.23144
-3 2 0.92514 -0.000469353 -0.0912836 -0.650877 0.00352314 5.72916
-4 1 -0.891964 0.000116952 2.76852 3.17186 0.0014363 -1.52231
-5 2 -1.43137 0.791127 2.86377 -1.95059 -4.67792 0.861555
-6 2 -1.43013 -0.791605 2.86488 -1.95795 4.67604 0.85497
-ITEM: TIMESTEP
-100
-ITEM: NUMBER OF ATOMS
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-ITEM: BOX BOUNDS ss ss ss
--1.4632357229999999e+00 9.3247372299999998e-01
--7.5570026690000003e-01 7.5527126690000002e-01
--8.9995638999999985e-03 2.9352285639000000e+00
-ITEM: ATOMS id type x y z fx fy fz
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-5 2 -1.45671 0.76736 2.88018 3.9012 0.426437 -0.678284
-6 2 -1.4555 -0.767854 2.88126 3.9018 -0.421357 -0.677675

examples/amoeba/dump.water_dimer.hippo.1

@@ -1,165 +0,0 @@
-ITEM: TIMESTEP
-0
-ITEM: NUMBER OF ATOMS
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-ITEM: BOX BOUNDS ss ss ss
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-ITEM: TIMESTEP
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-ITEM: NUMBER OF ATOMS
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-6 2 -1.42099 -0.791374 2.92075 -3.91591 4.87112 1.05588
-ITEM: TIMESTEP
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-ITEM: NUMBER OF ATOMS
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-ITEM: BOX BOUNDS ss ss ss
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-6 2 -1.46268 -0.753984 2.92608 4.55648 -4.84791 -1.47593
-ITEM: TIMESTEP
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-ITEM: NUMBER OF ATOMS
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-ITEM: BOX BOUNDS ss ss ss
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-5 2 -1.42536 0.788259 2.90023 -5.83991 -2.07218 1.27305
-6 2 -1.42412 -0.788676 2.90134 -5.84324 2.06468 1.27016
-ITEM: TIMESTEP
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-ITEM: NUMBER OF ATOMS
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-ITEM: BOX BOUNDS ss ss ss
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-ITEM: NUMBER OF ATOMS
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-ITEM: TIMESTEP
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-ITEM: NUMBER OF ATOMS
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-6 2 -1.47719 -0.753996 2.80876 4.79863 -4.81616 -0.498076
-ITEM: TIMESTEP
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-ITEM: NUMBER OF ATOMS
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-5 2 -1.4359 0.790393 2.75878 -3.89983 -4.84574 0.12595
-6 2 -1.43466 -0.791026 2.7599 -3.90736 4.83989 0.11913
-ITEM: TIMESTEP
-80
-ITEM: NUMBER OF ATOMS
-6
-ITEM: BOX BOUNDS ss ss ss
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-3 2 0.902079 -0.000521504 -0.139604 -1.23495 -0.0056704 -6.67396
-4 1 -0.883488 0.000127321 2.77377 -12.2256 -0.0109573 -1.83848
-5 2 -1.47309 0.755263 2.71301 6.16734 2.89071 0.796293
-6 2 -1.4719 -0.756019 2.71407 6.17192 -2.87983 0.800362
-ITEM: TIMESTEP
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-ITEM: NUMBER OF ATOMS
-6
-ITEM: BOX BOUNDS ss ss ss
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-6 2 -1.42478 -0.791209 2.68827 -3.94309 4.85389 -0.0130349
-ITEM: TIMESTEP
-100
-ITEM: NUMBER OF ATOMS
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-1 1 -0.0443853 -0.00113803 0.0410221 7.36858 0.0108291 7.15279
-2 2 -0.076648 -0.000485983 1.00287 -6.96363 -0.00585609 -0.543819
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-4 1 -0.880834 0.000124898 2.7674 -9.13947 -0.00841726 -1.90715
-5 2 -1.46341 0.754149 2.66816 4.55895 4.52404 1.01184
-6 2 -1.46222 -0.754952 2.66922 4.56597 -4.51554 1.01819

examples/amoeba/dump.water_dimer.hippo.4

@@ -1,165 +0,0 @@
-ITEM: TIMESTEP
-0
-ITEM: NUMBER OF ATOMS
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-1 1 -0.024616 -0.001154 -0.003748 6.77815 0.012441 10.1043
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-4 1 -0.892721 0.00012 2.77367 -11.9286 -0.00716387 3.29032
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-ITEM: TIMESTEP
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-4 1 -0.897884 0.000116793 2.77488 7.53966 0.00410482 -2.48587
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-6 2 -1.42099 -0.791374 2.92075 -3.91591 4.87112 1.05588
-ITEM: TIMESTEP
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-ITEM: TIMESTEP
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-6 2 -1.42412 -0.788676 2.90134 -5.84324 2.06468 1.27016
-ITEM: TIMESTEP
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-1 1 -0.0292005 -0.00114894 0.00855106 5.6712 0.00787804 4.86214
-2 2 -0.153199 -0.000576377 0.959922 -7.58451 -0.00449199 2.07976
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-4 1 -0.89217 0.000118771 2.77132 -5.68638 -0.00321013 1.64962
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-6 2 -1.46886 -0.752392 2.88844 3.11554 -6.73373 -0.972121
-ITEM: TIMESTEP
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-1 1 -0.0276682 -0.00114169 0.0171537 -7.90829 -0.012452 -8.85967
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-4 1 -0.895573 0.00011689 2.77245 11.8261 0.00822001 -1.54401
-5 2 -1.4336 0.787999 2.84603 -5.85703 -2.08185 0.681764
-6 2 -1.43237 -0.788505 2.84714 -5.86031 2.07358 0.678838
-ITEM: TIMESTEP
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-ITEM: NUMBER OF ATOMS
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examples/amoeba/dump.water_hexamer.amoeba.1

@@ -1,297 +0,0 @@
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-16 1 2.01083 1.04528 -0.114231 6.83173 -12.9986 1.26494
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-3 2 -1.97348 -0.365352 2.2852 -6.58467 -1.56222 9.05296
-4 1 -1.74352 -0.377279 -1.33693 -0.505822 0.308788 -3.25308
-5 2 -1.91188 -0.438855 -0.39405 1.95743 0.358158 9.20234
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-7 1 -0.571778 1.99034 -0.138544 1.3921 0.315501 -1.43854
-8 2 -0.938419 1.50232 0.602337 -1.22478 -1.30903 4.8686
-9 2 -0.959599 1.56918 -0.90914 -0.0288155 0.574454 -3.52808
-10 1 0.985435 -1.15713 1.41811 -6.25848 -6.25702 9.27302
-11 2 0.972167 -1.59168 0.560031 1.69554 -0.201305 -5.06875
-12 2 1.54032 -0.386652 1.30283 4.96928 5.72762 -4.15176
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examples/amoeba/dump.water_hexamer.amoeba.4

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-7 1 -0.571778 1.99034 -0.138544 1.3921 0.315501 -1.43854
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-9 2 -0.959599 1.56918 -0.90914 -0.0288155 0.574454 -3.52808
-10 1 0.985435 -1.15713 1.41811 -6.25848 -6.25702 9.27302
-11 2 0.972167 -1.59168 0.560031 1.69554 -0.201305 -5.06875
-12 2 1.54032 -0.386652 1.30283 4.96928 5.72762 -4.15176
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-8 2 -0.945484 1.51375 0.61188 -1.03442 -1.79649 -0.570033
-9 2 -0.936389 1.56212 -0.924193 -1.07342 -0.200973 1.02154
-10 1 0.975854 -1.15481 1.42351 1.86741 -2.52595 -4.21318
-11 2 0.98193 -1.53917 0.537259 -2.6087 -4.02599 1.03016
-12 2 1.52752 -0.379325 1.30866 2.98513 5.11632 2.51897
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-17 2 1.15126 1.49959 -0.126569 -0.261743 3.34267 -0.115684
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-ITEM: NUMBER OF ATOMS
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-4 1 -1.74898 -0.375873 -1.32741 -4.05983 -3.09974 1.92324
-5 2 -1.86884 -0.471305 -0.372769 3.24632 2.33491 1.76011
-6 2 -2.50916 -0.806172 -1.72327 1.14638 0.924599 -3.12385
-7 1 -0.564884 1.97778 -0.142101 -4.14881 -3.0738 -0.168062
-8 2 -0.958996 1.4911 0.595477 2.25574 1.20147 -1.85844
-9 2 -0.937749 1.56372 -0.930264 1.31445 2.00952 1.76263
-10 1 0.975211 -1.15256 1.42364 -0.947501 -4.6035 2.62584
-11 2 0.950951 -1.55837 0.541757 3.10583 4.89391 1.85772
-12 2 1.52342 -0.363228 1.34082 0.672959 -1.69053 -5.30235
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-16 1 2.00445 1.04687 -0.100669 -1.02523 8.04786 -0.336895
-17 2 1.16075 1.52969 -0.119062 2.24423 -4.67525 0.190963
-18 2 2.68635 1.72058 -0.160395 0.158945 -3.21195 0.180894

examples/amoeba/dump.water_hexamer.hippo.1

@@ -1,297 +0,0 @@
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-10 1 0.964803 -1.16576 1.43999 15.4285 1.35636 -21.3173
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-12 2 1.54222 -0.393692 1.34437 -5.98579 -2.68738 6.2337
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-9 2 -0.948386 1.59852 -0.906373 -0.161598 -1.83495 7.27882
-10 1 0.972994 -1.16632 1.4367 2.1365 -3.63541 -4.30666
-11 2 0.921471 -1.54563 0.536978 3.92948 8.96444 9.02535
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-8 2 -0.894989 1.49275 0.621756 1.9428 5.13739 2.3456
-9 2 -0.928333 1.53949 -0.878364 1.74391 4.55343 -2.63937
-10 1 0.983665 -1.17004 1.43811 2.15858 5.32924 -12.0192
-11 2 0.916986 -1.51176 0.532863 -0.801958 -4.34579 6.00669
-12 2 1.48632 -0.356933 1.30471 -0.115562 -1.35756 5.38685
-13 1 0.974155 -1.39809 -1.34091 -3.6872 9.81415 2.33229
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-17 2 1.15863 1.52924 -0.140109 2.7798 -3.05413 0.358119
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-5 2 -1.85923 -0.443728 -0.358889 -2.57415 -1.51426 3.86387
-6 2 -2.50599 -0.762479 -1.73443 -2.25678 -0.997735 0.886673
-7 1 -0.57869 2.00716 -0.122116 7.46708 7.5609 -0.932554
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-9 2 -0.906489 1.54888 -0.899539 -3.74504 -3.89196 0.775918
-10 1 0.993915 -1.16716 1.4314 -4.03671 -0.827424 10.5116
-11 2 0.932938 -1.58361 0.567361 1.80347 1.36047 -5.88474
-12 2 1.49414 -0.355801 1.3027 1.34198 0.116597 -4.03649
-13 1 0.970608 -1.38983 -1.33905 4.21477 -7.05635 0.421831
-14 2 0.0575618 -1.13428 -1.49637 -1.45416 4.35852 0.0411765
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-16 1 2.00096 1.05017 -0.124007 4.94447 -7.97826 1.06585
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-18 2 2.7082 1.68479 -0.23083 -0.128954 2.19398 -0.267092
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-ITEM: NUMBER OF ATOMS
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-7 1 -0.578876 1.99941 -0.124067 2.19183 2.88771 -2.2033
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-10 1 1.00066 -1.16525 1.43041 -2.12968 1.37125 11.5778
-11 2 0.974279 -1.60078 0.583019 -3.02955 -6.45349 -11.2722
-12 2 1.51087 -0.375422 1.25067 2.49642 6.22795 1.24643
-13 1 0.96952 -1.38626 -1.33641 3.1199 -1.09706 -1.06644
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-15 2 1.45433 -0.57243 -1.18601 5.63783 2.37426 1.20997
-16 1 1.9962 1.04317 -0.122075 10.6231 -9.89832 0.540427
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-18 2 2.71508 1.6609 -0.228386 3.66149 2.12531 -0.383549
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-ITEM: NUMBER OF ATOMS
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-4 1 -1.72947 -0.37135 -1.31158 7.45117 4.03521 -12.7525
-5 2 -1.85272 -0.46757 -0.370426 -4.08312 -1.86842 12.0545
-6 2 -2.4914 -0.737252 -1.75485 -4.03109 -2.01148 0.403261
-7 1 -0.581812 1.98886 -0.127591 8.73336 12.0451 -2.23223
-8 2 -0.927295 1.54015 0.641551 -4.26906 -6.45964 5.24049
-9 2 -0.953055 1.5416 -0.887204 -3.28906 -5.2042 -3.24355
-10 1 1.00866 -1.16393 1.43094 -5.76797 0.688141 16.3003
-11 2 0.941718 -1.59751 0.586621 -0.69625 -5.79697 -13.9615
-12 2 1.5005 -0.365594 1.24465 4.16474 6.46538 -1.29083
-13 1 0.968591 -1.37822 -1.33754 5.88173 -13.6635 -0.995409
-14 2 0.058765 -1.13465 -1.50083 -6.65826 5.43105 -0.991523
-15 2 1.47128 -0.574689 -1.20309 0.663977 7.53437 1.14922
-16 1 1.99172 1.03702 -0.120004 11.7209 -15.9347 1.25003
-17 2 1.18616 1.54124 -0.127765 -14.4197 10.6401 -0.950727
-18 2 2.7224 1.64022 -0.223578 2.05256 5.25094 -0.438473
-ITEM: TIMESTEP
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-ITEM: NUMBER OF ATOMS
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-4 1 -1.72371 -0.366036 -1.3145 0.154709 0.0103655 -5.79078
-5 2 -1.86537 -0.486382 -0.375504 0.204748 0.738589 9.60402
-6 2 -2.49691 -0.728317 -1.74343 -1.12209 -0.453095 -3.27306
-7 1 -0.582396 1.98478 -0.131637 3.0799 3.10149 -1.36944
-8 2 -0.917703 1.51358 0.63199 -1.67497 -1.52591 5.69623
-9 2 -0.95935 1.51373 -0.876424 -0.704912 -1.0485 -4.50039
-10 1 1.01141 -1.16147 1.43332 -7.40944 0.284109 12.5023
-11 2 0.911102 -1.56686 0.573359 1.73368 -3.47737 -10.1102
-12 2 1.49548 -0.352196 1.26684 4.34342 4.22027 -2.29553
-13 1 0.969684 -1.37685 -1.34222 -0.51092 -4.11589 -0.224969
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-15 2 1.44029 -0.555019 -1.20354 6.44357 4.32801 1.75924
-16 1 1.98854 1.02727 -0.117121 5.38674 -4.81439 0.472007
-17 2 1.17286 1.52668 -0.137432 -10.3716 4.01885 -0.196355
-18 2 2.69 1.66639 -0.213741 4.03261 1.60042 -0.312306
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-3 2 -1.9938 -0.405389 2.24937 -1.65789 -0.838399 2.61041
-4 1 -1.72181 -0.363627 -1.31513 2.63115 1.26887 -2.8752
-5 2 -1.86247 -0.45623 -0.365408 -2.65258 -1.1368 1.02525
-6 2 -2.4895 -0.712321 -1.77001 -0.898587 -0.369019 2.21573
-7 1 -0.583063 1.97962 -0.135858 1.67055 0.570004 -0.383383
-8 2 -0.908051 1.51128 0.64094 -1.16679 -0.0785678 -0.520586
-9 2 -0.943124 1.49995 -0.888932 -0.754685 -0.199723 0.596245
-10 1 1.00431 -1.15529 1.43647 -0.676345 0.911353 -2.95012
-11 2 0.95109 -1.53365 0.551095 -1.85378 -3.64627 0.0738184
-12 2 1.52689 -0.36229 1.29214 1.34973 2.90443 2.73267
-13 1 0.96764 -1.3732 -1.34735 0.830518 -7.82237 0.0710001
-14 2 0.049796 -1.13062 -1.50565 0.0671147 3.17314 0.120857
-15 2 1.46341 -0.566541 -1.18509 -0.178936 4.65822 -0.507667
-16 1 1.98438 1.02188 -0.114233 -0.881295 -2.57322 0.275288
-17 2 1.13419 1.48172 -0.149659 1.87909 1.86036 0.463365
-18 2 2.6735 1.67987 -0.202074 -0.651386 1.64881 -0.399918
-ITEM: TIMESTEP
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-ITEM: NUMBER OF ATOMS
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-ITEM: ATOMS id type x y z fx fy fz
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-2 2 -0.617503 -0.581602 1.56045 -17.3455 8.85736 -2.90765
-3 2 -1.99215 -0.403845 2.25671 0.833211 1.42908 -3.53001
-4 1 -1.71857 -0.360372 -1.31644 -7.32338 -2.11362 6.45601
-5 2 -1.89982 -0.440583 -0.365391 4.39327 0.727605 -4.87947
-6 2 -2.49827 -0.701359 -1.75982 2.51785 1.20426 -1.18541
-7 1 -0.581108 1.97455 -0.140769 -3.87733 -3.80002 1.10694
-8 2 -0.928789 1.51932 0.641149 2.19408 2.20718 -5.07369
-9 2 -0.943839 1.48954 -0.89443 1.32563 2.05291 3.72773
-10 1 0.995847 -1.14613 1.43537 0.755936 -5.6909 -0.46639
-11 2 0.966841 -1.55186 0.550806 1.56938 7.42451 5.54707
-12 2 1.55511 -0.362342 1.35836 -2.79165 -2.9995 -5.36768
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-8 2 -0.945449 1.52054 0.635243 4.66427 4.57627 -6.94972
-9 2 -0.952686 1.48464 -0.897126 3.60343 4.09955 4.74753
-10 1 0.988258 -1.14419 1.44127 11.1074 1.88534 -20.9154
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-12 2 1.5415 -0.356231 1.32305 -5.76468 -4.25266 5.91571
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-6 2 -2.51926 -0.676876 -1.74282 3.42966 1.20159 -1.20299
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-8 2 -0.935394 1.51644 0.636953 2.89489 2.96603 -9.31226
-9 2 -0.942573 1.488 -0.91114 1.96254 2.34604 7.29302
-10 1 0.988651 -1.14425 1.44045 0.840008 -1.36718 -7.83612
-11 2 0.899639 -1.53136 0.543246 5.64911 9.69241 11.7913
-12 2 1.49178 -0.318235 1.33897 -3.7582 -9.86315 -4.79205
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examples/amoeba/dump.water_hexamer.hippo.4

