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

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This commit is contained in:
Axel Kohlmeyer
2022-07-05 06:59:31 -04:00
parent 574818c3e9
commit f58d413fbd
35 changed files with 1233 additions and 31175 deletions
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52
examples/amoeba/Compare.sh
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@ -1,52 +0,0 @@
# compare test runs to original runs
# dimer
kdiff.py log.water_dimer.amoeba.1 log.water_dimer.amoeba.1.test
kdiff.py dump.water_dimer.amoeba.1 dump.water_dimer.amoeba.1.test
kdiff.py log.water_dimer.amoeba.4 log.water_dimer.amoeba.4.test
kdiff.py dump.water_dimer.amoeba.4 dump.water_dimer.amoeba.4.test
kdiff.py log.water_dimer.hippo.1 log.water_dimer.hippo.1.test
kdiff.py dump.water_dimer.hippo.1 dump.water_dimer.hippo.1.test
kdiff.py log.water_dimer.hippo.4 log.water_dimer.hippo.4.test
kdiff.py dump.water_dimer.hippo.4 dump.water_dimer.hippo.4.test
# hexamer
kdiff.py log.water_hexamer.amoeba.1 log.water_hexamer.amoeba.1.test
kdiff.py dump.water_hexamer.amoeba.1 dump.water_hexamer.amoeba.1.test
kdiff.py log.water_hexamer.amoeba.4 log.water_hexamer.amoeba.4.test
kdiff.py dump.water_hexamer.amoeba.4 dump.water_hexamer.amoeba.4.test
kdiff.py log.water_hexamer.hippo.1 log.water_hexamer.hippo.1.test
kdiff.py dump.water_hexamer.hippo.1 dump.water_hexamer.hippo.1.test
kdiff.py log.water_hexamer.hippo.4 log.water_hexamer.hippo.4.test
kdiff.py dump.water_hexamer.hippo.4 dump.water_hexamer.hippo.4.test
# water box
kdiff.py log.water_box.amoeba.1 log.water_box.amoeba.1.test
kdiff.py dump.water_box.amoeba.1 dump.water_box.amoeba.1.test
kdiff.py log.water_box.amoeba.32 log.water_box.amoeba.32.test
kdiff.py dump.water_box.amoeba.32 dump.water_box.amoeba.32.test
kdiff.py log.water_box.hippo.1 log.water_box.hippo.1.test
kdiff.py dump.water_box.hippo.1 dump.water_box.hippo.1.test
kdiff.py log.water_box.hippo.32 log.water_box.hippo.32.test
kdiff.py dump.water_box.hippo.32 dump.water_box.hippo.32.test
# ubiquitin
kdiff.py log.ubiquitin.1 log.ubiquitin.1.test
kdiff.py dump.ubiquitin.1 dump.ubiquitin.1.test
kdiff.py log.ubiquitin.32 log.ubiquitin.32.test
kdiff.py dump.ubiquitin.32 dump.ubiquitin.32.test

68
examples/amoeba/Test.sh Normal file → Executable file
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@ -1,66 +1,34 @@
# run test problems
#!/bin/sh
# run test problems.
EXE=${1-../../src/lmp_mpi}
DATE=$(date +%1d%b%y)
# dimer
../../src/lmp_mpi < in.water_dimer.amoeba.test
mv log.lammps log.water_dimer.amoeba.1.test
mv dump.water_dimer dump.water_dimer.amoeba.1.test
${EXE} -in in.water_dimer.amoeba -log log.${DATE}.water_dimer.amoeba.g++.1
mpirun -np 4 ${EXE} -in in.water_dimer.amoeba -log log.${DATE}.water_dimer.amoeba.g++.4
mpirun -np 4 ../../src/lmp_mpi < in.water_dimer.amoeba.test
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.test
mv log.lammps log.water_dimer.hippo.1.test
mv dump.water_dimer dump.water_dimer.hippo.1.test
mpirun -np 4 ../../src/lmp_mpi < in.water_dimer.hippo.test
mv log.lammps log.water_dimer.hippo.4.test
mv dump.water_dimer dump.water_dimer.hippo.4.test
${EXE} -in in.water_dimer.hippo -log log.${DATE}.water_dimer.hippo.g++.1
mpirun -np 4 ${EXE} -in in.water_dimer.hippo -log log.${DATE}.water_dimer.hippo.g++.4
# hexamer
../../src/lmp_mpi < in.water_hexamer.amoeba.test
mv log.lammps log.water_hexamer.amoeba.1.test
mv dump.water_hexamer dump.water_hexamer.amoeba.1.test
${EXE} -in in.water_hexamer.amoeba -log log.${DATE}.water_hexamer.amoeba.g++.1
mpirun -np 4 ${EXE} -in in.water_hexamer.amoeba -log log.${DATE}.water_hexamer.amoeba.g++.4
mpirun -np 4 ../../src/lmp_mpi < in.water_hexamer.amoeba.test
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.test
mv log.lammps log.water_hexamer.hippo.1.test
mv dump.water_hexamer dump.water_hexamer.hippo.1.test
mpirun -np 4 ../../src/lmp_mpi < in.water_hexamer.hippo.test
mv log.lammps log.water_hexamer.hippo.4.test
mv dump.water_hexamer dump.water_hexamer.hippo.4.test
${EXE} -in in.water_hexamer.hippo -log log.${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
../../src/lmp_mpi < in.water_box.amoeba.test
mv log.lammps log.water_box.amoeba.1.test
mv dump.water_box dump.water_box.amoeba.1.test
${EXE} -in in.water_box.amoeba -log log.${DATE}.water_box.amoeba.g++.1
mpirun -np 4 ${EXE} -in in.water_box.amoeba -log log.${DATE}.water_box.amoeba.g++.4
mpirun -np 32 ../../src/lmp_mpi < in.water_box.amoeba.test
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.test
mv log.lammps log.water_box.hippo.1.test
mv dump.water_box dump.water_box.hippo.1.test
mpirun -np 32 ../../src/lmp_mpi < in.water_box.hippo.test
mv log.lammps log.water_box.hippo.32.test
mv dump.water_box dump.water_box.hippo.32.test
${EXE} -in in.water_box.hippo -log log.${DATE}.water_box.hippo.g++.1
mpirun -np 4 ${EXE} -in in.water_box.hippo -log log.${DATE}.water_box.hippo.g++.4
# ubiquitin
../../src/lmp_mpi < in.ubiquitin.test
mv log.lammps log.ubiquitin.1.test
mv dump.ubiquitin dump.ubiquitin.1.test
mpirun -np 32 ../../src/lmp_mpi < in.ubiquitin.test
mv log.lammps log.ubiquitin.32.test
mv dump.ubiquitin dump.ubiquitin.32.test
${EXE} -in in.ubiquitin -log log.${DATE}.ubiquitin.g++.1
mpirun -np 4 ${EXE} -in in.ubiquitin -log log.${DATE}.ubiquitin.g++.4

