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code tweaks and update of examples

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This commit is contained in:
Steve Plimpton
2022-07-07 14:33:19 -06:00
parent 212048d4cc
commit 6100e1fafb
31 changed files with 543 additions and 662 deletions
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34
examples/amoeba/Test.sh
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@ -1,34 +0,0 @@
#!/bin/sh
# run test problems.
EXE=${1-../../src/lmp_mpi}
DATE=$(date +%1d%b%y)
# dimer
${EXE} -in in.water_dimer.amoeba -log log.${DATE}.water_dimer.amoeba.g++.1
mpirun -np 4 ${EXE} -in in.water_dimer.amoeba -log log.${DATE}.water_dimer.amoeba.g++.4
${EXE} -in in.water_dimer.hippo -log log.${DATE}.water_dimer.hippo.g++.1
mpirun -np 4 ${EXE} -in in.water_dimer.hippo -log log.${DATE}.water_dimer.hippo.g++.4
# hexamer
${EXE} -in in.water_hexamer.amoeba -log log.${DATE}.water_hexamer.amoeba.g++.1
mpirun -np 4 ${EXE} -in in.water_hexamer.amoeba -log log.${DATE}.water_hexamer.amoeba.g++.4
${EXE} -in in.water_hexamer.hippo -log log.${DATE}.water_hexamer.hippo.g++.1
mpirun -np 4 ${EXE} -in in.water_hexamer.hippo -log log.${DATE}.water_hexamer.hippo.g++.4
# water box
${EXE} -in in.water_box.amoeba -log log.${DATE}.water_box.amoeba.g++.1
mpirun -np 4 ${EXE} -in in.water_box.amoeba -log log.${DATE}.water_box.amoeba.g++.4
${EXE} -in in.water_box.hippo -log log.${DATE}.water_box.hippo.g++.1
mpirun -np 4 ${EXE} -in in.water_box.hippo -log log.${DATE}.water_box.hippo.g++.4
# ubiquitin
${EXE} -in in.ubiquitin -log log.${DATE}.ubiquitin.g++.1
mpirun -np 4 ${EXE} -in in.ubiquitin -log log.${DATE}.ubiquitin.g++.4

8
examples/amoeba/in.ubiquitin
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@ -44,13 +44,9 @@ thermo_style custom step temp epair ebond eangle edihed eimp &
#dump 1 all custom 10 dump.ubiquitin id type x y z fx fy fz
#dump_modify 1 sort id
# zero step run
#run 0
# dynamics
fix 1 all nve
thermo 1
run 5
thermo 10
run 100

4
examples/amoeba/in.water_box.amoeba
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@ -35,10 +35,6 @@ thermo_style custom step temp epair ebond eangle edihed eimp &
#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

8
examples/amoeba/in.water_box.hippo
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@ -35,13 +35,9 @@ thermo_style custom step temp epair ebond eangle edihed eimp &
#dump 1 all custom 10 dump.water_box id type x y z fx fy fz
#dump_modify 1 sort id
# zero step run
#run 0
# dynamics
fix 1 all nve
thermo 1
run 5
thermo 10
run 100

8
examples/amoeba/in.water_dimer.amoeba
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@ -35,13 +35,9 @@ thermo_style custom step temp epair ebond eangle edihed eimp &
#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 1
run 5
thermo 10
run 100

8
examples/amoeba/in.water_dimer.hippo
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@ -35,13 +35,9 @@ thermo_style custom step temp epair ebond eangle edihed eimp &
#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 1
run 5
thermo 10
run 100

8
examples/amoeba/in.water_hexamer.amoeba
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@ -35,13 +35,9 @@ thermo_style custom step temp epair ebond eangle edihed eimp &
#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 1
run 5
thermo 10
run 100

8
examples/amoeba/in.water_hexamer.hippo
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@ -35,13 +35,9 @@ thermo_style custom step temp epair ebond eangle edihed eimp &
#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 1
run 5
thermo 10
run 100

150
examples/amoeba/log.5Jul22.water_box.hippo.g++.4
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@ -1,150 +0,0 @@
LAMMPS (23 Jun 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# water box with AMOEBA or HIPPO
units real
boundary p p p
atom_style amoeba
bond_style class2
angle_style amoeba
dihedral_style none
# per-atom properties required by AMOEBA or HIPPO
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom i_amgroup d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
# read data file
read_data data.water_box.hippo fix amtype NULL "Tinker Types"
Reading data file ...
orthogonal box = (0 0 0) to (18.643 18.643 18.643)
1 by 2 by 2 MPI processor grid
reading atoms ...
648 atoms
scanning bonds ...
2 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
432 bonds
reading angles ...
216 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.007 seconds
# force field
pair_style hippo
pair_coeff * * hippo_water.prm hippo_water_box.key
Reading potential file hippo_water.prm with DATE: 2022-07-05
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0.5 0.5 0.5
special bond factors coul: 0.5 0.5 0.5
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of 1-5 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
# thermo output
compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*]
#dump 1 all custom 10 dump.water_box id type x y z fx fy fz
#dump_modify 1 sort id
# zero step run
#run 0
# dynamics
fix 1 all nve
thermo 1
run 5
HIPPO force field settings
repulsion: cut 7 taper 6 rscale 0 0 1 1
qxfer: cut 7 taper 6 mscale 0 0 0.4 1
dispersion: cut 7 aewald 0.45 bsorder 4 FFT 16 16 16 dspscale 0 0 0.4 1
multipole: cut 7 aewald 0.4 bsorder 5 FFT 24 24 24 mscale 0 0 0.4 1
polar: cut 7 aewald 0.5 bsorder 5 FFT 24 24 24
pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 0.2 1 1 1 d/u scale 0 1
precondition: cut 4.5
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 9
ghost atom cutoff = 9
binsize = 4.5, bins = 5 5 5
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair hippo, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
HIPPO group count: 216
Per MPI rank memory allocation (min/avg/max) = 55.94 | 55.94 | 55.94 Mbytes
Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6]
0 0 -2188.594 166.82637 77.478353 0 0 244.30473 -1944.2893 -10859.589 -9285.4645 -11598.049 -11695.254 -282.7072 3164.4148 2495.2578
1 29.599499 -2189.0009 110.80903 70.640769 0 0 181.4498 -1950.466 -9781.8027 -8491.8338 -11237.523 -10824.225 -316.85579 2724.3099 2103.706
2 77.782401 -2189.0806 26.465487 53.091297 0 0 79.556784 -1959.5139 -5674.5913 -4709.6895 -8454.6227 -7034.3366 -270.02397 1600.8009 1104.5782
3 83.751912 -2189.1561 36.936027 32.349803 0 0 69.285831 -1958.3477 1505.3642 2789.4989 -1919.6532 227.71216 3.4467207 240.18575 -91.250567
4 59.186129 -2195.3882 116.40559 17.314099 0 0 133.71969 -1947.5231 7666.6109 9441.7634 4355.1915 6787.0543 329.33631 -768.83277 -966.66638
5 70.911532 -2215.1422 115.71443 14.75745 0 0 130.47188 -1947.9114 7292.9034 8506.6309 4019.0295 6458.6256 348.80878 -911.32703 -1060.6123
Loop time of 0.122 on 4 procs for 5 steps with 648 atoms
Performance: 3.541 ns/day, 6.778 hours/ns, 40.984 timesteps/s
98.6% CPU use with 4 MPI tasks x 1 OpenMP threads
HIPPO timing breakdown:
Init time: 0.000810221 0.67%
Repulse time: 0.0125366 10.36%
Disp time: 0.00623213 5.15%
Mpole time: 0.0210595 17.40%
Induce time: 0.0506279 41.83%
Polar time: 0.026832 22.17%
Qxfer time: 0.00292863 2.42%
Total time: 0.121027
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.12089 | 0.12109 | 0.12131 | 0.0 | 99.25
Bond | 4.8642e-05 | 5.2114e-05 | 6.0555e-05 | 0.0 | 0.04
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00035781 | 0.00058015 | 0.00076608 | 0.0 | 0.48
Output | 0.0001878 | 0.00022879 | 0.00026441 | 0.0 | 0.19
Modify | 1.7668e-05 | 1.8481e-05 | 1.9751e-05 | 0.0 | 0.02
Other | | 3.389e-05 | | | 0.03
Nlocal: 162 ave 166 max 159 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Nghost: 2582.75 ave 2600 max 2559 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Neighs: 24646.2 ave 25106 max 23932 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Total # of neighbors = 98585
Ave neighs/atom = 152.13735
Ave special neighs/atom = 2
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