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-9 2 -0.948386 1.59852 -0.906373 -0.161598 -1.83495 7.27882
-10 1 0.972994 -1.16632 1.4367 2.1365 -3.63541 -4.30666
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-11 2 0.916986 -1.51176 0.532863 -0.801958 -4.34579 6.00669
-12 2 1.48632 -0.356933 1.30471 -0.115562 -1.35756 5.38685
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-17 2 1.15863 1.52924 -0.140109 2.7798 -3.05413 0.358119
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-7 1 -0.57869 2.00716 -0.122116 7.46708 7.5609 -0.932554
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-9 2 -0.906489 1.54888 -0.899539 -3.74504 -3.89196 0.775918
-10 1 0.993915 -1.16716 1.4314 -4.03671 -0.827424 10.5116
-11 2 0.932938 -1.58361 0.567361 1.80347 1.36047 -5.88474
-12 2 1.49414 -0.355801 1.3027 1.34198 0.116597 -4.03649
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-14 2 0.0575618 -1.13428 -1.49637 -1.45416 4.35852 0.0411765
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-ITEM: NUMBER OF ATOMS
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-10 1 1.00066 -1.16525 1.43041 -2.12968 1.37125 11.5778
-11 2 0.974279 -1.60078 0.583019 -3.02955 -6.45349 -11.2722
-12 2 1.51087 -0.375422 1.25067 2.49642 6.22795 1.24643
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-6 2 -2.4914 -0.737252 -1.75485 -4.03109 -2.01148 0.403261
-7 1 -0.581812 1.98886 -0.127591 8.73336 12.0451 -2.23223
-8 2 -0.927295 1.54015 0.641551 -4.26906 -6.45964 5.24049
-9 2 -0.953055 1.5416 -0.887204 -3.28906 -5.2042 -3.24355
-10 1 1.00866 -1.16393 1.43094 -5.76797 0.688141 16.3003
-11 2 0.941718 -1.59751 0.586621 -0.69625 -5.79697 -13.9615
-12 2 1.5005 -0.365594 1.24465 4.16474 6.46538 -1.29083
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-15 2 1.47128 -0.574689 -1.20309 0.663977 7.53437 1.14922
-16 1 1.99172 1.03702 -0.120004 11.7209 -15.9347 1.25003
-17 2 1.18616 1.54124 -0.127765 -14.4197 10.6401 -0.950727
-18 2 2.7224 1.64022 -0.223578 2.05256 5.25094 -0.438473
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-ITEM: NUMBER OF ATOMS
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-5 2 -1.86537 -0.486382 -0.375504 0.204748 0.738589 9.60402
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-8 2 -0.917703 1.51358 0.63199 -1.67497 -1.52591 5.69623
-9 2 -0.95935 1.51373 -0.876424 -0.704912 -1.0485 -4.50039
-10 1 1.01141 -1.16147 1.43332 -7.40944 0.284109 12.5023
-11 2 0.911102 -1.56686 0.573359 1.73368 -3.47737 -10.1102
-12 2 1.49548 -0.352196 1.26684 4.34342 4.22027 -2.29553
-13 1 0.969684 -1.37685 -1.34222 -0.51092 -4.11589 -0.224969
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-15 2 1.44029 -0.555019 -1.20354 6.44357 4.32801 1.75924
-16 1 1.98854 1.02727 -0.117121 5.38674 -4.81439 0.472007
-17 2 1.17286 1.52668 -0.137432 -10.3716 4.01885 -0.196355
-18 2 2.69 1.66639 -0.213741 4.03261 1.60042 -0.312306
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-7 1 -0.583063 1.97962 -0.135858 1.67055 0.570004 -0.383383
-8 2 -0.908051 1.51128 0.64094 -1.16679 -0.0785678 -0.520586
-9 2 -0.943124 1.49995 -0.888932 -0.754685 -0.199723 0.596245
-10 1 1.00431 -1.15529 1.43647 -0.676345 0.911353 -2.95012
-11 2 0.95109 -1.53365 0.551095 -1.85378 -3.64627 0.0738184
-12 2 1.52689 -0.36229 1.29214 1.34973 2.90443 2.73267
-13 1 0.96764 -1.3732 -1.34735 0.830518 -7.82237 0.0710001
-14 2 0.049796 -1.13062 -1.50565 0.0671147 3.17314 0.120857
-15 2 1.46341 -0.566541 -1.18509 -0.178936 4.65822 -0.507667
-16 1 1.98438 1.02188 -0.114233 -0.881295 -2.57322 0.275288
-17 2 1.13419 1.48172 -0.149659 1.87909 1.86036 0.463365
-18 2 2.6735 1.67987 -0.202074 -0.651386 1.64881 -0.399918
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-ITEM: NUMBER OF ATOMS
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-2 2 -0.617503 -0.581602 1.56045 -17.3455 8.85736 -2.90765
-3 2 -1.99215 -0.403845 2.25671 0.833211 1.42908 -3.53001
-4 1 -1.71857 -0.360372 -1.31644 -7.32338 -2.11362 6.45601
-5 2 -1.89982 -0.440583 -0.365391 4.39327 0.727605 -4.87947
-6 2 -2.49827 -0.701359 -1.75982 2.51785 1.20426 -1.18541
-7 1 -0.581108 1.97455 -0.140769 -3.87733 -3.80002 1.10694
-8 2 -0.928789 1.51932 0.641149 2.19408 2.20718 -5.07369
-9 2 -0.943839 1.48954 -0.89443 1.32563 2.05291 3.72773
-10 1 0.995847 -1.14613 1.43537 0.755936 -5.6909 -0.46639
-11 2 0.966841 -1.55186 0.550806 1.56938 7.42451 5.54707
-12 2 1.55511 -0.362342 1.35836 -2.79165 -2.9995 -5.36768
-13 1 0.967816 -1.37465 -1.35163 -3.29308 4.65803 -0.872226
-14 2 0.0602027 -1.09254 -1.5264 2.56737 -3.64929 1.27094
-15 2 1.45854 -0.559392 -1.19328 1.84002 -1.84978 0.0538636
-16 1 1.98052 1.0158 -0.111184 -7.14388 11.5516 -0.816233
-17 2 1.12003 1.47724 -0.140032 8.70268 -6.85942 1.26876
-18 2 2.64114 1.706 -0.201685 0.0272078 -3.57662 -0.103793
-ITEM: TIMESTEP
-90
-ITEM: NUMBER OF ATOMS
-18
-ITEM: BOX BOUNDS ss ss ss
--2.5173543550999997e+00 2.6752353550999999e+00
--1.5223951870999999e+00 2.0181841871000001e+00
--1.7341615612999999e+00 2.2202425613000001e+00
-ITEM: ATOMS id type x y z fx fy fz
-1 1 -1.50003 -0.175917 1.46165 15.3898 -11.884 8.8546
-2 2 -0.608584 -0.600731 1.57129 -23.7815 11.9323 -1.75151
-3 2 -2.00991 -0.394435 2.25305 5.57059 1.55514 -7.64598
-4 1 -1.72137 -0.357368 -1.31563 -1.93902 -0.246344 7.85181
-5 2 -1.87234 -0.43987 -0.353482 -0.118832 -0.772284 -11.4834
-6 2 -2.49861 -0.682857 -1.77755 1.48512 0.513779 4.12935
-7 1 -0.579472 1.97061 -0.145894 -8.85759 -8.26094 2.77276
-8 2 -0.945449 1.52054 0.635243 4.66427 4.57627 -6.94972
-9 2 -0.952686 1.48464 -0.897126 3.60343 4.09955 4.74753
-10 1 0.988258 -1.14419 1.44127 11.1074 1.88534 -20.9154
-11 2 0.971991 -1.50516 0.531218 -4.29535 0.162687 14.3489
-12 2 1.5415 -0.356231 1.32305 -5.76468 -4.25266 5.91571
-13 1 0.969416 -1.37359 -1.35605 -1.23717 3.53556 0.174563
-14 2 0.053578 -1.1004 -1.52114 7.10928 -0.236326 1.96556
-15 2 1.49219 -0.569722 -1.21186 -5.0738 -3.24139 -1.5161
-16 1 1.97824 1.01566 -0.108279 -8.95647 8.69277 0.191958
-17 2 1.10027 1.45664 -0.104435 15.9218 -5.21388 -1.22481
-18 2 2.64464 1.70165 -0.21558 -4.82724 -2.84557 0.534172
-ITEM: TIMESTEP
-100
-ITEM: NUMBER OF ATOMS
-18
-ITEM: BOX BOUNDS ss ss ss
--2.5173543550999997e+00 2.6752353550999999e+00
--1.5223951870999999e+00 2.0181841871000001e+00
--1.7341615612999999e+00 2.2202425613000001e+00
-ITEM: ATOMS id type x y z fx fy fz
-1 1 -1.4951 -0.17739 1.46185 11.6291 -12.0775 13.5087
-2 2 -0.608426 -0.588808 1.60852 -19.0988 9.4339 -4.86631
-3 2 -2.01619 -0.397996 2.24676 4.77562 3.06476 -9.1756
-4 1 -1.72287 -0.352149 -1.31567 -8.10325 -4.84048 12.8242
-5 2 -1.86729 -0.479262 -0.356777 4.49726 3.58866 -11.0242
-6 2 -2.51926 -0.676876 -1.74282 3.42966 1.20159 -1.20299
-7 1 -0.581355 1.96754 -0.149521 -5.24612 -4.66563 2.71982
-8 2 -0.935394 1.51644 0.636953 2.89489 2.96603 -9.31226
-9 2 -0.942573 1.488 -0.91114 1.96254 2.34604 7.29302
-10 1 0.988651 -1.14425 1.44045 0.840008 -1.36718 -7.83612
-11 2 0.899639 -1.53136 0.543246 5.64911 9.69241 11.7913
-12 2 1.49178 -0.318235 1.33897 -3.7582 -9.86315 -4.79205
-13 1 0.974233 -1.37573 -1.35945 -3.77942 11.331 0.435153
-14 2 0.0583408 -1.08758 -1.49668 6.15796 -3.89994 -0.197074
-15 2 1.48764 -0.558876 -1.24121 -3.14566 -8.24544 0.525665
-16 1 1.97883 1.01496 -0.10404 -9.03485 15.6667 -0.929518
-17 2 1.11471 1.47883 -0.106249 11.9101 -8.77208 -0.858699
-18 2 2.63671 1.70526 -0.232286 -1.57994 -5.55972 1.09694

examples/amoeba/in.ubiquitin

@@ -41,8 +41,8 @@ compute         virial all pressure NULL virial
 thermo_style    custom step temp epair ebond eangle edihed eimp &
                 emol etotal press c_virial[*]
 
-dump            1 all custom 10 dump.ubiquitin id type x y z fx fy fz
+#dump            1 all custom 10 dump.ubiquitin id type x y z fx fy fz
-dump_modify     1 sort id
+#dump_modify     1 sort id
 
 # zero step run
 

examples/amoeba/in.water_box.amoeba

@@ -32,8 +32,8 @@ compute         virial all pressure NULL virial
 thermo_style    custom step temp epair ebond eangle edihed eimp &
                 emol etotal press c_virial[*]
 
-dump            1 all custom 10 dump.water_box id type x y z fx fy fz
+#dump            1 all custom 10 dump.water_box id type x y z fx fy fz
-dump_modify     1 sort id
+#dump_modify     1 sort id
 
 # zero step run
 

examples/amoeba/in.water_box.hippo

@@ -32,8 +32,8 @@ compute         virial all pressure NULL virial
 thermo_style    custom step temp epair ebond eangle edihed eimp &
                 emol etotal press c_virial[*]
 
-dump            1 all custom 10 dump.water_box id type x y z fx fy fz
+#dump            1 all custom 10 dump.water_box id type x y z fx fy fz
-dump_modify     1 sort id
+#dump_modify     1 sort id
 
 # zero step run
 

examples/amoeba/in.water_dimer.amoeba

@@ -32,8 +32,8 @@ compute         virial all pressure NULL virial
 thermo_style    custom step temp epair ebond eangle edihed eimp &
                 emol etotal press c_virial[*]
 
-dump            1 all custom 10 dump.water_dimer id type x y z fx fy fz
+#dump            1 all custom 10 dump.water_dimer id type x y z fx fy fz
-dump_modify     1 sort id
+#dump_modify     1 sort id
 
 # zero step run
 

examples/amoeba/in.water_dimer.hippo

@@ -32,8 +32,8 @@ compute         virial all pressure NULL virial
 thermo_style    custom step temp epair ebond eangle edihed eimp &
                 emol etotal press c_virial[*]
 
-dump            1 all custom 10 dump.water_dimer id type x y z fx fy fz
+#dump            1 all custom 10 dump.water_dimer id type x y z fx fy fz
-dump_modify     1 sort id
+#dump_modify     1 sort id
 
 # zero step run
 

examples/amoeba/in.water_hexamer.amoeba

@@ -32,8 +32,8 @@ compute         virial all pressure NULL virial
 thermo_style    custom step temp epair ebond eangle edihed eimp &
                 emol etotal press c_virial[*]
 
-dump            1 all custom 10 dump.water_hexamer id type x y z fx fy fz
+#dump            1 all custom 10 dump.water_hexamer id type x y z fx fy fz
-dump_modify     1 sort id
+#dump_modify     1 sort id
 
 # zero step run
 

examples/amoeba/in.water_hexamer.hippo

@@ -32,8 +32,8 @@ compute         virial all pressure NULL virial
 thermo_style    custom step temp epair ebond eangle edihed eimp &
                 emol etotal press c_virial[*]
 
-dump            1 all custom 10 dump.water_hexamer id type x y z fx fy fz
+#dump            1 all custom 10 dump.water_hexamer id type x y z fx fy fz
-dump_modify     1 sort id
+#dump_modify     1 sort id
 