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examples/amoeba/dump.water_box.amoeba.1
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7227
examples/amoeba/dump.water_box.amoeba.32
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7227
examples/amoeba/dump.water_box.hippo.1
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7227
examples/amoeba/dump.water_box.hippo.32
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165
examples/amoeba/dump.water_dimer.amoeba.1
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@ -1,165 +0,0 @@
ITEM: TIMESTEP
0
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS ss ss ss
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ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
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ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
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ITEM: ATOMS id type x y z fx fy fz
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5 2 -1.45804 0.75449 2.94684 5.21348 5.11475 -1.77652
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ITEM: TIMESTEP
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ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
-1.4632357229999999e+00 9.3247372299999998e-01
-7.5570026690000003e-01 7.5527126690000002e-01
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ITEM: ATOMS id type x y z fx fy fz
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3 2 0.92432 -0.000494304 -0.125343 2.07038 0.00615069 6.42537
4 1 -0.900866 0.00010992 2.76846 11.0986 0.00640696 -3.42785
5 2 -1.40977 0.795072 2.93807 -5.57817 -3.04583 1.75974
6 2 -1.40852 -0.795411 2.93919 -5.58301 3.03943 1.75548
ITEM: TIMESTEP
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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 -0.171607 -0.000594964 0.954009 -8.40692 -0.00484075 2.50346
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ITEM: TIMESTEP
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ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
-1.4632357229999999e+00 9.3247372299999998e-01
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ITEM: ATOMS id type x y z fx fy fz
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ITEM: TIMESTEP
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ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
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ITEM: TIMESTEP
70
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS ss ss ss
-1.4632357229999999e+00 9.3247372299999998e-01
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ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
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ITEM: ATOMS id type x y z fx fy fz
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ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
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ITEM: ATOMS id type x y z fx fy fz
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ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
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ITEM: ATOMS id type x y z fx fy fz
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5 2 -1.45671 0.76736 2.88018 3.9012 0.426437 -0.678284
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165
examples/amoeba/dump.water_dimer.amoeba.4
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@ -1,165 +0,0 @@
ITEM: TIMESTEP
0
ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
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ITEM: ATOMS id type x y z fx fy fz
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ITEM: TIMESTEP
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ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
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ITEM: ATOMS id type x y z fx fy fz
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ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
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ITEM: ATOMS id type x y z fx fy fz
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ITEM: TIMESTEP
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ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS ss ss ss
-1.4632357229999999e+00 9.3247372299999998e-01
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ITEM: ATOMS id type x y z fx fy fz
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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
4 1 -0.900866 0.00010992 2.76846 11.0986 0.00640696 -3.42785
5 2 -1.40977 0.795072 2.93807 -5.57817 -3.04583 1.75974
6 2 -1.40852 -0.795411 2.93919 -5.58301 3.03943 1.75548
ITEM: TIMESTEP
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ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS ss ss ss
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ITEM: ATOMS id type x y z fx fy fz
1 1 -0.0269208 -0.00114842 0.00674288 5.42877 0.00730481 4.31748
2 2 -0.171607 -0.000594964 0.954009 -8.40692 -0.00484075 2.50346
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5 2 -1.45218 0.754436 2.95353 3.40261 6.39649 -1.53879
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ITEM: TIMESTEP
50
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS ss ss ss
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ITEM: TIMESTEP
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ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
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ITEM: ATOMS id type x y z fx fy fz
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5 2 -1.45749 0.757284 2.91975 3.48398 5.14308 -1.14726
6 2 -1.4563 -0.757724 2.92081 3.49211 -5.13915 -1.14003
ITEM: TIMESTEP
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ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
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ITEM: ATOMS id type x y z fx fy fz
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4 1 -0.894893 0.000114175 2.76783 7.43985 0.00424265 -2.1131
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6 2 -1.42292 -0.792944 2.88751 -3.94318 3.53329 1.14403
ITEM: TIMESTEP
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ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS ss ss ss
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ITEM: ATOMS id type x y z fx fy fz
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4 1 -0.888796 0.000119275 2.76827 -9.03539 -0.00642914 1.05959
5 2 -1.46214 0.762697 2.87512 4.48797 2.10983 -0.617778
6 2 -1.46094 -0.763208 2.87619 4.49133 -2.10357 -0.61482
ITEM: TIMESTEP
90
ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
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ITEM: ATOMS id type x y z fx fy fz
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4 1 -0.891964 0.000116952 2.76852 3.17186 0.0014363 -1.52231
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6 2 -1.43013 -0.791605 2.86488 -1.95795 4.67604 0.85497
ITEM: TIMESTEP
100
ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
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ITEM: ATOMS id type x y z fx fy fz
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2 2 -0.203569 -0.000615753 0.960107 -6.40597 -0.00736639 -3.30674
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4 1 -0.889443 0.000116814 2.76553 -7.7691 -0.0050422 1.37075
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165
examples/amoeba/dump.water_dimer.hippo.1
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@ -1,165 +0,0 @@
ITEM: TIMESTEP
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ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
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ITEM: ATOMS id type x y z fx fy fz
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ITEM: TIMESTEP
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ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
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ITEM: ATOMS id type x y z fx fy fz
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6 2 -1.42099 -0.791374 2.92075 -3.91591 4.87112 1.05588
ITEM: TIMESTEP
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ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
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ITEM: ATOMS id type x y z fx fy fz
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4 1 -0.893054 0.000118973 2.77259 -8.83712 -0.00512625 2.54445
5 2 -1.46387 0.753541 2.92502 4.54888 4.85296 -1.48277
6 2 -1.46268 -0.753984 2.92608 4.55648 -4.84791 -1.47593
ITEM: TIMESTEP
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ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
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ITEM: ATOMS id type x y z fx fy fz
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3 2 0.923032 -0.000493736 -0.123121 1.75879 0.00552582 5.88556
4 1 -0.897978 0.000115451 2.77309 11.6501 0.00727223 -2.82116
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6 2 -1.42412 -0.788676 2.90134 -5.84324 2.06468 1.27016
ITEM: TIMESTEP
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ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
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ITEM: ATOMS id type x y z fx fy fz
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2 2 -0.153199 -0.000576377 0.959922 -7.58451 -0.00449199 2.07976
3 2 0.919336 -0.000480028 -0.0995905 1.37912 -0.00359093 -6.63778
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6 2 -1.46886 -0.752392 2.88844 3.11554 -6.73373 -0.972121
ITEM: TIMESTEP
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ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
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ITEM: ATOMS id type x y z fx fy fz
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5 2 -1.4336 0.787999 2.84603 -5.85703 -2.08185 0.681764
6 2 -1.43237 -0.788505 2.84714 -5.86031 2.07358 0.678838
ITEM: TIMESTEP
60
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS ss ss ss
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ITEM: ATOMS id type x y z fx fy fz
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2 2 -0.113434 -0.000533921 0.975674 -7.44659 -0.00496006 1.26816
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4 1 -0.888126 0.000122907 2.77269 -9.08281 -0.00670232 0.725333
5 2 -1.47838 0.753365 2.8077 4.79099 4.82306 -0.504859
6 2 -1.47719 -0.753996 2.80876 4.79863 -4.81616 -0.498076
ITEM: TIMESTEP
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ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
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ITEM: ATOMS id type x y z fx fy fz
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3 2 0.899135 -0.000560623 -0.191768 0.56204 0.00474764 6.11404
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6 2 -1.43466 -0.791026 2.7599 -3.90736 4.83989 0.11913
ITEM: TIMESTEP
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ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
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ITEM: ATOMS id type x y z fx fy fz
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4 1 -0.883488 0.000127321 2.77377 -12.2256 -0.0109573 -1.83848
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6 2 -1.4719 -0.756019 2.71407 6.17192 -2.87983 0.800362
ITEM: TIMESTEP
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ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
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ITEM: ATOMS id type x y z fx fy fz
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3 2 0.889431 -0.00057205 -0.197356 0.916 0.00477871 5.76452
4 1 -0.886952 0.000122589 2.77093 7.29365 0.00587785 0.155791
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6 2 -1.42478 -0.791209 2.68827 -3.94309 4.85389 -0.0130349
ITEM: TIMESTEP
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ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
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ITEM: ATOMS id type x y z fx fy fz
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165
examples/amoeba/dump.water_dimer.hippo.4
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ITEM: NUMBER OF ATOMS
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ITEM: ATOMS id type x y z fx fy fz
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ITEM: TIMESTEP
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ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
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ITEM: ATOMS id type x y z fx fy fz
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ITEM: TIMESTEP
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ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
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ITEM: ATOMS id type x y z fx fy fz
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ITEM: TIMESTEP
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ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
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ITEM: TIMESTEP
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ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
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ITEM: ATOMS id type x y z fx fy fz
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4 1 -0.89217 0.000118771 2.77132 -5.68638 -0.00321013 1.64962
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ITEM: TIMESTEP
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ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
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ITEM: ATOMS id type x y z fx fy fz
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2 2 -0.185755 -0.000598779 0.964286 5.83022 0.00671605 3.0354
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4 1 -0.895573 0.00011689 2.77245 11.8261 0.00822001 -1.54401
5 2 -1.4336 0.787999 2.84603 -5.85703 -2.08185 0.681764
6 2 -1.43237 -0.788505 2.84714 -5.86031 2.07358 0.678838
ITEM: TIMESTEP
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ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
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ITEM: ATOMS id type x y z fx fy fz
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2 2 -0.113434 -0.000533921 0.975674 -7.44659 -0.00496006 1.26816
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4 1 -0.888126 0.000122907 2.77269 -9.08281 -0.00670232 0.725333
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6 2 -1.47719 -0.753996 2.80876 4.79863 -4.81616 -0.498076
ITEM: TIMESTEP
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ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
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ITEM: ATOMS id type x y z fx fy fz
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ITEM: NUMBER OF ATOMS
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ITEM: ATOMS id type x y z fx fy fz
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ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
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ITEM: TIMESTEP
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ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
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297
examples/amoeba/dump.water_hexamer.amoeba.1
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ITEM: TIMESTEP
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ITEM: NUMBER OF ATOMS
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ITEM: ATOMS id type x y z fx fy fz
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ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
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ITEM: TIMESTEP
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ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
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12 2 1.55686 -0.401102 1.29785 -3.41945 -1.35828 5.31582
13 1 0.971997 -1.39727 -1.33295 -3.50737 11.1512 0.685267
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ITEM: TIMESTEP
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ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
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ITEM: ATOMS id type x y z fx fy fz
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ITEM: TIMESTEP
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ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
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ITEM: ATOMS id type x y z fx fy fz
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8 2 -0.992092 1.48382 0.567817 1.09284 0.418387 6.78235
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10 1 1.00941 -1.17308 1.4189 -1.85973 4.64458 1.0889
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12 2 1.53559 -0.396477 1.19908 0.544307 1.46508 3.63166
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15 2 1.46633 -0.576681 -1.19175 5.00795 0.70617 0.521536
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17 2 1.19121 1.55327 -0.120038 -7.25224 2.19125 0.154184
18 2 2.71636 1.68982 -0.237383 1.31607 -0.463304 0.195666
ITEM: TIMESTEP
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ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
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ITEM: ATOMS id type x y z fx fy fz
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3 2 -2.07217 -0.405364 2.23045 -0.725799 -0.490948 1.77161
4 1 -1.74113 -0.378171 -1.32957 5.99712 2.85952 -9.13842
5 2 -1.82713 -0.447378 -0.375703 -3.89226 -1.3818 7.11516
6 2 -2.4999 -0.790471 -1.74187 -3.02333 -1.60416 1.77146
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8 2 -0.97832 1.50522 0.591572 -4.4866 -5.64841 2.33138
9 2 -0.951447 1.66071 -0.944057 -3.97244 -4.92262 -1.79974
10 1 1.01358 -1.17192 1.41393 -6.48605 2.83151 13.495
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12 2 1.53449 -0.394669 1.19537 2.46945 2.14925 -1.89795
13 1 0.966791 -1.38037 -1.31946 4.73561 -12.449 -1.17286
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15 2 1.48076 -0.580834 -1.19775 0.0522693 6.36707 0.249418
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ITEM: TIMESTEP
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ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
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8 2 -0.97416 1.49195 0.577492 -1.32391 -2.58987 8.72867
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10 1 1.00791 -1.1681 1.41401 -6.20027 1.07549 12.575
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12 2 1.54632 -0.404877 1.20306 3.83119 5.88484 -0.834958
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ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
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10 1 0.996682 -1.16249 1.41603 -5.52393 -2.7768 9.00886
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ITEM: TIMESTEP
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ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
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ITEM: ATOMS id type x y z fx fy fz
