test scripts

examples/amoeba/Compare.sh

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

examples/amoeba/Test.sh

@@ -0,0 +1,66 @@
+# run test problems
+
+# dimer
+
+../../src/lmp_mpi < in.water_dimer.amoeba
+mv log.lammps log.water_dimer.amoeba.1.test
+mv dump.water_dimer dump.water_dimer.amoeba.1.test
+
+mpirun -np 4 ../../src/lmp_mpi < in.water_dimer.amoeba
+mv log.lammps log.water_dimer.amoeba.4.test
+mv dump.water_dimer dump.water_dimer.amoeba.4.test
+
+../../src/lmp_mpi < in.water_dimer.hippo
+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
+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
+mv log.lammps log.water_hexamer.amoeba.1.test
+mv dump.water_hexamer dump.water_hexamer.amoeba.1.test
+
+mpirun -np 4 ../../src/lmp_mpi < in.water_hexamer.amoeba
+mv log.lammps log.water_hexamer.amoeba.4.test
+mv dump.water_hexamer dump.water_hexamer.amoeba.4.test
+
+../../src/lmp_mpi < in.water_hexamer.hippo
+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
+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
+mv log.lammps log.water_box.amoeba.1.test
+mv dump.water_box dump.water_box.amoeba.1.test
+
+mpirun -np 32 ../../src/lmp_mpi < in.water_box.amoeba
+mv log.lammps log.water_box.amoeba.32.test
+mv dump.water_box dump.water_box.amoeba.32.test
+
+../../src/lmp_mpi < in.water_box.hippo
+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
+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
+mv log.lammps log.ubi.1.test
+mv dump.ubi dump.ubi.1.test
+
+mpirun -np 32 ../../src/lmp_mpi < in.ubiquitin
+mv log.lammps log.ubi.32.test
+mv dump.ubi dump.ubi.32.test
+

examples/amoeba/dump.water_dimer.amoeba.1

@@ -0,0 +1,165 @@
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+ITEM: NUMBER OF ATOMS
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+ITEM: BOX BOUNDS ss ss ss
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+-7.5570026690000003e-01 7.5527126690000002e-01
+-8.9995638999999985e-03 2.9352285639000000e+00
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+6 2 -1.46181 -0.755549 2.93493 6.40581 -4.05491 -1.70517
+ITEM: TIMESTEP
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+ITEM: NUMBER OF ATOMS
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+ITEM: NUMBER OF ATOMS
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+ITEM: NUMBER OF ATOMS
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+ITEM: NUMBER OF ATOMS
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+ITEM: NUMBER OF ATOMS
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+ITEM: NUMBER OF ATOMS
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examples/amoeba/dump.water_dimer.amoeba.4

@@ -0,0 +1,165 @@
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+ITEM: NUMBER OF ATOMS
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+ITEM: BOX BOUNDS ss ss ss
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+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
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+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
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+-7.5570026690000003e-01 7.5527126690000002e-01
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+ITEM: ATOMS id type x y z fx fy fz
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+2 2 -0.171607 -0.000594964 0.954009 -8.40692 -0.00484075 2.50346
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+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
+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
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+2 2 -0.230937 -0.000644481 0.949766 5.72493 0.00756591 4.36142
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+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
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+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
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examples/amoeba/dump.water_dimer.hippo.1

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examples/amoeba/dump.water_dimer.hippo.4

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examples/amoeba/dump.water_hexamer.amoeba.1

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examples/amoeba/dump.water_hexamer.hippo.1

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examples/amoeba/dump.water_hexamer.hippo.4

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+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

@@ -36,19 +36,21 @@ special_bonds   lj/coul 0.5 0.5 0.5 one/five yes
 
 # thermo output
 
-compute virial all pressure NULL virial
+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.ubi id type x y z fx fy fz
+dump_modify     1 sort id
+
 # zero step run
 
-dump            1 all custom 10 dump.ubi id type x y z fx fy fz
-run             0
+#run             0
 
 # dynamics
 
-#fix             1 all nve
+fix            1 all nve
 
-#thermo          10
-#run             100
+thermo         1
+run            10

examples/amoeba/in.water_box.amoeba

@@ -33,12 +33,16 @@ 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
 
-thermo          1
 fix             1 all nve
+
+thermo          10
 run             100

examples/amoeba/in.water_box.hippo

@@ -33,12 +33,16 @@ 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
 
-thermo          1
 fix             1 all nve
+
+thermo          10
 run             100

examples/amoeba/in.water_dimer.amoeba

@@ -33,12 +33,16 @@ 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_modify     1 sort id
+
 # zero step run
 
 #run             0
 
 # dynamics
 
-thermo          1
 fix             1 all nve
+
+thermo          10
 run             100

examples/amoeba/in.water_dimer.hippo

@@ -33,12 +33,16 @@ 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_modify     1 sort id
+
 # zero step run
 
 #run             0
 
 # dynamics
 
-thermo          1
 fix             1 all nve
+
+thermo          10
 run             100

examples/amoeba/in.water_hexamer.amoeba

@@ -33,12 +33,16 @@ 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_modify     1 sort id
+
 # zero step run
 
-run             0
+#run             0
 
 # dynamics
 
-#thermo          1
-#fix             1 all nve
-#run             100
+fix             1 all nve
+
+thermo          10
+run             100

examples/amoeba/in.water_hexamer.hippo

@@ -33,12 +33,16 @@ 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_modify     1 sort id
+
 # zero step run
 
-run             0
+#run             0
 
 # dynamics
 
-#thermo          1
-#fix             1 all nve
-#run             100
+fix             1 all nve
+
+thermo          10
+run             100