 # zero step run
 

examples/amoeba/log.5Jul22.ubiquitin.g++.1

@@ -0,0 +1,162 @@
+LAMMPS (23 Jun 2022)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
+# solvated ubiquitin molecule with AMOEBA force field
+
+units           real
+boundary        p p p
+atom_modify     sort 0 0.0
+
+atom_style      amoeba
+
+bond_style      class2
+angle_style     amoeba
+dihedral_style  fourier
+improper_style  amoeba
+
+# per-atom properties required by AMOEBA or HIPPO
+
+fix             amtype all property/atom i_amtype ghost yes
+fix             extra all property/atom i_amgroup d_redID d_pval ghost yes
+fix             extra2 all property/atom i_polaxe d2_xyzaxis 3
+
+fix             pit all amoeba/pitorsion
+fix_modify      pit energy yes
+fix             bit all amoeba/bitorsion bitorsion.ubiquitin.data
+fix_modify      bit energy yes
+
+# read data file
+
+read_data       data.ubiquitin fix amtype NULL "Tinker Types"                 fix pit "pitorsion types" "PiTorsion Coeffs"                 fix pit pitorsions PiTorsions                 fix bit bitorsions BiTorsions
+Reading data file ...
+  orthogonal box = (0 0 0) to (54.99 41.91 41.91)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  9737 atoms
+  scanning bonds ...
+  4 = max bonds/atom
+  scanning angles ...
+  6 = max angles/atom
+  scanning dihedrals ...
+  18 = max dihedrals/atom
+  scanning impropers ...
+  3 = max impropers/atom
+  reading bonds ...
+  6908 bonds
+  reading angles ...
+  5094 angles
+  reading dihedrals ...
+  3297 dihedrals
+  reading impropers ...
+  651 impropers
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0        0        0       
+  special bond factors coul:  0        0        0       
+     4 = max # of 1-2 neighbors
+     9 = max # of 1-3 neighbors
+    19 = max # of 1-4 neighbors
+    21 = max # of special neighbors
+  special bonds CPU = 0.003 seconds
+  read_data CPU = 0.042 seconds
+
+pair_style      amoeba
+pair_coeff      * * amoeba_ubiquitin.prm amoeba_ubiquitin.key
+Skipping section:   AMOEBA Protein Force Field Atom Classes  
+Skipping section:   Torsion-Torsion Parameters  
+Skipping section:   Biopolymer Atom Type Conversions  
+
+special_bonds   lj/coul 0.5 0.5 0.5 one/five yes
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0.5      0.5      0.5     
+  special bond factors coul:  0.5      0.5      0.5     
+     4 = max # of 1-2 neighbors
+     9 = max # of 1-3 neighbors
+    19 = max # of 1-4 neighbors
+    58 = max # of 1-5 neighbors
+    21 = max # of special neighbors
+  special bonds CPU = 0.004 seconds
+
+# thermo output
+
+compute         virial all pressure NULL virial
+
+thermo_style    custom step temp epair ebond eangle edihed eimp                 emol etotal press c_virial[*]
+
+#dump            1 all custom 10 dump.ubiquitin id type x y z fx fy fz
+#dump_modify     1 sort id
+
+# zero step run
+
+#run             0
+
+# dynamics
+
+fix            1 all nve
+
+thermo         1
+run            5
+AMOEBA force field settings
+  hal: cut 12 taper 10.8 vscale 0 0 1 1
+  multipole: cut 7 aewald 0.4 bsorder 5 FFT 60 48 48 mscale 0 0 0.4 1
+  polar: cut 7 aewald 0.5 bsorder 5 FFT 60 48 48
+         pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 1 1 1 1 d/u scale 0 1
+  precondition: cut 4.5
+Generated 0 of 15 mixed pair_coeff terms from geometric mixing rule
+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 = 8 6 6
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair amoeba, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d
+      bin: standard
+  AMOEBA group count: 3196
+Per MPI rank memory allocation (min/avg/max) = 258.3 | 258.3 | 258.3 Mbytes
+   Step          Temp          E_pair         E_bond        E_angle        E_dihed        E_impro         E_mol          TotEng         Press       c_virial[1]    c_virial[2]    c_virial[3]    c_virial[4]    c_virial[5]    c_virial[6]  
+         0   0             -35338.057      2856.5938      1955.5431      224.37609      65.00809       5101.5211     -30247.585     -6336.5196     -5795.4272     -6329.8149     -6884.3167      349.52657      77.164877      652.41925    
+         1   29.61379      -35356.153      2037.3541      1840.7883      223.90217      64.293945      4166.3385     -30341.522     -6486.773      -6452.8463     -6841.5982     -7386.1106      311.38025      120.72605      545.35513    
+         2   78.518242     -35383.65       825.39919      1538.3909      222.55095      62.191009      2648.5321     -30467.814     -5502.9841     -6410.2998     -6396.1829     -6937.8137      217.3515       210.76948      294.28051    
+         3   88.8921       -35402.11       938.99299      1162.2914      220.5271       58.832521      2380.644      -30453.516     -1929.5417     -3331.1291     -2769.7218     -3350.5733      117.32302      279.72705      31.237776    
+         4   68.740402     -35477.589      2048.0659      858.03795      218.14277      54.460022      3178.7066     -30316.325      2041.1138      594.25938      1665.7799      1030.8539      66.230421      304.28296     -155.80224    
+         5   76.267862     -35707.869      2206.6534      736.37385      215.75693      49.401674      3208.1859     -30299.377      2276.9276      536.21124      1893.4621      1258.492       92.097191      299.65604     -228.58369    
+Loop time of 6.52854 on 1 procs for 5 steps with 9737 atoms
+
+Performance: 0.066 ns/day, 362.697 hours/ns, 0.766 timesteps/s
+99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+AMOEBA timing breakdown:
+  Init    time: 0.0100839      0.15%
+  Hal     time: 1.54573       23.70%
+  Mpole   time: 0.806911      12.37%
+  Induce  time: 2.63878       40.46%
+  Polar   time: 1.51971       23.30%
+  Total   time: 6.52122     
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 6.5212     | 6.5212     | 6.5212     |   0.0 | 99.89
+Bond    | 0.0049597  | 0.0049597  | 0.0049597  |   0.0 |  0.08
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.0010627  | 0.0010627  | 0.0010627  |   0.0 |  0.02
+Output  | 0.00032106 | 0.00032106 | 0.00032106 |   0.0 |  0.00
+Modify  | 0.00083249 | 0.00083249 | 0.00083249 |   0.0 |  0.01
+Other   |            | 0.0001265  |            |       |  0.00
+
+Nlocal:           9737 ave        9737 max        9737 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:          31511 ave       31511 max       31511 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:     5.6393e+06 ave  5.6393e+06 max  5.6393e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 5639296
+Ave neighs/atom = 579.16155
+Ave special neighs/atom = 3.1364897
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:08

examples/amoeba/log.5Jul22.ubiquitin.g++.4

@@ -0,0 +1,162 @@
+LAMMPS (23 Jun 2022)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
+# solvated ubiquitin molecule with AMOEBA force field
+
+units           real
+boundary        p p p
+atom_modify     sort 0 0.0
+
+atom_style      amoeba
+
+bond_style      class2
+angle_style     amoeba
+dihedral_style  fourier
+improper_style  amoeba
+
+# per-atom properties required by AMOEBA or HIPPO
+
+fix             amtype all property/atom i_amtype ghost yes
+fix             extra all property/atom i_amgroup d_redID d_pval ghost yes
+fix             extra2 all property/atom i_polaxe d2_xyzaxis 3
+
+fix             pit all amoeba/pitorsion
+fix_modify      pit energy yes
+fix             bit all amoeba/bitorsion bitorsion.ubiquitin.data
+fix_modify      bit energy yes
+
+# read data file
+
+read_data       data.ubiquitin fix amtype NULL "Tinker Types"                 fix pit "pitorsion types" "PiTorsion Coeffs"                 fix pit pitorsions PiTorsions                 fix bit bitorsions BiTorsions
+Reading data file ...
+  orthogonal box = (0 0 0) to (54.99 41.91 41.91)
+  2 by 1 by 2 MPI processor grid
+  reading atoms ...
+  9737 atoms
+  scanning bonds ...
+  4 = max bonds/atom
+  scanning angles ...
+  6 = max angles/atom
+  scanning dihedrals ...
+  18 = max dihedrals/atom
+  scanning impropers ...
+  3 = max impropers/atom
+  reading bonds ...
+  6908 bonds
+  reading angles ...
+  5094 angles
+  reading dihedrals ...
+  3297 dihedrals
+  reading impropers ...
+  651 impropers
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0        0        0       
+  special bond factors coul:  0        0        0       
+     4 = max # of 1-2 neighbors
+     9 = max # of 1-3 neighbors
+    19 = max # of 1-4 neighbors
+    21 = max # of special neighbors
+  special bonds CPU = 0.001 seconds
+  read_data CPU = 0.049 seconds
+
+pair_style      amoeba
+pair_coeff      * * amoeba_ubiquitin.prm amoeba_ubiquitin.key
+Skipping section:   AMOEBA Protein Force Field Atom Classes  
+Skipping section:   Torsion-Torsion Parameters  
+Skipping section:   Biopolymer Atom Type Conversions  
+
+special_bonds   lj/coul 0.5 0.5 0.5 one/five yes
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0.5      0.5      0.5     
+  special bond factors coul:  0.5      0.5      0.5     
+     4 = max # of 1-2 neighbors
+     9 = max # of 1-3 neighbors
+    19 = max # of 1-4 neighbors
+    58 = max # of 1-5 neighbors
+    21 = max # of special neighbors
+  special bonds CPU = 0.001 seconds
+
+# thermo output
+
+compute         virial all pressure NULL virial
+
+thermo_style    custom step temp epair ebond eangle edihed eimp                 emol etotal press c_virial[*]
+
+#dump            1 all custom 10 dump.ubiquitin id type x y z fx fy fz
+#dump_modify     1 sort id
+
+# zero step run
+
+#run             0
+
+# dynamics
+
+fix            1 all nve
+
+thermo         1
+run            5
+AMOEBA force field settings
+  hal: cut 12 taper 10.8 vscale 0 0 1 1
+  multipole: cut 7 aewald 0.4 bsorder 5 FFT 60 48 48 mscale 0 0 0.4 1
+  polar: cut 7 aewald 0.5 bsorder 5 FFT 60 48 48
+         pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 1 1 1 1 d/u scale 0 1
+  precondition: cut 4.5
+Generated 0 of 15 mixed pair_coeff terms from geometric mixing rule
+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 = 8 6 6
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair amoeba, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d
+      bin: standard
+  AMOEBA group count: 3196
+Per MPI rank memory allocation (min/avg/max) = 144.2 | 144.7 | 145.4 Mbytes
+   Step          Temp          E_pair         E_bond        E_angle        E_dihed        E_impro         E_mol          TotEng         Press       c_virial[1]    c_virial[2]    c_virial[3]    c_virial[4]    c_virial[5]    c_virial[6]  
+         0   0             -35338.057      2856.5938      1955.5431      224.37609      65.00809       5101.5211     -30247.585     -6336.5196     -5795.4272     -6329.8149     -6884.3167      349.52657      77.164877      652.41925    
+         1   29.61379      -35356.153      2037.3541      1840.7883      223.90217      64.293945      4166.3385     -30341.522     -6486.773      -6452.8463     -6841.5982     -7386.1106      311.38025      120.72605      545.35513    
+         2   78.518242     -35383.65       825.39919      1538.3909      222.55095      62.191009      2648.5321     -30467.814     -5502.9841     -6410.2998     -6396.1829     -6937.8137      217.3515       210.76948      294.28051    
+         3   88.8921       -35402.11       938.99299      1162.2914      220.5271       58.832521      2380.644      -30453.516     -1929.5417     -3331.1291     -2769.7218     -3350.5733      117.32302      279.72705      31.237776    
+         4   68.740402     -35477.589      2048.0659      858.03795      218.14277      54.460022      3178.7066     -30316.325      2041.1138      594.25938      1665.7799      1030.8539      66.230421      304.28296     -155.80224    
+         5   76.267862     -35707.869      2206.6534      736.37385      215.75693      49.401674      3208.1859     -30299.377      2276.9276      536.21124      1893.4621      1258.492       92.097191      299.65604     -228.58369    
+Loop time of 2.20325 on 4 procs for 5 steps with 9737 atoms
+
+Performance: 0.196 ns/day, 122.403 hours/ns, 2.269 timesteps/s
+99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+AMOEBA timing breakdown:
+  Init    time: 0.0117181      0.53%
+  Hal     time: 0.442973      20.14%
+  Mpole   time: 0.287778      13.09%
+  Induce  time: 0.94261       42.86%
+  Polar   time: 0.514081      23.38%
+  Total   time: 2.19916     
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 2.1991     | 2.1992     | 2.1996     |   0.0 | 99.82
+Bond    | 0.0011873  | 0.0014547  | 0.0016743  |   0.5 |  0.07
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.0014371  | 0.0018264  | 0.0020772  |   0.6 |  0.08
+Output  | 0.0002413  | 0.00029218 | 0.00037812 |   0.0 |  0.01
+Modify  | 0.0002694  | 0.00029873 | 0.00032365 |   0.0 |  0.01
+Other   |            | 0.000135   |            |       |  0.01
+
+Nlocal:        2434.25 ave        2498 max        2390 min
+Histogram: 1 1 0 0 1 0 0 0 0 1
+Nghost:        16683.2 ave       16765 max       16568 min
+Histogram: 1 0 0 1 0 0 0 0 0 2
+Neighs:    1.40982e+06 ave 1.52088e+06 max 1.30717e+06 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+
+Total # of neighbors = 5639296
+Ave neighs/atom = 579.16155
+Ave special neighs/atom = 3.1364897
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:02

examples/amoeba/log.5Jul22.water_box.amoeba.g++.1

@@ -0,0 +1,150 @@
+LAMMPS (23 Jun 2022)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
+# replicate water box with AMOEBA or HIPPO
+
+units           real
+boundary        p p p
+
+atom_style      amoeba
+bond_style      class2
+angle_style     amoeba
+dihedral_style  none
+
+# per-atom properties required by AMOEBA or HIPPO
+
+fix             amtype all property/atom i_amtype ghost yes
+fix             extra all property/atom i_amgroup d_redID d_pval ghost yes
+fix             extra2 all property/atom i_polaxe d2_xyzaxis 3
+
+# read data file
+
+read_data       data.water_box.amoeba fix amtype NULL "Tinker Types"
+Reading data file ...
+  orthogonal box = (0 0 0) to (18.643 18.643 18.643)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  648 atoms
+  scanning bonds ...
+  2 = max bonds/atom
+  scanning angles ...
+  1 = max angles/atom
+  reading bonds ...
+  432 bonds
+  reading angles ...
+  216 angles
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0        0        0       
+  special bond factors coul:  0        0        0       
+     2 = max # of 1-2 neighbors
+     1 = max # of 1-3 neighbors
+     1 = max # of 1-4 neighbors
+     2 = max # of special neighbors
+  special bonds CPU = 0.000 seconds
+  read_data CPU = 0.004 seconds
+
+# force field
+
+pair_style      amoeba
+pair_coeff      * * amoeba_water.prm amoeba_water_box.key
+
+special_bonds   lj/coul 0.5 0.5 0.5 one/five yes
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0.5      0.5      0.5     
+  special bond factors coul:  0.5      0.5      0.5     
+     2 = max # of 1-2 neighbors
+     1 = max # of 1-3 neighbors
+     1 = max # of 1-4 neighbors
+     2 = max # of 1-5 neighbors
+     2 = max # of special neighbors
+  special bonds CPU = 0.000 seconds
+
+# thermo output
+
+compute         virial all pressure NULL virial
+
+thermo_style    custom step temp epair ebond eangle edihed eimp                 emol etotal press c_virial[*]
+
+#dump            1 all custom 10 dump.water_box id type x y z fx fy fz
+#dump_modify     1 sort id
+
+# zero step run
+
+#run             0
+
+# dynamics
+
+fix             1 all nve
+
+thermo          10
+run             100
+AMOEBA force field settings
+  hal: cut 7 taper 6 vscale 0 0 1 1
+  multipole: cut 7 aewald 0.4 bsorder 5 FFT 24 24 24 mscale 0 0 0.4 1
+  polar: cut 7 aewald 0.5 bsorder 5 FFT 24 24 24
+         pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 1 1 1 1 d/u scale 0 1
+  precondition: cut 4.5
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 9
+  ghost atom cutoff = 9
+  binsize = 4.5, bins = 5 5 5
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair amoeba, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d
+      bin: standard
+  AMOEBA group count: 216
+Per MPI rank memory allocation (min/avg/max) = 56.94 | 56.94 | 56.94 Mbytes
+   Step          Temp          E_pair         E_bond        E_angle        E_dihed        E_impro         E_mol          TotEng         Press       c_virial[1]    c_virial[2]    c_virial[3]    c_virial[4]    c_virial[5]    c_virial[6]  
+         0   0             -2172.0637      166.82637      83.732524      0              0              250.5589      -1921.5048     -6181.4178     -4772.1682     -6954.8414     -6817.2437     -272.19967      3173.3481      2229.9454    
+        10   105.50186     -2373.7036      136.67877      106.86833      0              0              243.5471      -1926.6873     -8440.8076     -10450.396     -9513.7369     -9664.6007     -301.7395       322.28511      1917.0314    
+        20   143.89822     -2358.363       70.950306      76.775658      0              0              147.72596     -1933.1172     -7370.2083     -7728.5515     -11580.39      -8675.2341     -806.78779      780.67516      2096.34      
+        30   157.22465     -2375.4739      50.393531      87.108003      0              0              137.50153     -1934.7514     -4449.577      -6946.7795     -7865.2165     -4954.2358     -417.69587     -1004.2877     -36.388669    
+        40   150.92481     -2354.1892      78.482464      53.798462      0              0              132.28093     -1930.8371      353.42948     -939.14353     -4636.5062      475.58057     -1073.8523     -1583.9471     -574.21807    
+        50   153.0181      -2388.7322      100.20232      65.813823      0              0              166.01614     -1927.6078      3975.1981      1368.1361      425.64533      3886.0124     -1806.8586     -2534.5272     -2118.2395    
+        60   155.01494     -2364.3168      92.946192      44.248949      0              0              137.19514     -1928.1623      5793.7546      3524.7523      1420.4096      6108.7958     -1536.5261     -2558.8204     -1501.5292    
+        70   166.70755     -2383.503       76.491199      55.01988       0              0              131.51108     -1930.4824      4744.1583      1919.3954      2838.7666      2669.745      -169.21643     -188.08678     -2256.4142    
+        80   171.83506     -2388.0612      76.465932      49.1299        0              0              125.59583     -1931.067       2210.3658     -318.23867      330.74353     -395.26693     -43.142216      252.53012     -1987.0412    
+        90   175.73401     -2423.8154      90.786573      63.719496      0              0              154.50607     -1930.3915     -916.91571     -3942.3954     -2566.5361     -3414.8202      199.82369      2365.9443     -266.38604    
+       100   173.72684     -2422.367       99.75941       57.294464      0              0              157.05387     -1930.2663     -3585.8356     -5734.1341     -5882.0146     -6232.4353     -227.79935      959.68225      404.47924    
+Loop time of 9.20176 on 1 procs for 100 steps with 648 atoms
+
+Performance: 0.939 ns/day, 25.560 hours/ns, 10.867 timesteps/s
+99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+AMOEBA timing breakdown:
+  Init    time: 0.0197604      0.22%
+  Hal     time: 0.384028       4.18%
+  Mpole   time: 0.939829      10.23%
+  Induce  time: 6.03232       65.64%
+  Polar   time: 1.81401       19.74%
+  Total   time: 9.18998     
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 9.1903     | 9.1903     | 9.1903     |   0.0 | 99.88
+Bond    | 0.0024644  | 0.0024644  | 0.0024644  |   0.0 |  0.03
+Neigh   | 0.0045623  | 0.0045623  | 0.0045623  |   0.0 |  0.05
+Comm    | 0.0024492  | 0.0024492  | 0.0024492  |   0.0 |  0.03
+Output  | 0.00046866 | 0.00046866 | 0.00046866 |   0.0 |  0.01
+Modify  | 0.00071308 | 0.00071308 | 0.00071308 |   0.0 |  0.01
+Other   |            | 0.000819   |            |       |  0.01
+
+Nlocal:            648 ave         648 max         648 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:           4290 ave        4290 max        4290 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:          98545 ave       98545 max       98545 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 98545
+Ave neighs/atom = 152.07562
+Ave special neighs/atom = 2
+Neighbor list builds = 2
+Dangerous builds = 0
+Total wall time: 0:00:09