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4 1 -1.74352 -0.377279 -1.33693 -0.505822 0.308788 -3.25308
5 2 -1.91188 -0.438855 -0.39405 1.95743 0.358158 9.20234
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8 2 -0.938419 1.50232 0.602337 -1.22478 -1.30903 4.8686
9 2 -0.959599 1.56918 -0.90914 -0.0288155 0.574454 -3.52808
10 1 0.985435 -1.15713 1.41811 -6.25848 -6.25702 9.27302
11 2 0.972167 -1.59168 0.560031 1.69554 -0.201305 -5.06875
12 2 1.54032 -0.386652 1.30283 4.96928 5.72762 -4.15176
13 1 0.963614 -1.3793 -1.33436 0.183354 -1.1048 0.823621
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15 2 1.49256 -0.587857 -1.21654 4.36346 2.23441 0.338535
16 1 2.00803 1.04345 -0.110717 3.61274 -3.25471 0.639326
17 2 1.16919 1.51061 -0.133404 -8.46417 2.50048 0.10369
18 2 2.67828 1.72068 -0.16597 4.94198 1.56662 -0.49597
ITEM: TIMESTEP
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ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
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ITEM: ATOMS id type x y z fx fy fz
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2 2 -0.637201 -0.589948 1.58141 9.00709 -5.13609 3.43504
3 2 -1.97805 -0.327506 2.28752 -1.76215 -2.05269 5.01359
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5 2 -1.87141 -0.433051 -0.37781 -3.50795 -2.5324 4.09176
6 2 -2.48522 -0.804273 -1.77362 -2.18894 -1.0456 2.79096
7 1 -0.568425 1.98378 -0.140489 1.33268 1.60885 -0.760228
8 2 -0.945484 1.51375 0.61188 -1.03442 -1.79649 -0.570033
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ITEM: TIMESTEP
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ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
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ITEM: ATOMS id type x y z fx fy fz
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297
examples/amoeba/dump.water_hexamer.amoeba.4
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ITEM: NUMBER OF ATOMS
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ITEM: ATOMS id type x y z fx fy fz
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ITEM: TIMESTEP
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ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
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ITEM: ATOMS id type x y z fx fy fz
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ITEM: TIMESTEP
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ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
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ITEM: ATOMS id type x y z fx fy fz
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10 1 0.981527 -1.16776 1.43139 8.19382 2.30469 -14.0571
11 2 0.999682 -1.57682 0.548153 -4.17545 -1.46604 7.90595
12 2 1.55686 -0.401102 1.29785 -3.41945 -1.35828 5.31582
13 1 0.971997 -1.39727 -1.33295 -3.50737 11.1512 0.685267
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17 2 1.16008 1.5422 -0.129327 5.1837 -4.83397 0.46283
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ITEM: TIMESTEP
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ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
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ITEM: ATOMS id type x y z fx fy fz
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10 1 0.998541 -1.16996 1.42191 -2.76709 -0.0175982 4.85417
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18 2 2.71517 1.69464 -0.239075 -2.32089 0.157967 0.209615
ITEM: TIMESTEP
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ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
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ITEM: ATOMS id type x y z fx fy fz
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10 1 1.00941 -1.17308 1.4189 -1.85973 4.64458 1.0889
11 2 0.973659 -1.6403 0.580693 -1.69219 -4.78957 -3.29195
12 2 1.53559 -0.396477 1.19908 0.544307 1.46508 3.63166
13 1 0.969009 -1.38744 -1.3228 -0.275569 1.85307 -0.63583
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15 2 1.46633 -0.576681 -1.19175 5.00795 0.70617 0.521536
16 1 2.01183 1.05054 -0.121932 4.41526 -1.70685 -0.0836272
17 2 1.19121 1.55327 -0.120038 -7.25224 2.19125 0.154184
18 2 2.71636 1.68982 -0.237383 1.31607 -0.463304 0.195666
ITEM: TIMESTEP
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ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
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ITEM: ATOMS id type x y z fx fy fz
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3 2 -2.07217 -0.405364 2.23045 -0.725799 -0.490948 1.77161
4 1 -1.74113 -0.378171 -1.32957 5.99712 2.85952 -9.13842
5 2 -1.82713 -0.447378 -0.375703 -3.89226 -1.3818 7.11516
6 2 -2.4999 -0.790471 -1.74187 -3.02333 -1.60416 1.77146
7 1 -0.579496 1.99691 -0.128028 9.72738 10.7655 -0.463519
8 2 -0.97832 1.50522 0.591572 -4.4866 -5.64841 2.33138
9 2 -0.951447 1.66071 -0.944057 -3.97244 -4.92262 -1.79974
10 1 1.01358 -1.17192 1.41393 -6.48605 2.83151 13.495
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12 2 1.53449 -0.394669 1.19537 2.46945 2.14925 -1.89795
13 1 0.966791 -1.38037 -1.31946 4.73561 -12.449 -1.17286
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15 2 1.48076 -0.580834 -1.19775 0.0522693 6.36707 0.249418
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18 2 2.72824 1.67508 -0.226016 0.699647 3.77524 -0.159727
ITEM: TIMESTEP
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ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
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ITEM: ATOMS id type x y z fx fy fz
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8 2 -0.97416 1.49195 0.577492 -1.32391 -2.58987 8.72867
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10 1 1.00791 -1.1681 1.41401 -6.20027 1.07549 12.575
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12 2 1.54632 -0.404877 1.20306 3.83119 5.88484 -0.834958
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15 2 1.45394 -0.565765 -1.20718 7.01226 4.42564 1.66198
16 1 2.01308 1.04537 -0.116618 6.94232 -7.944 0.350248
17 2 1.19126 1.53332 -0.135036 -13.3157 5.74475 0.221956
18 2 2.70715 1.69348 -0.205764 4.95008 2.7812 -0.398561
ITEM: TIMESTEP
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ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
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ITEM: ATOMS id type x y z fx fy fz
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8 2 -0.93279 1.50467 0.607511 -5.01196 -5.05095 3.69276
9 2 -0.967697 1.61396 -0.924499 -2.96791 -3.60448 -2.11522
10 1 0.996682 -1.16249 1.41603 -5.52393 -2.7768 9.00886
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13 1 0.964232 -1.37715 -1.32734 3.83388 -12.0598 -0.0980446
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18 2 2.7022 1.69874 -0.182183 2.76884 5.3999 -0.639748
ITEM: TIMESTEP
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ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
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ITEM: ATOMS id type x y z fx fy fz
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10 1 0.985435 -1.15713 1.41811 -6.25848 -6.25702 9.27302
11 2 0.972167 -1.59168 0.560031 1.69554 -0.201305 -5.06875
12 2 1.54032 -0.386652 1.30283 4.96928 5.72762 -4.15176
13 1 0.963614 -1.3793 -1.33436 0.183354 -1.1048 0.823621
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15 2 1.49256 -0.587857 -1.21654 4.36346 2.23441 0.338535
16 1 2.00803 1.04345 -0.110717 3.61274 -3.25471 0.639326
17 2 1.16919 1.51061 -0.133404 -8.46417 2.50048 0.10369
18 2 2.67828 1.72068 -0.16597 4.94198 1.56662 -0.49597
ITEM: TIMESTEP
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ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
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ITEM: ATOMS id type x y z fx fy fz
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10 1 0.975854 -1.15481 1.42351 1.86741 -2.52595 -4.21318
11 2 0.98193 -1.53917 0.537259 -2.6087 -4.02599 1.03016
12 2 1.52752 -0.379325 1.30866 2.98513 5.11632 2.51897
13 1 0.962056 -1.37771 -1.33914 1.58342 -3.36145 0.893222
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15 2 1.52774 -0.603203 -1.25083 -2.15602 1.98356 -0.537593
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ITEM: TIMESTEP
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ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
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ITEM: ATOMS id type x y z fx fy fz
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297
examples/amoeba/dump.water_hexamer.hippo.1
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ITEM: NUMBER OF ATOMS
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ITEM: ATOMS id type x y z fx fy fz
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12 2 1.54222 -0.393692 1.34437 -5.98579 -2.68738 6.2337
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ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
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ITEM: TIMESTEP
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ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
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6 2 -2.51909 -0.769609 -1.71571 1.56589 0.868196 -2.04346
7 1 -0.571857 2.01726 -0.121524 -4.42229 -10.7497 0.101549
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10 1 0.983665 -1.17004 1.43811 2.15858 5.32924 -12.0192
11 2 0.916986 -1.51176 0.532863 -0.801958 -4.34579 6.00669
12 2 1.48632 -0.356933 1.30471 -0.115562 -1.35756 5.38685
13 1 0.974155 -1.39809 -1.34091 -3.6872 9.81415 2.33229
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16 1 2.0041 1.05318 -0.12468 -4.82863 5.07797 -0.287867
17 2 1.15863 1.52924 -0.140109 2.7798 -3.05413 0.358119
18 2 2.67895 1.72504 -0.234758 0.77424 -2.65718 0.249897
ITEM: TIMESTEP
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ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
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ITEM: ATOMS id type x y z fx fy fz
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5 2 -1.85923 -0.443728 -0.358889 -2.57415 -1.51426 3.86387
6 2 -2.50599 -0.762479 -1.73443 -2.25678 -0.997735 0.886673
7 1 -0.57869 2.00716 -0.122116 7.46708 7.5609 -0.932554
8 2 -0.891326 1.5227 0.646189 -3.77932 -4.24552 -0.379656
9 2 -0.906489 1.54888 -0.899539 -3.74504 -3.89196 0.775918
10 1 0.993915 -1.16716 1.4314 -4.03671 -0.827424 10.5116
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12 2 1.49414 -0.355801 1.3027 1.34198 0.116597 -4.03649
13 1 0.970608 -1.38983 -1.33905 4.21477 -7.05635 0.421831
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15 2 1.48422 -0.594211 -1.16216 -2.77696 3.0816 -1.11496
16 1 2.00096 1.05017 -0.124007 4.94447 -7.97826 1.06585
17 2 1.17138 1.53183 -0.140668 -5.63771 5.40691 -0.274313
18 2 2.7082 1.68479 -0.23083 -0.128954 2.19398 -0.267092
ITEM: TIMESTEP
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ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
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ITEM: ATOMS id type x y z fx fy fz
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2 2 -0.687962 -0.594151 1.59127 27.1026 -13.0552 4.45143
3 2 -2.07116 -0.378379 2.19317 -1.29427 -1.5252 3.96365
4 1 -1.73305 -0.375414 -1.31137 2.16372 2.0419 -7.75161
5 2 -1.87951 -0.450834 -0.370226 0.624847 -0.775772 11.2387
6 2 -2.50254 -0.754697 -1.72909 -2.50645 -1.07375 -3.54713
7 1 -0.578876 1.99941 -0.124067 2.19183 2.88771 -2.2033
8 2 -0.936478 1.52242 0.623048 -0.431918 -2.06784 8.93732
9 2 -0.943689 1.52907 -0.872983 -0.503357 -0.655131 -7.36871
10 1 1.00066 -1.16525 1.43041 -2.12968 1.37125 11.5778
11 2 0.974279 -1.60078 0.583019 -3.02955 -6.45349 -11.2722
12 2 1.51087 -0.375422 1.25067 2.49642 6.22795 1.24643
13 1 0.96952 -1.38626 -1.33641 3.1199 -1.09706 -1.06644
14 2 0.0736705 -1.0998 -1.50988 -8.20047 -1.85824 -0.95018
15 2 1.45433 -0.57243 -1.18601 5.63783 2.37426 1.20997
16 1 1.9962 1.04317 -0.122075 10.6231 -9.89832 0.540427
17 2 1.19663 1.55837 -0.138658 -15.3708 7.22601 0.146924
18 2 2.71508 1.6609 -0.228386 3.66149 2.12531 -0.383549
ITEM: TIMESTEP
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ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
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ITEM: ATOMS id type x y z fx fy fz
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2 2 -0.679923 -0.574818 1.57581 25.4624 -12.0419 4.4477
3 2 -2.05017 -0.382025 2.20867 -3.53537 -2.33472 6.62258
4 1 -1.72947 -0.37135 -1.31158 7.45117 4.03521 -12.7525
5 2 -1.85272 -0.46757 -0.370426 -4.08312 -1.86842 12.0545
6 2 -2.4914 -0.737252 -1.75485 -4.03109 -2.01148 0.403261
7 1 -0.581812 1.98886 -0.127591 8.73336 12.0451 -2.23223
8 2 -0.927295 1.54015 0.641551 -4.26906 -6.45964 5.24049
9 2 -0.953055 1.5416 -0.887204 -3.28906 -5.2042 -3.24355
10 1 1.00866 -1.16393 1.43094 -5.76797 0.688141 16.3003
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12 2 1.5005 -0.365594 1.24465 4.16474 6.46538 -1.29083
13 1 0.968591 -1.37822 -1.33754 5.88173 -13.6635 -0.995409
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15 2 1.47128 -0.574689 -1.20309 0.663977 7.53437 1.14922
16 1 1.99172 1.03702 -0.120004 11.7209 -15.9347 1.25003
17 2 1.18616 1.54124 -0.127765 -14.4197 10.6401 -0.950727
18 2 2.7224 1.64022 -0.223578 2.05256 5.25094 -0.438473
ITEM: TIMESTEP
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ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
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ITEM: ATOMS id type x y z fx fy fz
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7 1 -0.582396 1.98478 -0.131637 3.0799 3.10149 -1.36944
8 2 -0.917703 1.51358 0.63199 -1.67497 -1.52591 5.69623
9 2 -0.95935 1.51373 -0.876424 -0.704912 -1.0485 -4.50039
10 1 1.01141 -1.16147 1.43332 -7.40944 0.284109 12.5023
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12 2 1.49548 -0.352196 1.26684 4.34342 4.22027 -2.29553
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15 2 1.44029 -0.555019 -1.20354 6.44357 4.32801 1.75924
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17 2 1.17286 1.52668 -0.137432 -10.3716 4.01885 -0.196355
18 2 2.69 1.66639 -0.213741 4.03261 1.60042 -0.312306
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ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
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ITEM: ATOMS id type x y z fx fy fz
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9 2 -0.943124 1.49995 -0.888932 -0.754685 -0.199723 0.596245
10 1 1.00431 -1.15529 1.43647 -0.676345 0.911353 -2.95012
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12 2 1.52689 -0.36229 1.29214 1.34973 2.90443 2.73267
13 1 0.96764 -1.3732 -1.34735 0.830518 -7.82237 0.0710001
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16 1 1.98438 1.02188 -0.114233 -0.881295 -2.57322 0.275288
17 2 1.13419 1.48172 -0.149659 1.87909 1.86036 0.463365
18 2 2.6735 1.67987 -0.202074 -0.651386 1.64881 -0.399918
ITEM: TIMESTEP
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ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
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ITEM: ATOMS id type x y z fx fy fz
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4 1 -1.71857 -0.360372 -1.31644 -7.32338 -2.11362 6.45601
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9 2 -0.943839 1.48954 -0.89443 1.32563 2.05291 3.72773
10 1 0.995847 -1.14613 1.43537 0.755936 -5.6909 -0.46639
11 2 0.966841 -1.55186 0.550806 1.56938 7.42451 5.54707
12 2 1.55511 -0.362342 1.35836 -2.79165 -2.9995 -5.36768
13 1 0.967816 -1.37465 -1.35163 -3.29308 4.65803 -0.872226
14 2 0.0602027 -1.09254 -1.5264 2.56737 -3.64929 1.27094
15 2 1.45854 -0.559392 -1.19328 1.84002 -1.84978 0.0538636
16 1 1.98052 1.0158 -0.111184 -7.14388 11.5516 -0.816233
17 2 1.12003 1.47724 -0.140032 8.70268 -6.85942 1.26876
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ITEM: TIMESTEP
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ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
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ITEM: ATOMS id type x y z fx fy fz
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3 2 -2.00991 -0.394435 2.25305 5.57059 1.55514 -7.64598
4 1 -1.72137 -0.357368 -1.31563 -1.93902 -0.246344 7.85181
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6 2 -2.49861 -0.682857 -1.77755 1.48512 0.513779 4.12935
7 1 -0.579472 1.97061 -0.145894 -8.85759 -8.26094 2.77276
8 2 -0.945449 1.52054 0.635243 4.66427 4.57627 -6.94972
9 2 -0.952686 1.48464 -0.897126 3.60343 4.09955 4.74753
10 1 0.988258 -1.14419 1.44127 11.1074 1.88534 -20.9154
11 2 0.971991 -1.50516 0.531218 -4.29535 0.162687 14.3489
12 2 1.5415 -0.356231 1.32305 -5.76468 -4.25266 5.91571
13 1 0.969416 -1.37359 -1.35605 -1.23717 3.53556 0.174563
14 2 0.053578 -1.1004 -1.52114 7.10928 -0.236326 1.96556
15 2 1.49219 -0.569722 -1.21186 -5.0738 -3.24139 -1.5161
16 1 1.97824 1.01566 -0.108279 -8.95647 8.69277 0.191958
17 2 1.10027 1.45664 -0.104435 15.9218 -5.21388 -1.22481
18 2 2.64464 1.70165 -0.21558 -4.82724 -2.84557 0.534172
ITEM: TIMESTEP
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ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
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ITEM: ATOMS id type x y z fx fy fz
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examples/amoeba/dump.water_hexamer.hippo.4
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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: BOX BOUNDS ss ss ss
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ITEM: NUMBER OF ATOMS
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12 2 1.51087 -0.375422 1.25067 2.49642 6.22795 1.24643
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ITEM: TIMESTEP
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ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
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ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
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12 2 1.49548 -0.352196 1.26684 4.34342 4.22027 -2.29553
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ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
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ITEM: NUMBER OF ATOMS
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ITEM: NUMBER OF ATOMS
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12 2 1.5415 -0.356231 1.32305 -5.76468 -4.25266 5.91571
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18 2 2.64464 1.70165 -0.21558 -4.82724 -2.84557 0.534172
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ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS ss ss ss
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8 2 -0.935394 1.51644 0.636953 2.89489 2.96603 -9.31226
9 2 -0.942573 1.488 -0.91114 1.96254 2.34604 7.29302
10 1 0.988651 -1.14425 1.44045 0.840008 -1.36718 -7.83612
11 2 0.899639 -1.53136 0.543246 5.64911 9.69241 11.7913
12 2 1.49178 -0.318235 1.33897 -3.7582 -9.86315 -4.79205
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