examples/amoeba/log.ubi.1

@@ -0,0 +1,162 @@
+LAMMPS (24 Mar 2022)
+# 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             pit all amoeba/pitorsion
+fix_modify      pit energy yes
+fix             bit all amoeba/bitorsion bitorsion.ubiquitin.data
+fix_modify      bit energy yes
+
+fix             extra all property/atom                 i_amgroup d_redID d_xaxis d_yaxis d_zaxis d_pval ghost yes
+fix             extra2 all property/atom i_polaxe
+
+#read_data       data.ubiquitin fix amtype NULL "Tinker Types"
+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 = 0.004 seconds
+  read_data CPU = 0.075 seconds
+
+pair_style      amoeba
+pair_coeff      * * amoeba_ubiquitin.prm amoeba_ubiquitin.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     
+     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 = 0.006 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.ubi 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            10
+AMOEBA/HIPPO 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/HIPPO group count: 3196
+Per MPI rank memory allocation (min/avg/max) = 98.55 | 98.55 | 98.55 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    
+         6   118.24373     -36092.77       1166.179       815.59206      213.67399      44.022297      2239.4673     -30435.629     -1677.8051     -3988.2428     -2669.6848     -3247.7207      197.42472      285.87129     -162.35459    
+         7   137.7204      -36521.444      782.87113      1026.745       212.04289      38.686259      2060.3452     -30479.082     -5987.83       -8386.8104     -7363.188      -7888.261       357.00835      253.66346      32.827786    
+         8   112.66452     -36897.181      1750.0569      1269.152       210.83571      33.742799      3263.7874     -30379.432     -7886.4081     -9703.2601     -9043.015      -9555.2908      490.76046      182.31259      278.727      
+         9   88.237359     -37209.906      2695.1766      1454.55        209.91331      29.503458      4389.1434     -30276.565     -8202.16       -9492.368      -9110.7037     -9639.2288      502.55699      107.82333      443.6705     
+
+AMEOBA/HIPPO timing info:
+  Init   time: 0.0257147 0.00113515
+  Hal    time: 7.6011 33.5542
+  Mpole  time: 2.25841 9.96952
+  Induce time: 8.18934 36.151
+  Polar  time: 4.5786 20.2117
+  Total  time: 22.6532
+
+        10   108.86756     -37474.988      2240.4603      1523.7936      209.10313      26.208515      3999.5656     -30333.279     -8468.4347     -9956.923      -9709.5874     -10224.682      365.98214      95.262991      425.12746    
+Loop time of 22.6992 on 1 procs for 10 steps with 9737 atoms
+
+Performance: 0.038 ns/day, 630.534 hours/ns, 0.441 timesteps/s
+98.8% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 22.653     | 22.653     | 22.653     |   0.0 | 99.80
+Bond    | 0.014323   | 0.014323   | 0.014323   |   0.0 |  0.06
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.0035064  | 0.0035064  | 0.0035064  |   0.0 |  0.02
+Output  | 0.024558   | 0.024558   | 0.024558   |   0.0 |  0.11
+Modify  | 0.002901   | 0.002901   | 0.002901   |   0.0 |  0.01
+Other   |            | 0.0006384  |            |       |  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: 0:00:25

examples/amoeba/log.ubi.32

@@ -0,0 +1,162 @@
+LAMMPS (24 Mar 2022)
+# 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             pit all amoeba/pitorsion
+fix_modify      pit energy yes
+fix             bit all amoeba/bitorsion bitorsion.ubiquitin.data
+fix_modify      bit energy yes
+
+fix             extra all property/atom                 i_amgroup d_redID d_xaxis d_yaxis d_zaxis d_pval ghost yes
+fix             extra2 all property/atom i_polaxe
+
+#read_data       data.ubiquitin fix amtype NULL "Tinker Types"
+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)
+  4 by 2 by 4 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 = 0.002 seconds
+  read_data CPU = 0.125 seconds
+
+pair_style      amoeba
+pair_coeff      * * amoeba_ubiquitin.prm amoeba_ubiquitin.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     
+     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 = 0.002 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.ubi 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            10
+AMOEBA/HIPPO 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/HIPPO group count: 3196
+Per MPI rank memory allocation (min/avg/max) = 26.19 | 26.49 | 27.59 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    
+         6   118.24373     -36092.77       1166.179       815.59206      213.67399      44.022297      2239.4673     -30435.629     -1677.8051     -3988.2428     -2669.6848     -3247.7207      197.42472      285.87129     -162.35459    
+         7   137.7204      -36521.444      782.87113      1026.745       212.04289      38.686259      2060.3452     -30479.082     -5987.83       -8386.8104     -7363.188      -7888.261       357.00835      253.66346      32.827786    
+         8   112.66452     -36897.181      1750.0569      1269.152       210.83571      33.742799      3263.7874     -30379.432     -7886.4081     -9703.2601     -9043.015      -9555.2908      490.76046      182.31259      278.727      
+         9   88.237359     -37209.906      2695.1766      1454.55        209.91331      29.503458      4389.1434     -30276.565     -8202.16       -9492.368      -9110.7037     -9639.2288      502.55699      107.82333      443.6705     
+
+AMEOBA/HIPPO timing info:
+  Init   time: 0.0350369 0.0194083
+  Hal    time: 0.274414 15.2009
+  Mpole  time: 0.209885 11.6263
+  Induce time: 1.00414 55.6234
+  Polar  time: 0.281769 15.6083
+  Total  time: 1.80525
+
+        10   108.86756     -37474.988      2240.4603      1523.7936      209.10313      26.208515      3999.5656     -30333.279     -8468.4347     -9956.923      -9709.5874     -10224.682      365.98214      95.262991      425.12746    
+Loop time of 1.82311 on 32 procs for 10 steps with 9737 atoms
+
+Performance: 0.474 ns/day, 50.642 hours/ns, 5.485 timesteps/s
+99.1% CPU use with 32 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 1.805      | 1.8057     | 1.8065     |   0.0 | 99.05
+Bond    | 0.00027    | 0.00076775 | 0.0023491  |   0.0 |  0.04
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.0098412  | 0.011853   | 0.013048   |   0.8 |  0.65
+Output  | 0.0038478  | 0.0041268  | 0.0045236  |   0.2 |  0.23
+Modify  | 0.00019451 | 0.00034384 | 0.00063207 |   0.0 |  0.02
+Other   |            | 0.0003186  |            |       |  0.02
+
+Nlocal:        304.281 ave         326 max         273 min
+Histogram: 1 1 0 5 2 8 3 6 4 2
+Nghost:        7618.59 ave        7678 max        7545 min
+Histogram: 1 1 4 4 5 5 2 2 4 4
+Neighs:         176228 ave      204476 max      149390 min
+Histogram: 3 3 3 2 6 2 5 4 2 2
+
+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.water_box.amoeba.1