49
examples/amoeba/log.5Jul22.ubiquitin.g++.1 → examples/amoeba/log.7Jul22.ubiquitin.g++.1
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@ -1,6 +1,4 @@
LAMMPS (23 Jun 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# solvated ubiquitin molecule with AMOEBA force field
units real
@ -56,7 +54,7 @@ Finding 1-2 1-3 1-4 neighbors ...
9 = max # of 1-3 neighbors
19 = max # of 1-4 neighbors
21 = max # of special neighbors
special bonds CPU = 0.003 seconds
special bonds CPU = 0.004 seconds
read_data CPU = 0.077 seconds
pair_style amoeba
@ -75,7 +73,7 @@ Finding 1-2 1-3 1-4 neighbors ...
19 = max # of 1-4 neighbors
58 = max # of 1-5 neighbors
21 = max # of special neighbors
special bonds CPU = 0.005 seconds
special bonds CPU = 0.006 seconds
# thermo output
@ -86,16 +84,12 @@ thermo_style custom step temp epair ebond eangle edihed eimp
#dump 1 all custom 10 dump.ubiquitin id type x y z fx fy fz
#dump_modify 1 sort id
# zero step run
#run 0
# dynamics
fix 1 all nve
thermo 1
run 5
run 10
AMOEBA force field settings
hal: cut 12 taper 10.8 vscale 0 0 1 1
multipole: cut 7 aewald 0.4 bsorder 5 FFT 60 48 48 mscale 0 0 0.4 1
@ -124,29 +118,34 @@ Per MPI rank memory allocation (min/avg/max) = 258.3 | 258.3 | 258.3 Mbytes
3 88.8921 -35402.11 938.99299 1162.2914 220.5271 58.832521 2380.644 -30453.516 -1929.5417 -3331.1291 -2769.7218 -3350.5733 117.32302 279.72705 31.237776
4 68.740402 -35477.589 2048.0659 858.03795 218.14277 54.460022 3178.7066 -30316.325 2041.1138 594.25938 1665.7799 1030.8539 66.230421 304.28296 -155.80224
5 76.267862 -35707.869 2206.6534 736.37385 215.75693 49.401674 3208.1859 -30299.377 2276.9276 536.21124 1893.4621 1258.492 92.097191 299.65604 -228.58369
Loop time of 6.65546 on 1 procs for 5 steps with 9737 atoms
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
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 24.1308 on 1 procs for 10 steps with 9737 atoms
Performance: 0.065 ns/day, 369.748 hours/ns, 0.751 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 0.036 ns/day, 670.300 hours/ns, 0.414 timesteps/s
99.4% CPU use with 1 MPI tasks x no OpenMP threads
AMOEBA timing breakdown:
Init time: 0.0105468 0.16%
Hal time: 1.57051 23.62%
Mpole time: 0.805631 12.12%
Induce time: 2.69099 40.48%
Polar time: 1.57015 23.62%
Total time: 6.64783
Init time: 0.0307243 0.13%
Hal time: 7.7896 32.31%
Mpole time: 2.35085 9.75%
Induce time: 9.19392 38.14%
Polar time: 4.74032 19.66%
Total time: 24.1054
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 6.6478 | 6.6478 | 6.6478 | 0.0 | 99.89
Bond | 0.0052138 | 0.0052138 | 0.0052138 | 0.0 | 0.08
Pair | 24.105 | 24.105 | 24.105 | 0.0 | 99.90
Bond | 0.016307 | 0.016307 | 0.016307 | 0.0 | 0.07
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0010535 | 0.0010535 | 0.0010535 | 0.0 | 0.02
Output | 0.00033674 | 0.00033674 | 0.00033674 | 0.0 | 0.01
Modify | 0.00085639 | 0.00085639 | 0.00085639 | 0.0 | 0.01
Other | | 0.000145 | | | 0.00
Comm | 0.0039483 | 0.0039483 | 0.0039483 | 0.0 | 0.02
Output | 0.001034 | 0.001034 | 0.001034 | 0.0 | 0.00
Modify | 0.0032551 | 0.0032551 | 0.0032551 | 0.0 | 0.01
Other | | 0.00076 | | | 0.00
Nlocal: 9737 ave 9737 max 9737 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -160,4 +159,4 @@ Ave neighs/atom = 579.16155
Ave special neighs/atom = 3.1364897
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:08
Total wall time: 0:00:27

51
examples/amoeba/log.5Jul22.ubiquitin.g++.4 → examples/amoeba/log.7Jul22.ubiquitin.g++.4
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@ -1,6 +1,4 @@
LAMMPS (23 Jun 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# solvated ubiquitin molecule with AMOEBA force field
units real
@ -56,8 +54,8 @@ Finding 1-2 1-3 1-4 neighbors ...
9 = max # of 1-3 neighbors
19 = max # of 1-4 neighbors
21 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.036 seconds
special bonds CPU = 0.002 seconds
read_data CPU = 0.100 seconds
pair_style amoeba
pair_coeff * * amoeba_ubiquitin.prm amoeba_ubiquitin.key
@ -75,7 +73,7 @@ Finding 1-2 1-3 1-4 neighbors ...
19 = max # of 1-4 neighbors
58 = max # of 1-5 neighbors
21 = max # of special neighbors
special bonds CPU = 0.001 seconds
special bonds CPU = 0.002 seconds
# thermo output
@ -86,16 +84,12 @@ thermo_style custom step temp epair ebond eangle edihed eimp
#dump 1 all custom 10 dump.ubiquitin id type x y z fx fy fz
#dump_modify 1 sort id
# zero step run
#run 0
# dynamics
fix 1 all nve
thermo 1
run 5
run 10
AMOEBA force field settings
hal: cut 12 taper 10.8 vscale 0 0 1 1
multipole: cut 7 aewald 0.4 bsorder 5 FFT 60 48 48 mscale 0 0 0.4 1
@ -124,29 +118,34 @@ Per MPI rank memory allocation (min/avg/max) = 144.2 | 144.7 | 145.4 Mbytes
3 88.8921 -35402.11 938.99299 1162.2914 220.5271 58.832521 2380.644 -30453.516 -1929.5417 -3331.1291 -2769.7218 -3350.5733 117.32302 279.72705 31.237776
4 68.740402 -35477.589 2048.0659 858.03795 218.14277 54.460022 3178.7066 -30316.325 2041.1138 594.25938 1665.7799 1030.8539 66.230421 304.28296 -155.80224
5 76.267862 -35707.869 2206.6534 736.37385 215.75693 49.401674 3208.1859 -30299.377 2276.9276 536.21124 1893.4621 1258.492 92.097191 299.65604 -228.58369
Loop time of 2.1516 on 4 procs for 5 steps with 9737 atoms
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
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 6.07676 on 4 procs for 10 steps with 9737 atoms
Performance: 0.201 ns/day, 119.533 hours/ns, 2.324 timesteps/s
99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 0.142 ns/day, 168.799 hours/ns, 1.646 timesteps/s
99.6% CPU use with 4 MPI tasks x no OpenMP threads
AMOEBA timing breakdown:
Init time: 0.0116891 0.54%
Hal time: 0.423411 19.72%
Mpole time: 0.269917 12.57%
Induce time: 0.929983 43.30%
Polar time: 0.512586 23.87%
Total time: 2.14759
Init time: 0.0182673 0.30%
Hal time: 1.89506 31.24%
Mpole time: 0.649816 10.71%
Induce time: 2.27346 37.48%
Polar time: 1.22947 20.27%
Total time: 6.06608
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.1477 | 2.1477 | 2.1477 | 0.0 | 99.82
Bond | 0.001184 | 0.0014529 | 0.0016771 | 0.5 | 0.07
Pair | 6.0656 | 6.0662 | 6.067 | 0.0 | 99.83
Bond | 0.0030706 | 0.0035014 | 0.0039085 | 0.5 | 0.06
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0015356 | 0.0017027 | 0.001922 | 0.4 | 0.08
Output | 0.00027025 | 0.0003219 | 0.00040484 | 0.0 | 0.01
Modify | 0.00028633 | 0.00030716 | 0.00032386 | 0.0 | 0.01
Other | | 0.0001328 | | | 0.01
Comm | 0.0045136 | 0.0052483 | 0.0058373 | 0.7 | 0.09
Output | 0.00065752 | 0.0007782 | 0.00099256 | 0.0 | 0.01
Modify | 0.00065468 | 0.0007142 | 0.00077861 | 0.0 | 0.01
Other | | 0.0003323 | | | 0.01
Nlocal: 2434.25 ave 2498 max 2390 min
Histogram: 1 1 0 0 1 0 0 0 0 1
@ -160,4 +159,4 @@ Ave neighs/atom = 579.16155
Ave special neighs/atom = 3.1364897
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:02
Total wall time: 0:00:07