4
examples/amoeba/in.ubiquitin
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@ -41,8 +41,8 @@ compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp &
emol etotal press c_virial[*]
dump 1 all custom 10 dump.ubiquitin id type x y z fx fy fz
dump_modify 1 sort id
#dump 1 all custom 10 dump.ubiquitin id type x y z fx fy fz
#dump_modify 1 sort id
# zero step run

4
examples/amoeba/in.water_box.amoeba
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@ -32,8 +32,8 @@ compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp &
emol etotal press c_virial[*]
dump 1 all custom 10 dump.water_box id type x y z fx fy fz
dump_modify 1 sort id
#dump 1 all custom 10 dump.water_box id type x y z fx fy fz
#dump_modify 1 sort id
# zero step run

4
examples/amoeba/in.water_box.hippo
View File

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

4
examples/amoeba/in.water_dimer.amoeba
View File

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

4
examples/amoeba/in.water_dimer.hippo
View File

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

4
examples/amoeba/in.water_hexamer.amoeba
View File

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

4
examples/amoeba/in.water_hexamer.hippo
View File

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

162
examples/amoeba/log.5Jul22.ubiquitin.g++.1 Normal file
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@ -0,0 +1,162 @@
LAMMPS (23 Jun 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# solvated ubiquitin molecule with AMOEBA force field
units real
boundary p p p
atom_modify sort 0 0.0
atom_style amoeba
bond_style class2
angle_style amoeba
dihedral_style fourier
improper_style amoeba
# per-atom properties required by AMOEBA or HIPPO
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom i_amgroup d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
fix pit all amoeba/pitorsion
fix_modify pit energy yes
fix bit all amoeba/bitorsion bitorsion.ubiquitin.data
fix_modify bit energy yes
# read data file
read_data data.ubiquitin fix amtype NULL "Tinker Types" fix pit "pitorsion types" "PiTorsion Coeffs" fix pit pitorsions PiTorsions fix bit bitorsions BiTorsions
Reading data file ...
orthogonal box = (0 0 0) to (54.99 41.91 41.91)
1 by 1 by 1 MPI processor grid
reading atoms ...
9737 atoms
scanning bonds ...
4 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
18 = max dihedrals/atom
scanning impropers ...
3 = max impropers/atom
reading bonds ...
6908 bonds
reading angles ...
5094 angles
reading dihedrals ...
3297 dihedrals
reading impropers ...
651 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
4 = max # of 1-2 neighbors
9 = max # of 1-3 neighbors
19 = max # of 1-4 neighbors
21 = max # of special neighbors
special bonds CPU = 0.003 seconds
read_data CPU = 0.042 seconds
pair_style amoeba
pair_coeff * * amoeba_ubiquitin.prm amoeba_ubiquitin.key
Skipping section: AMOEBA Protein Force Field Atom Classes
Skipping section: Torsion-Torsion Parameters
Skipping section: Biopolymer Atom Type Conversions
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0.5 0.5 0.5
special bond factors coul: 0.5 0.5 0.5
4 = max # of 1-2 neighbors
9 = max # of 1-3 neighbors
19 = max # of 1-4 neighbors
58 = max # of 1-5 neighbors
21 = max # of special neighbors
special bonds CPU = 0.004 seconds
# thermo output
compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*]
#dump 1 all custom 10 dump.ubiquitin id type x y z fx fy fz
#dump_modify 1 sort id
# zero step run
#run 0
# dynamics
fix 1 all nve
thermo 1
run 5
AMOEBA force field settings
hal: cut 12 taper 10.8 vscale 0 0 1 1
multipole: cut 7 aewald 0.4 bsorder 5 FFT 60 48 48 mscale 0 0 0.4 1
polar: cut 7 aewald 0.5 bsorder 5 FFT 60 48 48
pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 1 1 1 1 d/u scale 0 1
precondition: cut 4.5
Generated 0 of 15 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 8 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair amoeba, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
AMOEBA group count: 3196
Per MPI rank memory allocation (min/avg/max) = 258.3 | 258.3 | 258.3 Mbytes
Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6]
0 0 -35338.057 2856.5938 1955.5431 224.37609 65.00809 5101.5211 -30247.585 -6336.5196 -5795.4272 -6329.8149 -6884.3167 349.52657 77.164877 652.41925
1 29.61379 -35356.153 2037.3541 1840.7883 223.90217 64.293945 4166.3385 -30341.522 -6486.773 -6452.8463 -6841.5982 -7386.1106 311.38025 120.72605 545.35513
2 78.518242 -35383.65 825.39919 1538.3909 222.55095 62.191009 2648.5321 -30467.814 -5502.9841 -6410.2998 -6396.1829 -6937.8137 217.3515 210.76948 294.28051
3 88.8921 -35402.11 938.99299 1162.2914 220.5271 58.832521 2380.644 -30453.516 -1929.5417 -3331.1291 -2769.7218 -3350.5733 117.32302 279.72705 31.237776
4 68.740402 -35477.589 2048.0659 858.03795 218.14277 54.460022 3178.7066 -30316.325 2041.1138 594.25938 1665.7799 1030.8539 66.230421 304.28296 -155.80224
5 76.267862 -35707.869 2206.6534 736.37385 215.75693 49.401674 3208.1859 -30299.377 2276.9276 536.21124 1893.4621 1258.492 92.097191 299.65604 -228.58369
Loop time of 6.52854 on 1 procs for 5 steps with 9737 atoms
Performance: 0.066 ns/day, 362.697 hours/ns, 0.766 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
AMOEBA timing breakdown:
Init time: 0.0100839 0.15%
Hal time: 1.54573 23.70%
Mpole time: 0.806911 12.37%
Induce time: 2.63878 40.46%
Polar time: 1.51971 23.30%
Total time: 6.52122
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 6.5212 | 6.5212 | 6.5212 | 0.0 | 99.89
Bond | 0.0049597 | 0.0049597 | 0.0049597 | 0.0 | 0.08
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0010627 | 0.0010627 | 0.0010627 | 0.0 | 0.02
Output | 0.00032106 | 0.00032106 | 0.00032106 | 0.0 | 0.00
Modify | 0.00083249 | 0.00083249 | 0.00083249 | 0.0 | 0.01
Other | | 0.0001265 | | | 0.00
Nlocal: 9737 ave 9737 max 9737 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 31511 ave 31511 max 31511 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 5.6393e+06 ave 5.6393e+06 max 5.6393e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 5639296
Ave neighs/atom = 579.16155
Ave special neighs/atom = 3.1364897
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:08