@@ -0,0 +1,149 @@
+LAMMPS (24 Mar 2022)
+# 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_xaxis d_yaxis d_zaxis d_pval ghost yes
+fix             extra2 all property/atom i_polaxe
+
+# 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 = 0.011 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 = 0.001 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.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/HIPPO force field settings
+  hal: cut 7 taper 6 vscale 0 0 1 1
+  multipole: cut 7 aewald 0.4 bsorder 5 FFT 50 50 50 mscale 0 0 0.4 1
+  polar: cut 7 aewald 0.5 bsorder 5 FFT 50 50 50
+         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/HIPPO group count: 216
+Per MPI rank memory allocation (min/avg/max) = 10.9 | 10.9 | 10.9 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             -2172.0441      166.82637      83.732524      0              0              250.5589      -1921.4852     -6181.7112     -4771.8292     -6955.3278     -6817.9765     -272.19746      3173.3487      2229.6526    
+        10   105.50439     -2373.6865      136.67908      106.86552      0              0              243.54459     -1926.6678     -8441.2174     -10450.318     -9514.124      -9665.625      -301.45304      322.2435       1916.9694    
+        20   143.90097     -2358.3516      70.951764      76.777106      0              0              147.72887     -1933.0976     -7370.463      -7728.4884     -11580.562     -8676.0017     -807.21546      780.4123       2096.7667    
+        30   157.22768     -2375.4639      50.396281      87.108719      0              0              137.505       -1934.7321     -4449.9504     -6946.5881     -7865.3435     -4955.5443     -417.85139     -1004.0926     -36.630383    
+        40   150.92709     -2354.1768      78.484257      53.799494      0              0              132.28375     -1930.8175      353.40845     -939.7978      -4636.1858      475.75837     -1074.4762     -1584.304      -574.27211    
+        50   153.02614     -2388.7287      100.20124      65.814409      0              0              166.01565     -1927.5893      3975.1595      1366.008       426.2343       3887.1078     -1807.1658     -2534.8393     -2118.6912    
+        60   155.01798     -2364.31        92.948309      44.252938      0              0              137.20125     -1928.1435      5793.7978      3521.2541      1421.9416      6110.7678     -1536.937      -2559.5674     -1502.2038    
+        70   166.70629     -2383.4827      76.492455      55.020922      0              0              131.51338     -1930.4622      4743.9587      1916.6786      2839.9241      2670.7568     -169.67855     -187.58379     -2256.4529    
+        80   171.82933     -2388.0347      76.463333      49.138785      0              0              125.60212     -1931.0453      2210.1222     -319.99043      330.98785     -394.25628     -44.858027      252.35533     -1985.0908    
+        90   175.7327      -2423.7974      90.784969      63.725029      0              0              154.51        -1930.3722     -917.58179     -3941.9566     -2568.4278     -3415.3121      196.38051      2366.2885     -263.52434    
+
+AMEOBA/HIPPO timing info:
+  Init   time: 0.0251099 0.000637177
+  Hal    time: 0.924614 2.34626
+  Mpole  time: 2.51306 6.37702
+  Induce time: 29.8839 75.8319
+  Polar  time: 6.06136 15.381
+  Total  time: 39.408
+
+       100   173.73319     -2422.3616      99.761403      57.29505       0              0              157.05645     -1930.2461     -3586.4169     -5733.9943     -5881.4025     -6235.1905     -230.75166      959.02899      406.2349     
+Loop time of 39.4372 on 1 procs for 100 steps with 648 atoms
+
+Performance: 0.219 ns/day, 109.548 hours/ns, 2.536 timesteps/s
+99.6% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 39.408     | 39.408     | 39.408     |   0.0 | 99.93
+Bond    | 0.0033709  | 0.0033709  | 0.0033709  |   0.0 |  0.01
+Neigh   | 0.0054251  | 0.0054251  | 0.0054251  |   0.0 |  0.01
+Comm    | 0.0035919  | 0.0035919  | 0.0035919  |   0.0 |  0.01
+Output  | 0.014523   | 0.014523   | 0.014523   |   0.0 |  0.04
+Modify  | 0.00095298 | 0.00095298 | 0.00095298 |   0.0 |  0.00
+Other   |            | 0.001005   |            |       |  0.00
+
+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:          98543 ave       98543 max       98543 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 98543
+Ave neighs/atom = 152.07253
+Ave special neighs/atom = 2
+Neighbor list builds = 2
+Dangerous builds = 0
+Total wall time: 0:00:40

examples/amoeba/log.water_box.amoeba.32

@@ -0,0 +1,149 @@
+LAMMPS (24 Mar 2022)
+# 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_xaxis d_yaxis d_zaxis d_pval ghost yes
+fix             extra2 all property/atom i_polaxe
+
+# 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)
+  2 by 4 by 4 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 = 0.002 seconds
+  read_data CPU = 0.027 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 = 0.002 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/HIPPO force field settings
+  hal: cut 7 taper 6 vscale 0 0 1 1
+  multipole: cut 7 aewald 0.4 bsorder 5 FFT 50 50 50 mscale 0 0 0.4 1
+  polar: cut 7 aewald 0.5 bsorder 5 FFT 50 50 50
+         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/HIPPO group count: 216
+Per MPI rank memory allocation (min/avg/max) = 10.07 | 10.08 | 10.34 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             -2172.0441      166.82637      83.732524      0              0              250.5589      -1921.4852     -6181.7112     -4771.8292     -6955.3278     -6817.9765     -272.19746      3173.3487      2229.6526    
+        10   105.50439     -2373.6865      136.67908      106.86552      0              0              243.54459     -1926.6678     -8441.2174     -10450.318     -9514.124      -9665.625      -301.45304      322.2435       1916.9694    
+        20   143.90097     -2358.3516      70.951764      76.777106      0              0              147.72887     -1933.0976     -7370.463      -7728.4884     -11580.562     -8676.0017     -807.21546      780.4123       2096.7667    
+        30   157.22768     -2375.4639      50.396281      87.108719      0              0              137.505       -1934.7321     -4449.9504     -6946.5881     -7865.3435     -4955.5443     -417.85139     -1004.0926     -36.630383    
+        40   150.92709     -2354.1768      78.484257      53.799494      0              0              132.28375     -1930.8175      353.40845     -939.7978      -4636.1858      475.75837     -1074.4762     -1584.304      -574.27211    
+        50   153.02614     -2388.7287      100.20124      65.814409      0              0              166.01565     -1927.5893      3975.1595      1366.008       426.2343       3887.1078     -1807.1658     -2534.8393     -2118.6912    
+        60   155.01798     -2364.31        92.948309      44.252938      0              0              137.20125     -1928.1435      5793.7978      3521.2541      1421.9416      6110.7678     -1536.937      -2559.5674     -1502.2038    
+        70   166.70629     -2383.4827      76.492455      55.020922      0              0              131.51338     -1930.4622      4743.9587      1916.6786      2839.9241      2670.7568     -169.67855     -187.58379     -2256.4529    
+        80   171.82933     -2388.0347      76.463333      49.138785      0              0              125.60212     -1931.0453      2210.1222     -319.99043      330.98785     -394.25628     -44.858027      252.35533     -1985.0908    
+        90   175.7327      -2423.7974      90.784969      63.725029      0              0              154.51        -1930.3722     -917.58179     -3941.9566     -2568.4278     -3415.3121      196.38051      2366.2885     -263.52434    
+
+AMEOBA/HIPPO timing info:
+  Init   time: 0.0525488 0.00776173
+  Hal    time: 0.037136 0.548518
+  Mpole  time: 0.586998 8.67026
+  Induce time: 5.01628 74.093
+  Polar  time: 1.07725 15.9116
+  Total  time: 6.77025
+
+       100   173.73319     -2422.3616      99.761403      57.29505       0              0              157.05645     -1930.2461     -3586.4169     -5733.9943     -5881.4025     -6235.1905     -230.75166      959.02899      406.2349     
+Loop time of 6.80378 on 32 procs for 100 steps with 648 atoms
+
+Performance: 1.270 ns/day, 18.899 hours/ns, 14.698 timesteps/s
+99.7% CPU use with 32 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 6.7643     | 6.7717     | 6.779      |   0.2 | 99.53
+Bond    | 0.00031311 | 0.00044449 | 0.00060974 |   0.0 |  0.01
+Neigh   | 0.00039627 | 0.00047385 | 0.00058355 |   0.0 |  0.01
+Comm    | 0.018079   | 0.025388   | 0.03285    |   2.6 |  0.37
+Output  | 0.0036767  | 0.0037103  | 0.0039596  |   0.1 |  0.05
+Modify  | 0.00040095 | 0.00049993 | 0.00061333 |   0.0 |  0.01
+Other   |            | 0.001545   |            |       |  0.02
+
+Nlocal:          20.25 ave          26 max          12 min
+Histogram: 1 1 3 1 2 7 3 11 1 2
+Nghost:        1381.97 ave        1413 max        1354 min
+Histogram: 3 5 4 0 6 3 1 4 5 1
+Neighs:        3079.47 ave        4080 max        1858 min
+Histogram: 1 3 1 2 5 6 7 5 0 2
+
+Total # of neighbors = 98543
+Ave neighs/atom = 152.07253
+Ave special neighs/atom = 2
+Neighbor list builds = 2
+Dangerous builds = 0
+Total wall time: 0:00:06

