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updated examples

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This commit is contained in:
Steve Plimpton
2022-05-24 16:49:30 -06:00
parent ed0f53cfde
commit 97eb6c195f
22 changed files with 345 additions and 19855 deletions
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28
examples/amoeba/Test.sh
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@ -2,65 +2,65 @@
# dimer
../../src/lmp_mpi < in.water_dimer.amoeba
../../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
mpirun -np 4 ../../src/lmp_mpi < in.water_dimer.amoeba
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
../../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
mpirun -np 4 ../../src/lmp_mpi < in.water_dimer.hippo.test
mv log.lammps log.water_dimer.hippo.4.test
mv dump.water_dimer dump.water_dimer.hippo.4.test
# hexamer
../../src/lmp_mpi < in.water_hexamer.amoeba
../../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
mpirun -np 4 ../../src/lmp_mpi < in.water_hexamer.amoeba
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
../../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
mpirun -np 4 ../../src/lmp_mpi < in.water_hexamer.hippo.test
mv log.lammps log.water_hexamer.hippo.4.test
mv dump.water_hexamer dump.water_hexamer.hippo.4.test
# water box
../../src/lmp_mpi < in.water_box.amoeba
../../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
mpirun -np 32 ../../src/lmp_mpi < in.water_box.amoeba
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
../../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
mpirun -np 32 ../../src/lmp_mpi < in.water_box.hippo.test
mv log.lammps log.water_box.hippo.32.test
mv dump.water_box dump.water_box.hippo.32.test
# ubiquitin
../../src/lmp_mpi < in.ubiquitin
../../src/lmp_mpi < in.ubiquitin.test
mv log.lammps log.ubi.1.test
mv dump.ubi dump.ubi.1.test
mpirun -np 32 ../../src/lmp_mpi < in.ubiquitin
mpirun -np 32 ../../src/lmp_mpi < in.ubiquitin.test
mv log.lammps log.ubi.32.test
mv dump.ubi dump.ubi.32.test

19492
examples/amoeba/dump.ubi
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File diff suppressed because it is too large Load Diff

5
examples/amoeba/in.water_box.amoeba.test
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@ -11,9 +11,8 @@ dihedral_style none
# per-atom properties required by AMOEBA or HIPPO
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom &
i_amgroup d_redID d_xaxis d_yaxis d_zaxis d_pval ghost yes
fix extra2 all property/atom i_polaxe
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

5
examples/amoeba/in.water_box.hippo.test
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@ -11,9 +11,8 @@ dihedral_style none
# per-atom properties required by AMOEBA or HIPPO
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom &
i_amgroup d_redID d_xaxis d_yaxis d_zaxis d_pval ghost yes
fix extra2 all property/atom i_polaxe
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

5
examples/amoeba/in.water_dimer.amoeba.test
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@ -11,9 +11,8 @@ dihedral_style none
# per-atom properties required by AMOEBA or HIPPO
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom &
i_amgroup d_redID d_xaxis d_yaxis d_zaxis d_pval ghost yes
fix extra2 all property/atom i_polaxe
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

5
examples/amoeba/in.water_dimer.hippo.test
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@ -11,9 +11,8 @@ dihedral_style none
# per-atom properties required by AMOEBA or HIPPO
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom &
i_amgroup d_redID d_xaxis d_yaxis d_zaxis d_pval ghost yes
fix extra2 all property/atom i_polaxe
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

5
examples/amoeba/in.water_hexamer.amoeba.test
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@ -11,9 +11,8 @@ dihedral_style none
# per-atom properties required by AMOEBA or HIPPO
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom &
i_amgroup d_redID d_xaxis d_yaxis d_zaxis d_pval ghost yes
fix extra2 all property/atom i_polaxe
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

5
examples/amoeba/in.water_hexamer.hippo.test
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@ -11,9 +11,8 @@ dihedral_style none
# per-atom properties required by AMOEBA or HIPPO
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom &
i_amgroup d_redID d_xaxis d_yaxis d_zaxis d_pval ghost yes
fix extra2 all property/atom i_polaxe
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

48
examples/amoeba/log.ubi.1.test
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@ -15,15 +15,16 @@ 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
fix extra all property/atom i_amgroup d_redID d_xaxis d_yaxis d_zaxis d_pval ghost yes
fix extra2 all property/atom i_polaxe
# read data file
#read_data data.ubiquitin fix amtype NULL "Tinker Types"
read_data data.ubiquitin fix amtype NULL "Tinker Types" fix pit "pitorsion types" "PiTorsion Coeffs" fix pit pitorsions PiTorsions fix bit bitorsions BiTorsions
Reading data file ...
orthogonal box = (0 0 0) to (54.99 41.91 41.91)
@ -54,7 +55,7 @@ Finding 1-2 1-3 1-4 neighbors ...
19 = max # of 1-4 neighbors
21 = max # of special neighbors
special bonds CPU = 0.004 seconds
read_data CPU = 0.076 seconds
read_data CPU = 0.082 seconds
pair_style amoeba
pair_coeff * * amoeba_ubiquitin.prm amoeba_ubiquitin.key
@ -109,7 +110,7 @@ Neighbor list info ...
stencil: half/bin/3d
bin: standard
AMOEBA/HIPPO group count: 3196
Per MPI rank memory allocation (min/avg/max) = 98.55 | 98.55 | 98.55 Mbytes
Per MPI rank memory allocation (min/avg/max) = 260.4 | 260.4 | 260.4 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
@ -121,31 +122,30 @@ Per MPI rank memory allocation (min/avg/max) = 98.55 | 98.55 | 98.55 Mbytes
7 137.7204 -36521.444 782.87113 1026.745 212.04289 38.686259 2060.3452 -30479.082 -5987.83 -8386.8104 -7363.188 -7888.261 357.00835 253.66346 32.827786
8 112.66452 -36897.181 1750.0569 1269.152 210.83571 33.742799 3263.7874 -30379.432 -7886.4081 -9703.2601 -9043.015 -9555.2908 490.76046 182.31259 278.727
9 88.237359 -37209.906 2695.1766 1454.55 209.91331 29.503458 4389.1434 -30276.565 -8202.16 -9492.368 -9110.7037 -9639.2288 502.55699 107.82333 443.6705
AMEOBA/HIPPO timing info:
Init time: 0.0295323 0.00130007
Hal time: 7.40889 32.6154
Mpole time: 2.19209 9.65001
Induce time: 8.54492 37.6164
Polar time: 4.5405 19.9882
Total time: 22.7159
10 108.86756 -37474.988 2240.4603 1523.7936 209.10313 26.208515 3999.5656 -30333.279 -8468.4347 -9956.923 -9709.5874 -10224.682 365.98214 95.262991 425.12746
Loop time of 22.7636 on 1 procs for 10 steps with 9737 atoms
Loop time of 21.791 on 1 procs for 10 steps with 9737 atoms
Performance: 0.038 ns/day, 632.324 hours/ns, 0.439 timesteps/s
98.1% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 0.040 ns/day, 605.307 hours/ns, 0.459 timesteps/s
99.1% CPU use with 1 MPI tasks x no OpenMP threads
AMEOBA/HIPPO timing breakdown:
Init time: 0.0264311 0.00121566
Hal time: 7.15654 32.9156
Mpole time: 2.14232 9.85334
Induce time: 7.99277 36.7617
Polar time: 4.42403 20.3477
Total time: 21.7421
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 22.716 | 22.716 | 22.716 | 0.0 | 99.79
Bond | 0.015795 | 0.015795 | 0.015795 | 0.0 | 0.07
Pair | 21.742 | 21.742 | 21.742 | 0.0 | 99.78
Bond | 0.014806 | 0.014806 | 0.014806 | 0.0 | 0.07
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.003791 | 0.003791 | 0.003791 | 0.0 | 0.02
Output | 0.024013 | 0.024013 | 0.024013 | 0.0 | 0.11
Modify | 0.00335 | 0.00335 | 0.00335 | 0.0 | 0.01
Other | | 0.0006405 | | | 0.00
Comm | 0.0035774 | 0.0035774 | 0.0035774 | 0.0 | 0.02
Output | 0.026947 | 0.026947 | 0.026947 | 0.0 | 0.12
Modify | 0.0028419 | 0.0028419 | 0.0028419 | 0.0 | 0.01
Other | | 0.0007034 | | | 0.00
Nlocal: 9737 ave 9737 max 9737 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -159,4 +159,4 @@ Ave neighs/atom = 579.16155
Ave special neighs/atom = 3.1364897
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:26
Total wall time: 0:00:24