162
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@ -0,0 +1,162 @@
LAMMPS (23 Jun 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# solvated ubiquitin molecule with AMOEBA force field
units real
boundary p p p
atom_modify sort 0 0.0
atom_style amoeba
bond_style class2
angle_style amoeba
dihedral_style fourier
improper_style amoeba
# per-atom properties required by AMOEBA or HIPPO
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom i_amgroup d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
fix pit all amoeba/pitorsion
fix_modify pit energy yes
fix bit all amoeba/bitorsion bitorsion.ubiquitin.data
fix_modify bit energy yes
# read data file
read_data data.ubiquitin fix amtype NULL "Tinker Types" fix pit "pitorsion types" "PiTorsion Coeffs" fix pit pitorsions PiTorsions fix bit bitorsions BiTorsions
Reading data file ...
orthogonal box = (0 0 0) to (54.99 41.91 41.91)
2 by 1 by 2 MPI processor grid
reading atoms ...
9737 atoms
scanning bonds ...
4 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
18 = max dihedrals/atom
scanning impropers ...
3 = max impropers/atom
reading bonds ...
6908 bonds
reading angles ...
5094 angles
reading dihedrals ...
3297 dihedrals
reading impropers ...
651 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
4 = max # of 1-2 neighbors
9 = max # of 1-3 neighbors
19 = max # of 1-4 neighbors
21 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.049 seconds
pair_style amoeba
pair_coeff * * amoeba_ubiquitin.prm amoeba_ubiquitin.key
Skipping section: AMOEBA Protein Force Field Atom Classes
Skipping section: Torsion-Torsion Parameters
Skipping section: Biopolymer Atom Type Conversions
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0.5 0.5 0.5
special bond factors coul: 0.5 0.5 0.5
4 = max # of 1-2 neighbors
9 = max # of 1-3 neighbors
19 = max # of 1-4 neighbors
58 = max # of 1-5 neighbors
21 = max # of special neighbors
special bonds CPU = 0.001 seconds
# thermo output
compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*]
#dump 1 all custom 10 dump.ubiquitin id type x y z fx fy fz
#dump_modify 1 sort id
# zero step run
#run 0
# dynamics
fix 1 all nve
thermo 1
run 5
AMOEBA force field settings
hal: cut 12 taper 10.8 vscale 0 0 1 1
multipole: cut 7 aewald 0.4 bsorder 5 FFT 60 48 48 mscale 0 0 0.4 1
polar: cut 7 aewald 0.5 bsorder 5 FFT 60 48 48
pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 1 1 1 1 d/u scale 0 1
precondition: cut 4.5
Generated 0 of 15 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 8 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair amoeba, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
AMOEBA group count: 3196
Per MPI rank memory allocation (min/avg/max) = 144.2 | 144.7 | 145.4 Mbytes
Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6]
0 0 -35338.057 2856.5938 1955.5431 224.37609 65.00809 5101.5211 -30247.585 -6336.5196 -5795.4272 -6329.8149 -6884.3167 349.52657 77.164877 652.41925
1 29.61379 -35356.153 2037.3541 1840.7883 223.90217 64.293945 4166.3385 -30341.522 -6486.773 -6452.8463 -6841.5982 -7386.1106 311.38025 120.72605 545.35513
2 78.518242 -35383.65 825.39919 1538.3909 222.55095 62.191009 2648.5321 -30467.814 -5502.9841 -6410.2998 -6396.1829 -6937.8137 217.3515 210.76948 294.28051
3 88.8921 -35402.11 938.99299 1162.2914 220.5271 58.832521 2380.644 -30453.516 -1929.5417 -3331.1291 -2769.7218 -3350.5733 117.32302 279.72705 31.237776
4 68.740402 -35477.589 2048.0659 858.03795 218.14277 54.460022 3178.7066 -30316.325 2041.1138 594.25938 1665.7799 1030.8539 66.230421 304.28296 -155.80224
5 76.267862 -35707.869 2206.6534 736.37385 215.75693 49.401674 3208.1859 -30299.377 2276.9276 536.21124 1893.4621 1258.492 92.097191 299.65604 -228.58369
Loop time of 2.20325 on 4 procs for 5 steps with 9737 atoms
Performance: 0.196 ns/day, 122.403 hours/ns, 2.269 timesteps/s
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
AMOEBA timing breakdown:
Init time: 0.0117181 0.53%
Hal time: 0.442973 20.14%
Mpole time: 0.287778 13.09%
Induce time: 0.94261 42.86%
Polar time: 0.514081 23.38%
Total time: 2.19916
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.1991 | 2.1992 | 2.1996 | 0.0 | 99.82
Bond | 0.0011873 | 0.0014547 | 0.0016743 | 0.5 | 0.07
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0014371 | 0.0018264 | 0.0020772 | 0.6 | 0.08
Output | 0.0002413 | 0.00029218 | 0.00037812 | 0.0 | 0.01
Modify | 0.0002694 | 0.00029873 | 0.00032365 | 0.0 | 0.01
Other | | 0.000135 | | | 0.01
Nlocal: 2434.25 ave 2498 max 2390 min
Histogram: 1 1 0 0 1 0 0 0 0 1
Nghost: 16683.2 ave 16765 max 16568 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Neighs: 1.40982e+06 ave 1.52088e+06 max 1.30717e+06 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Total # of neighbors = 5639296
Ave neighs/atom = 579.16155
Ave special neighs/atom = 3.1364897
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:02

150
examples/amoeba/log.5Jul22.water_box.amoeba.g++.1 Normal file
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@ -0,0 +1,150 @@
LAMMPS (23 Jun 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# replicate water box with AMOEBA or HIPPO
units real
boundary p p p
atom_style amoeba
bond_style class2
angle_style amoeba
dihedral_style none
# per-atom properties required by AMOEBA or HIPPO
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom i_amgroup d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
# read data file
read_data data.water_box.amoeba fix amtype NULL "Tinker Types"
Reading data file ...
orthogonal box = (0 0 0) to (18.643 18.643 18.643)
1 by 1 by 1 MPI processor grid
reading atoms ...
648 atoms
scanning bonds ...
2 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
432 bonds
reading angles ...
216 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.004 seconds
# force field
pair_style amoeba
pair_coeff * * amoeba_water.prm amoeba_water_box.key
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0.5 0.5 0.5
special bond factors coul: 0.5 0.5 0.5
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of 1-5 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
# thermo output
compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*]
#dump 1 all custom 10 dump.water_box id type x y z fx fy fz
#dump_modify 1 sort id
# zero step run
#run 0
# dynamics
fix 1 all nve
thermo 10
run 100
AMOEBA force field settings
hal: cut 7 taper 6 vscale 0 0 1 1
multipole: cut 7 aewald 0.4 bsorder 5 FFT 24 24 24 mscale 0 0 0.4 1
polar: cut 7 aewald 0.5 bsorder 5 FFT 24 24 24
pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 1 1 1 1 d/u scale 0 1
precondition: cut 4.5
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 9
ghost atom cutoff = 9
binsize = 4.5, bins = 5 5 5
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair amoeba, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
AMOEBA group count: 216
Per MPI rank memory allocation (min/avg/max) = 56.94 | 56.94 | 56.94 Mbytes
Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6]
0 0 -2172.0637 166.82637 83.732524 0 0 250.5589 -1921.5048 -6181.4178 -4772.1682 -6954.8414 -6817.2437 -272.19967 3173.3481 2229.9454
10 105.50186 -2373.7036 136.67877 106.86833 0 0 243.5471 -1926.6873 -8440.8076 -10450.396 -9513.7369 -9664.6007 -301.7395 322.28511 1917.0314
20 143.89822 -2358.363 70.950306 76.775658 0 0 147.72596 -1933.1172 -7370.2083 -7728.5515 -11580.39 -8675.2341 -806.78779 780.67516 2096.34
30 157.22465 -2375.4739 50.393531 87.108003 0 0 137.50153 -1934.7514 -4449.577 -6946.7795 -7865.2165 -4954.2358 -417.69587 -1004.2877 -36.388669
40 150.92481 -2354.1892 78.482464 53.798462 0 0 132.28093 -1930.8371 353.42948 -939.14353 -4636.5062 475.58057 -1073.8523 -1583.9471 -574.21807
50 153.0181 -2388.7322 100.20232 65.813823 0 0 166.01614 -1927.6078 3975.1981 1368.1361 425.64533 3886.0124 -1806.8586 -2534.5272 -2118.2395
60 155.01494 -2364.3168 92.946192 44.248949 0 0 137.19514 -1928.1623 5793.7546 3524.7523 1420.4096 6108.7958 -1536.5261 -2558.8204 -1501.5292
70 166.70755 -2383.503 76.491199 55.01988 0 0 131.51108 -1930.4824 4744.1583 1919.3954 2838.7666 2669.745 -169.21643 -188.08678 -2256.4142
80 171.83506 -2388.0612 76.465932 49.1299 0 0 125.59583 -1931.067 2210.3658 -318.23867 330.74353 -395.26693 -43.142216 252.53012 -1987.0412
90 175.73401 -2423.8154 90.786573 63.719496 0 0 154.50607 -1930.3915 -916.91571 -3942.3954 -2566.5361 -3414.8202 199.82369 2365.9443 -266.38604
100 173.72684 -2422.367 99.75941 57.294464 0 0 157.05387 -1930.2663 -3585.8356 -5734.1341 -5882.0146 -6232.4353 -227.79935 959.68225 404.47924
Loop time of 9.20176 on 1 procs for 100 steps with 648 atoms
Performance: 0.939 ns/day, 25.560 hours/ns, 10.867 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
AMOEBA timing breakdown:
Init time: 0.0197604 0.22%
Hal time: 0.384028 4.18%
Mpole time: 0.939829 10.23%
Induce time: 6.03232 65.64%
Polar time: 1.81401 19.74%
Total time: 9.18998
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 9.1903 | 9.1903 | 9.1903 | 0.0 | 99.88
Bond | 0.0024644 | 0.0024644 | 0.0024644 | 0.0 | 0.03
Neigh | 0.0045623 | 0.0045623 | 0.0045623 | 0.0 | 0.05
Comm | 0.0024492 | 0.0024492 | 0.0024492 | 0.0 | 0.03
Output | 0.00046866 | 0.00046866 | 0.00046866 | 0.0 | 0.01
Modify | 0.00071308 | 0.00071308 | 0.00071308 | 0.0 | 0.01
Other | | 0.000819 | | | 0.01
Nlocal: 648 ave 648 max 648 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4290 ave 4290 max 4290 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 98545 ave 98545 max 98545 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 98545
Ave neighs/atom = 152.07562
Ave special neighs/atom = 2
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:00:09