examples/amoeba/log.water_box.hippo.1

@@ -0,0 +1,153 @@
+LAMMPS (24 Mar 2022)
+# 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_xaxis d_yaxis d_zaxis d_pval ghost yes
+fix             extra2 all property/atom i_polaxe
+
+# 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 = 0.010 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 = 0.001 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.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/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
+  AMOEBA/HIPPO group count: 216
+Per MPI rank memory allocation (min/avg/max) = 10.89 | 10.89 | 10.89 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    
+        10   100.94691     -2350.192       116.13156      88.56605       0              0              204.69761     -1950.8098     -11480.919     -13574.139     -12190.797     -12798.212     -263.77028      280.62864      1974.1486    
+        20   153.91622     -2358.3058      36.396961      66.22466       0              0              102.62162     -1958.8438     -7778.4529     -8492.3868     -11999.431     -9125.9998     -917.99962      589.09064      1788.2094    
+        30   145.5951      -2343.9956      39.651541      65.833248      0              0              105.48479     -1957.7184     -288.79965     -2574.4466     -3820.4824     -414.28285     -347.51491     -1147.3995     -126.71025    
+        40   126.87801     -2340.2623      102.93951      43.896946      0              0              146.83646     -1948.7309      6766.15        5908.7048      1280.0961      7930.8191     -1085.6811     -1596.6859     -714.82888    
+        50   134.52078     -2358.9232      107.49288      44.253826      0              0              151.74671     -1947.7419      8762.4348      6023.4661      5377.0189      9396.0316     -1629.1364     -1663.1666     -2381.51      
+        60   173.10181     -2374.3854      51.097314      33.03646       0              0              84.133774     -1956.4102      4614.2907      1719.1989      505.79149      4552.3167     -1661.1714     -587.92108     -1380.6732    
+        70   184.86849     -2391.6106      39.916931      35.978152      0              0              75.895083     -1959.1811     -2146.9339     -4993.4021     -4095.6729     -4897.5768     -833.09046      1542.411      -1539.5266    
+        80   164.75795     -2406.3017      101.94229      33.067832      0              0              135.01013     -1953.542      -8779.3265     -10545.409     -10418.702     -12098.858     -1319.194       1750.3511     -275.1272     
+        90   151.17491     -2434.6876      152.21826      41.301673      0              0              193.51993     -1949.6141     -13330.691     -15436.505     -13791.461     -16934.674      149.25497      2289.1026      976.14333    
+
+AMEOBA/HIPPO timing info:
+  Init   time: 0.0130348 0.00133126
+  Repls  time: 1.10221 11.257
+  Disp   time: 0.909199 9.28573
+  Mpole  time: 1.75286 17.9021
+  Induce time: 3.46637 35.4024
+  Polar  time: 2.22081 22.6813
+  Qxfer  time: 0.326863 3.33828
+  Total  time: 9.79136
+
+       100   166.99163     -2452.5298      143.57768      35.341459      0              0              178.91914     -1951.5533     -14918.51      -16077.49      -17353.738     -18140.466      19.009088      1487.0469      1084.0231    
+Loop time of 9.81706 on 1 procs for 100 steps with 648 atoms
+
+Performance: 0.880 ns/day, 27.270 hours/ns, 10.186 timesteps/s
+98.8% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 9.7915     | 9.7915     | 9.7915     |   0.0 | 99.74
+Bond    | 0.0024566  | 0.0024566  | 0.0024566  |   0.0 |  0.03
+Neigh   | 0.0056616  | 0.0056616  | 0.0056616  |   0.0 |  0.06
+Comm    | 0.0022387  | 0.0022387  | 0.0022387  |   0.0 |  0.02
+Output  | 0.013878   | 0.013878   | 0.013878   |   0.0 |  0.14
+Modify  | 0.00062189 | 0.00062189 | 0.00062189 |   0.0 |  0.01
+Other   |            | 0.0007035  |            |       |  0.01
+
+Nlocal:            648 ave         648 max         648 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:           4282 ave        4282 max        4282 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:          98490 ave       98490 max       98490 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 98490
+Ave neighs/atom = 151.99074
+Ave special neighs/atom = 2
+Neighbor list builds = 2
+Dangerous builds = 0
+Total wall time: 0:00:10