examples/amoeba/log.5Jul22.water_box.amoeba.g++.4

@@ -0,0 +1,150 @@
+LAMMPS (23 Jun 2022)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
+# replicate water box with AMOEBA or HIPPO
+
+units           real
+boundary        p p p
+
+atom_style      amoeba
+bond_style      class2
+angle_style     amoeba
+dihedral_style  none
+
+# per-atom properties required by AMOEBA or HIPPO
+
+fix             amtype all property/atom i_amtype ghost yes
+fix             extra all property/atom i_amgroup d_redID d_pval ghost yes
+fix             extra2 all property/atom i_polaxe d2_xyzaxis 3
+
+# read data file
+
+read_data       data.water_box.amoeba fix amtype NULL "Tinker Types"
+Reading data file ...
+  orthogonal box = (0 0 0) to (18.643 18.643 18.643)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  648 atoms
+  scanning bonds ...
+  2 = max bonds/atom
+  scanning angles ...
+  1 = max angles/atom
+  reading bonds ...
+  432 bonds
+  reading angles ...
+  216 angles
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0        0        0       
+  special bond factors coul:  0        0        0       
+     2 = max # of 1-2 neighbors
+     1 = max # of 1-3 neighbors
+     1 = max # of 1-4 neighbors
+     2 = max # of special neighbors
+  special bonds CPU = 0.000 seconds
+  read_data CPU = 0.004 seconds
+
+# force field
+
+pair_style      amoeba
+pair_coeff      * * amoeba_water.prm amoeba_water_box.key
+
+special_bonds   lj/coul 0.5 0.5 0.5 one/five yes
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0.5      0.5      0.5     
+  special bond factors coul:  0.5      0.5      0.5     
+     2 = max # of 1-2 neighbors
+     1 = max # of 1-3 neighbors
+     1 = max # of 1-4 neighbors
+     2 = max # of 1-5 neighbors
+     2 = max # of special neighbors
+  special bonds CPU = 0.000 seconds
+
+# thermo output
+
+compute         virial all pressure NULL virial
+
+thermo_style    custom step temp epair ebond eangle edihed eimp                 emol etotal press c_virial[*]
+
+#dump            1 all custom 10 dump.water_box id type x y z fx fy fz
+#dump_modify     1 sort id
+
+# zero step run
+
+#run             0
+
+# dynamics
+
+fix             1 all nve
+
+thermo          10
+run             100
+AMOEBA force field settings
+  hal: cut 7 taper 6 vscale 0 0 1 1
+  multipole: cut 7 aewald 0.4 bsorder 5 FFT 24 24 24 mscale 0 0 0.4 1
+  polar: cut 7 aewald 0.5 bsorder 5 FFT 24 24 24
+         pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 1 1 1 1 d/u scale 0 1
+  precondition: cut 4.5
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 9
+  ghost atom cutoff = 9
+  binsize = 4.5, bins = 5 5 5
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair amoeba, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d
+      bin: standard
+  AMOEBA group count: 216
+Per MPI rank memory allocation (min/avg/max) = 56.38 | 56.38 | 56.38 Mbytes
+   Step          Temp          E_pair         E_bond        E_angle        E_dihed        E_impro         E_mol          TotEng         Press       c_virial[1]    c_virial[2]    c_virial[3]    c_virial[4]    c_virial[5]    c_virial[6]  
+         0   0             -2172.0637      166.82637      83.732524      0              0              250.5589      -1921.5048     -6181.4178     -4772.1682     -6954.8414     -6817.2437     -272.19967      3173.3481      2229.9454    
+        10   105.50186     -2373.7036      136.67877      106.86833      0              0              243.5471      -1926.6873     -8440.8076     -10450.396     -9513.7369     -9664.6007     -301.7395       322.28511      1917.0314    
+        20   143.89822     -2358.363       70.950306      76.775658      0              0              147.72596     -1933.1172     -7370.2083     -7728.5515     -11580.39      -8675.2341     -806.78779      780.67516      2096.34      
+        30   157.22465     -2375.4739      50.393531      87.108003      0              0              137.50153     -1934.7514     -4449.577      -6946.7795     -7865.2165     -4954.2358     -417.69587     -1004.2877     -36.388669    
+        40   150.92481     -2354.1892      78.482464      53.798462      0              0              132.28093     -1930.8371      353.42948     -939.14353     -4636.5062      475.58057     -1073.8523     -1583.9471     -574.21807    
+        50   153.0181      -2388.7322      100.20232      65.813823      0              0              166.01614     -1927.6078      3975.1981      1368.1361      425.64533      3886.0124     -1806.8586     -2534.5272     -2118.2395    
+        60   155.01494     -2364.3168      92.946192      44.248949      0              0              137.19514     -1928.1623      5793.7546      3524.7523      1420.4096      6108.7958     -1536.5261     -2558.8204     -1501.5292    
+        70   166.70755     -2383.503       76.491199      55.01988       0              0              131.51108     -1930.4824      4744.1583      1919.3954      2838.7666      2669.745      -169.21643     -188.08678     -2256.4142    
+        80   171.83506     -2388.0612      76.465932      49.1299        0              0              125.59583     -1931.067       2210.3658     -318.23867      330.74353     -395.26693     -43.142216      252.53012     -1987.0412    
+        90   175.73401     -2423.8154      90.786573      63.719496      0              0              154.50607     -1930.3915     -916.91571     -3942.3954     -2566.5361     -3414.8202      199.82369      2365.9443     -266.38604    
+       100   173.72684     -2422.367       99.75941       57.294464      0              0              157.05387     -1930.2663     -3585.8356     -5734.1341     -5882.0146     -6232.4353     -227.79935      959.68225      404.47924    
+Loop time of 3.56288 on 4 procs for 100 steps with 648 atoms
+
+Performance: 2.425 ns/day, 9.897 hours/ns, 28.067 timesteps/s
+99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+AMOEBA timing breakdown:
+  Init    time: 0.0211994      0.60%
+  Hal     time: 0.112106       3.15%
+  Mpole   time: 0.321265       9.04%
+  Induce  time: 2.48321       69.88%
+  Polar   time: 0.61587       17.33%
+  Total   time: 3.55367     
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 3.5543     | 3.5544     | 3.5544     |   0.0 | 99.76
+Bond    | 0.00084867 | 0.0008661  | 0.00088053 |   0.0 |  0.02
+Neigh   | 0.0014115  | 0.0014132  | 0.0014157  |   0.0 |  0.04
+Comm    | 0.0044654  | 0.0045745  | 0.004671   |   0.1 |  0.13
+Output  | 0.00037263 | 0.00042347 | 0.00054242 |   0.0 |  0.01
+Modify  | 0.00035262 | 0.00036625 | 0.00037678 |   0.0 |  0.01
+Other   |            | 0.0008691  |            |       |  0.02
+
+Nlocal:            162 ave         164 max         159 min
+Histogram: 1 0 0 0 0 0 1 0 1 1
+Nghost:         2568.5 ave        2585 max        2544 min
+Histogram: 1 0 0 0 0 1 0 0 1 1
+Neighs:        24636.2 ave       25226 max       23891 min
+Histogram: 1 0 0 0 0 0 2 0 0 1
+
+Total # of neighbors = 98545
+Ave neighs/atom = 152.07562
+Ave special neighs/atom = 2
+Neighbor list builds = 2
+Dangerous builds = 0
+Total wall time: 0:00:03

examples/amoeba/log.5Jul22.water_box.hippo.g++.1

@@ -0,0 +1,149 @@
+LAMMPS (23 Jun 2022)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
+# water box with AMOEBA or HIPPO
+
+units           real
+boundary        p p p
+
+atom_style      amoeba
+bond_style      class2
+angle_style     amoeba
+dihedral_style  none
+
+# per-atom properties required by AMOEBA or HIPPO
+
+fix             amtype all property/atom i_amtype ghost yes
+fix             extra all property/atom i_amgroup d_redID d_pval ghost yes
+fix             extra2 all property/atom i_polaxe d2_xyzaxis 3
+
+# read data file
+
+read_data       data.water_box.hippo fix amtype NULL "Tinker Types"
+Reading data file ...
+  orthogonal box = (0 0 0) to (18.643 18.643 18.643)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  648 atoms
+  scanning bonds ...
+  2 = max bonds/atom
+  scanning angles ...
+  1 = max angles/atom
+  reading bonds ...
+  432 bonds
+  reading angles ...
+  216 angles
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0        0        0       
+  special bond factors coul:  0        0        0       
+     2 = max # of 1-2 neighbors
+     1 = max # of 1-3 neighbors
+     1 = max # of 1-4 neighbors
+     2 = max # of special neighbors
+  special bonds CPU = 0.000 seconds
+  read_data CPU = 0.004 seconds
+
+# force field
+
+pair_style      hippo
+pair_coeff      * * hippo_water.prm hippo_water_box.key
+
+special_bonds   lj/coul 0.5 0.5 0.5 one/five yes
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0.5      0.5      0.5     
+  special bond factors coul:  0.5      0.5      0.5     
+     2 = max # of 1-2 neighbors
+     1 = max # of 1-3 neighbors
+     1 = max # of 1-4 neighbors
+     2 = max # of 1-5 neighbors
+     2 = max # of special neighbors
+  special bonds CPU = 0.000 seconds
+
+# thermo output
+
+compute         virial all pressure NULL virial
+
+thermo_style    custom step temp epair ebond eangle edihed eimp                 emol etotal press c_virial[*]
+
+#dump            1 all custom 10 dump.water_box id type x y z fx fy fz
+#dump_modify     1 sort id
+
+# zero step run
+
+#run             0
+
+# dynamics
+
+fix             1 all nve
+
+thermo          1
+run             5
+HIPPO force field settings
+  repulsion: cut 7 taper 6 rscale 0 0 1 1
+  qxfer: cut 7 taper 6 mscale 0 0 0.4 1
+  dispersion: cut 7 aewald 0.45 bsorder 4 FFT 16 16 16 dspscale 0 0 0.4 1
+  multipole: cut 7 aewald 0.4 bsorder 5 FFT 24 24 24 mscale 0 0 0.4 1
+  polar: cut 7 aewald 0.5 bsorder 5 FFT 24 24 24
+         pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 0.2 1 1 1 d/u scale 0 1
+  precondition: cut 4.5
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 9
+  ghost atom cutoff = 9
+  binsize = 4.5, bins = 5 5 5
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair hippo, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d
+      bin: standard
+  HIPPO group count: 216
+Per MPI rank memory allocation (min/avg/max) = 56.46 | 56.46 | 56.46 Mbytes
+   Step          Temp          E_pair         E_bond        E_angle        E_dihed        E_impro         E_mol          TotEng         Press       c_virial[1]    c_virial[2]    c_virial[3]    c_virial[4]    c_virial[5]    c_virial[6]  
+         0   0             -2188.594       166.82637      77.478353      0              0              244.30473     -1944.2893     -10859.589     -9285.4645     -11598.049     -11695.254     -282.7072       3164.4148      2495.2578    
+         1   29.599499     -2189.0009      110.80903      70.640769      0              0              181.4498      -1950.466      -9781.8027     -8491.8338     -11237.523     -10824.225     -316.85579      2724.3099      2103.706     
+         2   77.782401     -2189.0806      26.465487      53.091297      0              0              79.556784     -1959.5139     -5674.5913     -4709.6895     -8454.6227     -7034.3366     -270.02397      1600.8009      1104.5782    
+         3   83.751912     -2189.1561      36.936027      32.349803      0              0              69.285831     -1958.3477      1505.3642      2789.4989     -1919.6532      227.71216      3.4467207      240.18575     -91.250567    
+         4   59.186129     -2195.3882      116.40559      17.314099      0              0              133.71969     -1947.5231      7666.6109      9441.7634      4355.1915      6787.0543      329.33631     -768.83277     -966.66638    
+         5   70.911532     -2215.1422      115.71443      14.75745       0              0              130.47188     -1947.9114      7292.9034      8506.6309      4019.0295      6458.6256      348.80878     -911.32703     -1060.6123    
+Loop time of 0.328811 on 1 procs for 5 steps with 648 atoms
+
+Performance: 1.314 ns/day, 18.267 hours/ns, 15.206 timesteps/s
+99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+HIPPO timing breakdown:
+  Init    time: 0.000849843    0.26%
+  Repulse time: 0.0386964     11.79%
+  Disp    time: 0.0176955      5.39%
+  Mpole   time: 0.0625716     19.06%
+  Induce  time: 0.122108      37.20%
+  Polar   time: 0.0762897     23.24%
+  Qxfer   time: 0.010031       3.06%
+  Total   time: 0.328242    
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.32826    | 0.32826    | 0.32826    |   0.0 | 99.83
+Bond    | 0.00014786 | 0.00014786 | 0.00014786 |   0.0 |  0.04
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 9.3603e-05 | 9.3603e-05 | 9.3603e-05 |   0.0 |  0.03
+Output  | 0.00022715 | 0.00022715 | 0.00022715 |   0.0 |  0.07
+Modify  | 5.5594e-05 | 5.5594e-05 | 5.5594e-05 |   0.0 |  0.02
+Other   |            | 2.723e-05  |            |       |  0.01
+
+Nlocal:            648 ave         648 max         648 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:           4302 ave        4302 max        4302 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:          98585 ave       98585 max       98585 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 98585
+Ave neighs/atom = 152.13735
+Ave special neighs/atom = 2
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:00