44
examples/amoeba/log.5Jul22.water_box.amoeba.g++.1 → examples/amoeba/log.7Jul22.water_box.amoeba.g++.1
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@ -1,6 +1,4 @@
LAMMPS (23 Jun 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# replicate water box with AMOEBA or HIPPO
units real
@ -40,8 +38,8 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.012 seconds
special bonds CPU = 0.000 seconds
read_data CPU = 0.011 seconds
# force field
@ -69,10 +67,6 @@ thermo_style custom step temp epair ebond eangle edihed eimp
#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
@ -112,29 +106,29 @@ Per MPI rank memory allocation (min/avg/max) = 56.94 | 56.94 | 56.94 Mbytes
80 171.83506 -2388.0612 76.465932 49.1299 0 0 125.59583 -1931.067 2210.3658 -318.23867 330.74353 -395.26693 -43.142216 252.53012 -1987.0412
90 175.73401 -2423.8154 90.786573 63.719496 0 0 154.50607 -1930.3915 -916.91571 -3942.3954 -2566.5361 -3414.8202 199.82369 2365.9443 -266.38604
100 173.72684 -2422.367 99.75941 57.294464 0 0 157.05387 -1930.2663 -3585.8356 -5734.1341 -5882.0146 -6232.4353 -227.79935 959.68225 404.47924
Loop time of 9.23157 on 1 procs for 100 steps with 648 atoms
Loop time of 13.2332 on 1 procs for 100 steps with 648 atoms
Performance: 0.936 ns/day, 25.643 hours/ns, 10.832 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 0.653 ns/day, 36.759 hours/ns, 7.557 timesteps/s
99.8% CPU use with 1 MPI tasks x no OpenMP threads
AMOEBA timing breakdown:
Init time: 0.0194993 0.21%
Hal time: 0.383028 4.15%
Mpole time: 0.935775 10.15%
Induce time: 6.06306 65.76%
Polar time: 1.81839 19.72%
Total time: 9.21978
Init time: 0.020242 0.15%
Hal time: 0.900253 6.81%
Mpole time: 1.29931 9.83%
Induce time: 8.37539 63.35%
Polar time: 2.62525 19.86%
Total time: 13.2205
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 9.2201 | 9.2201 | 9.2201 | 0.0 | 99.88
Bond | 0.0024949 | 0.0024949 | 0.0024949 | 0.0 | 0.03
Neigh | 0.0046051 | 0.0046051 | 0.0046051 | 0.0 | 0.05
Comm | 0.0023611 | 0.0023611 | 0.0023611 | 0.0 | 0.03
Output | 0.00045516 | 0.00045516 | 0.00045516 | 0.0 | 0.00
Modify | 0.00070554 | 0.00070554 | 0.00070554 | 0.0 | 0.01
Other | | 0.0008327 | | | 0.01
Pair | 13.221 | 13.221 | 13.221 | 0.0 | 99.90
Bond | 0.0027476 | 0.0027476 | 0.0027476 | 0.0 | 0.02
Neigh | 0.0055619 | 0.0055619 | 0.0055619 | 0.0 | 0.04
Comm | 0.002464 | 0.002464 | 0.002464 | 0.0 | 0.02
Output | 0.00041636 | 0.00041636 | 0.00041636 | 0.0 | 0.00
Modify | 0.00068882 | 0.00068882 | 0.00068882 | 0.0 | 0.01
Other | | 0.0007637 | | | 0.01
Nlocal: 648 ave 648 max 648 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -148,4 +142,4 @@ Ave neighs/atom = 152.07562
Ave special neighs/atom = 2
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:00:09
Total wall time: 0:00:13

46
examples/amoeba/log.5Jul22.water_box.amoeba.g++.4 → examples/amoeba/log.7Jul22.water_box.amoeba.g++.4
View File

@ -1,6 +1,4 @@
LAMMPS (23 Jun 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# replicate water box with AMOEBA or HIPPO
units real
@ -40,8 +38,8 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.005 seconds
special bonds CPU = 0.001 seconds
read_data CPU = 0.014 seconds
# force field
@ -58,7 +56,7 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-4 neighbors
2 = max # of 1-5 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
special bonds CPU = 0.001 seconds
# thermo output
@ -69,10 +67,6 @@ thermo_style custom step temp epair ebond eangle edihed eimp
#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
@ -112,29 +106,29 @@ Per MPI rank memory allocation (min/avg/max) = 56.38 | 56.38 | 56.38 Mbytes
80 171.83506 -2388.0612 76.465932 49.1299 0 0 125.59583 -1931.067 2210.3658 -318.23867 330.74353 -395.26693 -43.142216 252.53012 -1987.0412
90 175.73401 -2423.8154 90.786573 63.719496 0 0 154.50607 -1930.3915 -916.91571 -3942.3954 -2566.5361 -3414.8202 199.82369 2365.9443 -266.38604
100 173.72684 -2422.367 99.75941 57.294464 0 0 157.05387 -1930.2663 -3585.8356 -5734.1341 -5882.0146 -6232.4353 -227.79935 959.68225 404.47924
Loop time of 3.62992 on 4 procs for 100 steps with 648 atoms
Loop time of 5.51861 on 4 procs for 100 steps with 648 atoms
Performance: 2.380 ns/day, 10.083 hours/ns, 27.549 timesteps/s
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 1.566 ns/day, 15.329 hours/ns, 18.120 timesteps/s
100.0% CPU use with 4 MPI tasks x no OpenMP threads
AMOEBA timing breakdown:
Init time: 0.0211291 0.58%
Hal time: 0.114718 3.17%
Mpole time: 0.329891 9.11%
Induce time: 2.5339 69.99%
Polar time: 0.620639 17.14%
Total time: 3.6203
Init time: 0.0236604 0.43%
Hal time: 0.257977 4.69%
Mpole time: 0.530078 9.63%
Induce time: 3.72129 67.60%
Polar time: 0.972013 17.66%
Total time: 5.50503
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.6209 | 3.621 | 3.6211 | 0.0 | 99.75
Bond | 0.00085544 | 0.00087038 | 0.00090469 | 0.0 | 0.02
Neigh | 0.0014354 | 0.0014405 | 0.0014453 | 0.0 | 0.04
Comm | 0.004823 | 0.0048746 | 0.0049092 | 0.0 | 0.13
Output | 0.00038727 | 0.00043628 | 0.00055233 | 0.0 | 0.01
Modify | 0.00033814 | 0.0003491 | 0.00037267 | 0.0 | 0.01
Other | | 0.0009691 | | | 0.03
Pair | 5.5047 | 5.5054 | 5.5063 | 0.0 | 99.76
Bond | 0.00080214 | 0.00087764 | 0.00092311 | 0.0 | 0.02
Neigh | 0.0016691 | 0.001675 | 0.0016849 | 0.0 | 0.03
Comm | 0.0083938 | 0.0092735 | 0.010026 | 0.7 | 0.17
Output | 0.000358 | 0.00041667 | 0.00056168 | 0.0 | 0.01
Modify | 0.00022011 | 0.00024519 | 0.00025818 | 0.0 | 0.00
Other | | 0.0007611 | | | 0.01
Nlocal: 162 ave 164 max 159 min
Histogram: 1 0 0 0 0 0 1 0 1 1
@ -148,4 +142,4 @@ Ave neighs/atom = 152.07562
Ave special neighs/atom = 2
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:00:03
Total wall time: 0:00:05

79
examples/amoeba/log.5Jul22.water_box.hippo.g++.1 → examples/amoeba/log.7Jul22.water_box.hippo.g++.1
View File

@ -1,6 +1,4 @@
LAMMPS (23 Jun 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# water box with AMOEBA or HIPPO
units real
@ -40,8 +38,8 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.004 seconds
special bonds CPU = 0.001 seconds
read_data CPU = 0.012 seconds
# force field
@ -58,7 +56,7 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-4 neighbors
2 = max # of 1-5 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
special bonds CPU = 0.001 seconds
# thermo output
@ -69,16 +67,12 @@ thermo_style custom step temp epair ebond eangle edihed eimp
#dump 1 all custom 10 dump.water_box id type x y z fx fy fz
#dump_modify 1 sort id
# zero step run
#run 0
# dynamics
fix 1 all nve
thermo 1
run 5
thermo 10
run 100
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
@ -104,47 +98,52 @@ Neighbor list info ...
Per MPI rank memory allocation (min/avg/max) = 56.46 | 56.46 | 56.46 Mbytes
Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6]
0 0 -2188.594 166.82637 77.478353 0 0 244.30473 -1944.2893 -10859.589 -9285.4645 -11598.049 -11695.254 -282.7072 3164.4148 2495.2578
1 29.599499 -2189.0009 110.80903 70.640769 0 0 181.4498 -1950.466 -9781.8027 -8491.8338 -11237.523 -10824.225 -316.85579 2724.3099 2103.706
2 77.782401 -2189.0806 26.465487 53.091297 0 0 79.556784 -1959.5139 -5674.5913 -4709.6895 -8454.6227 -7034.3366 -270.02397 1600.8009 1104.5782
3 83.751912 -2189.1561 36.936027 32.349803 0 0 69.285831 -1958.3477 1505.3642 2789.4989 -1919.6532 227.71216 3.4467207 240.18575 -91.250567
4 59.186129 -2195.3882 116.40559 17.314099 0 0 133.71969 -1947.5231 7666.6109 9441.7634 4355.1915 6787.0543 329.33631 -768.83277 -966.66638
5 70.911532 -2215.1422 115.71443 14.75745 0 0 130.47188 -1947.9114 7292.9034 8506.6309 4019.0295 6458.6256 348.80878 -911.32703 -1060.6123
Loop time of 0.326218 on 1 procs for 5 steps with 648 atoms
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
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 10.7228 on 1 procs for 100 steps with 648 atoms
Performance: 1.324 ns/day, 18.123 hours/ns, 15.327 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 0.806 ns/day, 29.786 hours/ns, 9.326 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
HIPPO timing breakdown:
Init time: 0.000842282 0.26%
Repulse time: 0.0383544 11.78%
Disp time: 0.0173558 5.33%
Mpole time: 0.0613861 18.85%
Induce time: 0.121337 37.26%
Polar time: 0.0763061 23.43%
Qxfer time: 0.0101016 3.10%
Total time: 0.325683
Init time: 0.0153975 0.14%
Repulse time: 1.2388 11.57%
Disp time: 0.693631 6.48%
Mpole time: 2.01598 18.83%
Induce time: 3.8747 36.19%
Polar time: 2.52726 23.60%
Qxfer time: 0.341839 3.19%
Total time: 10.7076
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.3257 | 0.3257 | 0.3257 | 0.0 | 99.84
Bond | 0.00013737 | 0.00013737 | 0.00013737 | 0.0 | 0.04
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0001122 | 0.0001122 | 0.0001122 | 0.0 | 0.03
Output | 0.00020981 | 0.00020981 | 0.00020981 | 0.0 | 0.06
Modify | 3.4058e-05 | 3.4058e-05 | 3.4058e-05 | 0.0 | 0.01
Other | | 2.595e-05 | | | 0.01
Pair | 10.708 | 10.708 | 10.708 | 0.0 | 99.86
Bond | 0.0028607 | 0.0028607 | 0.0028607 | 0.0 | 0.03
Neigh | 0.0073977 | 0.0073977 | 0.0073977 | 0.0 | 0.07
Comm | 0.0026424 | 0.0026424 | 0.0026424 | 0.0 | 0.02
Output | 0.00048358 | 0.00048358 | 0.00048358 | 0.0 | 0.00
Modify | 0.00077694 | 0.00077694 | 0.00077694 | 0.0 | 0.01
Other | | 0.0008999 | | | 0.01
Nlocal: 648 ave 648 max 648 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4302 ave 4302 max 4302 min
Nghost: 4282 ave 4282 max 4282 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 98585 ave 98585 max 98585 min
Neighs: 98490 ave 98490 max 98490 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 98585
Ave neighs/atom = 152.13735
Total # of neighbors = 98490
Ave neighs/atom = 151.99074
Ave special neighs/atom = 2
Neighbor list builds = 0
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:00:00
Total wall time: 0:00:10