48
examples/amoeba/log.ubi.32.test
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@ -15,15 +15,16 @@ 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
fix extra all property/atom i_amgroup d_redID d_xaxis d_yaxis d_zaxis d_pval ghost yes
fix extra2 all property/atom i_polaxe
# read data file
#read_data data.ubiquitin fix amtype NULL "Tinker Types"
read_data data.ubiquitin fix amtype NULL "Tinker Types" fix pit "pitorsion types" "PiTorsion Coeffs" fix pit pitorsions PiTorsions fix bit bitorsions BiTorsions
Reading data file ...
orthogonal box = (0 0 0) to (54.99 41.91 41.91)
@ -54,7 +55,7 @@ Finding 1-2 1-3 1-4 neighbors ...
19 = max # of 1-4 neighbors
21 = max # of special neighbors
special bonds CPU = 0.002 seconds
read_data CPU = 0.120 seconds
read_data CPU = 0.112 seconds
pair_style amoeba
pair_coeff * * amoeba_ubiquitin.prm amoeba_ubiquitin.key
@ -109,7 +110,7 @@ Neighbor list info ...
stencil: half/bin/3d
bin: standard
AMOEBA/HIPPO group count: 3196
Per MPI rank memory allocation (min/avg/max) = 26.19 | 26.49 | 27.59 Mbytes
Per MPI rank memory allocation (min/avg/max) = 73.46 | 73.76 | 74.86 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 -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
@ -121,31 +122,30 @@ Per MPI rank memory allocation (min/avg/max) = 26.19 | 26.49 | 27.59 Mbytes
7 137.7204 -36521.444 782.87113 1026.745 212.04289 38.686259 2060.3452 -30479.082 -5987.83 -8386.8104 -7363.188 -7888.261 357.00835 253.66346 32.827786
8 112.66452 -36897.181 1750.0569 1269.152 210.83571 33.742799 3263.7874 -30379.432 -7886.4081 -9703.2601 -9043.015 -9555.2908 490.76046 182.31259 278.727
9 88.237359 -37209.906 2695.1766 1454.55 209.91331 29.503458 4389.1434 -30276.565 -8202.16 -9492.368 -9110.7037 -9639.2288 502.55699 107.82333 443.6705
AMEOBA/HIPPO timing info:
Init time: 0.0255174 0.0162332
Hal time: 0.273968 17.4289
Mpole time: 0.202832 12.9035
Induce time: 0.79876 50.8142
Polar time: 0.270839 17.2298
Total time: 1.57192
10 108.86756 -37474.988 2240.4603 1523.7936 209.10313 26.208515 3999.5656 -30333.279 -8468.4347 -9956.923 -9709.5874 -10224.682 365.98214 95.262991 425.12746
Loop time of 1.58782 on 32 procs for 10 steps with 9737 atoms
Loop time of 1.51355 on 32 procs for 10 steps with 9737 atoms
Performance: 0.544 ns/day, 44.106 hours/ns, 6.298 timesteps/s
99.3% CPU use with 32 MPI tasks x no OpenMP threads
Performance: 0.571 ns/day, 42.043 hours/ns, 6.607 timesteps/s
99.5% CPU use with 32 MPI tasks x no OpenMP threads
AMEOBA/HIPPO timing breakdown:
Init time: 0.0221241 0.0147382
Hal time: 0.27487 18.3107
Mpole time: 0.1964 13.0833
Induce time: 0.743514 49.5298
Polar time: 0.264231 17.602
Total time: 1.50114
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.5717 | 1.5724 | 1.5732 | 0.0 | 99.03
Bond | 0.00025512 | 0.00072817 | 0.0025027 | 0.0 | 0.05
Pair | 1.5006 | 1.5014 | 1.5026 | 0.1 | 99.20
Bond | 0.00023121 | 0.0006371 | 0.002095 | 0.0 | 0.04
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.008108 | 0.010596 | 0.011659 | 0.9 | 0.67
Output | 0.0032598 | 0.0035294 | 0.0038605 | 0.2 | 0.22
Modify | 0.00017743 | 0.00030162 | 0.00054742 | 0.0 | 0.02
Other | | 0.0002902 | | | 0.02
Comm | 0.0060146 | 0.008046 | 0.0092638 | 1.0 | 0.53
Output | 0.0028415 | 0.0030424 | 0.003441 | 0.2 | 0.20
Modify | 0.00011709 | 0.00019911 | 0.00036104 | 0.0 | 0.01
Other | | 0.0002509 | | | 0.02
Nlocal: 304.281 ave 326 max 273 min
Histogram: 1 1 0 5 2 8 3 6 4 2
@ -159,4 +159,4 @@ Ave neighs/atom = 579.16155
Ave special neighs/atom = 3.1364897
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:02
Total wall time: 0:00:01