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

149
examples/amoeba/log.5Jul22.water_box.hippo.g++.1 Normal file
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LAMMPS (23 Jun 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# water box with AMOEBA or HIPPO
units real
boundary p p p
atom_style amoeba
bond_style class2
angle_style amoeba
dihedral_style none
# per-atom properties required by AMOEBA or HIPPO
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom i_amgroup d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
# read data file
read_data data.water_box.hippo fix amtype NULL "Tinker Types"
Reading data file ...
orthogonal box = (0 0 0) to (18.643 18.643 18.643)
1 by 1 by 1 MPI processor grid
reading atoms ...
648 atoms
scanning bonds ...
2 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
432 bonds
reading angles ...
216 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.004 seconds
# force field
pair_style hippo
pair_coeff * * hippo_water.prm hippo_water_box.key
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0.5 0.5 0.5
special bond factors coul: 0.5 0.5 0.5
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of 1-5 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
# thermo output
compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*]
#dump 1 all custom 10 dump.water_box id type x y z fx fy fz
#dump_modify 1 sort id
# zero step run
#run 0
# dynamics
fix 1 all nve
thermo 1
run 5
HIPPO force field settings
repulsion: cut 7 taper 6 rscale 0 0 1 1
qxfer: cut 7 taper 6 mscale 0 0 0.4 1
dispersion: cut 7 aewald 0.45 bsorder 4 FFT 16 16 16 dspscale 0 0 0.4 1
multipole: cut 7 aewald 0.4 bsorder 5 FFT 24 24 24 mscale 0 0 0.4 1
polar: cut 7 aewald 0.5 bsorder 5 FFT 24 24 24
pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 0.2 1 1 1 d/u scale 0 1
precondition: cut 4.5
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 9
ghost atom cutoff = 9
binsize = 4.5, bins = 5 5 5
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair hippo, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
HIPPO group count: 216
Per MPI rank memory allocation (min/avg/max) = 56.46 | 56.46 | 56.46 Mbytes
Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6]
0 0 -2188.594 166.82637 77.478353 0 0 244.30473 -1944.2893 -10859.589 -9285.4645 -11598.049 -11695.254 -282.7072 3164.4148 2495.2578
1 29.599499 -2189.0009 110.80903 70.640769 0 0 181.4498 -1950.466 -9781.8027 -8491.8338 -11237.523 -10824.225 -316.85579 2724.3099 2103.706
2 77.782401 -2189.0806 26.465487 53.091297 0 0 79.556784 -1959.5139 -5674.5913 -4709.6895 -8454.6227 -7034.3366 -270.02397 1600.8009 1104.5782
3 83.751912 -2189.1561 36.936027 32.349803 0 0 69.285831 -1958.3477 1505.3642 2789.4989 -1919.6532 227.71216 3.4467207 240.18575 -91.250567
4 59.186129 -2195.3882 116.40559 17.314099 0 0 133.71969 -1947.5231 7666.6109 9441.7634 4355.1915 6787.0543 329.33631 -768.83277 -966.66638
5 70.911532 -2215.1422 115.71443 14.75745 0 0 130.47188 -1947.9114 7292.9034 8506.6309 4019.0295 6458.6256 348.80878 -911.32703 -1060.6123
Loop time of 0.328811 on 1 procs for 5 steps with 648 atoms
Performance: 1.314 ns/day, 18.267 hours/ns, 15.206 timesteps/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
HIPPO timing breakdown:
Init time: 0.000849843 0.26%
Repulse time: 0.0386964 11.79%
Disp time: 0.0176955 5.39%
Mpole time: 0.0625716 19.06%
Induce time: 0.122108 37.20%
Polar time: 0.0762897 23.24%
Qxfer time: 0.010031 3.06%
Total time: 0.328242
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.32826 | 0.32826 | 0.32826 | 0.0 | 99.83
Bond | 0.00014786 | 0.00014786 | 0.00014786 | 0.0 | 0.04
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 9.3603e-05 | 9.3603e-05 | 9.3603e-05 | 0.0 | 0.03
Output | 0.00022715 | 0.00022715 | 0.00022715 | 0.0 | 0.07
Modify | 5.5594e-05 | 5.5594e-05 | 5.5594e-05 | 0.0 | 0.02
Other | | 2.723e-05 | | | 0.01
Nlocal: 648 ave 648 max 648 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4302 ave 4302 max 4302 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 98585 ave 98585 max 98585 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 98585
Ave neighs/atom = 152.13735
Ave special neighs/atom = 2
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

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

71
examples/amoeba/log.water_dimer.amoeba.1 → examples/amoeba/log.5Jul22.water_dimer.amoeba.g++.1
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@ -1,4 +1,6 @@
LAMMPS (24 Mar 2022)
LAMMPS (23 Jun 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# water dimer with AMOEBA or HIPPO
units real
@ -39,7 +41,7 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.008 seconds
read_data CPU = 0.003 seconds
# force field
@ -63,8 +65,8 @@ compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*]
dump 1 all custom 10 dump.water_dimer id type x y z fx fy fz
dump_modify 1 sort id
#dump 1 all custom 10 dump.water_dimer id type x y z fx fy fz
#dump_modify 1 sort id
# zero step run
@ -74,15 +76,15 @@ dump_modify 1 sort id
fix 1 all nve
thermo 10
run 100
AMOEBA/HIPPO force field settings
thermo 1
run 5
AMOEBA force field settings
hal: cut 10 taper 8 vscale 0 0 1 1
multipole: cut 10 aewald 0 mscale 0 0 0.4 1
polar: cut 10 aewald 0
pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 1 1 1 1 d/u scale 0 1
precondition: cut 4.5
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
@ -95,44 +97,39 @@ Neighbor list info ...
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:974)
AMOEBA/HIPPO group count: 2
Per MPI rank memory allocation (min/avg/max) = 49.59 | 49.59 | 49.59 Mbytes
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/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
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 0.00655818 on 1 procs for 100 steps with 6 atoms
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 0.000286908 on 1 procs for 5 steps with 6 atoms
Performance: 1317.439 ns/day, 0.018 hours/ns, 15248.138 timesteps/s
98.5% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 1505.709 ns/day, 0.016 hours/ns, 17427.189 timesteps/s
98.6% CPU use with 1 MPI tasks x 1 OpenMP threads
AMEOBA/HIPPO timing breakdown:
Init time: 0.000126483 0.0233682
Hal time: 0.000471055 8.70292
Mpole time: 0.000619314 11.4421
Induce time: 0.00270856 50.0417
Polar time: 0.00147122 27.1814
Total time: 0.00541261
AMOEBA timing breakdown:
Init time: 7.417e-06 4.75%
Hal time: 8.458e-06 5.42%
Mpole time: 2.2734e-05 14.57%
Induce time: 7.4016e-05 47.43%
Polar time: 4.2972e-05 27.54%
Total time: 0.00015604
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.005443 | 0.005443 | 0.005443 | 0.0 | 83.00
Bond | 9.6579e-05 | 9.6579e-05 | 9.6579e-05 | 0.0 | 1.47
Pair | 0.00015922 | 0.00015922 | 0.00015922 | 0.0 | 55.49
Bond | 5.034e-06 | 5.034e-06 | 5.034e-06 | 0.0 | 1.75
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 1.7434e-05 | 1.7434e-05 | 1.7434e-05 | 0.0 | 0.27
Output | 0.0008951 | 0.0008951 | 0.0008951 | 0.0 | 13.65
Modify | 5.161e-05 | 5.161e-05 | 5.161e-05 | 0.0 | 0.79
Other | | 5.444e-05 | | | 0.83
Comm | 8.49e-07 | 8.49e-07 | 8.49e-07 | 0.0 | 0.30
Output | 0.00011336 | 0.00011336 | 0.00011336 | 0.0 | 39.51
Modify | 2.093e-06 | 2.093e-06 | 2.093e-06 | 0.0 | 0.73
Other | | 6.355e-06 | | | 2.21
Nlocal: 6 ave 6 max 6 min
Histogram: 1 0 0 0 0 0 0 0 0 0

71
examples/amoeba/log.water_dimer.amoeba.4 → examples/amoeba/log.5Jul22.water_dimer.amoeba.g++.4
View File

@ -1,4 +1,6 @@
LAMMPS (24 Mar 2022)
LAMMPS (23 Jun 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# water dimer with AMOEBA or HIPPO
units real
@ -39,7 +41,7 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.009 seconds
read_data CPU = 0.004 seconds
# force field
@ -63,8 +65,8 @@ compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*]
dump 1 all custom 10 dump.water_dimer id type x y z fx fy fz
dump_modify 1 sort id
#dump 1 all custom 10 dump.water_dimer id type x y z fx fy fz
#dump_modify 1 sort id
# zero step run
@ -74,15 +76,15 @@ dump_modify 1 sort id
fix 1 all nve
thermo 10
run 100
AMOEBA/HIPPO force field settings
thermo 1
run 5
AMOEBA force field settings
hal: cut 10 taper 8 vscale 0 0 1 1
multipole: cut 10 aewald 0 mscale 0 0 0.4 1
polar: cut 10 aewald 0
pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 1 1 1 1 d/u scale 0 1
precondition: cut 4.5
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
@ -95,44 +97,39 @@ Neighbor list info ...
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:974)
AMOEBA/HIPPO group count: 2
Per MPI rank memory allocation (min/avg/max) = 49.61 | 49.75 | 49.88 Mbytes
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/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
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 0.0167554 on 4 procs for 100 steps with 6 atoms
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 0.000582267 on 4 procs for 5 steps with 6 atoms
Performance: 515.654 ns/day, 0.047 hours/ns, 5968.213 timesteps/s
99.4% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 741.928 ns/day, 0.032 hours/ns, 8587.130 timesteps/s
99.5% CPU use with 4 MPI tasks x 1 OpenMP threads
AMEOBA/HIPPO timing breakdown:
Init time: 0.000555846 0.0390251
Hal time: 0.000129733 0.910835
Mpole time: 0.000783914 5.50375
Induce time: 0.0115771 81.2811
Polar time: 0.00118294 8.30522
Total time: 0.0142433
AMOEBA timing breakdown:
Init time: 1.3264e-05 3.71%
Hal time: 3.16275e-06 0.88%
Mpole time: 2.35955e-05 6.60%
Induce time: 0.000290896 81.33%
Polar time: 2.62723e-05 7.34%
Total time: 0.000357696
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.013911 | 0.014439 | 0.0147 | 0.3 | 86.18
Bond | 1.196e-05 | 4.4667e-05 | 8.5848e-05 | 0.0 | 0.27
Pair | 0.00036015 | 0.00038587 | 0.00040555 | 0.0 | 66.27
Bond | 1.441e-06 | 3.3365e-06 | 5.265e-06 | 0.0 | 0.57
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00060682 | 0.00082002 | 0.001342 | 0.0 | 4.89
Output | 0.00098235 | 0.0010281 | 0.0011458 | 0.2 | 6.14
Modify | 2.2946e-05 | 3.473e-05 | 4.2983e-05 | 0.0 | 0.21
Other | | 0.0003885 | | | 2.32
Comm | 2.1512e-05 | 3.3761e-05 | 4.9368e-05 | 0.0 | 5.80
Output | 0.00012269 | 0.00014666 | 0.00017989 | 0.0 | 25.19
Modify | 1.659e-06 | 2.0448e-06 | 2.275e-06 | 0.0 | 0.35
Other | | 1.059e-05 | | | 1.82
Nlocal: 1.5 ave 3 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 2

75
examples/amoeba/log.water_dimer.hippo.1 → examples/amoeba/log.5Jul22.water_dimer.hippo.g++.1
View File