examples/amoeba/log.water_box.hippo.32

@@ -0,0 +1,153 @@
+LAMMPS (24 Mar 2022)
+# 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_xaxis d_yaxis d_zaxis d_pval ghost yes
+fix             extra2 all property/atom i_polaxe
+
+# 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)
+  2 by 4 by 4 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 = 0.002 seconds
+  read_data CPU = 0.027 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 = 0.002 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/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
+  AMOEBA/HIPPO group count: 216
+Per MPI rank memory allocation (min/avg/max) = 10.07 | 10.08 | 10.34 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    
+        10   100.94691     -2350.192       116.13156      88.56605       0              0              204.69761     -1950.8098     -11480.919     -13574.139     -12190.797     -12798.212     -263.77028      280.62864      1974.1486    
+        20   153.91622     -2358.3058      36.396961      66.22466       0              0              102.62162     -1958.8438     -7778.4529     -8492.3868     -11999.431     -9125.9998     -917.99962      589.09064      1788.2094    
+        30   145.5951      -2343.9956      39.651541      65.833248      0              0              105.48479     -1957.7184     -288.79965     -2574.4466     -3820.4824     -414.28285     -347.51491     -1147.3995     -126.71025    
+        40   126.87801     -2340.2623      102.93951      43.896946      0              0              146.83646     -1948.7309      6766.15        5908.7048      1280.0961      7930.8191     -1085.6811     -1596.6859     -714.82888    
+        50   134.52078     -2358.9232      107.49288      44.253826      0              0              151.74671     -1947.7419      8762.4348      6023.4661      5377.0189      9396.0316     -1629.1364     -1663.1666     -2381.51      
+        60   173.10181     -2374.3854      51.097314      33.03646       0              0              84.133774     -1956.4102      4614.2907      1719.1989      505.79149      4552.3167     -1661.1714     -587.92108     -1380.6732    
+        70   184.86849     -2391.6106      39.916931      35.978152      0              0              75.895083     -1959.1811     -2146.9339     -4993.4021     -4095.6729     -4897.5768     -833.09046      1542.411      -1539.5266    
+        80   164.75795     -2406.3017      101.94229      33.067832      0              0              135.01013     -1953.542      -8779.3265     -10545.409     -10418.702     -12098.858     -1319.194       1750.3511     -275.1272     
+        90   151.17491     -2434.6876      152.21826      41.301673      0              0              193.51993     -1949.6141     -13330.691     -15436.505     -13791.461     -16934.674      149.25497      2289.1026      976.14333    
+
+AMEOBA/HIPPO timing info:
+  Init   time: 0.0225211 0.0138448
+  Repls  time: 0.0710727 4.36919
+  Disp   time: 0.147228 9.05085
+  Mpole  time: 0.271419 16.6855
+  Induce time: 0.760323 46.7408
+  Polar  time: 0.341361 20.9851
+  Qxfer  time: 0.0127489 0.783737
+  Total  time: 1.62668
+
+       100   166.99163     -2452.5298      143.57768      35.341459      0              0              178.91914     -1951.5533     -14918.51      -16077.49      -17353.738     -18140.466      19.009088      1487.0469      1084.0231    
+Loop time of 1.65072 on 32 procs for 100 steps with 648 atoms
+
+Performance: 5.234 ns/day, 4.585 hours/ns, 60.579 timesteps/s
+99.7% CPU use with 32 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 1.6233     | 1.6277     | 1.632      |   0.2 | 98.61
+Bond    | 0.0001841  | 0.00025145 | 0.00041274 |   0.0 |  0.02
+Neigh   | 0.00046301 | 0.00052361 | 0.00059181 |   0.0 |  0.03
+Comm    | 0.013032   | 0.017446   | 0.021961   |   1.7 |  1.06
+Output  | 0.0035779  | 0.0036051  | 0.0038143  |   0.1 |  0.22
+Modify  | 0.00011362 | 0.00018386 | 0.0002631  |   0.0 |  0.01
+Other   |            | 0.0009717  |            |       |  0.06
+
+Nlocal:          20.25 ave          27 max          12 min
+Histogram: 1 1 3 1 6 2 10 4 2 2
+Nghost:        1379.75 ave        1408 max        1345 min
+Histogram: 2 4 1 3 3 4 4 3 2 6
+Neighs:        3077.81 ave        4233 max        1858 min
+Histogram: 1 3 1 4 5 7 6 2 1 2
+
+Total # of neighbors = 98490
+Ave neighs/atom = 151.99074
+Ave special neighs/atom = 2
+Neighbor list builds = 2
+Dangerous builds = 0
+Total wall time: 0:00:01

examples/amoeba/log.water_dimer.amoeba.1

@@ -0,0 +1,150 @@
+LAMMPS (24 Mar 2022)
+# water dimer with AMOEBA or HIPPO
+
+units           real
+boundary        s s s
+
+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_xaxis d_yaxis d_zaxis d_pval ghost yes
+fix             extra2 all property/atom i_polaxe
+
+# read data file
+
+read_data       data.water_dimer.amoeba fix amtype NULL "Tinker Types"
+Reading data file ...
+  orthogonal box = (-1.463996 -0.756549 -0.009705) to (0.933234 0.75612 2.935934)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  6 atoms
+  scanning bonds ...
+  2 = max bonds/atom
+  scanning angles ...
+  1 = max angles/atom
+  reading bonds ...
+  4 bonds
+  reading angles ...
+  2 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      amoeba
+pair_coeff      * * amoeba_water.prm amoeba_water.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_dimer 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/HIPPO 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
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 12
+  ghost atom cutoff = 12
+  binsize = 6, bins = 1 1 1
+  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
+WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:974)
+  AMOEBA/HIPPO group count: 2
+Per MPI rank memory allocation (min/avg/max) = 9.855 | 9.855 | 9.855 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    
+        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    
+        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    
+        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    
+        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    
+        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     
+        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    
+
+AMEOBA/HIPPO timing info:
+  Init   time: 0.000126119 0.0205557
+  Hal    time: 0.000487693 7.94875
+  Mpole  time: 0.00066233 10.7951
+  Induce time: 0.00328101 53.4761
+  Polar  time: 0.0015627 25.4699
+  Total  time: 0.00613547
+
+       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 0.00720187 on 1 procs for 100 steps with 6 atoms
+
+Performance: 1199.688 ns/day, 0.020 hours/ns, 13885.283 timesteps/s
+83.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.0062208  | 0.0062208  | 0.0062208  |   0.0 | 86.38
+Bond    | 0.00010381 | 0.00010381 | 0.00010381 |   0.0 |  1.44
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 1.4955e-05 | 1.4955e-05 | 1.4955e-05 |   0.0 |  0.21
+Output  | 0.00075216 | 0.00075216 | 0.00075216 |   0.0 | 10.44
+Modify  | 4.5409e-05 | 4.5409e-05 | 4.5409e-05 |   0.0 |  0.63
+Other   |            | 6.472e-05  |            |       |  0.90
+
+Nlocal:              6 ave           6 max           6 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:             15 ave          15 max          15 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 15
+Ave neighs/atom = 2.5
+Ave special neighs/atom = 2
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:00