45
examples/amoeba/log.water_box.amoeba.1.test
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@ -12,8 +12,8 @@ dihedral_style none
# per-atom properties required by AMOEBA or HIPPO
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom i_amgroup d_redID d_xaxis d_yaxis d_zaxis d_pval ghost yes
fix extra2 all property/atom i_polaxe
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
@ -39,7 +39,7 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.010 seconds
read_data CPU = 0.012 seconds
# force field
@ -96,7 +96,7 @@ Neighbor list info ...
stencil: half/bin/3d
bin: standard
AMOEBA/HIPPO group count: 216
Per MPI rank memory allocation (min/avg/max) = 10.9 | 10.9 | 10.9 Mbytes
Per MPI rank memory allocation (min/avg/max) = 58.28 | 58.28 | 58.28 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 -2172.0441 166.82637 83.732524 0 0 250.5589 -1921.4852 -6181.7112 -4771.8292 -6955.3278 -6817.9765 -272.19746 3173.3487 2229.6526
10 105.50439 -2373.6865 136.67908 106.86552 0 0 243.54459 -1926.6678 -8441.2174 -10450.318 -9514.124 -9665.625 -301.45304 322.2435 1916.9694
@ -108,31 +108,30 @@ Per MPI rank memory allocation (min/avg/max) = 10.9 | 10.9 | 10.9 Mbytes
70 166.70629 -2383.4827 76.492455 55.020922 0 0 131.51338 -1930.4622 4743.9587 1916.6786 2839.9241 2670.7568 -169.67855 -187.58379 -2256.4529
80 171.82933 -2388.0347 76.463333 49.138785 0 0 125.60212 -1931.0453 2210.1222 -319.99043 330.98785 -394.25628 -44.858027 252.35533 -1985.0908
90 175.7327 -2423.7974 90.784969 63.725029 0 0 154.51 -1930.3722 -917.58179 -3941.9566 -2568.4278 -3415.3121 196.38051 2366.2885 -263.52434
AMEOBA/HIPPO timing info:
Init time: 0.0268067 0.000648832
Hal time: 0.950781 2.30127
Mpole time: 2.62623 6.35653
Induce time: 31.3736 75.9368
Polar time: 6.33798 15.3405
Total time: 41.3154
100 173.73319 -2422.3616 99.761403 57.29505 0 0 157.05645 -1930.2461 -3586.4169 -5733.9943 -5881.4025 -6235.1905 -230.75166 959.02899 406.2349
Loop time of 41.3458 on 1 procs for 100 steps with 648 atoms
Loop time of 38.7603 on 1 procs for 100 steps with 648 atoms
Performance: 0.209 ns/day, 114.849 hours/ns, 2.419 timesteps/s
Performance: 0.223 ns/day, 107.668 hours/ns, 2.580 timesteps/s
99.6% CPU use with 1 MPI tasks x no OpenMP threads
AMEOBA/HIPPO timing breakdown:
Init time: 0.0258209 0.000666708
Hal time: 0.889324 2.29628
Mpole time: 2.44816 6.32126
Induce time: 29.4141 75.9487
Polar time: 5.95145 15.3669
Total time: 38.7289
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 41.316 | 41.316 | 41.316 | 0.0 | 99.93
Bond | 0.0034989 | 0.0034989 | 0.0034989 | 0.0 | 0.01
Neigh | 0.0060545 | 0.0060545 | 0.0060545 | 0.0 | 0.01
Comm | 0.0037812 | 0.0037812 | 0.0037812 | 0.0 | 0.01
Output | 0.014701 | 0.014701 | 0.014701 | 0.0 | 0.04
Modify | 0.00098692 | 0.00098692 | 0.00098692 | 0.0 | 0.00
Other | | 0.001033 | | | 0.00
Pair | 38.729 | 38.729 | 38.729 | 0.0 | 99.92
Bond | 0.003226 | 0.003226 | 0.003226 | 0.0 | 0.01
Neigh | 0.0054679 | 0.0054679 | 0.0054679 | 0.0 | 0.01
Comm | 0.0036497 | 0.0036497 | 0.0036497 | 0.0 | 0.01
Output | 0.01663 | 0.01663 | 0.01663 | 0.0 | 0.04
Modify | 0.00088965 | 0.00088965 | 0.00088965 | 0.0 | 0.00
Other | | 0.001155 | | | 0.00
Nlocal: 648 ave 648 max 648 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -146,4 +145,4 @@ Ave neighs/atom = 152.07253
Ave special neighs/atom = 2
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:00:42
Total wall time: 0:00:39

45
examples/amoeba/log.water_box.amoeba.32.test
View File

@ -12,8 +12,8 @@ dihedral_style none
# per-atom properties required by AMOEBA or HIPPO
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom i_amgroup d_redID d_xaxis d_yaxis d_zaxis d_pval ghost yes
fix extra2 all property/atom i_polaxe
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
@ -39,7 +39,7 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.002 seconds
read_data CPU = 0.026 seconds
read_data CPU = 0.020 seconds
# force field
@ -55,7 +55,7 @@ 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 = 0.002 seconds
special bonds CPU = 0.001 seconds
# thermo output
@ -96,7 +96,7 @@ Neighbor list info ...
stencil: half/bin/3d
bin: standard
AMOEBA/HIPPO group count: 216
Per MPI rank memory allocation (min/avg/max) = 10.07 | 10.08 | 10.34 Mbytes
Per MPI rank memory allocation (min/avg/max) = 57.47 | 57.48 | 57.74 Mbytes
Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6]
0 0 -2172.0441 166.82637 83.732524 0 0 250.5589 -1921.4852 -6181.7112 -4771.8292 -6955.3278 -6817.9765 -272.19746 3173.3487 2229.6526
10 105.50439 -2373.6865 136.67908 106.86552 0 0 243.54459 -1926.6678 -8441.2174 -10450.318 -9514.124 -9665.625 -301.45304 322.2435 1916.9694
@ -108,31 +108,30 @@ Per MPI rank memory allocation (min/avg/max) = 10.07 | 10.08 | 10.34 Mbytes
70 166.70629 -2383.4827 76.492455 55.020922 0 0 131.51338 -1930.4622 4743.9587 1916.6786 2839.9241 2670.7568 -169.67855 -187.58379 -2256.4529
80 171.82933 -2388.0347 76.463333 49.138785 0 0 125.60212 -1931.0453 2210.1222 -319.99043 330.98785 -394.25628 -44.858027 252.35533 -1985.0908
90 175.7327 -2423.7974 90.784969 63.725029 0 0 154.51 -1930.3722 -917.58179 -3941.9566 -2568.4278 -3415.3121 196.38051 2366.2885 -263.52434
AMEOBA/HIPPO timing info:
Init time: 0.0370802 0.00577897
Hal time: 0.0365961 0.570352
Mpole time: 0.548509 8.54854
Induce time: 4.8345 75.346
Polar time: 0.95968 14.9567
Total time: 6.4164
100 173.73319 -2422.3616 99.761403 57.29505 0 0 157.05645 -1930.2461 -3586.4169 -5733.9943 -5881.4025 -6235.1905 -230.75166 959.02899 406.2349
Loop time of 6.44751 on 32 procs for 100 steps with 648 atoms
Loop time of 6.48935 on 32 procs for 100 steps with 648 atoms
Performance: 1.340 ns/day, 17.910 hours/ns, 15.510 timesteps/s
Performance: 1.331 ns/day, 18.026 hours/ns, 15.410 timesteps/s
99.8% CPU use with 32 MPI tasks x no OpenMP threads
AMEOBA/HIPPO timing breakdown:
Init time: 0.0357484 0.00553355
Hal time: 0.0364815 0.564704
Mpole time: 0.541384 8.38018
Induce time: 4.89091 75.7073
Polar time: 0.955739 14.794
Total time: 6.46029
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 6.4102 | 6.4179 | 6.4248 | 0.2 | 99.54
Bond | 0.00029057 | 0.00042623 | 0.00057421 | 0.0 | 0.01
Neigh | 0.00040172 | 0.00045575 | 0.00052495 | 0.0 | 0.01
Comm | 0.016267 | 0.023118 | 0.030703 | 2.6 | 0.36
Output | 0.0037201 | 0.003804 | 0.0040605 | 0.1 | 0.06
Modify | 0.00028994 | 0.00038094 | 0.0005128 | 0.0 | 0.01
Other | | 0.001461 | | | 0.02
Pair | 6.4536 | 6.4614 | 6.4698 | 0.2 | 99.57
Bond | 0.00025488 | 0.00038243 | 0.00051904 | 0.0 | 0.01
Neigh | 0.00033789 | 0.00036365 | 0.00040331 | 0.0 | 0.01
Comm | 0.013439 | 0.021894 | 0.02956 | 2.9 | 0.34
Output | 0.0038126 | 0.0038325 | 0.0040712 | 0.1 | 0.06
Modify | 0.00021256 | 0.00028049 | 0.00035212 | 0.0 | 0.00
Other | | 0.001189 | | | 0.02
Nlocal: 20.25 ave 26 max 12 min
Histogram: 1 1 3 1 2 7 3 11 1 2