149
examples/amoeba/log.7Jul22.water_box.hippo.g++.4 Normal file
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@ -0,0 +1,149 @@
LAMMPS (23 Jun 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_pval ghost yes
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
# read data file
read_data data.water_box.hippo fix amtype NULL "Tinker Types"
Reading data file ...
orthogonal box = (0 0 0) to (18.643 18.643 18.643)
1 by 2 by 2 MPI processor grid
reading atoms ...
648 atoms
scanning bonds ...
2 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
432 bonds
reading angles ...
216 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.012 seconds
# force field
pair_style hippo
pair_coeff * * hippo_water.prm hippo_water_box.key
Reading potential file hippo_water.prm with DATE: 2022-07-05
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
# dynamics
fix 1 all nve
thermo 10
run 100
HIPPO force field settings
repulsion: cut 7 taper 6 rscale 0 0 1 1
qxfer: cut 7 taper 6 mscale 0 0 0.4 1
dispersion: cut 7 aewald 0.45 bsorder 4 FFT 16 16 16 dspscale 0 0 0.4 1
multipole: cut 7 aewald 0.4 bsorder 5 FFT 24 24 24 mscale 0 0 0.4 1
polar: cut 7 aewald 0.5 bsorder 5 FFT 24 24 24
pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 0.2 1 1 1 d/u scale 0 1
precondition: cut 4.5
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 9
ghost atom cutoff = 9
binsize = 4.5, bins = 5 5 5
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair hippo, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
HIPPO group count: 216
Per MPI rank memory allocation (min/avg/max) = 55.94 | 55.94 | 55.94 Mbytes
Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6]
0 0 -2188.594 166.82637 77.478353 0 0 244.30473 -1944.2893 -10859.589 -9285.4645 -11598.049 -11695.254 -282.7072 3164.4148 2495.2578
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
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 3.56341 on 4 procs for 100 steps with 648 atoms
Performance: 2.425 ns/day, 9.898 hours/ns, 28.063 timesteps/s
100.0% CPU use with 4 MPI tasks x no OpenMP threads
HIPPO timing breakdown:
Init time: 0.0164761 0.47%
Repulse time: 0.329025 9.29%
Disp time: 0.240825 6.80%
Mpole time: 0.631085 17.81%
Induce time: 1.43692 40.56%
Polar time: 0.807046 22.78%
Qxfer time: 0.081509 2.30%
Total time: 3.5429
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.5358 | 3.5432 | 3.5499 | 0.3 | 99.43
Bond | 0.00065586 | 0.00073446 | 0.00079512 | 0.0 | 0.02
Neigh | 0.0016222 | 0.0016303 | 0.0016397 | 0.0 | 0.05
Comm | 0.0098332 | 0.016538 | 0.023936 | 4.9 | 0.46
Output | 0.00030555 | 0.00034729 | 0.00046611 | 0.0 | 0.01
Modify | 0.00020015 | 0.00022223 | 0.00025815 | 0.0 | 0.01
Other | | 0.0007117 | | | 0.02
Nlocal: 162 ave 166 max 160 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Nghost: 2563.25 ave 2589 max 2535 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Neighs: 24622.5 ave 25210 max 24056 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Total # of neighbors = 98490
Ave neighs/atom = 151.99074
Ave special neighs/atom = 2
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:00:03

59
examples/amoeba/log.5Jul22.water_dimer.amoeba.g++.1 → examples/amoeba/log.7Jul22.water_dimer.amoeba.g++.1
View File

@ -1,6 +1,4 @@
LAMMPS (23 Jun 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# water dimer with AMOEBA or HIPPO
units real
@ -41,7 +39,7 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.003 seconds
read_data CPU = 0.007 seconds
# force field
@ -69,16 +67,12 @@ thermo_style custom step temp epair ebond eangle edihed eimp
#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 1
run 5
thermo 10
run 100
AMOEBA force field settings
hal: cut 10 taper 8 vscale 0 0 1 1
multipole: cut 10 aewald 0 mscale 0 0 0.4 1
@ -98,39 +92,44 @@ Neighbor list info ...
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:970)
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:970)
AMOEBA group count: 2
Per MPI rank memory allocation (min/avg/max) = 48.33 | 48.33 | 48.33 Mbytes
Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6]
0 0 -5.1627563 0.025695395 0.71581114 0 0 0.74150653 -4.4212497 -12260.522 -43226.042 39448.214 -33003.739 -85.160886 -28101.905 -72.971988
1 3.4764991 -5.1500622 0.021865831 0.65347737 0 0 0.67534321 -4.4229051 -8987.9108 -37684.452 39410.243 -29356.236 -80.130511 -27322.706 -69.79235
2 12.286735 -5.1147506 0.014370337 0.49051077 0 0 0.50488111 -4.4267474 -865.99299 -23430.467 38420.372 -19944.197 -66.155435 -24835.896 -60.583907
3 22.599529 -5.0641035 0.0093422156 0.28736734 0 0 0.29670956 -4.4305695 7832.024 -6436.638 34275.274 -8676.6339 -46.038158 -20245.105 -46.202354
4 30.447598 -5.0072832 0.0076827791 0.11282886 0 0 0.12051164 -4.432979 12374.854 6652.5061 24658.364 -25.4576 -23.025707 -13137.295 -27.801932
5 33.189086 -4.9523094 0.0086012541 0.015399005 0 0 0.024000259 -4.4336573 10023.674 11810.883 8754.5769 3140.658 0.25267021 -3546.6216 -6.83205
Loop time of 0.000214688 on 1 procs for 5 steps with 6 atoms
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
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 0.0054238 on 1 procs for 100 steps with 6 atoms
Performance: 2012.222 ns/day, 0.012 hours/ns, 23289.611 timesteps/s
65.7% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 1592.978 ns/day, 0.015 hours/ns, 18437.244 timesteps/s
98.9% CPU use with 1 MPI tasks x no OpenMP threads
AMOEBA timing breakdown:
Init time: 5.306e-06 4.54%
Hal time: 6.681e-06 5.72%
Mpole time: 1.6221e-05 13.88%
Induce time: 5.6723e-05 48.54%
Polar time: 3.1532e-05 26.98%
Total time: 0.000116854
Init time: 0.000115142 2.36%
Hal time: 0.000417554 8.56%
Mpole time: 0.000572556 11.74%
Induce time: 0.00241105 49.43%
Polar time: 0.0013468 27.61%
Total time: 0.00487742
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00011888 | 0.00011888 | 0.00011888 | 0.0 | 55.37
Bond | 3.797e-06 | 3.797e-06 | 3.797e-06 | 0.0 | 1.77
Pair | 0.0049078 | 0.0049078 | 0.0049078 | 0.0 | 90.49
Bond | 8.5639e-05 | 8.5639e-05 | 8.5639e-05 | 0.0 | 1.58
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 7.24e-07 | 7.24e-07 | 7.24e-07 | 0.0 | 0.34
Output | 8.4738e-05 | 8.4738e-05 | 8.4738e-05 | 0.0 | 39.47
Modify | 1.53e-06 | 1.53e-06 | 1.53e-06 | 0.0 | 0.71
Other | | 5.022e-06 | | | 2.34
Comm | 1.3462e-05 | 1.3462e-05 | 1.3462e-05 | 0.0 | 0.25
Output | 0.00032702 | 0.00032702 | 0.00032702 | 0.0 | 6.03
Modify | 4.1776e-05 | 4.1776e-05 | 4.1776e-05 | 0.0 | 0.77
Other | | 4.812e-05 | | | 0.89
Nlocal: 6 ave 6 max 6 min
Histogram: 1 0 0 0 0 0 0 0 0 0