examples/amoeba/log.5Jul22.water_box.hippo.g++.4

@@ -0,0 +1,149 @@
+LAMMPS (23 Jun 2022)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
+# water box with AMOEBA or HIPPO
+
+units           real
+boundary        p p p
+
+atom_style      amoeba
+bond_style      class2
+angle_style     amoeba
+dihedral_style  none
+
+# per-atom properties required by AMOEBA or HIPPO
+
+fix             amtype all property/atom i_amtype ghost yes
+fix             extra all property/atom i_amgroup d_redID d_pval ghost yes
+fix             extra2 all property/atom i_polaxe d2_xyzaxis 3
+
+# read data file
+
+read_data       data.water_box.hippo fix amtype NULL "Tinker Types"
+Reading data file ...
+  orthogonal box = (0 0 0) to (18.643 18.643 18.643)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  648 atoms
+  scanning bonds ...
+  2 = max bonds/atom
+  scanning angles ...
+  1 = max angles/atom
+  reading bonds ...
+  432 bonds
+  reading angles ...
+  216 angles
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0        0        0       
+  special bond factors coul:  0        0        0       
+     2 = max # of 1-2 neighbors
+     1 = max # of 1-3 neighbors
+     1 = max # of 1-4 neighbors
+     2 = max # of special neighbors
+  special bonds CPU = 0.000 seconds
+  read_data CPU = 0.007 seconds
+
+# force field
+
+pair_style      hippo
+pair_coeff      * * hippo_water.prm hippo_water_box.key
+
+special_bonds   lj/coul 0.5 0.5 0.5 one/five yes
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0.5      0.5      0.5     
+  special bond factors coul:  0.5      0.5      0.5     
+     2 = max # of 1-2 neighbors
+     1 = max # of 1-3 neighbors
+     1 = max # of 1-4 neighbors
+     2 = max # of 1-5 neighbors
+     2 = max # of special neighbors
+  special bonds CPU = 0.000 seconds
+
+# thermo output
+
+compute         virial all pressure NULL virial
+
+thermo_style    custom step temp epair ebond eangle edihed eimp                 emol etotal press c_virial[*]
+
+#dump            1 all custom 10 dump.water_box id type x y z fx fy fz
+#dump_modify     1 sort id
+
+# zero step run
+
+#run             0
+
+# dynamics
+
+fix             1 all nve
+
+thermo          1
+run             5
+HIPPO force field settings
+  repulsion: cut 7 taper 6 rscale 0 0 1 1
+  qxfer: cut 7 taper 6 mscale 0 0 0.4 1
+  dispersion: cut 7 aewald 0.45 bsorder 4 FFT 16 16 16 dspscale 0 0 0.4 1
+  multipole: cut 7 aewald 0.4 bsorder 5 FFT 24 24 24 mscale 0 0 0.4 1
+  polar: cut 7 aewald 0.5 bsorder 5 FFT 24 24 24
+         pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 0.2 1 1 1 d/u scale 0 1
+  precondition: cut 4.5
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 9
+  ghost atom cutoff = 9
+  binsize = 4.5, bins = 5 5 5
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair hippo, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d
+      bin: standard
+  HIPPO group count: 216
+Per MPI rank memory allocation (min/avg/max) = 55.94 | 55.94 | 55.94 Mbytes
+   Step          Temp          E_pair         E_bond        E_angle        E_dihed        E_impro         E_mol          TotEng         Press       c_virial[1]    c_virial[2]    c_virial[3]    c_virial[4]    c_virial[5]    c_virial[6]  
+         0   0             -2188.594       166.82637      77.478353      0              0              244.30473     -1944.2893     -10859.589     -9285.4645     -11598.049     -11695.254     -282.7072       3164.4148      2495.2578    
+         1   29.599499     -2189.0009      110.80903      70.640769      0              0              181.4498      -1950.466      -9781.8027     -8491.8338     -11237.523     -10824.225     -316.85579      2724.3099      2103.706     
+         2   77.782401     -2189.0806      26.465487      53.091297      0              0              79.556784     -1959.5139     -5674.5913     -4709.6895     -8454.6227     -7034.3366     -270.02397      1600.8009      1104.5782    
+         3   83.751912     -2189.1561      36.936027      32.349803      0              0              69.285831     -1958.3477      1505.3642      2789.4989     -1919.6532      227.71216      3.4467207      240.18575     -91.250567    
+         4   59.186129     -2195.3882      116.40559      17.314099      0              0              133.71969     -1947.5231      7666.6109      9441.7634      4355.1915      6787.0543      329.33631     -768.83277     -966.66638    
+         5   70.911532     -2215.1422      115.71443      14.75745       0              0              130.47188     -1947.9114      7292.9034      8506.6309      4019.0295      6458.6256      348.80878     -911.32703     -1060.6123    
+Loop time of 0.122174 on 4 procs for 5 steps with 648 atoms
+
+Performance: 3.536 ns/day, 6.787 hours/ns, 40.925 timesteps/s
+98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+HIPPO timing breakdown:
+  Init    time: 0.00112002     0.93%
+  Repulse time: 0.0120679      9.97%
+  Disp    time: 0.00648732     5.36%
+  Mpole   time: 0.0211822     17.50%
+  Induce  time: 0.0497719     41.12%
+  Polar   time: 0.0274737     22.70%
+  Qxfer   time: 0.00294446     2.43%
+  Total   time: 0.121048    
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.12105    | 0.12112    | 0.12123    |   0.0 | 99.14
+Bond    | 5.27e-05   | 5.9124e-05 | 6.5605e-05 |   0.0 |  0.05
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.00038065 | 0.0005645  | 0.00066198 |   0.0 |  0.46
+Output  | 0.00030705 | 0.00035011 | 0.00042646 |   0.0 |  0.29
+Modify  | 2.8994e-05 | 3.163e-05  | 3.6394e-05 |   0.0 |  0.03
+Other   |            | 4.464e-05  |            |       |  0.04
+
+Nlocal:            162 ave         166 max         159 min
+Histogram: 2 0 0 0 0 0 0 1 0 1
+Nghost:        2582.75 ave        2600 max        2559 min
+Histogram: 1 0 0 1 0 0 0 0 0 2
+Neighs:        24646.2 ave       25106 max       23932 min
+Histogram: 1 0 0 0 0 0 1 0 1 1
+
+Total # of neighbors = 98585
+Ave neighs/atom = 152.13735
+Ave special neighs/atom = 2
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:00

examples/amoeba/log.5Jul22.water_dimer.amoeba.g++.1

@@ -1,4 +1,6 @@
-LAMMPS (24 Mar 2022)
+LAMMPS (23 Jun 2022)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
 # water dimer with AMOEBA or HIPPO
 
 units           real
@@ -39,7 +41,7 @@ Finding 1-2 1-3 1-4 neighbors ...
      1 = max # of 1-4 neighbors
      2 = max # of special neighbors
   special bonds CPU = 0.000 seconds
-  read_data CPU = 0.008 seconds
+  read_data CPU = 0.003 seconds
 
 # force field
 
@@ -63,8 +65,8 @@ compute         virial all pressure NULL virial
 
 thermo_style    custom step temp epair ebond eangle edihed eimp                 emol etotal press c_virial[*]
 
-dump            1 all custom 10 dump.water_dimer id type x y z fx fy fz
+#dump            1 all custom 10 dump.water_dimer id type x y z fx fy fz
-dump_modify     1 sort id
+#dump_modify     1 sort id
 
 # zero step run
 
@@ -74,15 +76,15 @@ dump_modify     1 sort id
 
 fix             1 all nve
 
-thermo          10
+thermo          1
-run             100
+run             5
-AMOEBA/HIPPO force field settings
+AMOEBA force field settings
   hal: cut 10 taper 8 vscale 0 0 1 1
   multipole: cut 10 aewald 0 mscale 0 0 0.4 1
   polar: cut 10 aewald 0
          pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 1 1 1 1 d/u scale 0 1
   precondition: cut 4.5
-  generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
 Neighbor list info ...
   update every 1 steps, delay 10 steps, check yes
   max neighbors/atom: 2000, page size: 100000
@@ -95,44 +97,39 @@ Neighbor list info ...
       pair build: half/bin/newton
       stencil: half/bin/3d
       bin: standard
-WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:974)
+WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:970)
-  AMOEBA/HIPPO group count: 2
+  AMOEBA group count: 2
-Per MPI rank memory allocation (min/avg/max) = 49.59 | 49.59 | 49.59 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 48.33 | 48.33 | 48.33 Mbytes
    Step          Temp          E_pair         E_bond        E_angle        E_dihed        E_impro         E_mol          TotEng         Press       c_virial[1]    c_virial[2]    c_virial[3]    c_virial[4]    c_virial[5]    c_virial[6]  
          0   0             -5.1627563      0.025695395    0.71581114     0              0              0.74150653    -4.4212497     -12260.522     -43226.042      39448.214     -33003.739     -85.160886     -28101.905     -72.971988    
-        10   1.1174766     -4.7928792      0.045080327    0.30848527     0              0              0.35356559    -4.4226587     -14728.416      11456.119     -52592.829     -3262.8454      70.868937      29494.268      57.977562    
+         1   3.4764991     -5.1500622      0.021865831    0.65347737     0              0              0.67534321    -4.4229051     -8987.9108     -37684.452      39410.243     -29356.236     -80.130511     -27322.706     -69.79235     
-        20   3.0821934     -5.1387316      0.013108182    0.65694692     0              0              0.6700551     -4.4227393      3007.4148     -25925.326      49641.41      -15284.933     -79.726771     -29005.234     -68.530079    
+         2   12.286735     -5.1147506      0.014370337    0.49051077     0              0              0.50488111    -4.4267474     -865.99299     -23430.467      38420.372     -19944.197     -66.155435     -24835.896     -60.583907    
-        30   3.461967      -4.8079248      0.013888863    0.31895667     0              0              0.33284554    -4.423482       8616.211       40027.877     -31134.295      16291.126      72.510013      23088.238      51.407946    
+         3   22.599529     -5.0641035      0.0093422156   0.28736734     0              0              0.29670956    -4.4305695      7832.024      -6436.638       34275.274     -8676.6339     -46.038158     -20245.105     -46.202354    
-        40   4.2181367     -5.0535921      0.0099009766   0.55796811     0              0              0.56786908    -4.4228557      24239.885     -5761.6967      62095.735      15576.675     -76.240192     -33057.385     -58.850871    
+         4   30.447598     -5.0072832      0.0076827791   0.11282886     0              0              0.12051164    -4.432979       12374.854      6652.5061      24658.364     -25.4576       -23.025707     -13137.295     -27.801932    
-        50   5.216657      -4.8012751      0.0053003148   0.29489399     0              0              0.30019431    -4.4233315      17728.056      44785.731     -21215.714      28613.715      66.24671       20292.137      51.010856    
+         5   33.189086     -4.9523094      0.0086012541   0.015399005    0              0              0.024000259   -4.4336573      10023.674      11810.883      8754.5769      3140.658       0.25267021    -3546.6216     -6.83205      
-        60   9.45101       -5.0818046      0.0043357361   0.5118733      0              0              0.51620903    -4.4247372      16893.135     -15068.961      50111.11       13824.77      -75.966047     -34809.168     -52.83183     
+Loop time of 0.000286908 on 1 procs for 5 steps with 6 atoms
-        70   10.385926     -4.8250769      0.022572262    0.22235766     0              0              0.24492992    -4.4253547     -1117.3665      19070.918     -36063.612      11648.813      61.067533      25754.59       53.919881    
-        80   12.797691     -5.123735       0.023756795    0.48275385     0              0              0.50651065    -4.4264869     -6491.9826     -28436.037      20681.908     -14176.121     -64.024669     -35737.052     -52.583533    
-        90   12.569481     -4.8303379      0.060369422    0.15670502     0              0              0.21707444    -4.4259273     -16762.536      1720.5855     -47624.986     -6793.7441      59.966729      30024.566      52.339671    
-       100   17.750788     -5.1195235      0.039885925    0.38711474     0              0              0.42700067    -4.4279642     -10817.92      -21833.456      4186.8301     -18211.329     -43.11086      -32664.671     -41.508916    
-Loop time of 0.00655818 on 1 procs for 100 steps with 6 atoms
 
-Performance: 1317.439 ns/day, 0.018 hours/ns, 15248.138 timesteps/s
+Performance: 1505.709 ns/day, 0.016 hours/ns, 17427.189 timesteps/s
-98.5% CPU use with 1 MPI tasks x no OpenMP threads
+98.6% CPU use with 1 MPI tasks x 1 OpenMP threads
 
-AMEOBA/HIPPO timing breakdown:
+AMOEBA timing breakdown:
-  Init    time: 0.000126483 0.0233682
+  Init    time: 7.417e-06      4.75%
-  Hal     time: 0.000471055 8.70292
+  Hal     time: 8.458e-06      5.42%
-  Mpole   time: 0.000619314 11.4421
+  Mpole   time: 2.2734e-05    14.57%
-  Induce  time: 0.00270856 50.0417
+  Induce  time: 7.4016e-05    47.43%
-  Polar   time: 0.00147122 27.1814
+  Polar   time: 4.2972e-05    27.54%
-  Total   time: 0.00541261
+  Total   time: 0.00015604  
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.005443   | 0.005443   | 0.005443   |   0.0 | 83.00
+Pair    | 0.00015922 | 0.00015922 | 0.00015922 |   0.0 | 55.49
-Bond    | 9.6579e-05 | 9.6579e-05 | 9.6579e-05 |   0.0 |  1.47
+Bond    | 5.034e-06  | 5.034e-06  | 5.034e-06  |   0.0 |  1.75
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 1.7434e-05 | 1.7434e-05 | 1.7434e-05 |   0.0 |  0.27
+Comm    | 8.49e-07   | 8.49e-07   | 8.49e-07   |   0.0 |  0.30
-Output  | 0.0008951  | 0.0008951  | 0.0008951  |   0.0 | 13.65
+Output  | 0.00011336 | 0.00011336 | 0.00011336 |   0.0 | 39.51
-Modify  | 5.161e-05  | 5.161e-05  | 5.161e-05  |   0.0 |  0.79
+Modify  | 2.093e-06  | 2.093e-06  | 2.093e-06  |   0.0 |  0.73
-Other   |            | 5.444e-05  |            |       |  0.83
+Other   |            | 6.355e-06  |            |       |  2.21
 
 Nlocal:              6 ave           6 max           6 min
 Histogram: 1 0 0 0 0 0 0 0 0 0

examples/amoeba/log.5Jul22.water_dimer.amoeba.g++.4

@@ -1,4 +1,6 @@
-LAMMPS (24 Mar 2022)
+LAMMPS (23 Jun 2022)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
 # water dimer with AMOEBA or HIPPO
 
 units           real
@@ -39,7 +41,7 @@ Finding 1-2 1-3 1-4 neighbors ...
      1 = max # of 1-4 neighbors
      2 = max # of special neighbors
   special bonds CPU = 0.000 seconds
-  read_data CPU = 0.009 seconds
+  read_data CPU = 0.004 seconds
 
 # force field
 
@@ -63,8 +65,8 @@ compute         virial all pressure NULL virial
 
 thermo_style    custom step temp epair ebond eangle edihed eimp                 emol etotal press c_virial[*]
 
-dump            1 all custom 10 dump.water_dimer id type x y z fx fy fz
+#dump            1 all custom 10 dump.water_dimer id type x y z fx fy fz
-dump_modify     1 sort id
+#dump_modify     1 sort id
 
 # zero step run
 
@@ -74,15 +76,15 @@ dump_modify     1 sort id
 
 fix             1 all nve
 
-thermo          10
+thermo          1
-run             100
+run             5
-AMOEBA/HIPPO force field settings
+AMOEBA force field settings
   hal: cut 10 taper 8 vscale 0 0 1 1
   multipole: cut 10 aewald 0 mscale 0 0 0.4 1
   polar: cut 10 aewald 0
          pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 1 1 1 1 d/u scale 0 1
   precondition: cut 4.5
-  generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
 Neighbor list info ...
   update every 1 steps, delay 10 steps, check yes
   max neighbors/atom: 2000, page size: 100000
@@ -95,44 +97,39 @@ Neighbor list info ...
       pair build: half/bin/newton
       stencil: half/bin/3d
       bin: standard
-WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:974)
+WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:970)
-  AMOEBA/HIPPO group count: 2
+  AMOEBA group count: 2
-Per MPI rank memory allocation (min/avg/max) = 49.61 | 49.75 | 49.88 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 48.35 | 48.48 | 48.62 Mbytes
    Step          Temp          E_pair         E_bond        E_angle        E_dihed        E_impro         E_mol          TotEng         Press       c_virial[1]    c_virial[2]    c_virial[3]    c_virial[4]    c_virial[5]    c_virial[6]  
          0   0             -5.1627563      0.025695395    0.71581114     0              0              0.74150653    -4.4212497     -12260.522     -43226.042      39448.214     -33003.739     -85.160886     -28101.905     -72.971988    
-        10   1.1174766     -4.7928792      0.045080327    0.30848527     0              0              0.35356559    -4.4226587     -14728.416      11456.119     -52592.829     -3262.8454      70.868937      29494.268      57.977562    
+         1   3.4764991     -5.1500622      0.021865831    0.65347737     0              0              0.67534321    -4.4229051     -8987.9108     -37684.452      39410.243     -29356.236     -80.130511     -27322.706     -69.79235     
-        20   3.0821934     -5.1387316      0.013108182    0.65694692     0              0              0.6700551     -4.4227393      3007.4148     -25925.326      49641.41      -15284.933     -79.726771     -29005.234     -68.530079    
+         2   12.286735     -5.1147506      0.014370337    0.49051077     0              0              0.50488111    -4.4267474     -865.99299     -23430.467      38420.372     -19944.197     -66.155435     -24835.896     -60.583907    
-        30   3.461967      -4.8079248      0.013888863    0.31895667     0              0              0.33284554    -4.423482       8616.211       40027.877     -31134.295      16291.126      72.510013      23088.238      51.407946    
+         3   22.599529     -5.0641035      0.0093422156   0.28736734     0              0              0.29670956    -4.4305695      7832.024      -6436.638       34275.274     -8676.6339     -46.038158     -20245.105     -46.202354    
-        40   4.2181367     -5.0535921      0.0099009766   0.55796811     0              0              0.56786908    -4.4228557      24239.885     -5761.6967      62095.735      15576.675     -76.240192     -33057.385     -58.850871    
+         4   30.447598     -5.0072832      0.0076827791   0.11282886     0              0              0.12051164    -4.432979       12374.854      6652.5061      24658.364     -25.4576       -23.025707     -13137.295     -27.801932    
-        50   5.216657      -4.8012751      0.0053003148   0.29489399     0              0              0.30019431    -4.4233315      17728.056      44785.731     -21215.714      28613.715      66.24671       20292.137      51.010856    
+         5   33.189086     -4.9523094      0.0086012541   0.015399005    0              0              0.024000259   -4.4336573      10023.674      11810.883      8754.5769      3140.658       0.25267021    -3546.6216     -6.83205      
-        60   9.45101       -5.0818046      0.0043357361   0.5118733      0              0              0.51620903    -4.4247372      16893.135     -15068.961      50111.11       13824.77      -75.966047     -34809.168     -52.83183     
+Loop time of 0.000582267 on 4 procs for 5 steps with 6 atoms
-        70   10.385926     -4.8250769      0.022572262    0.22235766     0              0              0.24492992    -4.4253547     -1117.3665      19070.918     -36063.612      11648.813      61.067533      25754.59       53.919881    
-        80   12.797691     -5.123735       0.023756795    0.48275385     0              0              0.50651065    -4.4264869     -6491.9826     -28436.037      20681.908     -14176.121     -64.024669     -35737.052     -52.583533    
-        90   12.569481     -4.8303379      0.060369422    0.15670502     0              0              0.21707444    -4.4259273     -16762.536      1720.5855     -47624.986     -6793.7441      59.966729      30024.566      52.339671    
-       100   17.750788     -5.1195235      0.039885925    0.38711474     0              0              0.42700067    -4.4279642     -10817.92      -21833.456      4186.8301     -18211.329     -43.11086      -32664.671     -41.508916    
-Loop time of 0.0167554 on 4 procs for 100 steps with 6 atoms
 
-Performance: 515.654 ns/day, 0.047 hours/ns, 5968.213 timesteps/s
+Performance: 741.928 ns/day, 0.032 hours/ns, 8587.130 timesteps/s
-99.4% CPU use with 4 MPI tasks x no OpenMP threads
+99.5% CPU use with 4 MPI tasks x 1 OpenMP threads
 