53
examples/amoeba/log.water_box.hippo.1.test
View File

@ -12,8 +12,8 @@ dihedral_style none
# per-atom properties required by AMOEBA or HIPPO
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom i_amgroup d_redID d_xaxis d_yaxis d_zaxis d_pval ghost yes
fix extra2 all property/atom i_polaxe
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
@ -39,7 +39,7 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.007 seconds
read_data CPU = 0.012 seconds
# force field
@ -55,7 +55,7 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-4 neighbors
2 = max # of 1-5 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
special bonds CPU = 0.001 seconds
# thermo output
@ -98,7 +98,7 @@ Neighbor list info ...
stencil: half/bin/3d
bin: standard
AMOEBA/HIPPO group count: 216
Per MPI rank memory allocation (min/avg/max) = 10.89 | 10.89 | 10.89 Mbytes
Per MPI rank memory allocation (min/avg/max) = 57.8 | 57.8 | 57.8 Mbytes
Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6]
0 0 -2188.594 166.82637 77.478353 0 0 244.30473 -1944.2893 -10859.589 -9285.4645 -11598.049 -11695.254 -282.7072 3164.4148 2495.2578
10 100.94691 -2350.192 116.13156 88.56605 0 0 204.69761 -1950.8098 -11480.919 -13574.139 -12190.797 -12798.212 -263.77028 280.62864 1974.1486
@ -110,33 +110,32 @@ Per MPI rank memory allocation (min/avg/max) = 10.89 | 10.89 | 10.89 Mbytes
70 184.86849 -2391.6106 39.916931 35.978152 0 0 75.895083 -1959.1811 -2146.9339 -4993.4021 -4095.6729 -4897.5768 -833.09046 1542.411 -1539.5266
80 164.75795 -2406.3017 101.94229 33.067832 0 0 135.01013 -1953.542 -8779.3265 -10545.409 -10418.702 -12098.858 -1319.194 1750.3511 -275.1272
90 151.17491 -2434.6876 152.21826 41.301673 0 0 193.51993 -1949.6141 -13330.691 -15436.505 -13791.461 -16934.674 149.25497 2289.1026 976.14333
AMEOBA/HIPPO timing info:
Init time: 0.0135815 0.00137415
Repls time: 1.1283 11.4159
Disp time: 0.913907 9.24672
Mpole time: 1.76939 17.9023
Induce time: 3.50511 35.4639
Polar time: 2.23426 22.6058
Qxfer time: 0.319009 3.22767
Total time: 9.88358
100 166.99163 -2452.5298 143.57768 35.341459 0 0 178.91914 -1951.5533 -14918.51 -16077.49 -17353.738 -18140.466 19.009088 1487.0469 1084.0231
Loop time of 9.91124 on 1 procs for 100 steps with 648 atoms
Loop time of 9.27469 on 1 procs for 100 steps with 648 atoms
Performance: 0.872 ns/day, 27.531 hours/ns, 10.090 timesteps/s
98.6% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 0.932 ns/day, 25.763 hours/ns, 10.782 timesteps/s
99.0% CPU use with 1 MPI tasks x no OpenMP threads
AMEOBA/HIPPO timing breakdown:
Init time: 0.012403 0.00134127
Repulse time: 1.04474 11.2979
Disp time: 0.83125 8.98919
Mpole time: 1.66803 18.0382
Induce time: 3.2846 35.5199
Polar time: 2.12371 22.9659
Qxfer time: 0.282486 3.05482
Total time: 9.24722
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 9.8837 | 9.8837 | 9.8837 | 0.0 | 99.72
Bond | 0.0026063 | 0.0026063 | 0.0026063 | 0.0 | 0.03
Neigh | 0.0058854 | 0.0058854 | 0.0058854 | 0.0 | 0.06
Comm | 0.002753 | 0.002753 | 0.002753 | 0.0 | 0.03
Output | 0.014779 | 0.014779 | 0.014779 | 0.0 | 0.15
Modify | 0.00071385 | 0.00071385 | 0.00071385 | 0.0 | 0.01
Other | | 0.0007555 | | | 0.01
Pair | 9.2473 | 9.2473 | 9.2473 | 0.0 | 99.70
Bond | 0.0023727 | 0.0023727 | 0.0023727 | 0.0 | 0.03
Neigh | 0.0055338 | 0.0055338 | 0.0055338 | 0.0 | 0.06
Comm | 0.0021428 | 0.0021428 | 0.0021428 | 0.0 | 0.02
Output | 0.016044 | 0.016044 | 0.016044 | 0.0 | 0.17
Modify | 0.00059122 | 0.00059122 | 0.00059122 | 0.0 | 0.01
Other | | 0.0006893 | | | 0.01
Nlocal: 648 ave 648 max 648 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -150,4 +149,4 @@ Ave neighs/atom = 151.99074
Ave special neighs/atom = 2
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:00:10
Total wall time: 0:00:09