61
examples/amoeba/log.5Jul22.water_dimer.amoeba.g++.4 → examples/amoeba/log.7Jul22.water_dimer.amoeba.g++.4
View File

@ -1,6 +1,4 @@
LAMMPS (23 Jun 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# water dimer with AMOEBA or HIPPO
units real
@ -41,7 +39,7 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.004 seconds
read_data CPU = 0.009 seconds
# force field
@ -58,7 +56,7 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-4 neighbors
2 = max # of 1-5 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
special bonds CPU = 0.001 seconds
# thermo output
@ -69,16 +67,12 @@ thermo_style custom step temp epair ebond eangle edihed eimp
#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 1
run 5
thermo 10
run 100
AMOEBA force field settings
hal: cut 10 taper 8 vscale 0 0 1 1
multipole: cut 10 aewald 0 mscale 0 0 0.4 1
@ -98,39 +92,44 @@ Neighbor list info ...
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:970)
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:970)
AMOEBA group count: 2
Per MPI rank memory allocation (min/avg/max) = 48.35 | 48.48 | 48.62 Mbytes
Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6]
0 0 -5.1627563 0.025695395 0.71581114 0 0 0.74150653 -4.4212497 -12260.522 -43226.042 39448.214 -33003.739 -85.160886 -28101.905 -72.971988
1 3.4764991 -5.1500622 0.021865831 0.65347737 0 0 0.67534321 -4.4229051 -8987.9108 -37684.452 39410.243 -29356.236 -80.130511 -27322.706 -69.79235
2 12.286735 -5.1147506 0.014370337 0.49051077 0 0 0.50488111 -4.4267474 -865.99299 -23430.467 38420.372 -19944.197 -66.155435 -24835.896 -60.583907
3 22.599529 -5.0641035 0.0093422156 0.28736734 0 0 0.29670956 -4.4305695 7832.024 -6436.638 34275.274 -8676.6339 -46.038158 -20245.105 -46.202354
4 30.447598 -5.0072832 0.0076827791 0.11282886 0 0 0.12051164 -4.432979 12374.854 6652.5061 24658.364 -25.4576 -23.025707 -13137.295 -27.801932
5 33.189086 -4.9523094 0.0086012541 0.015399005 0 0 0.024000259 -4.4336573 10023.674 11810.883 8754.5769 3140.658 0.25267021 -3546.6216 -6.83205
Loop time of 0.000598353 on 4 procs for 5 steps with 6 atoms
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
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 0.0160572 on 4 procs for 100 steps with 6 atoms
Performance: 721.982 ns/day, 0.033 hours/ns, 8356.278 timesteps/s
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 538.077 ns/day, 0.045 hours/ns, 6227.743 timesteps/s
99.9% CPU use with 4 MPI tasks x no OpenMP threads
AMOEBA timing breakdown:
Init time: 1.3678e-05 3.81%
Hal time: 3.5045e-06 0.97%
Mpole time: 2.3748e-05 6.61%
Induce time: 0.000284514 79.15%
Polar time: 3.3521e-05 9.33%
Total time: 0.000359445
Init time: 0.000593411 4.20%
Hal time: 0.000115521 0.82%
Mpole time: 0.000734892 5.20%
Induce time: 0.0115567 81.83%
Polar time: 0.00110812 7.85%
Total time: 0.0141227
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00035282 | 0.00038565 | 0.00040584 | 0.0 | 64.45
Bond | 1.637e-06 | 3.2485e-06 | 4.816e-06 | 0.0 | 0.54
Pair | 0.013932 | 0.014334 | 0.014559 | 0.2 | 89.27
Bond | 1.1551e-05 | 4.3997e-05 | 8.2514e-05 | 0.0 | 0.27
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 1.4157e-05 | 3.2696e-05 | 5.1431e-05 | 0.0 | 5.46
Output | 0.00014589 | 0.0001627 | 0.00018978 | 0.0 | 27.19
Modify | 1.649e-06 | 2.0097e-06 | 2.209e-06 | 0.0 | 0.34
Other | | 1.205e-05 | | | 2.01
Comm | 0.00064766 | 0.00080925 | 0.0012349 | 0.0 | 5.04
Output | 0.00037674 | 0.00043125 | 0.0005388 | 0.0 | 2.69
Modify | 2.9613e-05 | 3.9056e-05 | 4.4592e-05 | 0.0 | 0.24
Other | | 0.0003995 | | | 2.49
Nlocal: 1.5 ave 3 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 2

63
examples/amoeba/log.5Jul22.water_dimer.hippo.g++.1 → examples/amoeba/log.7Jul22.water_dimer.hippo.g++.1
View File

@ -1,6 +1,4 @@
LAMMPS (23 Jun 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# water dimer with AMOEBA or HIPPO
units real
@ -41,7 +39,7 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.003 seconds
read_data CPU = 0.007 seconds
# force field
@ -69,16 +67,12 @@ thermo_style custom step temp epair ebond eangle edihed eimp
#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 1
run 5
thermo 10
run 100
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
@ -100,41 +94,46 @@ Neighbor list info ...
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:970)
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:970)
HIPPO group count: 2
Per MPI rank memory allocation (min/avg/max) = 47.9 | 47.9 | 47.9 Mbytes
Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6]
0 0 -5.0101954 0.025695395 0.51472748 0 0 0.54042288 -4.4697726 -11875.159 -38149.178 29162.678 -26638.977 -70.63422 -24614.614 -58.505595
1 2.8239917 -5.0023563 0.021919009 0.46718 0 0 0.48909901 -4.4711684 -8777.4654 -33285.75 30332.24 -23920.463 -67.159404 -23940.605 -56.913519
2 9.9359188 -4.9806071 0.014704278 0.34344685 0 0 0.35815113 -4.4743705 -1094.2989 -20777.766 32507.918 -16918.53 -57.217298 -21702.479 -51.827962
3 18.15288 -4.9496234 0.010334146 0.19125791 0 0 0.20159205 -4.47748 7115.3453 -5853.149 32274.916 -8557.0355 -41.982111 -17374.865 -42.455978
4 24.248994 -4.9153331 0.0093063079 0.065238074 0 0 0.074544382 -4.4793805 11356.801 5716.9586 25838.412 -2135.3667 -22.820662 -10495.224 -28.045156
5 26.136423 -4.8829114 0.0095061937 0.0039834608 0 0 0.013489654 -4.4798832 9044.3732 10498.874 11345.536 276.34491 -1.1467483 -1185.8556 -8.820154
Loop time of 0.000210439 on 1 procs for 5 steps with 6 atoms
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
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 0.00549002 on 1 procs for 100 steps with 6 atoms
Performance: 2052.851 ns/day, 0.012 hours/ns, 23759.854 timesteps/s
98.4% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 1573.763 ns/day, 0.015 hours/ns, 18214.853 timesteps/s
98.3% CPU use with 1 MPI tasks x no OpenMP threads
HIPPO timing breakdown:
Init time: 5.006e-06 4.58%
Repulse time: 1.3587e-05 12.42%
Disp time: 5.471e-06 5.00%
Mpole time: 2.1321e-05 19.49%
Induce time: 3.7665e-05 34.43%
Polar time: 2.3919e-05 21.87%
Qxfer time: 2.295e-06 2.10%
Total time: 0.000109391
Init time: 0.000118122 2.43%
Repulse time: 0.000596081 12.26%
Disp time: 0.000298407 6.14%
Mpole time: 0.000966546 19.89%
Induce time: 0.00167417 34.45%
Polar time: 0.00105479 21.70%
Qxfer time: 0.000147142 3.03%
Total time: 0.00486031
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00011125 | 0.00011125 | 0.00011125 | 0.0 | 52.86
Bond | 3.062e-06 | 3.062e-06 | 3.062e-06 | 0.0 | 1.46
Pair | 0.0048915 | 0.0048915 | 0.0048915 | 0.0 | 89.10
Bond | 7.8835e-05 | 7.8835e-05 | 7.8835e-05 | 0.0 | 1.44
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 6.3e-07 | 6.3e-07 | 6.3e-07 | 0.0 | 0.30
Output | 8.8087e-05 | 8.8087e-05 | 8.8087e-05 | 0.0 | 41.86
Modify | 1.664e-06 | 1.664e-06 | 1.664e-06 | 0.0 | 0.79
Other | | 5.749e-06 | | | 2.73
Comm | 1.3993e-05 | 1.3993e-05 | 1.3993e-05 | 0.0 | 0.25
Output | 0.00039472 | 0.00039472 | 0.00039472 | 0.0 | 7.19
Modify | 4.5208e-05 | 4.5208e-05 | 4.5208e-05 | 0.0 | 0.82
Other | | 6.581e-05 | | | 1.20
Nlocal: 6 ave 6 max 6 min
Histogram: 1 0 0 0 0 0 0 0 0 0

63
examples/amoeba/log.5Jul22.water_dimer.hippo.g++.4 → examples/amoeba/log.7Jul22.water_dimer.hippo.g++.4
View File

