diff --git a/examples/amoeba/log.7Jul22.ubiquitin.g++.1 b/examples/amoeba/log.7Jul22.ubiquitin.g++.1 new file mode 100644 index 0000000000..d10a114126 --- /dev/null +++ b/examples/amoeba/log.7Jul22.ubiquitin.g++.1 @@ -0,0 +1,163 @@ +LAMMPS (23 Jun 2022) +# solvated ubiquitin molecule with AMOEBA force field + +units real +boundary p p p +atom_modify sort 0 0.0 + +atom_style amoeba + +bond_style class2 +angle_style amoeba +dihedral_style fourier +improper_style amoeba + +# per-atom properties required by AMOEBA or HIPPO + +fix amtype all property/atom i_amtype ghost yes +fix 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 = 0.004 seconds + read_data CPU = 0.091 seconds + +pair_style amoeba +pair_coeff * * amoeba_ubiquitin.prm amoeba_ubiquitin.key +Reading potential file amoeba_ubiquitin.prm with DATE: 2022-07-05 +Skipping section: AMOEBA Protein Force Field Atom Classes +Skipping section: Torsion-Torsion Parameters +Skipping section: Biopolymer Atom Type Conversions +Reading potential file amoeba_ubiquitin.key with DATE: 2022-07-05 + +special_bonds lj/coul 0.5 0.5 0.5 one/five yes +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0.5 0.5 0.5 + special bond factors coul: 0.5 0.5 0.5 + 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 = 0.007 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 + +# dynamics + +fix 1 all nve + +thermo 1 +run 10 +AMOEBA force field settings + hal: cut 12 taper 10.8 vscale 0 0 1 1 + multipole: cut 7 aewald 0.4 bsorder 5 FFT 60 48 48 mscale 0 0 0.4 1 + 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 + 6 118.24373 -36092.77 1166.179 815.59206 213.67399 44.022297 2239.4673 -30435.629 -1677.8051 -3988.2428 -2669.6848 -3247.7207 197.42472 285.87129 -162.35459 + 7 137.7204 -36521.444 782.87113 1026.745 212.04289 38.686259 2060.3452 -30479.082 -5987.83 -8386.8104 -7363.188 -7888.261 357.00835 253.66346 32.827786 + 8 112.66452 -36897.181 1750.0569 1269.152 210.83571 33.742799 3263.7874 -30379.432 -7886.4081 -9703.2601 -9043.015 -9555.2908 490.76046 182.31259 278.727 + 9 88.237359 -37209.906 2695.1766 1454.55 209.91331 29.503458 4389.1434 -30276.565 -8202.16 -9492.368 -9110.7037 -9639.2288 502.55699 107.82333 443.6705 + 10 108.86756 -37474.988 2240.4603 1523.7936 209.10313 26.208515 3999.5656 -30333.279 -8468.4347 -9956.923 -9709.5874 -10224.682 365.98214 95.262991 425.12746 +Loop time of 24.2102 on 1 procs for 10 steps with 9737 atoms + +Performance: 0.036 ns/day, 672.507 hours/ns, 0.413 timesteps/s +97.8% CPU use with 1 MPI tasks x no OpenMP threads + +AMOEBA timing breakdown: + Init time: 0.0401664 0.17% + Hal time: 7.62094 31.51% + Mpole time: 2.44622 10.12% + Induce time: 9.28925 38.41% + Polar time: 4.78631 19.79% + Total time: 24.1829 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 24.183 | 24.183 | 24.183 | 0.0 | 99.89 +Bond | 0.016031 | 0.016031 | 0.016031 | 0.0 | 0.07 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.004396 | 0.004396 | 0.004396 | 0.0 | 0.02 +Output | 0.0011692 | 0.0011692 | 0.0011692 | 0.0 | 0.00 +Modify | 0.0044765 | 0.0044765 | 0.0044765 | 0.0 | 0.02 +Other | | 0.001194 | | | 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: 0:00:27 diff --git a/examples/amoeba/log.7Jul22.ubiquitin.g++.4 b/examples/amoeba/log.7Jul22.ubiquitin.g++.4 new file mode 100644 index 0000000000..50bbd6ce03 --- /dev/null +++ b/examples/amoeba/log.7Jul22.ubiquitin.g++.4 @@ -0,0 +1,163 @@ +LAMMPS (23 Jun 2022) +# solvated ubiquitin molecule with AMOEBA force field + +units real +boundary p p p +atom_modify sort 0 0.0 + +atom_style amoeba + +bond_style class2 +angle_style amoeba +dihedral_style fourier +improper_style amoeba + +# per-atom properties required by AMOEBA or HIPPO + +fix amtype all property/atom i_amtype ghost yes +fix 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 = 0.072 seconds + +pair_style amoeba +pair_coeff * * amoeba_ubiquitin.prm amoeba_ubiquitin.key +Reading potential file amoeba_ubiquitin.prm with DATE: 2022-07-05 +Skipping section: AMOEBA Protein Force Field Atom Classes +Skipping section: Torsion-Torsion Parameters +Skipping section: Biopolymer Atom Type Conversions +Reading potential file amoeba_ubiquitin.key with DATE: 2022-07-05 + +special_bonds lj/coul 0.5 0.5 0.5 one/five yes +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0.5 0.5 0.5 + special bond factors coul: 0.5 0.5 0.5 + 4 = max # of 1-2 neighbors + 9 = max # of 1-3 neighbors + 19 = max # of 1-4 neighbors + 58 = max # of 1-5 neighbors + 21 = max # of special neighbors + special bonds CPU = 0.002 seconds + +# thermo output + +compute virial all pressure NULL virial + +thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*] + +#dump 1 all custom 10 dump.ubiquitin id type x y z fx fy fz +#dump_modify 1 sort id + +# dynamics + +fix 1 all nve + +thermo 1 +run 10 +AMOEBA force field settings + hal: cut 12 taper 10.8 vscale 0 0 1 1 + multipole: cut 7 aewald 0.4 bsorder 5 FFT 60 48 48 mscale 0 0 0.4 1 + 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 + 6 118.24373 -36092.77 1166.179 815.59206 213.67399 44.022297 2239.4673 -30435.629 -1677.8051 -3988.2428 -2669.6848 -3247.7207 197.42472 285.87129 -162.35459 + 7 137.7204 -36521.444 782.87113 1026.745 212.04289 38.686259 2060.3452 -30479.082 -5987.83 -8386.8104 -7363.188 -7888.261 357.00835 253.66346 32.827786 + 8 112.66452 -36897.181 1750.0569 1269.152 210.83571 33.742799 3263.7874 -30379.432 -7886.4081 -9703.2601 -9043.015 -9555.2908 490.76046 182.31259 278.727 + 9 88.237359 -37209.906 2695.1766 1454.55 209.91331 29.503458 4389.1434 -30276.565 -8202.16 -9492.368 -9110.7037 -9639.2288 502.55699 107.82333 443.6705 + 10 108.86756 -37474.988 2240.4603 1523.7936 209.10313 26.208515 3999.5656 -30333.279 -8468.4347 -9956.923 -9709.5874 -10224.682 365.98214 95.262991 425.12746 +Loop time of 6.03244 on 4 procs for 10 steps with 9737 atoms + +Performance: 0.143 ns/day, 167.568 hours/ns, 1.658 timesteps/s +99.7% CPU use with 4 MPI tasks x no OpenMP threads + +AMOEBA timing breakdown: + Init time: 0.0192504 0.32% + Hal time: 1.86975 31.05% + Mpole time: 0.633256 10.52% + Induce time: 2.26029 37.54% + Polar time: 1.23884 20.57% + Total time: 6.02139 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 6.0202 | 6.0215 | 6.0228 | 0.0 | 99.82 +Bond | 0.0029895 | 0.0033805 | 0.0036579 | 0.4 | 0.06 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.0044978 | 0.0059188 | 0.0070446 | 1.5 | 0.10 +Output | 0.00055049 | 0.00062352 | 0.00079826 | 0.0 | 0.01 +Modify | 0.00067451 | 0.00071394 | 0.00074612 | 0.0 | 0.01 +Other | | 0.0003294 | | | 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: 0:00:07 diff --git a/examples/amoeba/log.7Jul22.water_box.amoeba.g++.1 b/examples/amoeba/log.7Jul22.water_box.amoeba.g++.1 new file mode 100644 index 0000000000..f0b1ed83e5 --- /dev/null +++ b/examples/amoeba/log.7Jul22.water_box.amoeba.g++.1 @@ -0,0 +1,146 @@ +LAMMPS (23 Jun 2022) +# 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 = 0.010 seconds + +# force field + +pair_style amoeba +pair_coeff * * amoeba_water.prm amoeba_water_box.key +Reading potential file amoeba_water.prm with DATE: 2022-07-05 +Reading potential file amoeba_water_box.key with DATE: 2022-07-05 + +special_bonds lj/coul 0.5 0.5 0.5 one/five yes +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0.5 0.5 0.5 + special bond factors coul: 0.5 0.5 0.5 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of 1-5 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.001 seconds + +# thermo output + +compute virial all pressure NULL virial + +thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*] + +#dump 1 all custom 10 dump.water_box id type x y z fx fy fz +#dump_modify 1 sort id + +# dynamics + +fix 1 all nve + +thermo 10 +run 100 +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 14.5572 on 1 procs for 100 steps with 648 atoms + +Performance: 0.594 ns/day, 40.437 hours/ns, 6.869 timesteps/s +99.9% CPU use with 1 MPI tasks x no OpenMP threads + +AMOEBA timing breakdown: + Init time: 0.0224497 0.15% + Hal time: 1.00248 6.90% + Mpole time: 1.42229 9.78% + Induce time: 9.23983 63.55% + Polar time: 2.8515 19.61% + Total time: 14.5386 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 14.539 | 14.539 | 14.539 | 0.0 | 99.87 +Bond | 0.0029302 | 0.0029302 | 0.0029302 | 0.0 | 0.02 +Neigh | 0.010789 | 0.010789 | 0.010789 | 0.0 | 0.07 +Comm | 0.0027888 | 0.0027888 | 0.0027888 | 0.0 | 0.02 +Output | 0.00040039 | 0.00040039 | 0.00040039 | 0.0 | 0.00 +Modify | 0.0007305 | 0.0007305 | 0.0007305 | 0.0 | 0.01 +Other | | 0.0008703 | | | 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: 0:00:14 diff --git a/examples/amoeba/log.7Jul22.water_box.amoeba.g++.4 b/examples/amoeba/log.7Jul22.water_box.amoeba.g++.4 new file mode 100644 index 0000000000..f813feadb9 --- /dev/null +++ b/examples/amoeba/log.7Jul22.water_box.amoeba.g++.4 @@ -0,0 +1,146 @@ +LAMMPS (23 Jun 2022) +# 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 = 0.001 seconds + read_data CPU = 0.011 seconds + +# force field + +pair_style amoeba +pair_coeff * * amoeba_water.prm amoeba_water_box.key +Reading potential file amoeba_water.prm with DATE: 2022-07-05 +Reading potential file amoeba_water_box.key with DATE: 2022-07-05 + +special_bonds lj/coul 0.5 0.5 0.5 one/five yes +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0.5 0.5 0.5 + special bond factors coul: 0.5 0.5 0.5 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of 1-5 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.001 seconds + +# thermo output + +compute virial all pressure NULL virial + +thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*] + +#dump 1 all custom 10 dump.water_box id type x y z fx fy fz +#dump_modify 1 sort id + +# dynamics + +fix 1 all nve + +thermo 10 +run 100 +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 5.22237 on 4 procs for 100 steps with 648 atoms + +Performance: 1.654 ns/day, 14.507 hours/ns, 19.148 timesteps/s +100.0% CPU use with 4 MPI tasks x no OpenMP threads + +AMOEBA timing breakdown: + Init time: 0.0217547 0.42% + Hal time: 0.246901 4.74% + Mpole time: 0.489975 9.41% + Induce time: 3.54999 68.15% + Polar time: 0.900374 17.28% + Total time: 5.20901 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 5.2084 | 5.2093 | 5.2114 | 0.1 | 99.75 +Bond | 0.00074127 | 0.00080769 | 0.00084525 | 0.0 | 0.02 +Neigh | 0.0014801 | 0.001481 | 0.0014832 | 0.0 | 0.03 +Comm | 0.007438 | 0.0095884 | 0.010526 | 1.3 | 0.18 +Output | 0.00028866 | 0.00033051 | 0.00044509 | 0.0 | 0.01 +Modify | 0.00020399 | 0.00020969 | 0.00021248 | 0.0 | 0.00 +Other | | 0.000658 | | | 0.01 + +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: 0:00:05 diff --git a/examples/amoeba/log.7Jul22.water_box.hippo.g++.1 b/examples/amoeba/log.7Jul22.water_box.hippo.g++.1 new file mode 100644 index 0000000000..0c4d2a2ebf --- /dev/null +++ b/examples/amoeba/log.7Jul22.water_box.hippo.g++.1 @@ -0,0 +1,150 @@ +LAMMPS (23 Jun 2022) +# water box with AMOEBA or HIPPO + +units real +boundary p p p + +atom_style amoeba +bond_style class2 +angle_style amoeba +dihedral_style none + +# per-atom properties required by AMOEBA or HIPPO + +fix amtype all property/atom i_amtype ghost yes +fix extra all property/atom i_amgroup d_redID d_pval ghost yes +fix extra2 all property/atom i_polaxe d2_xyzaxis 3 + +# read data file + +read_data data.water_box.hippo fix amtype NULL "Tinker Types" +Reading data file ... + orthogonal box = (0 0 0) to (18.643 18.643 18.643) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 648 atoms + scanning bonds ... + 2 = max bonds/atom + scanning angles ... + 1 = max angles/atom + reading bonds ... + 432 bonds + reading angles ... + 216 angles +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.011 seconds + +# force field + +pair_style hippo +pair_coeff * * hippo_water.prm hippo_water_box.key +Reading potential file hippo_water.prm with DATE: 2022-07-05 +Reading potential file hippo_water_box.key with DATE: 2022-07-05 + +special_bonds lj/coul 0.5 0.5 0.5 one/five yes +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0.5 0.5 0.5 + special bond factors coul: 0.5 0.5 0.5 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of 1-5 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.001 seconds + +# thermo output + +compute virial all pressure NULL virial + +thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*] + +#dump 1 all custom 10 dump.water_box id type x y z fx fy fz +#dump_modify 1 sort id + +# dynamics + +fix 1 all nve + +thermo 10 +run 100 +HIPPO force field settings + repulsion: cut 7 taper 6 rscale 0 0 1 1 + qxfer: cut 7 taper 6 mscale 0 0 0.4 1 + dispersion: cut 7 aewald 0.45 bsorder 4 FFT 16 16 16 dspscale 0 0 0.4 1 + multipole: cut 7 aewald 0.4 bsorder 5 FFT 24 24 24 mscale 0 0 0.4 1 + polar: cut 7 aewald 0.5 bsorder 5 FFT 24 24 24 + pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 0.2 1 1 1 d/u scale 0 1 + precondition: cut 4.5 +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 9 + ghost atom cutoff = 9 + binsize = 4.5, bins = 5 5 5 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair hippo, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + HIPPO group count: 216 +Per MPI rank memory allocation (min/avg/max) = 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 + 10 100.94691 -2350.192 116.13156 88.56605 0 0 204.69761 -1950.8098 -11480.919 -13574.139 -12190.797 -12798.212 -263.77028 280.62864 1974.1486 + 20 153.91622 -2358.3058 36.396961 66.22466 0 0 102.62162 -1958.8438 -7778.4529 -8492.3868 -11999.431 -9125.9998 -917.99962 589.09064 1788.2094 + 30 145.5951 -2343.9956 39.651541 65.833248 0 0 105.48479 -1957.7184 -288.79965 -2574.4466 -3820.4824 -414.28285 -347.51491 -1147.3995 -126.71025 + 40 126.87801 -2340.2623 102.93951 43.896946 0 0 146.83646 -1948.7309 6766.15 5908.7048 1280.0961 7930.8191 -1085.6811 -1596.6859 -714.82888 + 50 134.52078 -2358.9232 107.49288 44.253826 0 0 151.74671 -1947.7419 8762.4348 6023.4661 5377.0189 9396.0316 -1629.1364 -1663.1666 -2381.51 + 60 173.10181 -2374.3854 51.097314 33.03646 0 0 84.133774 -1956.4102 4614.2907 1719.1989 505.79149 4552.3167 -1661.1714 -587.92108 -1380.6732 + 70 184.86849 -2391.6106 39.916931 35.978152 0 0 75.895083 -1959.1811 -2146.9339 -4993.4021 -4095.6729 -4897.5768 -833.09046 1542.411 -1539.5266 + 80 164.75795 -2406.3017 101.94229 33.067832 0 0 135.01013 -1953.542 -8779.3265 -10545.409 -10418.702 -12098.858 -1319.194 1750.3511 -275.1272 + 90 151.17491 -2434.6876 152.21826 41.301673 0 0 193.51993 -1949.6141 -13330.691 -15436.505 -13791.461 -16934.674 149.25497 2289.1026 976.14333 + 100 166.99163 -2452.5298 143.57768 35.341459 0 0 178.91914 -1951.5533 -14918.51 -16077.49 -17353.738 -18140.466 19.009088 1487.0469 1084.0231 +Loop time of 9.10254 on 1 procs for 100 steps with 648 atoms + +Performance: 0.949 ns/day, 25.285 hours/ns, 10.986 timesteps/s +99.8% CPU use with 1 MPI tasks x no OpenMP threads + +HIPPO timing breakdown: + Init time: 0.0131104 0.14% + Repulse time: 1.06663 11.73% + Disp time: 0.585678 6.44% + Mpole time: 1.7162 18.88% + Induce time: 3.27504 36.03% + Polar time: 2.14366 23.58% + Qxfer time: 0.289804 3.19% + Total time: 9.09012 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 9.0902 | 9.0902 | 9.0902 | 0.0 | 99.86 +Bond | 0.0024561 | 0.0024561 | 0.0024561 | 0.0 | 0.03 +Neigh | 0.005878 | 0.005878 | 0.005878 | 0.0 | 0.06 +Comm | 0.0023344 | 0.0023344 | 0.0023344 | 0.0 | 0.03 +Output | 0.00036107 | 0.00036107 | 0.00036107 | 0.0 | 0.00 +Modify | 0.00062368 | 0.00062368 | 0.00062368 | 0.0 | 0.01 +Other | | 0.0006736 | | | 0.01 + +Nlocal: 648 ave 648 max 648 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 4282 ave 4282 max 4282 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 98490 ave 98490 max 98490 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 98490 +Ave neighs/atom = 151.99074 +Ave special neighs/atom = 2 +Neighbor list builds = 2 +Dangerous builds = 0 +Total wall time: 0:00:09 diff --git a/examples/amoeba/log.7Jul22.water_box.hippo.g++.4 b/examples/amoeba/log.7Jul22.water_box.hippo.g++.4 new file mode 100644 index 0000000000..0cb1e8a934 --- /dev/null +++ b/examples/amoeba/log.7Jul22.water_box.hippo.g++.4 @@ -0,0 +1,150 @@ +LAMMPS (23 Jun 2022) +# water box with AMOEBA or HIPPO + +units real +boundary p p p + +atom_style amoeba +bond_style class2 +angle_style amoeba +dihedral_style none + +# per-atom properties required by AMOEBA or HIPPO + +fix amtype all property/atom i_amtype ghost yes +fix extra all property/atom i_amgroup d_redID d_pval ghost yes +fix extra2 all property/atom i_polaxe d2_xyzaxis 3 + +# read data file + +read_data data.water_box.hippo fix amtype NULL "Tinker Types" +Reading data file ... + orthogonal box = (0 0 0) to (18.643 18.643 18.643) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 648 atoms + scanning bonds ... + 2 = max bonds/atom + scanning angles ... + 1 = max angles/atom + reading bonds ... + 432 bonds + reading angles ... + 216 angles +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_data CPU = 0.013 seconds + +# force field + +pair_style hippo +pair_coeff * * hippo_water.prm