@ -1,4 +1,6 @@
LAMMPS (24 Mar 2022)
LAMMPS (23 Jun 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# water dimer with AMOEBA or HIPPO
units real
@ -39,7 +41,7 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.008 seconds
read_data CPU = 0.003 seconds
# force field
@ -63,8 +65,8 @@ compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*]
dump 1 all custom 10 dump.water_dimer id type x y z fx fy fz
dump_modify 1 sort id
#dump 1 all custom 10 dump.water_dimer id type x y z fx fy fz
#dump_modify 1 sort id
# zero step run
@ -74,9 +76,9 @@ dump_modify 1 sort id
fix 1 all nve
thermo 10
run 100
AMOEBA/HIPPO force field settings
thermo 1
run 5
HIPPO force field settings
repulsion: cut 10 taper 8 rscale 0 0 1 1
qxfer: cut 10 taper 8 mscale 0 0 0.4 1
dispersion: cut 10 aewald 0 dspscale 0 0 0.4 1
@ -84,7 +86,7 @@ AMOEBA/HIPPO force field settings
polar: cut 10 aewald 0
pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 0.2 1 1 1 d/u scale 0 1
precondition: cut 4.5
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
@ -97,46 +99,41 @@ Neighbor list info ...
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:974)
AMOEBA/HIPPO group count: 2
Per MPI rank memory allocation (min/avg/max) = 49.15 | 49.15 | 49.15 Mbytes
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/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
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 0.00568827 on 1 procs for 100 steps with 6 atoms
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 0.000211279 on 1 procs for 5 steps with 6 atoms
Performance: 1518.916 ns/day, 0.016 hours/ns, 17580.041 timesteps/s
76.9% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 2044.690 ns/day, 0.012 hours/ns, 23665.390 timesteps/s
98.4% CPU use with 1 MPI tasks x 1 OpenMP threads
AMEOBA/HIPPO timing breakdown:
Init time: 0.00011293 0.024348
Repulse time: 0.000604058 13.0236
Disp time: 0.000336908 7.26382
Mpole time: 0.000853828 18.4087
Induce time: 0.00158723 34.2211
Polar time: 0.000996193 21.4782
Qxfer time: 0.000142246 3.06686
Total time: 0.00463817
HIPPO timing breakdown:
Init time: 4.768e-06 4.20%
Repulse time: 1.3408e-05 11.81%
Disp time: 9.476e-06 8.35%
Mpole time: 2.1547e-05 18.98%
Induce time: 3.7631e-05 33.14%
Polar time: 2.4333e-05 21.43%
Qxfer time: 2.244e-06 1.98%
Total time: 0.000113542
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0046663 | 0.0046663 | 0.0046663 | 0.0 | 82.03
Bond | 7.8168e-05 | 7.8168e-05 | 7.8168e-05 | 0.0 | 1.37
Pair | 0.00011535 | 0.00011535 | 0.00011535 | 0.0 | 54.60
Bond | 3.239e-06 | 3.239e-06 | 3.239e-06 | 0.0 | 1.53
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 1.3206e-05 | 1.3206e-05 | 1.3206e-05 | 0.0 | 0.23
Output | 0.00084402 | 0.00084402 | 0.00084402 | 0.0 | 14.84
Modify | 3.8896e-05 | 3.8896e-05 | 3.8896e-05 | 0.0 | 0.68
Other | | 4.77e-05 | | | 0.84
Comm | 6.41e-07 | 6.41e-07 | 6.41e-07 | 0.0 | 0.30
Output | 8.5752e-05 | 8.5752e-05 | 8.5752e-05 | 0.0 | 40.59
Modify | 1.55e-06 | 1.55e-06 | 1.55e-06 | 0.0 | 0.73
Other | | 4.744e-06 | | | 2.25
Nlocal: 6 ave 6 max 6 min
Histogram: 1 0 0 0 0 0 0 0 0 0

77
examples/amoeba/log.water_dimer.hippo.4 → examples/amoeba/log.5Jul22.water_dimer.hippo.g++.4
View File

@ -1,4 +1,6 @@
LAMMPS (24 Mar 2022)
LAMMPS (23 Jun 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# water dimer with AMOEBA or HIPPO
units real
@ -39,7 +41,7 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.009 seconds
read_data CPU = 0.004 seconds
# force field
@ -55,7 +57,7 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-4 neighbors
2 = max # of 1-5 neighbors
2 = max # of special neighbors
special bonds CPU = 0.001 seconds
special bonds CPU = 0.000 seconds
# thermo output
@ -63,8 +65,8 @@ compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*]
dump 1 all custom 10 dump.water_dimer id type x y z fx fy fz
dump_modify 1 sort id
#dump 1 all custom 10 dump.water_dimer id type x y z fx fy fz
#dump_modify 1 sort id
# zero step run
@ -74,9 +76,9 @@ dump_modify 1 sort id
fix 1 all nve
thermo 10
run 100
AMOEBA/HIPPO force field settings
thermo 1
run 5
HIPPO force field settings
repulsion: cut 10 taper 8 rscale 0 0 1 1
qxfer: cut 10 taper 8 mscale 0 0 0.4 1
dispersion: cut 10 aewald 0 dspscale 0 0 0.4 1
@ -84,7 +86,7 @@ AMOEBA/HIPPO force field settings
polar: cut 10 aewald 0
pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 0.2 1 1 1 d/u scale 0 1
precondition: cut 4.5
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
@ -97,46 +99,41 @@ Neighbor list info ...
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:974)
AMOEBA/HIPPO group count: 2
Per MPI rank memory allocation (min/avg/max) = 49.18 | 49.31 | 49.44 Mbytes
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/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
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 0.0133873 on 4 procs for 100 steps with 6 atoms
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 0.000515971 on 4 procs for 5 steps with 6 atoms
Performance: 645.386 ns/day, 0.037 hours/ns, 7469.744 timesteps/s
98.4% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 837.257 ns/day, 0.029 hours/ns, 9690.472 timesteps/s
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
AMEOBA/HIPPO timing breakdown:
Init time: 0.000581606 0.0545512
Repulse time: 0.000622984 5.84322
Disp time: 0.000115637 1.0846
Mpole time: 0.000994723 9.32991
Induce time: 0.00737161 69.1413
Polar time: 0.00091816 8.61179
Qxfer time: 5.1997e-05 0.487701
Total time: 0.0106617
HIPPO timing breakdown:
Init time: 1.26765e-05 4.09%
Repulse time: 1.99082e-05 6.43%
Disp time: 3.16825e-06 1.02%
Mpole time: 3.4956e-05 11.29%
Induce time: 0.000205268 66.29%
Polar time: 3.1924e-05 10.31%
Qxfer time: 1.5545e-06 0.50%
Total time: 0.000309632
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.010579 | 0.010896 | 0.011085 | 0.2 | 81.39
Bond | 1.3578e-05 | 4.3855e-05 | 7.6592e-05 | 0.0 | 0.33
Pair | 0.0003033 | 0.00032943 | 0.00034747 | 0.0 | 63.85
Bond | 1.237e-06 | 2.778e-06 | 4.775e-06 | 0.0 | 0.54
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00058533 | 0.00080957 | 0.0011064 | 0.0 | 6.05
Output | 0.0011175 | 0.0011761 | 0.0013051 | 0.2 | 8.78
Modify | 2.4304e-05 | 3.4805e-05 | 4.2149e-05 | 0.0 | 0.26
Other | | 0.0004266 | | | 3.19
Comm | 1.2356e-05 | 3.1848e-05 | 4.3553e-05 | 0.0 | 6.17
Output | 0.00012443 | 0.0001412 | 0.00015698 | 0.0 | 27.37
Modify | 1.428e-06 | 2.0447e-06 | 2.545e-06 | 0.0 | 0.40
Other | | 8.678e-06 | | | 1.68
Nlocal: 1.5 ave 3 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 2

69
examples/amoeba/log.water_hexamer.amoeba.1 → examples/amoeba/log.5Jul22.water_hexamer.amoeba.g++.1
View File

@ -1,4 +1,6 @@
LAMMPS (24 Mar 2022)
LAMMPS (23 Jun 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# water hexamer with AMOEBA or HIPPO
units real
@ -39,7 +41,7 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.009 seconds
read_data CPU = 0.003 seconds
# force field
@ -63,8 +65,8 @@ compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*]
dump 1 all custom 10 dump.water_hexamer id type x y z fx fy fz
dump_modify 1 sort id
#dump 1 all custom 10 dump.water_hexamer id type x y z fx fy fz
#dump_modify 1 sort id
# zero step run
@ -74,15 +76,15 @@ dump_modify 1 sort id
fix 1 all nve
thermo 10
run 100
AMOEBA/HIPPO force field settings
thermo 1
run 5
AMOEBA force field settings
hal: cut 10 taper 8 vscale 0 0 1 1
multipole: cut 10 aewald 0 mscale 0 0 0.4 1
polar: cut 10 aewald 0
pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 1 1 1 1 d/u scale 0 1
precondition: cut 4.5
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
@ -95,43 +97,38 @@ Neighbor list info ...
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
AMOEBA/HIPPO group count: 6
Per MPI rank memory allocation (min/avg/max) = 49.53 | 49.53 | 49.53 Mbytes
AMOEBA group count: 6
Per MPI rank memory allocation (min/avg/max) = 48.28 | 48.28 | 48.28 Mbytes
Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6]
0 0 -48.469664 1.9820353 2.2499329 0 0 4.2319683 -44.237696 -26322.671 -28303.103 -27669.614 -22995.296 1312.6688 2624.8394 4042.0489
10 6.3616471 -46.626437 1.7910812 0.25704063 0 0 2.0481218 -44.255947 -23813.06 -24671.886 -17167.34 -30208.043 -474.208 -8339.5934 -5278.359
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 0.0438592 on 1 procs for 100 steps with 18 atoms
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 0.00100021 on 1 procs for 5 steps with 18 atoms
Performance: 196.994 ns/day, 0.122 hours/ns, 2280.022 timesteps/s
95.1% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 431.907 ns/day, 0.056 hours/ns, 4998.925 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
AMEOBA/HIPPO timing breakdown:
Init time: 0.000324764 0.00770058
Hal time: 0.00500441 11.8661
Mpole time: 0.00442974 10.5035
Induce time: 0.0210286 49.8617
Polar time: 0.0113696 26.9588
Total time: 0.042174
AMOEBA timing breakdown:
Init time: 1.2295e-05 1.38%
Hal time: 6.2308e-05 6.98%
Mpole time: 0.000124591 13.97%
Induce time: 0.000432719 48.51%
Polar time: 0.000259676 29.11%
Total time: 0.000892068
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.042221 | 0.042221 | 0.042221 | 0.0 | 96.26
Bond | 0.00021632 | 0.00021632 | 0.00021632 | 0.0 | 0.49
Pair | 0.00089392 | 0.00089392 | 0.00089392 | 0.0 | 89.37
Bond | 6.685e-06 | 6.685e-06 | 6.685e-06 | 0.0 | 0.67
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 1.6322e-05 | 1.6322e-05 | 1.6322e-05 | 0.0 | 0.04
Output | 0.0012472 | 0.0012472 | 0.0012472 | 0.0 | 2.84
Modify | 7.9638e-05 | 7.9638e-05 | 7.9638e-05 | 0.0 | 0.18
Other | | 7.889e-05 | | | 0.18
Comm | 6.67e-07 | 6.67e-07 | 6.67e-07 | 0.0 | 0.07
Output | 9.0869e-05 | 9.0869e-05 | 9.0869e-05 | 0.0 | 9.08
Modify | 2.517e-06 | 2.517e-06 | 2.517e-06 | 0.0 | 0.25
Other | | 5.561e-06 | | | 0.56
Nlocal: 18 ave 18 max 18 min
Histogram: 1 0 0 0 0 0 0 0 0 0

71
examples/amoeba/log.water_hexamer.amoeba.4 → examples/amoeba/log.5Jul22.water_hexamer.amoeba.g++.4
View File