49
examples/amoeba/log.water_box.hippo.32.test
View File

@ -12,8 +12,8 @@ dihedral_style none
# per-atom properties required by AMOEBA or HIPPO
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom i_amgroup d_redID d_xaxis d_yaxis d_zaxis d_pval ghost yes
fix extra2 all property/atom i_polaxe
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
@ -39,7 +39,7 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.002 seconds
read_data CPU = 0.026 seconds
read_data CPU = 0.020 seconds
# force field
@ -98,7 +98,7 @@ Neighbor list info ...
stencil: half/bin/3d
bin: standard
AMOEBA/HIPPO group count: 216
Per MPI rank memory allocation (min/avg/max) = 10.07 | 10.08 | 10.34 Mbytes
Per MPI rank memory allocation (min/avg/max) = 57.03 | 57.04 | 57.3 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 -2188.594 166.82637 77.478353 0 0 244.30473 -1944.2893 -10859.589 -9285.4645 -11598.049 -11695.254 -282.7072 3164.4148 2495.2578
10 100.94691 -2350.192 116.13156 88.56605 0 0 204.69761 -1950.8098 -11480.919 -13574.139 -12190.797 -12798.212 -263.77028 280.62864 1974.1486
@ -110,33 +110,32 @@ Per MPI rank memory allocation (min/avg/max) = 10.07 | 10.08 | 10.34 Mbytes
70 184.86849 -2391.6106 39.916931 35.978152 0 0 75.895083 -1959.1811 -2146.9339 -4993.4021 -4095.6729 -4897.5768 -833.09046 1542.411 -1539.5266
80 164.75795 -2406.3017 101.94229 33.067832 0 0 135.01013 -1953.542 -8779.3265 -10545.409 -10418.702 -12098.858 -1319.194 1750.3511 -275.1272
90 151.17491 -2434.6876 152.21826 41.301673 0 0 193.51993 -1949.6141 -13330.691 -15436.505 -13791.461 -16934.674 149.25497 2289.1026 976.14333
AMEOBA/HIPPO timing info:
Init time: 0.0207283 0.0128038
Repls time: 0.0699766 4.32242
Disp time: 0.149724 9.24836
Mpole time: 0.274572 16.9601
Induce time: 0.755302 46.6545
Polar time: 0.336004 20.7548
Qxfer time: 0.0126115 0.779003
Total time: 1.61892
100 166.99163 -2452.5298 143.57768 35.341459 0 0 178.91914 -1951.5533 -14918.51 -16077.49 -17353.738 -18140.466 19.009088 1487.0469 1084.0231
Loop time of 1.64289 on 32 procs for 100 steps with 648 atoms
Loop time of 1.60312 on 32 procs for 100 steps with 648 atoms
Performance: 5.259 ns/day, 4.564 hours/ns, 60.868 timesteps/s
99.7% CPU use with 32 MPI tasks x no OpenMP threads
Performance: 5.389 ns/day, 4.453 hours/ns, 62.378 timesteps/s
99.8% CPU use with 32 MPI tasks x no OpenMP threads
AMEOBA/HIPPO timing breakdown:
Init time: 0.019742 0.012493
Repulse time: 0.0675395 4.27399
Disp time: 0.142632 9.02596
Mpole time: 0.265051 16.7728
Induce time: 0.740525 46.8614
Polar time: 0.332551 21.0442
Qxfer time: 0.0121995 0.772001
Total time: 1.58025
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.6154 | 1.62 | 1.6242 | 0.2 | 98.61
Bond | 0.00017997 | 0.0002499 | 0.00040555 | 0.0 | 0.02
Neigh | 0.00042001 | 0.00048474 | 0.00059125 | 0.0 | 0.03
Comm | 0.012961 | 0.017336 | 0.021852 | 1.7 | 1.06
Output | 0.0036708 | 0.0037324 | 0.0039355 | 0.1 | 0.23
Modify | 0.0001113 | 0.00018285 | 0.00027874 | 0.0 | 0.01
Other | | 0.0009209 | | | 0.06
Pair | 1.5773 | 1.5814 | 1.5855 | 0.2 | 98.65
Bond | 0.00015755 | 0.00023663 | 0.0003199 | 0.0 | 0.01
Neigh | 0.00036065 | 0.00038248 | 0.00042908 | 0.0 | 0.02
Comm | 0.01209 | 0.016226 | 0.020477 | 1.7 | 1.01
Output | 0.0037797 | 0.0038027 | 0.0040217 | 0.1 | 0.24
Modify | 0.00010094 | 0.00013624 | 0.00018983 | 0.0 | 0.01
Other | | 0.0008996 | | | 0.06
Nlocal: 20.25 ave 27 max 12 min
Histogram: 1 1 3 1 6 2 10 4 2 2

43
examples/amoeba/log.water_dimer.amoeba.1.test
View File

@ -12,8 +12,8 @@ dihedral_style none
# per-atom properties required by AMOEBA or HIPPO
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom i_amgroup d_redID d_xaxis d_yaxis d_zaxis d_pval ghost yes
fix extra2 all property/atom i_polaxe
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
@ -39,7 +39,7 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.007 seconds
read_data CPU = 0.008 seconds
# force field
@ -97,7 +97,7 @@ Neighbor list info ...
bin: standard
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:974)
AMOEBA/HIPPO group count: 2
Per MPI rank memory allocation (min/avg/max) = 9.855 | 9.855 | 9.855 Mbytes
Per MPI rank memory allocation (min/avg/max) = 49.59 | 49.59 | 49.59 Mbytes
Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6]
0 0 -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
@ -109,31 +109,30 @@ Per MPI rank memory allocation (min/avg/max) = 9.855 | 9.855 | 9.855 Mbytes
70 10.385926 -4.8250769 0.022572262 0.22235766 0 0 0.24492992 -4.4253547 -1117.3665 19070.918 -36063.612 11648.813 61.067533 25754.59 53.919881
80 12.797691 -5.123735 0.023756795 0.48275385 0 0 0.50651065 -4.4264869 -6491.9826 -28436.037 20681.908 -14176.121 -64.024669 -35737.052 -52.583533
90 12.569481 -4.8303379 0.060369422 0.15670502 0 0 0.21707444 -4.4259273 -16762.536 1720.5855 -47624.986 -6793.7441 59.966729 30024.566 52.339671
AMEOBA/HIPPO timing info:
Init time: 0.000111558 0.0206865
Hal time: 0.000425262 7.88575
Mpole time: 0.000608653 11.2864
Induce time: 0.00283871 52.6391
Polar time: 0.00139471 25.8625
Total time: 0.00539279
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 0.00640556 on 1 procs for 100 steps with 6 atoms
Loop time of 0.00655818 on 1 procs for 100 steps with 6 atoms
Performance: 1348.828 ns/day, 0.018 hours/ns, 15611.435 timesteps/s
79.3% CPU use with 1 MPI tasks x no OpenMP threads
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
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
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0054675 | 0.0054675 | 0.0054675 | 0.0 | 85.36
Bond | 9.3071e-05 | 9.3071e-05 | 9.3071e-05 | 0.0 | 1.45
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
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 1.5103e-05 | 1.5103e-05 | 1.5103e-05 | 0.0 | 0.24
Output | 0.00072279 | 0.00072279 | 0.00072279 | 0.0 | 11.28
Modify | 4.4005e-05 | 4.4005e-05 | 4.4005e-05 | 0.0 | 0.69
Other | | 6.307e-05 | | | 0.98
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
Nlocal: 6 ave 6 max 6 min
Histogram: 1 0 0 0 0 0 0 0 0 0