@ -1,6 +1,4 @@
LAMMPS (23 Jun 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# water dimer with AMOEBA or HIPPO
units real
@ -41,7 +39,7 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.004 seconds
read_data CPU = 0.007 seconds
# force field
@ -69,16 +67,12 @@ thermo_style custom step temp epair ebond eangle edihed eimp
#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 1
run 5
thermo 10
run 100
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
@ -100,41 +94,46 @@ Neighbor list info ...
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:970)
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:970)
HIPPO group count: 2
Per MPI rank memory allocation (min/avg/max) = 47.91 | 48.04 | 48.18 Mbytes
Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6]
0 0 -5.0101954 0.025695395 0.51472748 0 0 0.54042288 -4.4697726 -11875.159 -38149.178 29162.678 -26638.977 -70.63422 -24614.614 -58.505595
1 2.8239917 -5.0023563 0.021919009 0.46718 0 0 0.48909901 -4.4711684 -8777.4654 -33285.75 30332.24 -23920.463 -67.159404 -23940.605 -56.913519
2 9.9359188 -4.9806071 0.014704278 0.34344685 0 0 0.35815113 -4.4743705 -1094.2989 -20777.766 32507.918 -16918.53 -57.217298 -21702.479 -51.827962
3 18.15288 -4.9496234 0.010334146 0.19125791 0 0 0.20159205 -4.47748 7115.3453 -5853.149 32274.916 -8557.0355 -41.982111 -17374.865 -42.455978
4 24.248994 -4.9153331 0.0093063079 0.065238074 0 0 0.074544382 -4.4793805 11356.801 5716.9586 25838.412 -2135.3667 -22.820662 -10495.224 -28.045156
5 26.136423 -4.8829114 0.0095061937 0.0039834608 0 0 0.013489654 -4.4798832 9044.3732 10498.874 11345.536 276.34491 -1.1467483 -1185.8556 -8.820154
Loop time of 0.000488464 on 4 procs for 5 steps with 6 atoms
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
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 0.0111155 on 4 procs for 100 steps with 6 atoms
Performance: 884.405 ns/day, 0.027 hours/ns, 10236.169 timesteps/s
70.9% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 777.294 ns/day, 0.031 hours/ns, 8996.461 timesteps/s
98.1% CPU use with 4 MPI tasks x no OpenMP threads
HIPPO timing breakdown:
Init time: 1.2924e-05 4.50%
Repulse time: 2.01283e-05 7.01%
Disp time: 3.04475e-06 1.06%
Mpole time: 3.51807e-05 12.25%
Induce time: 0.000183034 63.71%
Polar time: 3.13832e-05 10.92%
Qxfer time: 1.44475e-06 0.50%
Total time: 0.000287298
Init time: 0.000522591 5.56%
Repulse time: 0.000518986 5.52%
Disp time: 7.85217e-05 0.84%
Mpole time: 0.000799739 8.51%
Induce time: 0.00666551 70.95%
Polar time: 0.000761531 8.11%
Qxfer time: 4.34115e-05 0.46%
Total time: 0.00939447
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00028193 | 0.00030553 | 0.00032173 | 0.0 | 62.55
Bond | 1.317e-06 | 2.7712e-06 | 4.847e-06 | 0.0 | 0.57
Pair | 0.0093886 | 0.0095904 | 0.009719 | 0.1 | 86.28
Bond | 1.1102e-05 | 3.5048e-05 | 6.4101e-05 | 0.0 | 0.32
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 1.3015e-05 | 3.0698e-05 | 4.1342e-05 | 0.0 | 6.28
Output | 0.00012315 | 0.00013964 | 0.00015356 | 0.0 | 28.59
Modify | 1.445e-06 | 1.881e-06 | 2.366e-06 | 0.0 | 0.39
Other | | 7.949e-06 | | | 1.63
Comm | 0.00058179 | 0.0007073 | 0.00089017 | 0.0 | 6.36
Output | 0.00033655 | 0.00038862 | 0.00047709 | 0.0 | 3.50
Modify | 2.5893e-05 | 3.3791e-05 | 3.9341e-05 | 0.0 | 0.30
Other | | 0.0003603 | | | 3.24
Nlocal: 1.5 ave 3 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 2

57
examples/amoeba/log.5Jul22.water_hexamer.amoeba.g++.1 → examples/amoeba/log.7Jul22.water_hexamer.amoeba.g++.1
View File

@ -1,6 +1,4 @@
LAMMPS (23 Jun 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# water hexamer with AMOEBA or HIPPO
units real
@ -41,7 +39,7 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.003 seconds
read_data CPU = 0.007 seconds
# force field
@ -69,16 +67,12 @@ thermo_style custom step temp epair ebond eangle edihed eimp
#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 1
run 5
thermo 10
run 100
AMOEBA force field settings
hal: cut 10 taper 8 vscale 0 0 1 1
multipole: cut 10 aewald 0 mscale 0 0 0.4 1
@ -102,34 +96,39 @@ Neighbor list info ...
Per MPI rank memory allocation (min/avg/max) = 48.28 | 48.28 | 48.28 Mbytes
Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6]
0 0 -48.469664 1.9820353 2.2499329 0 0 4.2319683 -44.237696 -26322.671 -28303.103 -27669.614 -22995.296 1312.6688 2624.8394 4042.0489
1 5.318656 -48.202382 1.5369859 2.1322394 0 0 3.6692253 -44.26364 -20236.446 -20385.617 -23104.961 -17727.152 417.52781 2728.2976 3750.7708
2 14.415671 -47.491537 0.6389772 1.8136212 0 0 2.4525984 -44.308442 -4127.4968 1051.8436 -10980.156 -3832.1256 -2285.3376 2991.8274 2945.888
3 15.996484 -46.59119 0.087228651 1.3862662 0 0 1.4734948 -44.307093 15705.166 28374.161 4124.662 13087.621 -6242.1769 3159.6508 1787.4159
4 10.888785 -45.839064 0.062461924 0.96598997 0 0 1.0284519 -44.258837 30226.38 48920.372 15666.108 25051.837 -9443.9251 2603.8275 435.5257
5 10.58575 -45.503287 0.071817565 0.64254674 0 0 0.71436431 -44.252503 31899.04 51066.283 18170.57 25448.409 -9478.6752 638.72265 -1011.7679
Loop time of 0.00100127 on 1 procs for 5 steps with 18 atoms
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
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 0.0422729 on 1 procs for 100 steps with 18 atoms
Performance: 431.450 ns/day, 0.056 hours/ns, 4993.633 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 204.386 ns/day, 0.117 hours/ns, 2365.584 timesteps/s
99.1% CPU use with 1 MPI tasks x no OpenMP threads
AMOEBA timing breakdown:
Init time: 1.2944e-05 1.45%
Hal time: 6.4578e-05 7.21%
Mpole time: 0.000124703 13.93%
Induce time: 0.000435232 48.60%
Polar time: 0.000257613 28.77%
Total time: 0.000895454
Init time: 0.000326361 0.79%
Hal time: 0.00514709 12.41%
Mpole time: 0.00443325 10.69%
Induce time: 0.0203454 49.05%
Polar time: 0.0112122 27.03%
Total time: 0.0414795
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00089735 | 0.00089735 | 0.00089735 | 0.0 | 89.62
Bond | 6.783e-06 | 6.783e-06 | 6.783e-06 | 0.0 | 0.68
Pair | 0.041518 | 0.041518 | 0.041518 | 0.0 | 98.21
Bond | 0.00021732 | 0.00021732 | 0.00021732 | 0.0 | 0.51
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 6.36e-07 | 6.36e-07 | 6.36e-07 | 0.0 | 0.06
Output | 8.9119e-05 | 8.9119e-05 | 8.9119e-05 | 0.0 | 8.90
Modify | 2.385e-06 | 2.385e-06 | 2.385e-06 | 0.0 | 0.24
Other | | 4.998e-06 | | | 0.50
Comm | 1.4363e-05 | 1.4363e-05 | 1.4363e-05 | 0.0 | 0.03
Output | 0.00037904 | 0.00037904 | 0.00037904 | 0.0 | 0.90
Modify | 7.8692e-05 | 7.8692e-05 | 7.8692e-05 | 0.0 | 0.19
Other | | 6.519e-05 | | | 0.15
Nlocal: 18 ave 18 max 18 min
Histogram: 1 0 0 0 0 0 0 0 0 0

59
examples/amoeba/log.5Jul22.water_hexamer.amoeba.g++.4 → examples/amoeba/log.7Jul22.water_hexamer.amoeba.g++.4
View File