-AMEOBA/HIPPO timing breakdown:
+AMOEBA timing breakdown:
-  Init    time: 0.000555846 0.0390251
+  Init    time: 1.3264e-05     3.71%
-  Hal     time: 0.000129733 0.910835
+  Hal     time: 3.16275e-06    0.88%
-  Mpole   time: 0.000783914 5.50375
+  Mpole   time: 2.35955e-05    6.60%
-  Induce  time: 0.0115771 81.2811
+  Induce  time: 0.000290896   81.33%
-  Polar   time: 0.00118294 8.30522
+  Polar   time: 2.62723e-05    7.34%
-  Total   time: 0.0142433
+  Total   time: 0.000357696 
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.013911   | 0.014439   | 0.0147     |   0.3 | 86.18
+Pair    | 0.00036015 | 0.00038587 | 0.00040555 |   0.0 | 66.27
-Bond    | 1.196e-05  | 4.4667e-05 | 8.5848e-05 |   0.0 |  0.27
+Bond    | 1.441e-06  | 3.3365e-06 | 5.265e-06  |   0.0 |  0.57
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.00060682 | 0.00082002 | 0.001342   |   0.0 |  4.89
+Comm    | 2.1512e-05 | 3.3761e-05 | 4.9368e-05 |   0.0 |  5.80
-Output  | 0.00098235 | 0.0010281  | 0.0011458  |   0.2 |  6.14
+Output  | 0.00012269 | 0.00014666 | 0.00017989 |   0.0 | 25.19
-Modify  | 2.2946e-05 | 3.473e-05  | 4.2983e-05 |   0.0 |  0.21
+Modify  | 1.659e-06  | 2.0448e-06 | 2.275e-06  |   0.0 |  0.35
-Other   |            | 0.0003885  |            |       |  2.32
+Other   |            | 1.059e-05  |            |       |  1.82
 
 Nlocal:            1.5 ave           3 max           0 min
 Histogram: 2 0 0 0 0 0 0 0 0 2

examples/amoeba/log.5Jul22.water_dimer.hippo.g++.1

@@ -1,4 +1,6 @@
-LAMMPS (24 Mar 2022)
+LAMMPS (23 Jun 2022)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
 # water dimer with AMOEBA or HIPPO
 
 units           real
@@ -39,7 +41,7 @@ Finding 1-2 1-3 1-4 neighbors ...
      1 = max # of 1-4 neighbors
      2 = max # of special neighbors
   special bonds CPU = 0.000 seconds
-  read_data CPU = 0.008 seconds
+  read_data CPU = 0.003 seconds
 
 # force field
 
@@ -63,8 +65,8 @@ compute         virial all pressure NULL virial
 
 thermo_style    custom step temp epair ebond eangle edihed eimp                 emol etotal press c_virial[*]
 
-dump            1 all custom 10 dump.water_dimer id type x y z fx fy fz
+#dump            1 all custom 10 dump.water_dimer id type x y z fx fy fz
-dump_modify     1 sort id
+#dump_modify     1 sort id
 
 # zero step run
 
@@ -74,9 +76,9 @@ dump_modify     1 sort id
 
 fix             1 all nve
 
-thermo          10
+thermo          1
-run             100
+run             5
-AMOEBA/HIPPO force field settings
+HIPPO force field settings
   repulsion: cut 10 taper 8 rscale 0 0 1 1
   qxfer: cut 10 taper 8 mscale 0 0 0.4 1
   dispersion: cut 10 aewald 0 dspscale 0 0 0.4 1
@@ -84,7 +86,7 @@ AMOEBA/HIPPO force field settings
   polar: cut 10 aewald 0
          pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 0.2 1 1 1 d/u scale 0 1
   precondition: cut 4.5
-  generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
 Neighbor list info ...
   update every 1 steps, delay 10 steps, check yes
   max neighbors/atom: 2000, page size: 100000
@@ -97,46 +99,41 @@ Neighbor list info ...
       pair build: half/bin/newton
       stencil: half/bin/3d
       bin: standard
-WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:974)
+WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:970)
-  AMOEBA/HIPPO group count: 2
+  HIPPO group count: 2
-Per MPI rank memory allocation (min/avg/max) = 49.15 | 49.15 | 49.15 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 47.9 | 47.9 | 47.9 Mbytes
    Step          Temp          E_pair         E_bond        E_angle        E_dihed        E_impro         E_mol          TotEng         Press       c_virial[1]    c_virial[2]    c_virial[3]    c_virial[4]    c_virial[5]    c_virial[6]  
          0   0             -5.0101954      0.025695395    0.51472748     0              0              0.54042288    -4.4697726     -11875.159     -38149.178      29162.678     -26638.977     -70.63422      -24614.614     -58.505595    
-        10   0.75132894    -4.7952077      0.028216017    0.28494196     0              0              0.31315798    -4.4708519     -13243.822      12661.254     -49613.657     -2923.1497      69.449413      29456.684      56.087663    
+         1   2.8239917     -5.0023563      0.021919009    0.46718        0              0              0.48909901    -4.4711684     -8777.4654     -33285.75       30332.24      -23920.463     -67.159404     -23940.605     -56.913519    
-        20   2.1716525     -5.0036265      0.011809223    0.48875837     0              0              0.50056759    -4.4706925      4371.5298     -22102.532      47044.297     -12243.648     -74.588915     -28903.762     -64.48154     
+         2   9.9359188     -4.9806071      0.014704278    0.34344685     0              0              0.35815113    -4.4743705     -1094.2989     -20777.766      32507.918     -16918.53      -57.217298     -21702.479     -51.827962    
-        30   2.9930198     -4.8261906      0.0091463366   0.30162756     0              0              0.3107739     -4.4708086      9992.4549      41973.539     -20985.339      8415.1715      67.458145      25027.414      40.261795    
+         3   18.15288      -4.9496234      0.010334146    0.19125791     0              0              0.20159205    -4.47748        7115.3453     -5853.149       32274.916     -8557.0355     -41.982111     -17374.865     -42.455978    
-        40   3.312268      -4.9802484      0.010400667    0.45076258     0              0              0.46116325    -4.4697189      21565.307     -11602.414      65186.215      10476.902     -83.374203     -33222.094     -64.700001    
+         4   24.248994     -4.9153331      0.0093063079   0.065238074    0              0              0.074544382   -4.4793805      11356.801      5716.9586      25838.412     -2135.3667     -22.820662     -10495.224     -28.045156    
-        50   4.3187397     -4.8535614      0.0060313545   0.31244652     0              0              0.31847788    -4.4707168      11344.244      45839.35      -21073.749      8438.8954      73.345039      29422.636      43.897876    
+         5   26.136423     -4.8829114      0.0095061937   0.0039834608   0              0              0.013489654   -4.4798832      9044.3732      10498.874      11345.536      276.34491     -1.1467483     -1185.8556     -8.820154     
-        60   4.9127902     -5.0035271      0.0070589202   0.45246538     0              0              0.4595243     -4.4707824      6529.9354     -37107.891      46740.24       9015.2973     -90.41111      -34402.095     -53.57079     
+Loop time of 0.000211279 on 1 procs for 5 steps with 6 atoms
-        70   5.3145827     -4.8748857      0.025797484    0.29875503     0              0              0.32455252    -4.4711244     -10208.876      26324.134     -49272.688     -8697.2875      84.479942      36185.667      57.000355    
-        80   3.8409793     -5.0262066      0.027669388    0.47104466     0              0              0.49871405    -4.4702464     -9777.1809     -52088.554      28053.855     -6033.4555     -94.607853     -44638.417     -59.108505    
-        90   3.0683704     -4.8369716      0.035455716    0.28466932     0              0              0.32012503    -4.4711155     -10626.245      31066.635     -49425.925     -14107.889      87.765958      34632.905      52.101981    
-       100   3.5262799     -4.9906817      0.016687539    0.45011301     0              0              0.46680055    -4.4713252      5216.7691     -34991.221      43883.163      6082.1058     -95.830393     -48645.129     -64.784334    
-Loop time of 0.00568827 on 1 procs for 100 steps with 6 atoms
 
-Performance: 1518.916 ns/day, 0.016 hours/ns, 17580.041 timesteps/s
+Performance: 2044.690 ns/day, 0.012 hours/ns, 23665.390 timesteps/s
-76.9% CPU use with 1 MPI tasks x no OpenMP threads
+98.4% CPU use with 1 MPI tasks x 1 OpenMP threads
 
-AMEOBA/HIPPO timing breakdown:
+HIPPO timing breakdown:
-  Init    time: 0.00011293 0.024348
+  Init    time: 4.768e-06      4.20%
-  Repulse time: 0.000604058 13.0236
+  Repulse time: 1.3408e-05    11.81%
-  Disp    time: 0.000336908 7.26382
+  Disp    time: 9.476e-06      8.35%
-  Mpole   time: 0.000853828 18.4087
+  Mpole   time: 2.1547e-05    18.98%
-  Induce  time: 0.00158723 34.2211
+  Induce  time: 3.7631e-05    33.14%
-  Polar   time: 0.000996193 21.4782
+  Polar   time: 2.4333e-05    21.43%
-  Qxfer   time: 0.000142246 3.06686
+  Qxfer   time: 2.244e-06      1.98%
-  Total   time: 0.00463817
+  Total   time: 0.000113542 
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.0046663  | 0.0046663  | 0.0046663  |   0.0 | 82.03
+Pair    | 0.00011535 | 0.00011535 | 0.00011535 |   0.0 | 54.60
-Bond    | 7.8168e-05 | 7.8168e-05 | 7.8168e-05 |   0.0 |  1.37
+Bond    | 3.239e-06  | 3.239e-06  | 3.239e-06  |   0.0 |  1.53
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 1.3206e-05 | 1.3206e-05 | 1.3206e-05 |   0.0 |  0.23
+Comm    | 6.41e-07   | 6.41e-07   | 6.41e-07   |   0.0 |  0.30
-Output  | 0.00084402 | 0.00084402 | 0.00084402 |   0.0 | 14.84
+Output  | 8.5752e-05 | 8.5752e-05 | 8.5752e-05 |   0.0 | 40.59
-Modify  | 3.8896e-05 | 3.8896e-05 | 3.8896e-05 |   0.0 |  0.68
+Modify  | 1.55e-06   | 1.55e-06   | 1.55e-06   |   0.0 |  0.73
-Other   |            | 4.77e-05   |            |       |  0.84
+Other   |            | 4.744e-06  |            |       |  2.25
 
 Nlocal:              6 ave           6 max           6 min
 Histogram: 1 0 0 0 0 0 0 0 0 0

examples/amoeba/log.5Jul22.water_dimer.hippo.g++.4

@@ -1,4 +1,6 @@
-LAMMPS (24 Mar 2022)
+LAMMPS (23 Jun 2022)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
 # water dimer with AMOEBA or HIPPO
 
 units           real
@@ -39,7 +41,7 @@ Finding 1-2 1-3 1-4 neighbors ...
      1 = max # of 1-4 neighbors
      2 = max # of special neighbors
   special bonds CPU = 0.000 seconds
-  read_data CPU = 0.009 seconds
+  read_data CPU = 0.004 seconds
 
 # force field
 
@@ -55,7 +57,7 @@ Finding 1-2 1-3 1-4 neighbors ...
      1 = max # of 1-4 neighbors
      2 = max # of 1-5 neighbors
      2 = max # of special neighbors
-  special bonds CPU = 0.001 seconds
+  special bonds CPU = 0.000 seconds
 
 # thermo output
 
@@ -63,8 +65,8 @@ compute         virial all pressure NULL virial
 
 thermo_style    custom step temp epair ebond eangle edihed eimp                 emol etotal press c_virial[*]
 
-dump            1 all custom 10 dump.water_dimer id type x y z fx fy fz
+#dump            1 all custom 10 dump.water_dimer id type x y z fx fy fz
-dump_modify     1 sort id
+#dump_modify     1 sort id
 
 # zero step run
 
@@ -74,9 +76,9 @@ dump_modify     1 sort id
 
 fix             1 all nve
 
-thermo          10
+thermo          1
-run             100
+run             5
-AMOEBA/HIPPO force field settings
+HIPPO force field settings
   repulsion: cut 10 taper 8 rscale 0 0 1 1
   qxfer: cut 10 taper 8 mscale 0 0 0.4 1
   dispersion: cut 10 aewald 0 dspscale 0 0 0.4 1
@@ -84,7 +86,7 @@ AMOEBA/HIPPO force field settings
   polar: cut 10 aewald 0
          pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 0.2 1 1 1 d/u scale 0 1
   precondition: cut 4.5
-  generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
 Neighbor list info ...
   update every 1 steps, delay 10 steps, check yes
   max neighbors/atom: 2000, page size: 100000
@@ -97,46 +99,41 @@ Neighbor list info ...
       pair build: half/bin/newton
       stencil: half/bin/3d
       bin: standard
-WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:974)
+WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:970)
-  AMOEBA/HIPPO group count: 2
+  HIPPO group count: 2
-Per MPI rank memory allocation (min/avg/max) = 49.18 | 49.31 | 49.44 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 47.91 | 48.04 | 48.18 Mbytes
    Step          Temp          E_pair         E_bond        E_angle        E_dihed        E_impro         E_mol          TotEng         Press       c_virial[1]    c_virial[2]    c_virial[3]    c_virial[4]    c_virial[5]    c_virial[6]  
          0   0             -5.0101954      0.025695395    0.51472748     0              0              0.54042288    -4.4697726     -11875.159     -38149.178      29162.678     -26638.977     -70.63422      -24614.614     -58.505595    
-        10   0.75132894    -4.7952077      0.028216017    0.28494196     0              0              0.31315798    -4.4708519     -13243.822      12661.254     -49613.657     -2923.1497      69.449413      29456.684      56.087663    
+         1   2.8239917     -5.0023563      0.021919009    0.46718        0              0              0.48909901    -4.4711684     -8777.4654     -33285.75       30332.24      -23920.463     -67.159404     -23940.605     -56.913519    
-        20   2.1716525     -5.0036265      0.011809223    0.48875837     0              0              0.50056759    -4.4706925      4371.5298     -22102.532      47044.297     -12243.648     -74.588915     -28903.762     -64.48154     
+         2   9.9359188     -4.9806071      0.014704278    0.34344685     0              0              0.35815113    -4.4743705     -1094.2989     -20777.766      32507.918     -16918.53      -57.217298     -21702.479     -51.827962    
-        30   2.9930198     -4.8261906      0.0091463366   0.30162756     0              0              0.3107739     -4.4708086      9992.4549      41973.539     -20985.339      8415.1715      67.458145      25027.414      40.261795    
+         3   18.15288      -4.9496234      0.010334146    0.19125791     0              0              0.20159205    -4.47748        7115.3453     -5853.149       32274.916     -8557.0355     -41.982111     -17374.865     -42.455978    
-        40   3.312268      -4.9802484      0.010400667    0.45076258     0              0              0.46116325    -4.4697189      21565.307     -11602.414      65186.215      10476.902     -83.374203     -33222.094     -64.700001    
+         4   24.248994     -4.9153331      0.0093063079   0.065238074    0              0              0.074544382   -4.4793805      11356.801      5716.9586      25838.412     -2135.3667     -22.820662     -10495.224     -28.045156    
-        50   4.3187397     -4.8535614      0.0060313545   0.31244652     0              0              0.31847788    -4.4707168      11344.244      45839.35      -21073.749      8438.8954      73.345039      29422.636      43.897876    
+         5   26.136423     -4.8829114      0.0095061937   0.0039834608   0              0              0.013489654   -4.4798832      9044.3732      10498.874      11345.536      276.34491     -1.1467483     -1185.8556     -8.820154     
-        60   4.9127902     -5.0035271      0.0070589202   0.45246538     0              0              0.4595243     -4.4707824      6529.9354     -37107.891      46740.24       9015.2973     -90.41111      -34402.095     -53.57079     
+Loop time of 0.000515971 on 4 procs for 5 steps with 6 atoms
-        70   5.3145827     -4.8748857      0.025797484    0.29875503     0              0              0.32455252    -4.4711244     -10208.876      26324.134     -49272.688     -8697.2875      84.479942      36185.667      57.000355    
-        80   3.8409793     -5.0262066      0.027669388    0.47104466     0              0              0.49871405    -4.4702464     -9777.1809     -52088.554      28053.855     -6033.4555     -94.607853     -44638.417     -59.108505    
-        90   3.0683704     -4.8369716      0.035455716    0.28466932     0              0              0.32012503    -4.4711155     -10626.245      31066.635     -49425.925     -14107.889      87.765958      34632.905      52.101981    
-       100   3.5262799     -4.9906817      0.016687539    0.45011301     0              0              0.46680055    -4.4713252      5216.7691     -34991.221      43883.163      6082.1058     -95.830393     -48645.129     -64.784334    
-Loop time of 0.0133873 on 4 procs for 100 steps with 6 atoms
 
-Performance: 645.386 ns/day, 0.037 hours/ns, 7469.744 timesteps/s
+Performance: 837.257 ns/day, 0.029 hours/ns, 9690.472 timesteps/s
-98.4% CPU use with 4 MPI tasks x no OpenMP threads
+99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
 