43
examples/amoeba/log.water_dimer.amoeba.4.test
View File

@ -12,8 +12,8 @@ dihedral_style none
# per-atom properties required by AMOEBA or HIPPO
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom i_amgroup d_redID d_xaxis d_yaxis d_zaxis d_pval ghost yes
fix extra2 all property/atom i_polaxe
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
@ -39,7 +39,7 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.008 seconds
read_data CPU = 0.009 seconds
# force field
@ -55,7 +55,7 @@ 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
@ -97,7 +97,7 @@ Neighbor list info ...
bin: standard
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:974)
AMOEBA/HIPPO group count: 2
Per MPI rank memory allocation (min/avg/max) = 9.883 | 10.02 | 10.15 Mbytes
Per MPI rank memory allocation (min/avg/max) = 49.61 | 49.75 | 49.88 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
@ -109,31 +109,30 @@ Per MPI rank memory allocation (min/avg/max) = 9.883 | 10.02 | 10.15 Mbytes
70 10.385926 -4.8250769 0.022572262 0.22235766 0 0 0.24492992 -4.4253547 -1117.3665 19070.918 -36063.612 11648.813 61.067533 25754.59 53.919881
80 12.797691 -5.123735 0.023756795 0.48275385 0 0 0.50651065 -4.4264869 -6491.9826 -28436.037 20681.908 -14176.121 -64.024669 -35737.052 -52.583533
90 12.569481 -4.8303379 0.060369422 0.15670502 0 0 0.21707444 -4.4259273 -16762.536 1720.5855 -47624.986 -6793.7441 59.966729 30024.566 52.339671
AMEOBA/HIPPO timing info:
Init time: 0.000634572 0.0450252
Hal time: 0.000117808 0.835889
Mpole time: 0.000691769 4.90835
Induce time: 0.0116228 82.4677
Polar time: 0.0010122 7.18191
Total time: 0.0140937
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 0.0169629 on 4 procs for 100 steps with 6 atoms
Loop time of 0.0167554 on 4 procs for 100 steps with 6 atoms
Performance: 509.347 ns/day, 0.047 hours/ns, 5895.222 timesteps/s
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
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
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.014227 | 0.014356 | 0.014521 | 0.1 | 84.63
Bond | 2.4327e-05 | 5.1278e-05 | 8.6189e-05 | 0.0 | 0.30
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
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00067884 | 0.00079493 | 0.00099578 | 0.0 | 4.69
Output | 0.0011363 | 0.0012476 | 0.0013572 | 0.2 | 7.35
Modify | 3.5088e-05 | 3.8645e-05 | 4.4792e-05 | 0.0 | 0.23
Other | | 0.0004741 | | | 2.79
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
Nlocal: 1.5 ave 3 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 2

47
examples/amoeba/log.water_dimer.hippo.1.test
View File

@ -12,8 +12,8 @@ dihedral_style none
# per-atom properties required by AMOEBA or HIPPO
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom i_amgroup d_redID d_xaxis d_yaxis d_zaxis d_pval ghost yes
fix extra2 all property/atom i_polaxe
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
@ -39,7 +39,7 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.006 seconds
read_data CPU = 0.008 seconds
# force field
@ -99,7 +99,7 @@ Neighbor list info ...
bin: standard
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:974)
AMOEBA/HIPPO group count: 2
Per MPI rank memory allocation (min/avg/max) = 9.855 | 9.855 | 9.855 Mbytes
Per MPI rank memory allocation (min/avg/max) = 49.15 | 49.15 | 49.15 Mbytes
Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6]
0 0 -5.0101954 0.025695395 0.51472748 0 0 0.54042288 -4.4697726 -11875.159 -38149.178 29162.678 -26638.977 -70.63422 -24614.614 -58.505595
10 0.75132894 -4.7952077 0.028216017 0.28494196 0 0 0.31315798 -4.4708519 -13243.822 12661.254 -49613.657 -2923.1497 69.449413 29456.684 56.087663
@ -111,33 +111,32 @@ Per MPI rank memory allocation (min/avg/max) = 9.855 | 9.855 | 9.855 Mbytes
70 5.3145827 -4.8748857 0.025797484 0.29875503 0 0 0.32455252 -4.4711244 -10208.876 26324.134 -49272.688 -8697.2875 84.479942 36185.667 57.000355
80 3.8409793 -5.0262066 0.027669388 0.47104466 0 0 0.49871405 -4.4702464 -9777.1809 -52088.554 28053.855 -6033.4555 -94.607853 -44638.417 -59.108505
90 3.0683704 -4.8369716 0.035455716 0.28466932 0 0 0.32012503 -4.4711155 -10626.245 31066.635 -49425.925 -14107.889 87.765958 34632.905 52.101981
AMEOBA/HIPPO timing info:
Init time: 0.000122127 0.0207713
Repls time: 0.000661596 11.2524
Disp time: 0.000406536 6.91434
Mpole time: 0.00103934 17.677
Induce time: 0.00224082 38.1118
Polar time: 0.00123925 21.0772
Qxfer time: 0.000164716 2.80148
Total time: 0.00587961
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 0.00703205 on 1 procs for 100 steps with 6 atoms
Loop time of 0.00568827 on 1 procs for 100 steps with 6 atoms
Performance: 1228.660 ns/day, 0.020 hours/ns, 14220.604 timesteps/s
94.9% CPU use with 1 MPI tasks x no OpenMP threads
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
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
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0059768 | 0.0059768 | 0.0059768 | 0.0 | 84.99
Bond | 9.2998e-05 | 9.2998e-05 | 9.2998e-05 | 0.0 | 1.32
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
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 1.7052e-05 | 1.7052e-05 | 1.7052e-05 | 0.0 | 0.24
Output | 0.00082231 | 0.00082231 | 0.00082231 | 0.0 | 11.69
Modify | 5.0238e-05 | 5.0238e-05 | 5.0238e-05 | 0.0 | 0.71
Other | | 7.262e-05 | | | 1.03
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
Nlocal: 6 ave 6 max 6 min
Histogram: 1 0 0 0 0 0 0 0 0 0