@ -1,6 +1,4 @@
LAMMPS (23 Jun 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# water hexamer with AMOEBA or HIPPO
units real
@ -41,7 +39,7 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.004 seconds
read_data CPU = 0.008 seconds
# force field
@ -69,16 +67,12 @@ thermo_style custom step temp epair ebond eangle edihed eimp
#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 1
run 5
thermo 10
run 100
AMOEBA force field settings
hal: cut 10 taper 8 vscale 0 0 1 1
multipole: cut 10 aewald 0 mscale 0 0 0.4 1
@ -98,39 +92,44 @@ Neighbor list info ...
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:970)
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:970)
AMOEBA group count: 6
Per MPI rank memory allocation (min/avg/max) = 48.3 | 48.3 | 48.3 Mbytes
Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6]
0 0 -48.469664 1.9820353 2.2499329 0 0 4.2319683 -44.237696 -26322.671 -28303.103 -27669.614 -22995.296 1312.6688 2624.8394 4042.0489
1 5.318656 -48.202382 1.5369859 2.1322394 0 0 3.6692253 -44.26364 -20236.446 -20385.617 -23104.961 -17727.152 417.52781 2728.2976 3750.7708
2 14.415671 -47.491537 0.6389772 1.8136212 0 0 2.4525984 -44.308442 -4127.4968 1051.8436 -10980.156 -3832.1256 -2285.3376 2991.8274 2945.888
3 15.996484 -46.59119 0.087228651 1.3862662 0 0 1.4734948 -44.307093 15705.166 28374.161 4124.662 13087.621 -6242.1769 3159.6508 1787.4159
4 10.888785 -45.839064 0.062461924 0.96598997 0 0 1.0284519 -44.258837 30226.38 48920.372 15666.108 25051.837 -9443.9251 2603.8275 435.5257
5 10.58575 -45.503287 0.071817565 0.64254674 0 0 0.71436431 -44.252503 31899.04 51066.283 18170.57 25448.409 -9478.6752 638.72265 -1011.7679
Loop time of 0.00124102 on 4 procs for 5 steps with 18 atoms
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
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 0.0414203 on 4 procs for 100 steps with 18 atoms
Performance: 348.100 ns/day, 0.069 hours/ns, 4028.938 timesteps/s
99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 208.593 ns/day, 0.115 hours/ns, 2414.273 timesteps/s
100.0% CPU use with 4 MPI tasks x no OpenMP threads
AMOEBA timing breakdown:
Init time: 1.93587e-05 1.89%
Hal time: 2.20198e-05 2.15%
Mpole time: 0.0001019 9.94%
Induce time: 0.000717017 69.95%
Polar time: 0.000164237 16.02%
Total time: 0.00102505
Init time: 0.000755971 1.92%
Hal time: 0.00126807 3.22%
Mpole time: 0.00372714 9.45%
Induce time: 0.0278954 70.76%
Polar time: 0.00576419 14.62%
Total time: 0.0394242
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0010331 | 0.0010362 | 0.0010375 | 0.0 | 83.50
Bond | 3.723e-06 | 5.0355e-06 | 5.6e-06 | 0.0 | 0.41
Pair | 0.039586 | 0.039644 | 0.039746 | 0.0 | 95.71
Bond | 6.0994e-05 | 8.2233e-05 | 9.988e-05 | 0.0 | 0.20
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 1.7872e-05 | 4.1093e-05 | 6.4155e-05 | 0.0 | 3.31
Output | 0.00012756 | 0.00014764 | 0.00016933 | 0.0 | 11.90
Modify | 1.808e-06 | 2.4647e-06 | 2.74e-06 | 0.0 | 0.20
Other | | 8.565e-06 | | | 0.69
Comm | 0.00069921 | 0.00087777 | 0.001002 | 0.0 | 2.12
Output | 0.00035764 | 0.00040122 | 0.00052238 | 0.0 | 0.97
Modify | 4.6185e-05 | 5.6938e-05 | 6.2738e-05 | 0.0 | 0.14
Other | | 0.0003586 | | | 0.87
Nlocal: 4.5 ave 6 max 3 min
Histogram: 1 0 0 1 0 0 1 0 0 1

61
examples/amoeba/log.5Jul22.water_hexamer.hippo.g++.1 → examples/amoeba/log.7Jul22.water_hexamer.hippo.g++.1
View File

@ -1,6 +1,4 @@
LAMMPS (23 Jun 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# water hexamer with AMOEBA or HIPPO
units real
@ -41,7 +39,7 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.003 seconds
read_data CPU = 0.007 seconds
# force field
@ -69,16 +67,12 @@ thermo_style custom step temp epair ebond eangle edihed eimp
#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 1
run 5
thermo 10
run 100
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
@ -104,36 +98,41 @@ Neighbor list info ...
Per MPI rank memory allocation (min/avg/max) = 47.84 | 47.84 | 47.84 Mbytes
Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6]
0 0 -47.362156 1.9820353 1.6634749 0 0 3.6455102 -43.716646 -34513.768 -42206.078 -31383.641 -29951.584 2850.1184 3579.9253 5768.3698
1 7.1819351 -47.135822 1.4553325 1.5620463 0 0 3.0173788 -43.754508 -26763.923 -32046.377 -25919.73 -23012.16 1848.028 3578.5744 5396.0234
2 18.776762 -46.526843 0.46636815 1.2906982 0 0 1.7570664 -43.818287 -6352.6601 -4602.4631 -11460.465 -4789.8629 -1296.5558 3625.7641 4391.7607
3 19.013509 -45.750445 0.043880608 0.9336078 0 0 0.97748841 -43.809471 18351.549 29896.314 6275.5012 17065.39 -6055.8639 3664.6024 3015.6633
4 11.017518 -45.12347 0.24124811 0.58878104 0 0 0.83002915 -43.735142 35358.63 54252.632 19050.919 31719.21 -9822.7607 3160.7845 1520.1368
5 12.143149 -44.904245 0.22320916 0.3270434 0 0 0.55025256 -43.738653 35160.919 53395.572 20272.979 30653.482 -9511.0241 1392.4959 35.692826
Loop time of 0.000984386 on 1 procs for 5 steps with 18 atoms
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
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 0.0380494 on 1 procs for 100 steps with 18 atoms
Performance: 438.852 ns/day, 0.055 hours/ns, 5079.308 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 227.073 ns/day, 0.106 hours/ns, 2628.163 timesteps/s
99.8% CPU use with 1 MPI tasks x no OpenMP threads
HIPPO timing breakdown:
Init time: 1.2669e-05 1.45%
Repulse time: 0.000132325 15.15%
Disp time: 4.2534e-05 4.87%
Mpole time: 0.000177341 20.30%
Induce time: 0.000303723 34.77%
Polar time: 0.000179318 20.53%
Qxfer time: 2.5413e-05 2.91%
Total time: 0.000873466
Init time: 0.000298991 0.80%
Repulse time: 0.00610364 16.36%
Disp time: 0.00215934 5.79%
Mpole time: 0.00717983 19.24%
Induce time: 0.0128706 34.49%
Polar time: 0.00726207 19.46%
Qxfer time: 0.00143879 3.86%
Total time: 0.0373178
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00087559 | 0.00087559 | 0.00087559 | 0.0 | 88.95
Bond | 6.455e-06 | 6.455e-06 | 6.455e-06 | 0.0 | 0.66
Pair | 0.037354 | 0.037354 | 0.037354 | 0.0 | 98.17
Bond | 0.0001712 | 0.0001712 | 0.0001712 | 0.0 | 0.45
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 7.87e-07 | 7.87e-07 | 7.87e-07 | 0.0 | 0.08
Output | 9.3142e-05 | 9.3142e-05 | 9.3142e-05 | 0.0 | 9.46
Modify | 2.351e-06 | 2.351e-06 | 2.351e-06 | 0.0 | 0.24
Other | | 6.065e-06 | | | 0.62
Comm | 1.5977e-05 | 1.5977e-05 | 1.5977e-05 | 0.0 | 0.04
Output | 0.00036487 | 0.00036487 | 0.00036487 | 0.0 | 0.96
Modify | 6.9428e-05 | 6.9428e-05 | 6.9428e-05 | 0.0 | 0.18
Other | | 7.438e-05 | | | 0.20
Nlocal: 18 ave 18 max 18 min
Histogram: 1 0 0 0 0 0 0 0 0 0

65
examples/amoeba/log.5Jul22.water_hexamer.hippo.g++.4 → examples/amoeba/log.7Jul22.water_hexamer.hippo.g++.4
View File