-AMEOBA/HIPPO timing breakdown:
+HIPPO timing breakdown:
-  Init    time: 0.000581606 0.0545512
+  Init    time: 1.26765e-05    4.09%
-  Repulse time: 0.000622984 5.84322
+  Repulse time: 1.99082e-05    6.43%
-  Disp    time: 0.000115637 1.0846
+  Disp    time: 3.16825e-06    1.02%
-  Mpole   time: 0.000994723 9.32991
+  Mpole   time: 3.4956e-05    11.29%
-  Induce  time: 0.00737161 69.1413
+  Induce  time: 0.000205268   66.29%
-  Polar   time: 0.00091816 8.61179
+  Polar   time: 3.1924e-05    10.31%
-  Qxfer   time: 5.1997e-05 0.487701
+  Qxfer   time: 1.5545e-06     0.50%
-  Total   time: 0.0106617
+  Total   time: 0.000309632 
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.010579   | 0.010896   | 0.011085   |   0.2 | 81.39
+Pair    | 0.0003033  | 0.00032943 | 0.00034747 |   0.0 | 63.85
-Bond    | 1.3578e-05 | 4.3855e-05 | 7.6592e-05 |   0.0 |  0.33
+Bond    | 1.237e-06  | 2.778e-06  | 4.775e-06  |   0.0 |  0.54
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.00058533 | 0.00080957 | 0.0011064  |   0.0 |  6.05
+Comm    | 1.2356e-05 | 3.1848e-05 | 4.3553e-05 |   0.0 |  6.17
-Output  | 0.0011175  | 0.0011761  | 0.0013051  |   0.2 |  8.78
+Output  | 0.00012443 | 0.0001412  | 0.00015698 |   0.0 | 27.37
-Modify  | 2.4304e-05 | 3.4805e-05 | 4.2149e-05 |   0.0 |  0.26
+Modify  | 1.428e-06  | 2.0447e-06 | 2.545e-06  |   0.0 |  0.40
-Other   |            | 0.0004266  |            |       |  3.19
+Other   |            | 8.678e-06  |            |       |  1.68
 
 Nlocal:            1.5 ave           3 max           0 min
 Histogram: 2 0 0 0 0 0 0 0 0 2

examples/amoeba/log.5Jul22.water_hexamer.amoeba.g++.1

@@ -1,4 +1,6 @@
-LAMMPS (24 Mar 2022)
+LAMMPS (23 Jun 2022)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
 # water hexamer with AMOEBA or HIPPO
 
 units           real
@@ -39,7 +41,7 @@ Finding 1-2 1-3 1-4 neighbors ...
      1 = max # of 1-4 neighbors
      2 = max # of special neighbors
   special bonds CPU = 0.000 seconds
-  read_data CPU = 0.009 seconds
+  read_data CPU = 0.003 seconds
 
 # force field
 
@@ -63,8 +65,8 @@ compute         virial all pressure NULL virial
 
 thermo_style    custom step temp epair ebond eangle edihed eimp                 emol etotal press c_virial[*]
 
-dump            1 all custom 10 dump.water_hexamer id type x y z fx fy fz
+#dump            1 all custom 10 dump.water_hexamer id type x y z fx fy fz
-dump_modify     1 sort id
+#dump_modify     1 sort id
 
 # zero step run
 
@@ -74,15 +76,15 @@ dump_modify     1 sort id
 
 fix             1 all nve
 
-thermo          10
+thermo          1
-run             100
+run             5
-AMOEBA/HIPPO force field settings
+AMOEBA force field settings
   hal: cut 10 taper 8 vscale 0 0 1 1
   multipole: cut 10 aewald 0 mscale 0 0 0.4 1
   polar: cut 10 aewald 0
          pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 1 1 1 1 d/u scale 0 1
   precondition: cut 4.5
-  generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
 Neighbor list info ...
   update every 1 steps, delay 10 steps, check yes
   max neighbors/atom: 2000, page size: 100000
@@ -95,43 +97,38 @@ Neighbor list info ...
       pair build: half/bin/newton
       stencil: half/bin/3d
       bin: standard
-  AMOEBA/HIPPO group count: 6
+  AMOEBA group count: 6
-Per MPI rank memory allocation (min/avg/max) = 49.53 | 49.53 | 49.53 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 48.28 | 48.28 | 48.28 Mbytes
    Step          Temp          E_pair         E_bond        E_angle        E_dihed        E_impro         E_mol          TotEng         Press       c_virial[1]    c_virial[2]    c_virial[3]    c_virial[4]    c_virial[5]    c_virial[6]  
          0   0             -48.469664      1.9820353      2.2499329      0              0              4.2319683     -44.237696     -26322.671     -28303.103     -27669.614     -22995.296      1312.6688      2624.8394      4042.0489    
-        10   6.3616471     -46.626437      1.7910812      0.25704063     0              0              2.0481218     -44.255947     -23813.06      -24671.886     -17167.34      -30208.043     -474.208       -8339.5934     -5278.359     
+         1   5.318656      -48.202382      1.5369859      2.1322394      0              0              3.6692253     -44.26364      -20236.446     -20385.617     -23104.961     -17727.152      417.52781      2728.2976      3750.7708    
-        20   15.149798     -48.177533      1.1130818      2.007499       0              0              3.1205807     -44.289255     -16468.855     -20150.975     -18596.629     -12107.083      885.52697      6320.1867      3064.949     
+         2   14.415671     -47.491537      0.6389772      1.8136212      0              0              2.4525984     -44.308442     -4127.4968      1051.8436     -10980.156     -3832.1256     -2285.3376      2991.8274      2945.888     
-        30   17.896968     -45.959274      0.54802739     0.19519937     0              0              0.74322676    -44.309141     -4749.0624     -9053.7792     -182.37209     -6721.7499     -2003.7641     -627.56998     -1658.1301    
+         3   15.996484     -46.59119       0.087228651    1.3862662      0              0              1.4734948     -44.307093      15705.166      28374.161      4124.662       13087.621     -6242.1769      3159.6508      1787.4159    
-        40   16.203813     -46.840973      0.1371751      1.5793326      0              0              1.7165077     -44.303357      9267.4858      6108.7966      4116.4548      16028.336      380.03787      8468.0648      4492.3331    
+         4   10.888785     -45.839064      0.062461924    0.96598997     0              0              1.0284519     -44.258837      30226.38       48920.372      15666.108      25051.837     -9443.9251      2603.8275      435.5257     
-        50   11.584975     -45.166711      0.017120512    0.28622888     0              0              0.30334939    -44.276308      22189.511      21453.083      22339.471      21668.607      150.93139      1059.5253      200.0668     
+         5   10.58575      -45.503287      0.071817565    0.64254674     0              0              0.71436431    -44.252503      31899.04       51066.283      18170.57       25448.409     -9478.6752      638.72265     -1011.7679    
-        60   10.002055     -45.994946      0.037889337    1.1987062      0              0              1.2365956     -44.251509      30944.004      35801.925      19832.696      36241.326      2042.3054      2320.5193      1660.0834    
+Loop time of 0.00100021 on 1 procs for 5 steps with 18 atoms
-        70   11.272241     -45.411622      0.07431614     0.51778317     0              0              0.59209931    -44.248316      32055.564      39306.193      30181.52       25601.501      1373.4778     -4501.0686     -2570.4767    
-        80   14.011502     -46.081444      0.089688317    1.006928       0              0              1.0966163     -44.274812      25661.838      38836.598      12603.734      24205.867     -867.36437     -4211.9639     -2820.6725    
-        90   17.659498     -46.247295      0.21744649     0.82687716     0              0              1.0443237     -44.308098      12101.207      19426.995      14142.311      1046.299      -2157.5418     -2141.2454     -2621.456     
-       100   17.630532     -46.788272      0.61811601     0.9654966      0              0              1.5836126     -44.311254     -4455.3587      3961.5737     -11554.095     -7458.8012     -3120.9771     -1532.1706     -1499.0117    
-Loop time of 0.0438592 on 1 procs for 100 steps with 18 atoms
 
-Performance: 196.994 ns/day, 0.122 hours/ns, 2280.022 timesteps/s
+Performance: 431.907 ns/day, 0.056 hours/ns, 4998.925 timesteps/s
-95.1% CPU use with 1 MPI tasks x no OpenMP threads
+99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
 
-AMEOBA/HIPPO timing breakdown:
+AMOEBA timing breakdown:
-  Init    time: 0.000324764 0.00770058
+  Init    time: 1.2295e-05     1.38%
-  Hal     time: 0.00500441 11.8661
+  Hal     time: 6.2308e-05     6.98%
-  Mpole   time: 0.00442974 10.5035
+  Mpole   time: 0.000124591   13.97%
-  Induce  time: 0.0210286 49.8617
+  Induce  time: 0.000432719   48.51%
-  Polar   time: 0.0113696 26.9588
+  Polar   time: 0.000259676   29.11%
-  Total   time: 0.042174
+  Total   time: 0.000892068 
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.042221   | 0.042221   | 0.042221   |   0.0 | 96.26
+Pair    | 0.00089392 | 0.00089392 | 0.00089392 |   0.0 | 89.37
-Bond    | 0.00021632 | 0.00021632 | 0.00021632 |   0.0 |  0.49
+Bond    | 6.685e-06  | 6.685e-06  | 6.685e-06  |   0.0 |  0.67
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 1.6322e-05 | 1.6322e-05 | 1.6322e-05 |   0.0 |  0.04
+Comm    | 6.67e-07   | 6.67e-07   | 6.67e-07   |   0.0 |  0.07
-Output  | 0.0012472  | 0.0012472  | 0.0012472  |   0.0 |  2.84
+Output  | 9.0869e-05 | 9.0869e-05 | 9.0869e-05 |   0.0 |  9.08
-Modify  | 7.9638e-05 | 7.9638e-05 | 7.9638e-05 |   0.0 |  0.18
+Modify  | 2.517e-06  | 2.517e-06  | 2.517e-06  |   0.0 |  0.25
-Other   |            | 7.889e-05  |            |       |  0.18
+Other   |            | 5.561e-06  |            |       |  0.56
 
 Nlocal:             18 ave          18 max          18 min
 Histogram: 1 0 0 0 0 0 0 0 0 0

examples/amoeba/log.5Jul22.water_hexamer.amoeba.g++.4

@@ -1,4 +1,6 @@
-LAMMPS (24 Mar 2022)
+LAMMPS (23 Jun 2022)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
 # water hexamer with AMOEBA or HIPPO
 
 units           real
@@ -39,7 +41,7 @@ Finding 1-2 1-3 1-4 neighbors ...
      1 = max # of 1-4 neighbors
      2 = max # of special neighbors
   special bonds CPU = 0.000 seconds
-  read_data CPU = 0.008 seconds
+  read_data CPU = 0.004 seconds
 
 # force field
 
@@ -63,8 +65,8 @@ compute         virial all pressure NULL virial
 
 thermo_style    custom step temp epair ebond eangle edihed eimp                 emol etotal press c_virial[*]
 
-dump            1 all custom 10 dump.water_hexamer id type x y z fx fy fz
+#dump            1 all custom 10 dump.water_hexamer id type x y z fx fy fz
-dump_modify     1 sort id
+#dump_modify     1 sort id
 
 # zero step run
 
@@ -74,15 +76,15 @@ dump_modify     1 sort id
 
 fix             1 all nve
 
-thermo          10
+thermo          1
-run             100
+run             5
-AMOEBA/HIPPO force field settings
+AMOEBA force field settings
   hal: cut 10 taper 8 vscale 0 0 1 1
   multipole: cut 10 aewald 0 mscale 0 0 0.4 1
   polar: cut 10 aewald 0
          pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 1 1 1 1 d/u scale 0 1
   precondition: cut 4.5
-  generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
 Neighbor list info ...
   update every 1 steps, delay 10 steps, check yes
   max neighbors/atom: 2000, page size: 100000
@@ -95,44 +97,39 @@ Neighbor list info ...
       pair build: half/bin/newton
       stencil: half/bin/3d
       bin: standard
-WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:974)
+WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:970)
-  AMOEBA/HIPPO group count: 6
+  AMOEBA group count: 6
-Per MPI rank memory allocation (min/avg/max) = 49.56 | 49.56 | 49.56 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 48.3 | 48.3 | 48.3 Mbytes
    Step          Temp          E_pair         E_bond        E_angle        E_dihed        E_impro         E_mol          TotEng         Press       c_virial[1]    c_virial[2]    c_virial[3]    c_virial[4]    c_virial[5]    c_virial[6]  
          0   0             -48.469664      1.9820353      2.2499329      0              0              4.2319683     -44.237696     -26322.671     -28303.103     -27669.614     -22995.296      1312.6688      2624.8394      4042.0489    
-        10   6.3616471     -46.626437      1.7910812      0.25704063     0              0              2.0481218     -44.255947     -23813.06      -24671.886     -17167.34      -30208.043     -474.208       -8339.5934     -5278.359     
+         1   5.318656      -48.202382      1.5369859      2.1322394      0              0              3.6692253     -44.26364      -20236.446     -20385.617     -23104.961     -17727.152      417.52781      2728.2976      3750.7708    
-        20   15.149798     -48.177533      1.1130818      2.007499       0              0              3.1205807     -44.289255     -16468.855     -20150.975     -18596.629     -12107.083      885.52697      6320.1867      3064.949     
+         2   14.415671     -47.491537      0.6389772      1.8136212      0              0              2.4525984     -44.308442     -4127.4968      1051.8436     -10980.156     -3832.1256     -2285.3376      2991.8274      2945.888     
-        30   17.896968     -45.959274      0.54802739     0.19519937     0              0              0.74322676    -44.309141     -4749.0624     -9053.7792     -182.37209     -6721.7499     -2003.7641     -627.56998     -1658.1301    
+         3   15.996484     -46.59119       0.087228651    1.3862662      0              0              1.4734948     -44.307093      15705.166      28374.161      4124.662       13087.621     -6242.1769      3159.6508      1787.4159    
-        40   16.203813     -46.840973      0.1371751      1.5793326      0              0              1.7165077     -44.303357      9267.4858      6108.7966      4116.4548      16028.336      380.03787      8468.0648      4492.3331    
+         4   10.888785     -45.839064      0.062461924    0.96598997     0              0              1.0284519     -44.258837      30226.38       48920.372      15666.108      25051.837     -9443.9251      2603.8275      435.5257     
-        50   11.584975     -45.166711      0.017120512    0.28622888     0              0              0.30334939    -44.276308      22189.511      21453.083      22339.471      21668.607      150.93139      1059.5253      200.0668     
+         5   10.58575      -45.503287      0.071817565    0.64254674     0              0              0.71436431    -44.252503      31899.04       51066.283      18170.57       25448.409     -9478.6752      638.72265     -1011.7679    
-        60   10.002055     -45.994946      0.037889337    1.1987062      0              0              1.2365956     -44.251509      30944.004      35801.925      19832.696      36241.326      2042.3054      2320.5193      1660.0834    
+Loop time of 0.0015204 on 4 procs for 5 steps with 18 atoms
-        70   11.272241     -45.411622      0.07431614     0.51778317     0              0              0.59209931    -44.248316      32055.564      39306.193      30181.52       25601.501      1373.4778     -4501.0686     -2570.4767    
-        80   14.011502     -46.081444      0.089688317    1.006928       0              0              1.0966163     -44.274812      25661.838      38836.598      12603.734      24205.867     -867.36437     -4211.9639     -2820.6725    
-        90   17.659498     -46.247295      0.21744649     0.82687716     0              0              1.0443237     -44.308098      12101.207      19426.995      14142.311      1046.299      -2157.5418     -2141.2454     -2621.456     
-       100   17.630532     -46.788272      0.61811601     0.9654966      0              0              1.5836126     -44.311254     -4455.3587      3961.5737     -11554.095     -7458.8012     -3120.9771     -1532.1706     -1499.0117    
-Loop time of 0.0405754 on 4 procs for 100 steps with 18 atoms
 
-Performance: 212.937 ns/day, 0.113 hours/ns, 2464.547 timesteps/s
+Performance: 284.136 ns/day, 0.084 hours/ns, 3288.611 timesteps/s
-98.9% CPU use with 4 MPI tasks x no OpenMP threads
+98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
 
-AMEOBA/HIPPO timing breakdown:
+AMOEBA timing breakdown:
-  Init    time: 0.000756446 0.0198927
+  Init    time: 2.00392e-05    1.57%
-  Hal     time: 0.00120064 3.15739
+  Hal     time: 2.58605e-05    2.02%
-  Mpole   time: 0.00338295 8.89637
+  Mpole   time: 0.000137192   10.74%
-  Induce  time: 0.0273688 71.9733
+  Induce  time: 0.000858714   67.22%
-  Polar   time: 0.00530425 13.9489
+  Polar   time: 0.00023507    18.40%
-  Total   time: 0.0380263
+  Total   time: 0.00127742  
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.03816    | 0.038221   | 0.038312   |   0.0 | 94.20
+Pair    | 0.0012876  | 0.0012913  | 0.0012951  |   0.0 | 84.93
-Bond    | 7.0759e-05 | 8.5222e-05 | 0.00010449 |   0.0 |  0.21
+Bond    | 4.076e-06  | 6.434e-06  | 1.0051e-05 |   0.0 |  0.42
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.00065721 | 0.00081724 | 0.00093857 |   0.0 |  2.01
+Comm    | 1.4924e-05 | 5.9337e-05 | 8.3417e-05 |   0.0 |  3.90
-Output  | 0.0010275  | 0.0010663  | 0.0011758  |   0.2 |  2.63
+Output  | 0.00012796 | 0.00014846 | 0.00018928 |   0.0 |  9.76
-Modify  | 3.3884e-05 | 4.422e-05  | 5.7037e-05 |   0.0 |  0.11
+Modify  | 2.066e-06  | 2.5358e-06 | 3.07e-06   |   0.0 |  0.17
-Other   |            | 0.000341   |            |       |  0.84
+Other   |            | 1.236e-05  |            |       |  0.81
 