examples/amoeba/log.water_dimer.amoeba.4

@@ -0,0 +1,150 @@
+LAMMPS (24 Mar 2022)
+# water dimer with AMOEBA or HIPPO
+
+units           real
+boundary        s s s
+
+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_xaxis d_yaxis d_zaxis d_pval ghost yes
+fix             extra2 all property/atom i_polaxe
+
+# read data file
+
+read_data       data.water_dimer.amoeba fix amtype NULL "Tinker Types"
+Reading data file ...
+  orthogonal box = (-1.463996 -0.756549 -0.009705) to (0.933234 0.75612 2.935934)
+  2 by 1 by 2 MPI processor grid
+  reading atoms ...
+  6 atoms
+  scanning bonds ...
+  2 = max bonds/atom
+  scanning angles ...
+  1 = max angles/atom
+  reading bonds ...
+  4 bonds
+  reading angles ...
+  2 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 = 0.009 seconds
+
+# force field
+
+pair_style      amoeba
+pair_coeff      * * amoeba_water.prm amoeba_water.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 = 0.001 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.water_dimer 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/HIPPO 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
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 12
+  ghost atom cutoff = 12
+  binsize = 6, bins = 1 1 1
+  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
+WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:974)
+  AMOEBA/HIPPO group count: 2
+Per MPI rank memory allocation (min/avg/max) = 9.883 | 10.02 | 10.15 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    
+        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    
+        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    
+        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    
+        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    
+        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     
+        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    
+
+AMEOBA/HIPPO timing info:
+  Init   time: 0.000562834 0.0392455
+  Hal    time: 0.000119032 0.829992
+  Mpole  time: 0.000759989 5.29928
+  Induce time: 0.0118027 82.2984
+  Polar  time: 0.00108262 7.54891
+  Total  time: 0.0143414
+
+       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 0.0169266 on 4 procs for 100 steps with 6 atoms
+
+Performance: 510.439 ns/day, 0.047 hours/ns, 5907.863 timesteps/s
+99.7% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.014229   | 0.01457    | 0.014803   |   0.2 | 86.08
+Bond    | 1.311e-05  | 4.1295e-05 | 6.8411e-05 |   0.0 |  0.24
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.00067827 | 0.0008315  | 0.0011965  |   0.0 |  4.91
+Output  | 0.00094515 | 0.0010124  | 0.0011247  |   0.2 |  5.98
+Modify  | 2.1384e-05 | 4.0305e-05 | 5.4006e-05 |   0.0 |  0.24
+Other   |            | 0.0004309  |            |       |  2.55
+
+Nlocal:            1.5 ave           3 max           0 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost:            4.5 ave           6 max           3 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs:           3.75 ave          12 max           0 min
+Histogram: 2 0 1 0 0 0 0 0 0 1
+
+Total # of neighbors = 15
+Ave neighs/atom = 2.5
+Ave special neighs/atom = 2
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:00

examples/amoeba/log.water_dimer.hippo.1

@@ -0,0 +1,154 @@
+LAMMPS (24 Mar 2022)
+# water dimer with AMOEBA or HIPPO
+
+units           real
+boundary        s s s
+
+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_xaxis d_yaxis d_zaxis d_pval ghost yes
+fix             extra2 all property/atom i_polaxe
+
+# read data file
+
+read_data       data.water_dimer.hippo fix amtype NULL "Tinker Types"
+Reading data file ...
+  orthogonal box = (-1.463996 -0.756549 -0.009705) to (0.933234 0.75612 2.935934)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  6 atoms
+  scanning bonds ...
+  2 = max bonds/atom
+  scanning angles ...
+  1 = max angles/atom
+  reading bonds ...
+  4 bonds
+  reading angles ...
+  2 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.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_dimer 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/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
+  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 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 = 12
+  ghost atom cutoff = 12
+  binsize = 6, bins = 1 1 1
+  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
+WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:974)
+  AMOEBA/HIPPO group count: 2
+Per MPI rank memory allocation (min/avg/max) = 9.855 | 9.855 | 9.855 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    
+        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     
+        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    
+        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    
+        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    
+        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     
+        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    
+
+AMEOBA/HIPPO timing info:
+  Init   time: 0.000114914 0.0215289
+  Repls  time: 0.000617533 11.5693
+  Disp   time: 0.000365952 6.85603
+  Mpole  time: 0.000944495 17.6949
+  Induce time: 0.00199722 37.4176
+  Polar  time: 0.0011473 21.4944
+  Qxfer  time: 0.000145366 2.7234
+  Total  time: 0.00533767
+
+       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 0.0063791 on 1 procs for 100 steps with 6 atoms
+
+Performance: 1354.423 ns/day, 0.018 hours/ns, 15676.190 timesteps/s
+98.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.005435   | 0.005435   | 0.005435   |   0.0 | 85.20
+Bond    | 8.7439e-05 | 8.7439e-05 | 8.7439e-05 |   0.0 |  1.37
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 1.447e-05  | 1.447e-05  | 1.447e-05  |   0.0 |  0.23
+Output  | 0.00073302 | 0.00073302 | 0.00073302 |   0.0 | 11.49
+Modify  | 4.6662e-05 | 4.6662e-05 | 4.6662e-05 |   0.0 |  0.73
+Other   |            | 6.248e-05  |            |       |  0.98
+
+Nlocal:              6 ave           6 max           6 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:             15 ave          15 max          15 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 15
+Ave neighs/atom = 2.5
+Ave special neighs/atom = 2
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:00