hippo_water_box.key +Reading potential file hippo_water.prm with DATE: 2022-07-05 +Reading potential file hippo_water_box.key with DATE: 2022-07-05 + +special_bonds lj/coul 0.5 0.5 0.5 one/five yes +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0.5 0.5 0.5 + special bond factors coul: 0.5 0.5 0.5 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of 1-5 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.001 seconds + +# thermo output + +compute virial all pressure NULL virial + +thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*] + +#dump 1 all custom 10 dump.water_box id type x y z fx fy fz +#dump_modify 1 sort id + +# dynamics + +fix 1 all nve + +thermo 10 +run 100 +HIPPO force field settings + repulsion: cut 7 taper 6 rscale 0 0 1 1 + qxfer: cut 7 taper 6 mscale 0 0 0.4 1 + dispersion: cut 7 aewald 0.45 bsorder 4 FFT 16 16 16 dspscale 0 0 0.4 1 + multipole: cut 7 aewald 0.4 bsorder 5 FFT 24 24 24 mscale 0 0 0.4 1 + polar: cut 7 aewald 0.5 bsorder 5 FFT 24 24 24 + pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 0.2 1 1 1 d/u scale 0 1 + precondition: cut 4.5 +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 9 + ghost atom cutoff = 9 + binsize = 4.5, bins = 5 5 5 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair hippo, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + HIPPO group count: 216 +Per MPI rank memory allocation (min/avg/max) = 55.94 | 55.94 | 55.94 Mbytes + Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6] + 0 0 -2188.594 166.82637 77.478353 0 0 244.30473 -1944.2893 -10859.589 -9285.4645 -11598.049 -11695.254 -282.7072 3164.4148 2495.2578 + 10 100.94691 -2350.192 116.13156 88.56605 0 0 204.69761 -1950.8098 -11480.919 -13574.139 -12190.797 -12798.212 -263.77028 280.62864 1974.1486 + 20 153.91622 -2358.3058 36.396961 66.22466 0 0 102.62162 -1958.8438 -7778.4529 -8492.3868 -11999.431 -9125.9998 -917.99962 589.09064 1788.2094 + 30 145.5951 -2343.9956 39.651541 65.833248 0 0 105.48479 -1957.7184 -288.79965 -2574.4466 -3820.4824 -414.28285 -347.51491 -1147.3995 -126.71025 + 40 126.87801 -2340.2623 102.93951 43.896946 0 0 146.83646 -1948.7309 6766.15 5908.7048 1280.0961 7930.8191 -1085.6811 -1596.6859 -714.82888 + 50 134.52078 -2358.9232 107.49288 44.253826 0 0 151.74671 -1947.7419 8762.4348 6023.4661 5377.0189 9396.0316 -1629.1364 -1663.1666 -2381.51 + 60 173.10181 -2374.3854 51.097314 33.03646 0 0 84.133774 -1956.4102 4614.2907 1719.1989 505.79149 4552.3167 -1661.1714 -587.92108 -1380.6732 + 70 184.86849 -2391.6106 39.916931 35.978152 0 0 75.895083 -1959.1811 -2146.9339 -4993.4021 -4095.6729 -4897.5768 -833.09046 1542.411 -1539.5266 + 80 164.75795 -2406.3017 101.94229 33.067832 0 0 135.01013 -1953.542 -8779.3265 -10545.409 -10418.702 -12098.858 -1319.194 1750.3511 -275.1272 + 90 151.17491 -2434.6876 152.21826 41.301673 0 0 193.51993 -1949.6141 -13330.691 -15436.505 -13791.461 -16934.674 149.25497 2289.1026 976.14333 + 100 166.99163 -2452.5298 143.57768 35.341459 0 0 178.91914 -1951.5533 -14918.51 -16077.49 -17353.738 -18140.466 19.009088 1487.0469 1084.0231 +Loop time of 3.60321 on 4 procs for 100 steps with 648 atoms + +Performance: 2.398 ns/day, 10.009 hours/ns, 27.753 timesteps/s +100.0% CPU use with 4 MPI tasks x no OpenMP threads + +HIPPO timing breakdown: + Init time: 0.0162772 0.45% + Repulse time: 0.329178 9.19% + Disp time: 0.244602 6.83% + Mpole time: 0.640969 17.89% + Induce time: 1.44984 