@ -1,6 +1,4 @@
LAMMPS (23 Jun 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# water hexamer with AMOEBA or HIPPO
units real
@ -41,7 +39,7 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.004 seconds
read_data CPU = 0.008 seconds
# force field
@ -58,7 +56,7 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-4 neighbors
2 = max # of 1-5 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
special bonds CPU = 0.001 seconds
# thermo output
@ -69,16 +67,12 @@ thermo_style custom step temp epair ebond eangle edihed eimp
#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 1
run 5
thermo 10
run 100
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
@ -100,41 +94,46 @@ Neighbor list info ...
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:970)
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:970)
HIPPO group count: 6
Per MPI rank memory allocation (min/avg/max) = 47.86 | 47.86 | 47.86 Mbytes
Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6]
0 0 -47.362156 1.9820353 1.6634749 0 0 3.6455102 -43.716646 -34513.768 -42206.078 -31383.641 -29951.584 2850.1184 3579.9253 5768.3698
1 7.1819351 -47.135822 1.4553325 1.5620463 0 0 3.0173788 -43.754508 -26763.923 -32046.377 -25919.73 -23012.16 1848.028 3578.5744 5396.0234
2 18.776762 -46.526843 0.46636815 1.2906982 0 0 1.7570664 -43.818287 -6352.6601 -4602.4631 -11460.465 -4789.8629 -1296.5558 3625.7641 4391.7607
3 19.013509 -45.750445 0.043880608 0.9336078 0 0 0.97748841 -43.809471 18351.549 29896.314 6275.5012 17065.39 -6055.8639 3664.6024 3015.6633
4 11.017518 -45.12347 0.24124811 0.58878104 0 0 0.83002915 -43.735142 35358.63 54252.632 19050.919 31719.21 -9822.7607 3160.7845 1520.1368
5 12.143149 -44.904245 0.22320916 0.3270434 0 0 0.55025256 -43.738653 35160.919 53395.572 20272.979 30653.482 -9511.0241 1392.4959 35.692826
Loop time of 0.00126451 on 4 procs for 5 steps with 18 atoms
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
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 0.0319956 on 4 procs for 100 steps with 18 atoms
Performance: 341.634 ns/day, 0.070 hours/ns, 3954.096 timesteps/s
92.2% CPU use with 4 MPI tasks x 1 OpenMP threads
Performance: 270.038 ns/day, 0.089 hours/ns, 3125.434 timesteps/s
99.7% CPU use with 4 MPI tasks x no OpenMP threads
HIPPO timing breakdown:
Init time: 1.75712e-05 1.72%
Repulse time: 0.000116156 11.39%
Disp time: 1.69788e-05 1.66%
Mpole time: 0.000178714 17.52%
Induce time: 0.000515806 50.57%
Polar time: 0.0001659 16.27%
Qxfer time: 8.64975e-06 0.85%
Total time: 0.00101993
Init time: 0.000692588 2.32%
Repulse time: 0.00294464 9.88%
Disp time: 0.000526361 1.77%
Mpole time: 0.00377225 12.66%
Induce time: 0.0178884 60.04%
Polar time: 0.00361349 12.13%
Qxfer time: 0.000349507 1.17%
Total time: 0.0297917
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0010223 | 0.0010316 | 0.001045 | 0.0 | 81.58
Bond | 3.062e-06 | 4.3805e-06 | 5.123e-06 | 0.0 | 0.35
Pair | 0.029692 | 0.029996 | 0.030382 | 0.2 | 93.75
Bond | 5.5693e-05 | 6.9151e-05 | 8.2812e-05 | 0.0 | 0.22
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 1.4853e-05 | 6.5245e-05 | 9.2753e-05 | 0.0 | 5.16
Output | 0.0001294 | 0.00014959 | 0.00018927 | 0.0 | 11.83
Modify | 1.595e-06 | 2.2495e-06 | 2.798e-06 | 0.0 | 0.18
Other | | 1.145e-05 | | | 0.91
Comm | 0.00066534 | 0.0011191 | 0.0014774 | 1.0 | 3.50
Output | 0.00036537 | 0.00040732 | 0.00052168 | 0.0 | 1.27
Modify | 4.6407e-05 | 5.1041e-05 | 5.4068e-05 | 0.0 | 0.16
Other | | 0.0003526 | | | 1.10
Nlocal: 4.5 ave 6 max 3 min
Histogram: 1 0 0 1 0 0 1 0 0 1

3
src/AMOEBA/amoeba_induce.cpp
View File

@ -388,7 +388,8 @@ void PairAmoeba::induce()
// NOTE: could make this an error
if (iter >= maxiter || eps > epsold)
if (comm->me == 0) error->warning(FLERR,"AMOEBA induced dipoles did not converge");
if (comm->me == 0)
error->warning(FLERR,"AMOEBA induced dipoles did not converge");
}
// update the lists of previous induced dipole values

2
src/AMOEBA/amoeba_utils.cpp
View File

@ -74,7 +74,7 @@ void PairAmoeba::kmpole()
// create a sorted version of bond/angle neighs from special[][]
// NOTE: this is to try and do it identically to Tinker
// b/c I think in Tinker, atom order matters as to which case is seen fist
// b/c I think in Tinker, which case is seen first can depend on atom order
for (j = 0; j < nspecial[i][0]; j++)
bondneigh[j] = special[i][j];

2
src/AMOEBA/fix_amoeba_bitorsion.cpp
View File

@ -778,7 +778,7 @@ void FixAmoebaBiTorsion::read_grid_data(char *bitorsion_file)
memory->create(tty[itype],ny,"bitorsion:tty");
memory->create(tbf[itype],nx*ny,"bitorsion:tbf");
// NOTE: should read this chunk of lines with utils in single read
// NOTE: could read this chunk of lines with utils in single read?
if (me == 0) {
for (int iy = 0; iy < ny; iy++) {

12
src/AMOEBA/pair_amoeba.cpp
View File

@ -552,11 +552,14 @@ void PairAmoeba::allocate()
/* ----------------------------------------------------------------------
global settings
NOTE: these undocumented args are only for debugging
------------------------------------------------------------------------- */
void PairAmoeba::settings(int narg, char **arg)
{
// turn on all FF components by default
// first 4 lines are non-bonded terms
// last 2 lines are bonded terms
hal_flag = repulse_flag = qxfer_flag = 1;
disp_rspace_flag = disp_kspace_flag = 1;
@ -616,6 +619,12 @@ void PairAmoeba::settings(int narg, char **arg)
else if (strcmp(arg[iarg],"bitorsion") == 0) bitorsion_flag = newvalue;
else error->all(FLERR,"Illegal pair_style command");
}
// cannot disable bond and dihedral terms b/c those classes not in AMOEBA pkg
if ((bond_flag == 0 || dihedral_flag == 0) && comm->me == 0)
error->warning(FLERR,"Cannot disable AMOEBA bonds or dihedrals - "
"use bond_style or dihedral_style none instead");
}
/* ----------------------------------------------------------------------
@ -1757,7 +1766,7 @@ void PairAmoeba::precond_neigh()
// rather all interactions in the precond neigh list are
// used every step until the neighbor list is rebuilt,
// this means the cutoff distance is not exactly enforced,
// on a later step atoms outside may contribute, atoms inside may not
// on later steps atoms outside may contribute, atoms inside may not
choose(USOLV);
@ -2067,6 +2076,7 @@ void *PairAmoeba::extract(const char *str, int &dim)
if (strcmp(str,"opbend_quartic") == 0) return (void *) &opbend_quartic;
if (strcmp(str,"opbend_pentic") == 0) return (void *) &opbend_pentic;
if (strcmp(str,"opbend_sextic") == 0) return (void *) &opbend_sextic;
return nullptr;
}

20
src/CLASS2/bond_class2.cpp
View File

@ -53,8 +53,6 @@ BondClass2::~BondClass2()
void BondClass2::compute(int eflag, int vflag)
{
if (disable) return;
int i1,i2,n,type;
double delx,dely,delz,ebond,fbond;
double rsq,r,dr,dr2,dr3,dr4,de_bond;
@ -157,24 +155,6 @@ void BondClass2::coeff(int narg, char **arg)
if (count == 0) error->all(FLERR,"Incorrect args for bond coefficients");
}
/* ---------------------------------------------------------------------- */
void BondClass2::init_style()
{
// check if PairAmoeba or PairHippo disabled bond terms
Pair *pair = NULL;
pair = force->pair_match("amoeba",1,0);
if (!pair) pair = force->pair_match("hippo",1,0);
if (!pair) disable = 0;
else {
int tmp;
int flag = *((int *) pair->extract("bond_flag",tmp));
disable = flag ? 0 : 1;
}
}
/* ----------------------------------------------------------------------
return an equilbrium bond length
------------------------------------------------------------------------- */

2
src/CLASS2/bond_class2.h
View File

@ -30,7 +30,6 @@ class BondClass2 : public Bond {
~BondClass2() override;
void compute(int, int) override;
void coeff(int, char **) override;
void init_style() override;
double equilibrium_distance(int) override;
void write_restart(FILE *) override;
void read_restart(FILE *) override;
@ -40,7 +39,6 @@ class BondClass2 : public Bond {
protected:
double *r0, *k2, *k3, *k4;
int disable;
void allocate();
};

20
src/EXTRA-MOLECULE/dihedral_fourier.cpp
View File

@ -69,8 +69,6 @@ DihedralFourier::~DihedralFourier()
void DihedralFourier::compute(int eflag, int vflag)
{
if (disable) return;
int i1,i2,i3,i4,i,j,m,n,type;
double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,vb2xm,vb2ym,vb2zm;
double edihedral,f1[3],f2[3],f3[3],f4[3];
@ -328,24 +326,6 @@ void DihedralFourier::coeff(int narg, char **arg)
if (count == 0) error->all(FLERR,"Incorrect args for dihedral coefficients");
}
/* ---------------------------------------------------------------------- */
void DihedralFourier::init_style()
{
// check if PairAmoeba or PairHippo disabled dihedral terms
Pair *pair = NULL;
pair = force->pair_match("amoeba",1,0);
if (!pair) pair = force->pair_match("hippo",1,0);
if (!pair) disable = 0;
else {
int tmp;
int flag = *((int *) pair->extract("dihedral_flag",tmp));
disable = flag ? 0 : 1;
}
}
/* ----------------------------------------------------------------------
proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */

2
src/EXTRA-MOLECULE/dihedral_fourier.h
View File

@ -30,7 +30,6 @@ class DihedralFourier : public Dihedral {
~DihedralFourier() override;
void compute(int, int) override;
void coeff(int, char **) override;
void init_style() override;
void write_restart(FILE *) override;
void read_restart(FILE *) override;
void write_data(FILE *) override;
@ -40,7 +39,6 @@ class DihedralFourier : public Dihedral {
int **multiplicity;
int *nterms;
int implicit, weightflag;
int disable;
void allocate();
};