examples/amoeba/log.water_dimer.hippo.4

@@ -0,0 +1,154 @@
+LAMMPS (24 Mar 2022)
+# water dimer with AMOEBA or HIPPO
+
+units           real
+boundary        s s s
+
+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_xaxis d_yaxis d_zaxis d_pval ghost yes
+fix             extra2 all property/atom i_polaxe
+
+# read data file
+
+read_data       data.water_dimer.hippo fix amtype NULL "Tinker Types"
+Reading data file ...
+  orthogonal box = (-1.463996 -0.756549 -0.009705) to (0.933234 0.75612 2.935934)
+  2 by 1 by 2 MPI processor grid
+  reading atoms ...
+  6 atoms
+  scanning bonds ...
+  2 = max bonds/atom
+  scanning angles ...
+  1 = max angles/atom
+  reading bonds ...
+  4 bonds
+  reading angles ...
+  2 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 = 0.009 seconds
+
+# force field
+
+pair_style      hippo
+pair_coeff      * * hippo_water.prm hippo_water.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 = 0.001 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.water_dimer 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/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
+  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 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 = 12
+  ghost atom cutoff = 12
+  binsize = 6, bins = 1 1 1
+  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
+WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:974)
+  AMOEBA/HIPPO group count: 2
+Per MPI rank memory allocation (min/avg/max) = 9.883 | 10.02 | 10.15 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    
+        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     
+        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    
+        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    
+        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    
+        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     
+        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    
+
+AMEOBA/HIPPO timing info:
+  Init   time: 0.000628997 0.0480375
+  Repls  time: 0.000859377 6.5632
+  Disp   time: 0.00015718 1.20041
+  Mpole  time: 0.00153385 11.7143
+  Induce time: 0.0085554 65.339
+  Polar  time: 0.00127985 9.77439
+  Qxfer  time: 7.40915e-05 0.565849
+  Total  time: 0.0130939
+
+       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 0.0163786 on 4 procs for 100 steps with 6 atoms
+
+Performance: 527.519 ns/day, 0.045 hours/ns, 6105.545 timesteps/s
+98.7% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.012747   | 0.013356   | 0.013763   |   0.3 | 81.55
+Bond    | 1.4562e-05 | 5.3301e-05 | 0.00010757 |   0.0 |  0.33
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.00061214 | 0.001076   | 0.0015518  |   1.0 |  6.57
+Output  | 0.0011991  | 0.0013282  | 0.0015124  |   0.3 |  8.11
+Modify  | 2.2511e-05 | 3.8778e-05 | 5.1854e-05 |   0.0 |  0.24
+Other   |            | 0.0005259  |            |       |  3.21
+
+Nlocal:            1.5 ave           3 max           0 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost:            4.5 ave           6 max           3 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs:           3.75 ave          12 max           0 min
+Histogram: 2 0 1 0 0 0 0 0 0 1
+
+Total # of neighbors = 15
+Ave neighs/atom = 2.5
+Ave special neighs/atom = 2
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:00

examples/amoeba/log.water_hexamer.amoeba.1

@@ -0,0 +1,149 @@
+LAMMPS (24 Mar 2022)
+# water hexamer with AMOEBA or HIPPO
+
+units           real
+boundary        s s s
+
+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_xaxis d_yaxis d_zaxis d_pval ghost yes
+fix             extra2 all property/atom i_polaxe
+
+# read data file
+
+read_data       data.water_hexamer.amoeba fix amtype NULL "Tinker Types"
+Reading data file ...
+  orthogonal box = (-2.517835 -1.523041 -1.734766) to (2.675716 2.01883 2.220847)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  18 atoms
+  scanning bonds ...
+  2 = max bonds/atom
+  scanning angles ...
+  1 = max angles/atom
+  reading bonds ...
+  12 bonds
+  reading angles ...
+  6 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      amoeba
+pair_coeff      * * amoeba_water.prm amoeba_water.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_hexamer 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/HIPPO 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
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 12
+  ghost atom cutoff = 12
+  binsize = 6, bins = 1 1 1
+  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/HIPPO group count: 6
+Per MPI rank memory allocation (min/avg/max) = 9.804 | 9.804 | 9.804 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     
+        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     
+        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    
+        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    
+        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     
+        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    
+        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     
+
+AMEOBA/HIPPO timing info:
+  Init   time: 0.000298703 0.00766228
+  Hal    time: 0.00477252 12.2424
+  Mpole  time: 0.00429886 11.0274
+  Induce time: 0.0189419 48.5895
+  Polar  time: 0.0106573 27.338
+  Total  time: 0.0389836
+
+       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 0.0403763 on 1 procs for 100 steps with 18 atoms
+
+Performance: 213.987 ns/day, 0.112 hours/ns, 2476.699 timesteps/s
+96.9% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.039062   | 0.039062   | 0.039062   |   0.0 | 96.74
+Bond    | 0.00018661 | 0.00018661 | 0.00018661 |   0.0 |  0.46
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 1.665e-05  | 1.665e-05  | 1.665e-05  |   0.0 |  0.04
+Output  | 0.0009741  | 0.0009741  | 0.0009741  |   0.0 |  2.41
+Modify  | 6.7026e-05 | 6.7026e-05 | 6.7026e-05 |   0.0 |  0.17
+Other   |            | 7.005e-05  |            |       |  0.17
+
+Nlocal:             18 ave          18 max          18 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:            153 ave         153 max         153 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 153
+Ave neighs/atom = 8.5
+Ave special neighs/atom = 2
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:00

examples/amoeba/log.water_hexamer.amoeba.4

@@ -0,0 +1,150 @@
+LAMMPS (24 Mar 2022)
+# water hexamer with AMOEBA or HIPPO
+
+units           real
+boundary        s s s
+
+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_xaxis d_yaxis d_zaxis d_pval ghost yes
+fix             extra2 all property/atom i_polaxe
+
+# read data file
+
+read_data       data.water_hexamer.amoeba fix amtype NULL "Tinker Types"
+Reading data file ...
+  orthogonal box = (-2.517835 -1.523041 -1.734766) to (2.675716 2.01883 2.220847)
+  2 by 1 by 2 MPI processor grid
+  reading atoms ...
+  18 atoms
+  scanning bonds ...
+  2 = max bonds/atom
+  scanning angles ...
+  1 = max angles/atom
+  reading bonds ...
+  12 bonds
+  reading angles ...
+  6 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 = 0.001 seconds
+  read_data CPU = 0.009 seconds
+
+# force field
+
+pair_style      amoeba
+pair_coeff      * * amoeba_water.prm amoeba_water.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 = 0.001 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.water_hexamer 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/HIPPO 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
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 12
+  ghost atom cutoff = 12
+  binsize = 6, bins = 1 1 1
+  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
+WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:974)
+  AMOEBA/HIPPO group count: 6
+Per MPI rank memory allocation (min/avg/max) = 9.833 | 9.833 | 9.833 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     
+        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     
+        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    
+        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    
+        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     
+        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    
+        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     
+
+AMEOBA/HIPPO timing info:
+  Init   time: 0.000875735 0.0198199
+  Hal    time: 0.00136658 3.09288
+  Mpole  time: 0.0042176 9.5454
+  Induce time: 0.0311498 70.4992
+  Polar  time: 0.00655957 14.8458
+  Total  time: 0.0441847
+
+       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 0.0471312 on 4 procs for 100 steps with 18 atoms
+
+Performance: 183.318 ns/day, 0.131 hours/ns, 2121.739 timesteps/s
+98.9% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.044346   | 0.044424   | 0.044557   |   0.0 | 94.26
+Bond    | 9.3929e-05 | 0.00010313 | 0.00011252 |   0.0 |  0.22
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.00071684 | 0.00091755 | 0.0010385  |   0.0 |  1.95
+Output  | 0.0011333  | 0.0012027  | 0.0013253  |   0.2 |  2.55
+Modify  | 4.2618e-05 | 5.1978e-05 | 6.2018e-05 |   0.0 |  0.11
+Other   |            | 0.0004322  |            |       |  0.92
+
+Nlocal:            4.5 ave           6 max           3 min
+Histogram: 1 0 0 1 0 0 1 0 0 1
+Nghost:           13.5 ave          15 max          12 min
+Histogram: 1 0 0 1 0 0 1 0 0 1
+Neighs:          38.25 ave          77 max           9 min
+Histogram: 2 0 0 0 0 0 1 0 0 1
+
+Total # of neighbors = 153
+Ave neighs/atom = 8.5
+Ave special neighs/atom = 2
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:00