 Nlocal:            4.5 ave           6 max           3 min
 Histogram: 1 0 0 1 0 0 1 0 0 1

examples/amoeba/log.5Jul22.water_hexamer.hippo.g++.1

@@ -1,4 +1,6 @@
-LAMMPS (24 Mar 2022)
+LAMMPS (23 Jun 2022)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
 # water hexamer with AMOEBA or HIPPO
 
 units           real
@@ -39,7 +41,7 @@ Finding 1-2 1-3 1-4 neighbors ...
      1 = max # of 1-4 neighbors
      2 = max # of special neighbors
   special bonds CPU = 0.000 seconds
-  read_data CPU = 0.007 seconds
+  read_data CPU = 0.004 seconds
 
 # force field
 
@@ -63,8 +65,8 @@ compute         virial all pressure NULL virial
 
 thermo_style    custom step temp epair ebond eangle edihed eimp                 emol etotal press c_virial[*]
 
-dump            1 all custom 10 dump.water_hexamer id type x y z fx fy fz
+#dump            1 all custom 10 dump.water_hexamer id type x y z fx fy fz
-dump_modify     1 sort id
+#dump_modify     1 sort id
 
 # zero step run
 
@@ -74,9 +76,9 @@ dump_modify     1 sort id
 
 fix             1 all nve
 
-thermo          10
+thermo          1
-run             100
+run             5
-AMOEBA/HIPPO force field settings
+HIPPO force field settings
   repulsion: cut 10 taper 8 rscale 0 0 1 1
   qxfer: cut 10 taper 8 mscale 0 0 0.4 1
   dispersion: cut 10 aewald 0 dspscale 0 0 0.4 1
@@ -84,7 +86,7 @@ AMOEBA/HIPPO force field settings
   polar: cut 10 aewald 0
          pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 0.2 1 1 1 d/u scale 0 1
   precondition: cut 4.5
-  generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
 Neighbor list info ...
   update every 1 steps, delay 10 steps, check yes
   max neighbors/atom: 2000, page size: 100000
@@ -97,45 +99,40 @@ Neighbor list info ...
       pair build: half/bin/newton
       stencil: half/bin/3d
       bin: standard
-  AMOEBA/HIPPO group count: 6
+  HIPPO group count: 6
-Per MPI rank memory allocation (min/avg/max) = 49.1 | 49.1 | 49.1 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 47.84 | 47.84 | 47.84 Mbytes
    Step          Temp          E_pair         E_bond        E_angle        E_dihed        E_impro         E_mol          TotEng         Press       c_virial[1]    c_virial[2]    c_virial[3]    c_virial[4]    c_virial[5]    c_virial[6]  
          0   0             -47.362156      1.9820353      1.6634749      0              0              3.6455102     -43.716646     -34513.768     -42206.078     -31383.641     -29951.584      2850.1184      3579.9253      5768.3698    
-        10   11.52238      -45.959856      1.53397        0.085100522    0              0              1.6190706     -43.756903     -28644.676     -34867.94      -19324.955     -32842.522     -370.63233     -6452.0859     -4002.3535    
+         1   7.1819351     -47.135822      1.4553325      1.5620463      0              0              3.0173788     -43.754508     -26763.923     -32046.377     -25919.73      -23012.16       1848.028       3578.5744      5396.0234    
-        20   20.237283     -46.772008      0.54762833     1.3835192      0              0              1.9311476     -43.815361     -10546.356     -10116.359     -17063.425     -6393.701      -1166.7608      4243.6327      3493.9596    
+         2   18.776762     -46.526843      0.46636815     1.2906982      0              0              1.7570664     -43.818287     -6352.6601     -4602.4631     -11460.465     -4789.8629     -1296.5558      3625.7641      4391.7607    
-        30   20.666374     -45.011106      0.086797459    0.071122604    0              0              0.15792006    -43.805943      13150.762      15882.022      10964.553      10630.278     -6754.7642     -432.29165     -3783.115     
+         3   19.013509     -45.750445      0.043880608    0.9336078      0              0              0.97748841    -43.809471      18351.549      29896.314      6275.5012      17065.39      -6055.8639      3664.6024      3015.6633    
-        40   10.639014     -45.430939      0.18926921     0.96410995     0              0              1.1533792     -43.738441      33402.664      41252.58       19726.586      38211.875     -6166.03        6081.5692      1815.7739    
+         4   11.017518     -45.12347       0.24124811     0.58878104     0              0              0.83002915    -43.735142      35358.63       54252.632      19050.919      31719.21      -9822.7607      3160.7845      1520.1368    
-        50   10.992432     -44.741108      0.19575431     0.25851128     0              0              0.45426559    -43.729815      37696.923      41572.466      33299.43       37168.141     -3254.5134      2.9639226     -1017.3669    
+         5   12.143149     -44.904245      0.22320916     0.3270434      0              0              0.55025256    -43.738653      35160.919      53395.572      20272.979      30653.482     -9511.0241      1392.4959      35.692826    
-        60   19.748633     -45.461264      0.035287281    0.63217389     0              0              0.66746117    -43.793065      26212.839      28825.788      16048.096      31876.925      3504.5461      135.3505       420.28566    
+Loop time of 0.00117792 on 1 procs for 5 steps with 18 atoms
-        70   26.129957     -46.022729      0.30434543     0.56770169     0              0              0.87204711    -43.826579      3919.9866     -2755.6905      11500.428      517.54333      5626.9543     -2238.5786      86.305984    
-        80   17.768494     -46.309777      1.1680612      0.45551823     0              0              1.6235794     -43.785801     -18335.898     -22168.789     -14488.992     -20048.346      7343.173      -2646.2196     -2525.6625    
-        90   8.3822494     -47.063502      2.0182644      0.88875358     0              0              2.9070179     -43.731724     -33693.203     -43487.996     -15178.35      -43214.494      2412.6411      1993.0113      1780.7512    
-       100   8.6486333     -46.517402      1.9551958      0.38696887     0              0              2.3421647     -43.736979     -34734.97      -34372.659     -28372.146     -42286.799      226.18821      40.353457     -755.93912    
-Loop time of 0.0399433 on 1 procs for 100 steps with 18 atoms
 
-Performance: 216.307 ns/day, 0.111 hours/ns, 2503.548 timesteps/s
+Performance: 366.749 ns/day, 0.065 hours/ns, 4244.778 timesteps/s
-92.6% CPU use with 1 MPI tasks x no OpenMP threads
+95.2% CPU use with 1 MPI tasks x 1 OpenMP threads
 
-AMEOBA/HIPPO timing breakdown:
+HIPPO timing breakdown:
-  Init    time: 0.000295019 0.00770171
+  Init    time: 1.5876e-05     1.52%
-  Repulse time: 0.00594736 15.5261
+  Repulse time: 0.000160405   15.32%
-  Disp    time: 0.00261218 6.81931
+  Disp    time: 5.1301e-05     4.90%
-  Mpole   time: 0.0069314 18.095
+  Mpole   time: 0.000219996   21.01%
-  Induce  time: 0.013694 35.7492
+  Induce  time: 0.000352821   33.70%
-  Polar   time: 0.00744631 19.4392
+  Polar   time: 0.000218541   20.87%
-  Qxfer   time: 0.001375 3.58954
+  Qxfer   time: 2.7842e-05     2.66%
-  Total   time: 0.0383057
+  Total   time: 0.00104695  
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.038344   | 0.038344   | 0.038344   |   0.0 | 96.00
+Pair    | 0.0010494  | 0.0010494  | 0.0010494  |   0.0 | 89.09
-Bond    | 0.00017707 | 0.00017707 | 0.00017707 |   0.0 |  0.44
+Bond    | 7.408e-06  | 7.408e-06  | 7.408e-06  |   0.0 |  0.63
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 1.5549e-05 | 1.5549e-05 | 1.5549e-05 |   0.0 |  0.04
+Comm    | 1.032e-06  | 1.032e-06  | 1.032e-06  |   0.0 |  0.09
-Output  | 0.0012682  | 0.0012682  | 0.0012682  |   0.0 |  3.18
+Output  | 0.00011139 | 0.00011139 | 0.00011139 |   0.0 |  9.46
-Modify  | 7.0869e-05 | 7.0869e-05 | 7.0869e-05 |   0.0 |  0.18
+Modify  | 2.647e-06  | 2.647e-06  | 2.647e-06  |   0.0 |  0.22
-Other   |            | 6.745e-05  |            |       |  0.17
+Other   |            | 6.086e-06  |            |       |  0.52
 
 Nlocal:             18 ave          18 max          18 min
 Histogram: 1 0 0 0 0 0 0 0 0 0

examples/amoeba/log.5Jul22.water_hexamer.hippo.g++.4

@@ -1,4 +1,6 @@
-LAMMPS (24 Mar 2022)
+LAMMPS (23 Jun 2022)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
 # water hexamer with AMOEBA or HIPPO
 
 units           real
@@ -39,7 +41,7 @@ Finding 1-2 1-3 1-4 neighbors ...
      1 = max # of 1-4 neighbors
      2 = max # of special neighbors
   special bonds CPU = 0.000 seconds
-  read_data CPU = 0.008 seconds
+  read_data CPU = 0.003 seconds
 
 # force field
 
@@ -63,8 +65,8 @@ compute         virial all pressure NULL virial
 
 thermo_style    custom step temp epair ebond eangle edihed eimp                 emol etotal press c_virial[*]
 
-dump            1 all custom 10 dump.water_hexamer id type x y z fx fy fz
+#dump            1 all custom 10 dump.water_hexamer id type x y z fx fy fz
-dump_modify     1 sort id
+#dump_modify     1 sort id
 
 # zero step run
 
@@ -74,9 +76,9 @@ dump_modify     1 sort id
 
 fix             1 all nve
 
-thermo          10
+thermo          1
-run             100
+run             5
-AMOEBA/HIPPO force field settings
+HIPPO force field settings
   repulsion: cut 10 taper 8 rscale 0 0 1 1
   qxfer: cut 10 taper 8 mscale 0 0 0.4 1
   dispersion: cut 10 aewald 0 dspscale 0 0 0.4 1
@@ -84,7 +86,7 @@ AMOEBA/HIPPO force field settings
   polar: cut 10 aewald 0
          pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 0.2 1 1 1 d/u scale 0 1
   precondition: cut 4.5
-  generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
 Neighbor list info ...
   update every 1 steps, delay 10 steps, check yes
   max neighbors/atom: 2000, page size: 100000
@@ -97,46 +99,41 @@ Neighbor list info ...
       pair build: half/bin/newton
       stencil: half/bin/3d
       bin: standard
-WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:974)
+WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:970)
-  AMOEBA/HIPPO group count: 6
+  HIPPO group count: 6
-Per MPI rank memory allocation (min/avg/max) = 49.13 | 49.13 | 49.13 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 47.86 | 47.86 | 47.86 Mbytes
    Step          Temp          E_pair         E_bond        E_angle        E_dihed        E_impro         E_mol          TotEng         Press       c_virial[1]    c_virial[2]    c_virial[3]    c_virial[4]    c_virial[5]    c_virial[6]  
          0   0             -47.362156      1.9820353      1.6634749      0              0              3.6455102     -43.716646     -34513.768     -42206.078     -31383.641     -29951.584      2850.1184      3579.9253      5768.3698    
-        10   11.52238      -45.959856      1.53397        0.085100522    0              0              1.6190706     -43.756903     -28644.676     -34867.94      -19324.955     -32842.522     -370.63233     -6452.0859     -4002.3535    
+         1   7.1819351     -47.135822      1.4553325      1.5620463      0              0              3.0173788     -43.754508     -26763.923     -32046.377     -25919.73      -23012.16       1848.028       3578.5744      5396.0234    
-        20   20.237283     -46.772008      0.54762833     1.3835192      0              0              1.9311476     -43.815361     -10546.356     -10116.359     -17063.425     -6393.701      -1166.7608      4243.6327      3493.9596    
+         2   18.776762     -46.526843      0.46636815     1.2906982      0              0              1.7570664     -43.818287     -6352.6601     -4602.4631     -11460.465     -4789.8629     -1296.5558      3625.7641      4391.7607    
-        30   20.666374     -45.011106      0.086797459    0.071122604    0              0              0.15792006    -43.805943      13150.762      15882.022      10964.553      10630.278     -6754.7642     -432.29165     -3783.115     
+         3   19.013509     -45.750445      0.043880608    0.9336078      0              0              0.97748841    -43.809471      18351.549      29896.314      6275.5012      17065.39      -6055.8639      3664.6024      3015.6633    
-        40   10.639014     -45.430939      0.18926921     0.96410995     0              0              1.1533792     -43.738441      33402.664      41252.58       19726.586      38211.875     -6166.03        6081.5692      1815.7739    
+         4   11.017518     -45.12347       0.24124811     0.58878104     0              0              0.83002915    -43.735142      35358.63       54252.632      19050.919      31719.21      -9822.7607      3160.7845      1520.1368    
-        50   10.992432     -44.741108      0.19575431     0.25851128     0              0              0.45426559    -43.729815      37696.923      41572.466      33299.43       37168.141     -3254.5134      2.9639226     -1017.3669    
+         5   12.143149     -44.904245      0.22320916     0.3270434      0              0              0.55025256    -43.738653      35160.919      53395.572      20272.979      30653.482     -9511.0241      1392.4959      35.692826    
-        60   19.748633     -45.461264      0.035287281    0.63217389     0              0              0.66746117    -43.793065      26212.839      28825.788      16048.096      31876.925      3504.5461      135.3505       420.28566    
+Loop time of 0.000850973 on 4 procs for 5 steps with 18 atoms
-        70   26.129957     -46.022729      0.30434543     0.56770169     0              0              0.87204711    -43.826579      3919.9866     -2755.6905      11500.428      517.54333      5626.9543     -2238.5786      86.305984    
-        80   17.768494     -46.309777      1.1680612      0.45551823     0              0              1.6235794     -43.785801     -18335.898     -22168.789     -14488.992     -20048.346      7343.173      -2646.2196     -2525.6625    
-        90   8.3822494     -47.063502      2.0182644      0.88875358     0              0              2.9070179     -43.731724     -33693.203     -43487.996     -15178.35      -43214.494      2412.6411      1993.0113      1780.7512    
-       100   8.6486333     -46.517402      1.9551958      0.38696887     0              0              2.3421647     -43.736979     -34734.97      -34372.659     -28372.146     -42286.799      226.18821      40.353457     -755.93912    
-Loop time of 0.033787 on 4 procs for 100 steps with 18 atoms
 
-Performance: 255.719 ns/day, 0.094 hours/ns, 2959.715 timesteps/s
+Performance: 507.654 ns/day, 0.047 hours/ns, 5875.629 timesteps/s
-99.9% CPU use with 4 MPI tasks x no OpenMP threads
+99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
 
-AMEOBA/HIPPO timing breakdown:
+HIPPO timing breakdown:
-  Init    time: 0.000724905 0.0236438
+  Init    time: 1.6627e-05     2.46%
-  Repulse time: 0.00306516 9.99746
+  Repulse time: 9.88147e-05   14.60%
-  Disp    time: 0.000637502 2.07931
+  Disp    time: 1.35375e-05    2.00%
-  Mpole   time: 0.00397577 12.9676
+  Mpole   time: 0.000103418   15.28%
-  Induce  time: 0.0181268 59.123
+  Induce  time: 0.000343719   50.80%
-  Polar   time: 0.00377543 12.3141
+  Polar   time: 9.3749e-05    13.85%
-  Qxfer   time: 0.000349256 1.13915
+  Qxfer   time: 6.64925e-06    0.98%
-  Total   time: 0.0306594
+  Total   time: 0.000676665 
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.030576   | 0.030875   | 0.031306   |   0.2 | 91.38
+Pair    | 0.00068159 | 0.00068738 | 0.00069496 |   0.0 | 80.78
-Bond    | 6.4191e-05 | 7.956e-05  | 0.0001014  |   0.0 |  0.24
+Bond    | 3.506e-06  | 3.8025e-06 | 4.338e-06  |   0.0 |  0.45
 Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.00072972 | 0.0012341  | 0.0015501  |   1.0 |  3.65
+Comm    | 1.1451e-05 | 4.4141e-05 | 5.7694e-05 |   0.0 |  5.19
-Output  | 0.0011293  | 0.0011806  | 0.0012922  |   0.2 |  3.49
+Output  | 9.6072e-05 | 0.00010517 | 0.00013106 |   0.0 | 12.36
-Modify  | 4.0541e-05 | 4.5677e-05 | 5.4304e-05 |   0.0 |  0.14
+Modify  | 1.799e-06  | 1.9772e-06 | 2.149e-06  |   0.0 |  0.23
-Other   |            | 0.0003717  |            |       |  1.10
+Other   |            | 8.507e-06  |            |       |  1.00
 
 Nlocal:            4.5 ave           6 max           3 min
 Histogram: 1 0 0 1 0 0 1 0 0 1