49
examples/amoeba/log.water_dimer.hippo.4.test
View File

@ -12,8 +12,8 @@ dihedral_style none
# per-atom properties required by AMOEBA or HIPPO
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom i_amgroup d_redID d_xaxis d_yaxis d_zaxis d_pval ghost yes
fix extra2 all property/atom i_polaxe
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
@ -39,7 +39,7 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.008 seconds
read_data CPU = 0.009 seconds
# force field
@ -55,7 +55,7 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-4 neighbors
2 = max # of 1-5 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
special bonds CPU = 0.001 seconds
# thermo output
@ -99,7 +99,7 @@ Neighbor list info ...
bin: standard
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:974)
AMOEBA/HIPPO group count: 2
Per MPI rank memory allocation (min/avg/max) = 9.883 | 10.02 | 10.15 Mbytes
Per MPI rank memory allocation (min/avg/max) = 49.18 | 49.31 | 49.44 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
@ -111,33 +111,32 @@ Per MPI rank memory allocation (min/avg/max) = 9.883 | 10.02 | 10.15 Mbytes
70 5.3145827 -4.8748857 0.025797484 0.29875503 0 0 0.32455252 -4.4711244 -10208.876 26324.134 -49272.688 -8697.2875 84.479942 36185.667 57.000355
80 3.8409793 -5.0262066 0.027669388 0.47104466 0 0 0.49871405 -4.4702464 -9777.1809 -52088.554 28053.855 -6033.4555 -94.607853 -44638.417 -59.108505
90 3.0683704 -4.8369716 0.035455716 0.28466932 0 0 0.32012503 -4.4711155 -10626.245 31066.635 -49425.925 -14107.889 87.765958 34632.905 52.101981
AMEOBA/HIPPO timing info:
Init time: 0.00050652 0.0494826
Repls time: 0.00054788 5.35232
Disp time: 9.848e-05 0.962064
Mpole time: 0.000949974 9.28042
Induce time: 0.00725514 70.8764
Polar time: 0.000826552 8.0747
Qxfer time: 4.75238e-05 0.464266
Total time: 0.0102363
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 0.0126885 on 4 procs for 100 steps with 6 atoms
Loop time of 0.0133873 on 4 procs for 100 steps with 6 atoms
Performance: 680.931 ns/day, 0.035 hours/ns, 7881.149 timesteps/s
98.0% CPU use with 4 MPI tasks x no OpenMP threads
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
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
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.010297 | 0.010486 | 0.01066 | 0.1 | 82.64
Bond | 1.5435e-05 | 3.8769e-05 | 6.9606e-05 | 0.0 | 0.31
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
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00054274 | 0.00075815 | 0.00091745 | 0.0 | 5.98
Output | 0.00089374 | 0.00097565 | 0.0010809 | 0.0 | 7.69
Modify | 2.4069e-05 | 3.143e-05 | 3.8898e-05 | 0.0 | 0.25
Other | | 0.0003984 | | | 3.14
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
Nlocal: 1.5 ave 3 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 2

43
examples/amoeba/log.water_hexamer.amoeba.1.test
View File

@ -12,8 +12,8 @@ dihedral_style none
# per-atom properties required by AMOEBA or HIPPO
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom i_amgroup d_redID d_xaxis d_yaxis d_zaxis d_pval ghost yes
fix extra2 all property/atom i_polaxe
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
@ -39,7 +39,7 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.006 seconds
read_data CPU = 0.009 seconds
# force field
@ -96,7 +96,7 @@ Neighbor list info ...
stencil: half/bin/3d
bin: standard
AMOEBA/HIPPO group count: 6
Per MPI rank memory allocation (min/avg/max) = 9.804 | 9.804 | 9.804 Mbytes
Per MPI rank memory allocation (min/avg/max) = 49.53 | 49.53 | 49.53 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
@ -108,31 +108,30 @@ Per MPI rank memory allocation (min/avg/max) = 9.804 | 9.804 | 9.804 Mbytes
70 11.272241 -45.411622 0.07431614 0.51778317 0 0 0.59209931 -44.248316 32055.564 39306.193 30181.52 25601.501 1373.4778 -4501.0686 -2570.4767
80 14.011502 -46.081444 0.089688317 1.006928 0 0 1.0966163 -44.274812 25661.838 38836.598 12603.734 24205.867 -867.36437 -4211.9639 -2820.6725
90 17.659498 -46.247295 0.21744649 0.82687716 0 0 1.0443237 -44.308098 12101.207 19426.995 14142.311 1046.299 -2157.5418 -2141.2454 -2621.456
AMEOBA/HIPPO timing info:
Init time: 0.000317854 0.00755342
Hal time: 0.00509951 12.1184
Mpole time: 0.0045403 10.7895
Induce time: 0.0205332 48.7946
Polar time: 0.0115735 27.503
Total time: 0.0420808
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 0.0436474 on 1 procs for 100 steps with 18 atoms
Loop time of 0.0438592 on 1 procs for 100 steps with 18 atoms
Performance: 197.950 ns/day, 0.121 hours/ns, 2291.090 timesteps/s
98.0% CPU use with 1 MPI tasks x no OpenMP threads
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
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
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.042165 | 0.042165 | 0.042165 | 0.0 | 96.60
Bond | 0.00020639 | 0.00020639 | 0.00020639 | 0.0 | 0.47
Pair | 0.042221 | 0.042221 | 0.042221 | 0.0 | 96.26
Bond | 0.00021632 | 0.00021632 | 0.00021632 | 0.0 | 0.49
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 1.9457e-05 | 1.9457e-05 | 1.9457e-05 | 0.0 | 0.04
Output | 0.0011074 | 0.0011074 | 0.0011074 | 0.0 | 2.54
Modify | 7.3538e-05 | 7.3538e-05 | 7.3538e-05 | 0.0 | 0.17
Other | | 7.545e-05 | | | 0.17
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
Nlocal: 18 ave 18 max 18 min
Histogram: 1 0 0 0 0 0 0 0 0 0

43
examples/amoeba/log.water_hexamer.amoeba.4.test
View File

@ -12,8 +12,8 @@ dihedral_style none
# per-atom properties required by AMOEBA or HIPPO
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom i_amgroup d_redID d_xaxis d_yaxis d_zaxis d_pval ghost yes
fix extra2 all property/atom i_polaxe
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
@ -55,7 +55,7 @@ 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
@ -97,7 +97,7 @@ Neighbor list info ...
bin: standard
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:974)
AMOEBA/HIPPO group count: 6
Per MPI rank memory allocation (min/avg/max) = 9.833 | 9.833 | 9.833 Mbytes
Per MPI rank memory allocation (min/avg/max) = 49.56 | 49.56 | 49.56 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
@ -109,31 +109,30 @@ Per MPI rank memory allocation (min/avg/max) = 9.833 | 9.833 | 9.833 Mbytes
70 11.272241 -45.411622 0.07431614 0.51778317 0 0 0.59209931 -44.248316 32055.564 39306.193 30181.52 25601.501 1373.4778 -4501.0686 -2570.4767
80 14.011502 -46.081444 0.089688317 1.006928 0 0 1.0966163 -44.274812 25661.838 38836.598 12603.734 24205.867 -867.36437 -4211.9639 -2820.6725
90 17.659498 -46.247295 0.21744649 0.82687716 0 0 1.0443237 -44.308098 12101.207 19426.995 14142.311 1046.299 -2157.5418 -2141.2454 -2621.456
AMEOBA/HIPPO timing info:
Init time: 0.000876489 0.0216648
Hal time: 0.0012315 3.04398
Mpole time: 0.00349354 8.63522
Induce time: 0.0293642 72.5816
Polar time: 0.00547642 13.5365
Total time: 0.0404569
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 0.0431834 on 4 procs for 100 steps with 18 atoms
Loop time of 0.0405754 on 4 procs for 100 steps with 18 atoms
Performance: 200.077 ns/day, 0.120 hours/ns, 2315.706 timesteps/s
97.8% CPU use with 4 MPI tasks x no OpenMP threads
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
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
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.040628 | 0.040702 | 0.04082 | 0.0 | 94.25
Bond | 7.2822e-05 | 9.4953e-05 | 0.00011572 | 0.0 | 0.22
Pair | 0.03816 | 0.038221 | 0.038312 | 0.0 | 94.20
Bond | 7.0759e-05 | 8.5222e-05 | 0.00010449 | 0.0 | 0.21
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00067844 | 0.00088282 | 0.0010398 | 0.0 | 2.04
Output | 0.0010464 | 0.0010868 | 0.0011886 | 0.2 | 2.52
Modify | 4.2857e-05 | 5.2307e-05 | 6.3734e-05 | 0.0 | 0.12
Other | | 0.0003646 | | | 0.84
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
Nlocal: 4.5 ave 6 max 3 min
Histogram: 1 0 0 1 0 0 1 0 0 1