examples/amoeba/log.water_hexamer.hippo.1

@@ -0,0 +1,153 @@
+LAMMPS (24 Mar 2022)
+# water hexamer with AMOEBA or HIPPO
+
+units           real
+boundary        s s s
+
+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_xaxis d_yaxis d_zaxis d_pval ghost yes
+fix             extra2 all property/atom i_polaxe
+
+# read data file
+
+read_data       data.water_hexamer.hippo fix amtype NULL "Tinker Types"
+Reading data file ...
+  orthogonal box = (-2.517835 -1.523041 -1.734766) to (2.675716 2.01883 2.220847)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  18 atoms
+  scanning bonds ...
+  2 = max bonds/atom
+  scanning angles ...
+  1 = max angles/atom
+  reading bonds ...
+  12 bonds
+  reading angles ...
+  6 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.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_hexamer 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/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
+  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 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 = 12
+  ghost atom cutoff = 12
+  binsize = 6, bins = 1 1 1
+  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
+  AMOEBA/HIPPO group count: 6
+Per MPI rank memory allocation (min/avg/max) = 9.804 | 9.804 | 9.804 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    
+        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    
+        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     
+        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    
+        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    
+        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    
+        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    
+
+AMEOBA/HIPPO timing info:
+  Init   time: 0.000305988 0.00772963
+  Repls  time: 0.00615705 15.5535
+  Disp   time: 0.00270421 6.83116
+  Mpole  time: 0.00727575 18.3794
+  Induce time: 0.0137304 34.6848
+  Polar  time: 0.00789202 19.9362
+  Qxfer  time: 0.00151645 3.83073
+  Total  time: 0.0395864
+
+       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 0.0411107 on 1 procs for 100 steps with 18 atoms
+
+Performance: 210.164 ns/day, 0.114 hours/ns, 2432.456 timesteps/s
+94.5% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.039681   | 0.039681   | 0.039681   |   0.0 | 96.52
+Bond    | 0.00018196 | 0.00018196 | 0.00018196 |   0.0 |  0.44
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 1.8274e-05 | 1.8274e-05 | 1.8274e-05 |   0.0 |  0.04
+Output  | 0.0010806  | 0.0010806  | 0.0010806  |   0.0 |  2.63
+Modify  | 7.5438e-05 | 7.5438e-05 | 7.5438e-05 |   0.0 |  0.18
+Other   |            | 7.382e-05  |            |       |  0.18
+
+Nlocal:             18 ave          18 max          18 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:            153 ave         153 max         153 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 153
+Ave neighs/atom = 8.5
+Ave special neighs/atom = 2
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:00

examples/amoeba/log.water_hexamer.hippo.4

@@ -0,0 +1,154 @@
+LAMMPS (24 Mar 2022)
+# water hexamer with AMOEBA or HIPPO
+
+units           real
+boundary        s s s
+
+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_xaxis d_yaxis d_zaxis d_pval ghost yes
+fix             extra2 all property/atom i_polaxe
+
+# read data file
+
+read_data       data.water_hexamer.hippo fix amtype NULL "Tinker Types"
+Reading data file ...
+  orthogonal box = (-2.517835 -1.523041 -1.734766) to (2.675716 2.01883 2.220847)
+  2 by 1 by 2 MPI processor grid
+  reading atoms ...
+  18 atoms
+  scanning bonds ...
+  2 = max bonds/atom
+  scanning angles ...
+  1 = max angles/atom
+  reading bonds ...
+  12 bonds
+  reading angles ...
+  6 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.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_hexamer 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/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
+  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 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 = 12
+  ghost atom cutoff = 12
+  binsize = 6, bins = 1 1 1
+  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
+WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:974)
+  AMOEBA/HIPPO group count: 6
+Per MPI rank memory allocation (min/avg/max) = 9.833 | 9.833 | 9.833 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    
+        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    
+        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     
+        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    
+        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    
+        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    
+        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    
+
+AMEOBA/HIPPO timing info:
+  Init   time: 0.000674024 0.0214167
+  Repls  time: 0.00313927 9.97487
+  Disp   time: 0.000678053 2.15448
+  Mpole  time: 0.00411311 13.0692
+  Induce time: 0.018633 59.2054
+  Polar  time: 0.00385369 12.2449
+  Qxfer  time: 0.000376264 1.19556
+  Total  time: 0.0314718
+
+       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 0.0345189 on 4 procs for 100 steps with 18 atoms
+
+Performance: 250.298 ns/day, 0.096 hours/ns, 2896.962 timesteps/s
+97.4% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.031394   | 0.031738   | 0.032246   |   0.2 | 91.94
+Bond    | 5.8552e-05 | 7.4876e-05 | 9.4475e-05 |   0.0 |  0.22
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.00068606 | 0.0012736  | 0.0016838  |   1.2 |  3.69
+Output  | 0.00098398 | 0.0010248  | 0.0011389  |   0.2 |  2.97
+Modify  | 3.693e-05  | 4.5649e-05 | 5.4845e-05 |   0.0 |  0.13
+Other   |            | 0.0003625  |            |       |  1.05
+
+Nlocal:            4.5 ave           6 max           3 min
+Histogram: 1 0 0 1 0 0 1 0 0 1
+Nghost:           13.5 ave          15 max          12 min
+Histogram: 1 0 0 1 0 0 1 0 0 1
+Neighs:          38.25 ave          77 max           9 min
+Histogram: 2 0 0 0 0 0 1 0 0 1
+
+Total # of neighbors = 153
+Ave neighs/atom = 8.5
+Ave special neighs/atom = 2
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:00