@ -1,4 +1,6 @@
LAMMPS (24 Mar 2022)
LAMMPS (23 Jun 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# water hexamer with AMOEBA or HIPPO
units real
@ -39,7 +41,7 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.008 seconds
read_data CPU = 0.004 seconds
# force field
@ -63,8 +65,8 @@ compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*]
dump 1 all custom 10 dump.water_hexamer id type x y z fx fy fz
dump_modify 1 sort id
#dump 1 all custom 10 dump.water_hexamer id type x y z fx fy fz
#dump_modify 1 sort id
# zero step run
@ -74,15 +76,15 @@ dump_modify 1 sort id
fix 1 all nve
thermo 10
run 100
AMOEBA/HIPPO force field settings
thermo 1
run 5
AMOEBA force field settings
hal: cut 10 taper 8 vscale 0 0 1 1
multipole: cut 10 aewald 0 mscale 0 0 0.4 1
polar: cut 10 aewald 0
pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 1 1 1 1 d/u scale 0 1
precondition: cut 4.5
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
@ -95,44 +97,39 @@ Neighbor list info ...
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:974)
AMOEBA/HIPPO group count: 6
Per MPI rank memory allocation (min/avg/max) = 49.56 | 49.56 | 49.56 Mbytes
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/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
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 0.0405754 on 4 procs for 100 steps with 18 atoms
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 0.0015204 on 4 procs for 5 steps with 18 atoms
Performance: 212.937 ns/day, 0.113 hours/ns, 2464.547 timesteps/s
98.9% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 284.136 ns/day, 0.084 hours/ns, 3288.611 timesteps/s
98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
AMEOBA/HIPPO timing breakdown:
Init time: 0.000756446 0.0198927
Hal time: 0.00120064 3.15739
Mpole time: 0.00338295 8.89637
Induce time: 0.0273688 71.9733
Polar time: 0.00530425 13.9489
Total time: 0.0380263
AMOEBA timing breakdown:
Init time: 2.00392e-05 1.57%
Hal time: 2.58605e-05 2.02%
Mpole time: 0.000137192 10.74%
Induce time: 0.000858714 67.22%
Polar time: 0.00023507 18.40%
Total time: 0.00127742
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.03816 | 0.038221 | 0.038312 | 0.0 | 94.20
Bond | 7.0759e-05 | 8.5222e-05 | 0.00010449 | 0.0 | 0.21
Pair | 0.0012876 | 0.0012913 | 0.0012951 | 0.0 | 84.93
Bond | 4.076e-06 | 6.434e-06 | 1.0051e-05 | 0.0 | 0.42
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00065721 | 0.00081724 | 0.00093857 | 0.0 | 2.01
Output | 0.0010275 | 0.0010663 | 0.0011758 | 0.2 | 2.63
Modify | 3.3884e-05 | 4.422e-05 | 5.7037e-05 | 0.0 | 0.11
Other | | 0.000341 | | | 0.84
Comm | 1.4924e-05 | 5.9337e-05 | 8.3417e-05 | 0.0 | 3.90
Output | 0.00012796 | 0.00014846 | 0.00018928 | 0.0 | 9.76
Modify | 2.066e-06 | 2.5358e-06 | 3.07e-06 | 0.0 | 0.17
Other | | 1.236e-05 | | | 0.81
Nlocal: 4.5 ave 6 max 3 min
Histogram: 1 0 0 1 0 0 1 0 0 1

73
examples/amoeba/log.water_hexamer.hippo.1 → examples/amoeba/log.5Jul22.water_hexamer.hippo.g++.1
View File

@ -1,4 +1,6 @@
LAMMPS (24 Mar 2022)
LAMMPS (23 Jun 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# water hexamer with AMOEBA or HIPPO
units real
@ -39,7 +41,7 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.007 seconds
read_data CPU = 0.004 seconds
# force field
@ -63,8 +65,8 @@ compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*]
dump 1 all custom 10 dump.water_hexamer id type x y z fx fy fz
dump_modify 1 sort id
#dump 1 all custom 10 dump.water_hexamer id type x y z fx fy fz
#dump_modify 1 sort id
# zero step run
@ -74,9 +76,9 @@ dump_modify 1 sort id
fix 1 all nve
thermo 10
run 100
AMOEBA/HIPPO force field settings
thermo 1
run 5
HIPPO force field settings
repulsion: cut 10 taper 8 rscale 0 0 1 1
qxfer: cut 10 taper 8 mscale 0 0 0.4 1
dispersion: cut 10 aewald 0 dspscale 0 0 0.4 1
@ -84,7 +86,7 @@ AMOEBA/HIPPO force field settings
polar: cut 10 aewald 0
pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 0.2 1 1 1 d/u scale 0 1
precondition: cut 4.5
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
@ -97,45 +99,40 @@ Neighbor list info ...
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
AMOEBA/HIPPO group count: 6
Per MPI rank memory allocation (min/avg/max) = 49.1 | 49.1 | 49.1 Mbytes
HIPPO group count: 6
Per MPI rank memory allocation (min/avg/max) = 47.84 | 47.84 | 47.84 Mbytes
Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6]
0 0 -47.362156 1.9820353 1.6634749 0 0 3.6455102 -43.716646 -34513.768 -42206.078 -31383.641 -29951.584 2850.1184 3579.9253 5768.3698
10 11.52238 -45.959856 1.53397 0.085100522 0 0 1.6190706 -43.756903 -28644.676 -34867.94 -19324.955 -32842.522 -370.63233 -6452.0859 -4002.3535
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 0.0399433 on 1 procs for 100 steps with 18 atoms
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 0.00117792 on 1 procs for 5 steps with 18 atoms
Performance: 216.307 ns/day, 0.111 hours/ns, 2503.548 timesteps/s
92.6% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 366.749 ns/day, 0.065 hours/ns, 4244.778 timesteps/s
95.2% CPU use with 1 MPI tasks x 1 OpenMP threads
AMEOBA/HIPPO timing breakdown:
Init time: 0.000295019 0.00770171
Repulse time: 0.00594736 15.5261
Disp time: 0.00261218 6.81931
Mpole time: 0.0069314 18.095
Induce time: 0.013694 35.7492
Polar time: 0.00744631 19.4392
Qxfer time: 0.001375 3.58954
Total time: 0.0383057
HIPPO timing breakdown:
Init time: 1.5876e-05 1.52%
Repulse time: 0.000160405 15.32%
Disp time: 5.1301e-05 4.90%
Mpole time: 0.000219996 21.01%
Induce time: 0.000352821 33.70%
Polar time: 0.000218541 20.87%
Qxfer time: 2.7842e-05 2.66%
Total time: 0.00104695
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.038344 | 0.038344 | 0.038344 | 0.0 | 96.00
Bond | 0.00017707 | 0.00017707 | 0.00017707 | 0.0 | 0.44
Pair | 0.0010494 | 0.0010494 | 0.0010494 | 0.0 | 89.09
Bond | 7.408e-06 | 7.408e-06 | 7.408e-06 | 0.0 | 0.63
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 1.5549e-05 | 1.5549e-05 | 1.5549e-05 | 0.0 | 0.04
Output | 0.0012682 | 0.0012682 | 0.0012682 | 0.0 | 3.18
Modify | 7.0869e-05 | 7.0869e-05 | 7.0869e-05 | 0.0 | 0.18
Other | | 6.745e-05 | | | 0.17
Comm | 1.032e-06 | 1.032e-06 | 1.032e-06 | 0.0 | 0.09
Output | 0.00011139 | 0.00011139 | 0.00011139 | 0.0 | 9.46
Modify | 2.647e-06 | 2.647e-06 | 2.647e-06 | 0.0 | 0.22
Other | | 6.086e-06 | | | 0.52
Nlocal: 18 ave 18 max 18 min
Histogram: 1 0 0 0 0 0 0 0 0 0

75
examples/amoeba/log.water_hexamer.hippo.4 → examples/amoeba/log.5Jul22.water_hexamer.hippo.g++.4
View File

@ -1,4 +1,6 @@
LAMMPS (24 Mar 2022)
LAMMPS (23 Jun 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# water hexamer with AMOEBA or HIPPO
units real
@ -39,7 +41,7 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.008 seconds
read_data CPU = 0.003 seconds
# force field
@ -63,8 +65,8 @@ compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*]
dump 1 all custom 10 dump.water_hexamer id type x y z fx fy fz
dump_modify 1 sort id
#dump 1 all custom 10 dump.water_hexamer id type x y z fx fy fz
#dump_modify 1 sort id
# zero step run
@ -74,9 +76,9 @@ dump_modify 1 sort id
fix 1 all nve
thermo 10
run 100
AMOEBA/HIPPO force field settings
thermo 1
run 5
HIPPO force field settings
repulsion: cut 10 taper 8 rscale 0 0 1 1
qxfer: cut 10 taper 8 mscale 0 0 0.4 1
dispersion: cut 10 aewald 0 dspscale 0 0 0.4 1
@ -84,7 +86,7 @@ AMOEBA/HIPPO force field settings
polar: cut 10 aewald 0
pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 0.2 1 1 1 d/u scale 0 1
precondition: cut 4.5
generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
@ -97,46 +99,41 @@ Neighbor list info ...
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:974)
AMOEBA/HIPPO group count: 6
Per MPI rank memory allocation (min/avg/max) = 49.13 | 49.13 | 49.13 Mbytes
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/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
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 0.033787 on 4 procs for 100 steps with 18 atoms
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 0.000850973 on 4 procs for 5 steps with 18 atoms
Performance: 255.719 ns/day, 0.094 hours/ns, 2959.715 timesteps/s
99.9% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 507.654 ns/day, 0.047 hours/ns, 5875.629 timesteps/s
99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
AMEOBA/HIPPO timing breakdown:
Init time: 0.000724905 0.0236438
Repulse time: 0.00306516 9.99746
Disp time: 0.000637502 2.07931
Mpole time: 0.00397577 12.9676
Induce time: 0.0181268 59.123
Polar time: 0.00377543 12.3141
Qxfer time: 0.000349256 1.13915
Total time: 0.0306594
HIPPO timing breakdown:
Init time: 1.6627e-05 2.46%
Repulse time: 9.88147e-05 14.60%
Disp time: 1.35375e-05 2.00%
Mpole time: 0.000103418 15.28%
Induce time: 0.000343719 50.80%
Polar time: 9.3749e-05 13.85%
Qxfer time: 6.64925e-06 0.98%
Total time: 0.000676665
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.030576 | 0.030875 | 0.031306 | 0.2 | 91.38
Bond | 6.4191e-05 | 7.956e-05 | 0.0001014 | 0.0 | 0.24
Pair | 0.00068159 | 0.00068738 | 0.00069496 | 0.0 | 80.78
Bond | 3.506e-06 | 3.8025e-06 | 4.338e-06 | 0.0 | 0.45
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00072972 | 0.0012341 | 0.0015501 | 1.0 | 3.65
Output | 0.0011293 | 0.0011806 | 0.0012922 | 0.2 | 3.49
Modify | 4.0541e-05 | 4.5677e-05 | 5.4304e-05 | 0.0 | 0.14
Other | | 0.0003717 | | | 1.10
Comm | 1.1451e-05 | 4.4141e-05 | 5.7694e-05 | 0.0 | 5.19
Output | 9.6072e-05 | 0.00010517 | 0.00013106 | 0.0 | 12.36
Modify | 1.799e-06 | 1.9772e-06 | 2.149e-06 | 0.0 | 0.23
Other | | 8.507e-06 | | | 1.00
Nlocal: 4.5 ave 6 max 3 min
Histogram: 1 0 0 1 0 0 1 0 0 1