47
examples/amoeba/log.water_hexamer.hippo.1.test
View File

@ -12,8 +12,8 @@ dihedral_style none
# per-atom properties required by AMOEBA or HIPPO
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom i_amgroup d_redID d_xaxis d_yaxis d_zaxis d_pval ghost yes
fix extra2 all property/atom i_polaxe
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
@ -39,7 +39,7 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.006 seconds
read_data CPU = 0.007 seconds
# force field
@ -98,7 +98,7 @@ Neighbor list info ...
stencil: half/bin/3d
bin: standard
AMOEBA/HIPPO group count: 6
Per MPI rank memory allocation (min/avg/max) = 9.804 | 9.804 | 9.804 Mbytes
Per MPI rank memory allocation (min/avg/max) = 49.1 | 49.1 | 49.1 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
@ -110,33 +110,32 @@ Per MPI rank memory allocation (min/avg/max) = 9.804 | 9.804 | 9.804 Mbytes
70 26.129957 -46.022729 0.30434543 0.56770169 0 0 0.87204711 -43.826579 3919.9866 -2755.6905 11500.428 517.54333 5626.9543 -2238.5786 86.305984
80 17.768494 -46.309777 1.1680612 0.45551823 0 0 1.6235794 -43.785801 -18335.898 -22168.789 -14488.992 -20048.346 7343.173 -2646.2196 -2525.6625
90 8.3822494 -47.063502 2.0182644 0.88875358 0 0 2.9070179 -43.731724 -33693.203 -43487.996 -15178.35 -43214.494 2412.6411 1993.0113 1780.7512
AMEOBA/HIPPO timing info:
Init time: 0.000259847 0.00745584
Repls time: 0.00547792 15.7179
Disp time: 0.00244273 7.00898
Mpole time: 0.00635244 18.2272
Induce time: 0.0119383 34.2547
Polar time: 0.00698809 20.051
Qxfer time: 0.00138825 3.98334
Total time: 0.0348515
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 0.0363248 on 1 procs for 100 steps with 18 atoms
Loop time of 0.0399433 on 1 procs for 100 steps with 18 atoms
Performance: 237.854 ns/day, 0.101 hours/ns, 2752.942 timesteps/s
98.0% CPU use with 1 MPI tasks x no OpenMP threads
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
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
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.034944 | 0.034944 | 0.034944 | 0.0 | 96.20
Bond | 0.00016367 | 0.00016367 | 0.00016367 | 0.0 | 0.45
Pair | 0.038344 | 0.038344 | 0.038344 | 0.0 | 96.00
Bond | 0.00017707 | 0.00017707 | 0.00017707 | 0.0 | 0.44
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 1.8118e-05 | 1.8118e-05 | 1.8118e-05 | 0.0 | 0.05
Output | 0.0010588 | 0.0010588 | 0.0010588 | 0.0 | 2.91
Modify | 7.1169e-05 | 7.1169e-05 | 7.1169e-05 | 0.0 | 0.20
Other | | 6.941e-05 | | | 0.19
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
Nlocal: 18 ave 18 max 18 min
Histogram: 1 0 0 0 0 0 0 0 0 0

47
examples/amoeba/log.water_hexamer.hippo.4.test
View File

@ -12,8 +12,8 @@ dihedral_style none
# per-atom properties required by AMOEBA or HIPPO
fix amtype all property/atom i_amtype ghost yes
fix extra all property/atom i_amgroup d_redID d_xaxis d_yaxis d_zaxis d_pval ghost yes
fix extra2 all property/atom i_polaxe
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
@ -39,7 +39,7 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.009 seconds
read_data CPU = 0.008 seconds
# force field
@ -55,7 +55,7 @@ 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
@ -99,7 +99,7 @@ Neighbor list info ...
bin: standard
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:974)
AMOEBA/HIPPO group count: 6
Per MPI rank memory allocation (min/avg/max) = 9.833 | 9.833 | 9.833 Mbytes
Per MPI rank memory allocation (min/avg/max) = 49.13 | 49.13 | 49.13 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
@ -111,33 +111,32 @@ Per MPI rank memory allocation (min/avg/max) = 9.833 | 9.833 | 9.833 Mbytes
70 26.129957 -46.022729 0.30434543 0.56770169 0 0 0.87204711 -43.826579 3919.9866 -2755.6905 11500.428 517.54333 5626.9543 -2238.5786 86.305984
80 17.768494 -46.309777 1.1680612 0.45551823 0 0 1.6235794 -43.785801 -18335.898 -22168.789 -14488.992 -20048.346 7343.173 -2646.2196 -2525.6625
90 8.3822494 -47.063502 2.0182644 0.88875358 0 0 2.9070179 -43.731724 -33693.203 -43487.996 -15178.35 -43214.494 2412.6411 1993.0113 1780.7512
AMEOBA/HIPPO timing info:
Init time: 0.000745036 0.0228122
Repls time: 0.00327392 10.0244
Disp time: 0.000684259 2.09513
Mpole time: 0.00435168 13.3244
Induce time: 0.0190657 58.3773
Polar time: 0.00415392 12.7189
Qxfer time: 0.000380552 1.16521
Total time: 0.0326595
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 0.0358657 on 4 procs for 100 steps with 18 atoms
Loop time of 0.033787 on 4 procs for 100 steps with 18 atoms
Performance: 240.899 ns/day, 0.100 hours/ns, 2788.181 timesteps/s
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
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
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.032583 | 0.03291 | 0.033445 | 0.2 | 91.76
Bond | 5.6993e-05 | 8.0508e-05 | 9.8801e-05 | 0.0 | 0.22
Pair | 0.030576 | 0.030875 | 0.031306 | 0.2 | 91.38
Bond | 6.4191e-05 | 7.956e-05 | 0.0001014 | 0.0 | 0.24
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00070037 | 0.0013312 | 0.0017469 | 1.1 | 3.71
Output | 0.0010287 | 0.0010873 | 0.0012054 | 0.2 | 3.03
Modify | 4.2091e-05 | 5.3037e-05 | 6.0581e-05 | 0.0 | 0.15
Other | | 0.0004036 | | | 1.13
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
Nlocal: 4.5 ave 6 max 3 min
Histogram: 1 0 0 1 0 0 1 0 0 1