40.47% + Polar time: 0.821061 22.92% + Qxfer time: 0.0804381 2.25% + Total time: 3.58237 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 3.5752 | 3.5827 | 3.59 | 0.4 | 99.43 +Bond | 0.00065212 | 0.00072305 | 0.00075673 | 0.0 | 0.02 +Neigh | 0.0015663 | 0.0015681 | 0.00157 | 0.0 | 0.04 +Comm | 0.0097453 | 0.017024 | 0.024558 | 5.5 | 0.47 +Output | 0.00030331 | 0.0003444 | 0.00045896 | 0.0 | 0.01 +Modify | 0.00018335 | 0.00020346 | 0.00021611 | 0.0 | 0.01 +Other | | 0.0006822 | | | 0.02 + +Nlocal: 162 ave 166 max 160 min +Histogram: 2 0 0 1 0 0 0 0 0 1 +Nghost: 2563.25 ave 2589 max 2535 min +Histogram: 1 1 0 0 0 0 0 0 0 2 +Neighs: 24622.5 ave 25210 max 24056 min +Histogram: 1 0 1 0 0 0 0 1 0 1 + +Total # of neighbors = 98490 +Ave neighs/atom = 151.99074 +Ave special neighs/atom = 2 +Neighbor list builds = 2 +Dangerous builds = 0 +Total wall time: 0:00:03 diff --git a/examples/amoeba/log.7Jul22.water_dimer.amoeba.g++.1 b/examples/amoeba/log.7Jul22.water_dimer.amoeba.g++.1 new file mode 100644 index 0000000000..824e1df844 --- /dev/null +++ b/examples/amoeba/log.7Jul22.water_dimer.amoeba.g++.1 @@ -0,0 +1,147 @@ +LAMMPS (23 Jun 2022) +# water dimer with AMOEBA or HIPPO + +units real +boundary s s s + +atom_style amoeba +bond_style class2 +angle_style amoeba +dihedral_style none + +# per-atom properties required by AMOEBA or HIPPO + +fix amtype all property/atom i_amtype ghost yes +fix extra all property/atom i_amgroup d_redID d_pval ghost yes +fix extra2 all property/atom i_polaxe d2_xyzaxis 3 + +# read data file + +read_data data.water_dimer.amoeba fix amtype NULL "Tinker Types" +Reading data file ... + orthogonal box = (-1.463996 -0.756549 -0.009705) to (0.933234 0.75612 2.935934) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 6 atoms + scanning bonds ... + 2 = max bonds/atom + scanning angles ... + 1 = max angles/atom + reading bonds ... + 4 bonds + reading angles ... + 2 angles +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.007 seconds + +# force field + +pair_style amoeba +pair_coeff * * amoeba_water.prm amoeba_water.key +Reading potential file amoeba_water.prm with DATE: 2022-07-05 +Reading potential file amoeba_water.key with DATE: 2022-07-05 + +special_bonds lj/coul 0.5 0.5 0.5 one/five yes +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0.5 0.5 0.5 + special bond factors coul: 0.5 0.5 0.5 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of 1-5 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000 seconds + +# thermo output + +compute virial all pressure NULL virial + +thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*] + +#dump 1 all custom 10 dump.water_dimer id type x y z fx fy fz +#dump_modify 1 sort id + +# dynamics + +fix 1 all nve + +thermo 10 +run 100 +AMOEBA force field settings + hal: cut 10 taper 8 vscale 0 0 1 1 + multipole: cut 10 aewald 0 mscale 0 0 0.4 1 + polar: cut 10 aewald 0 + pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 1 1 1 1 d/u scale 0 1 + precondition: cut 4.5 +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12 + ghost atom cutoff = 12 + binsize = 6, bins = 1 1 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair amoeba, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp: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 0.00539351 on 1 procs for 100 steps with 6 atoms + +Performance: 1601.925 ns/day, 0.015 hours/ns, 18540.802 timesteps/s +97.1% CPU use with 1 MPI tasks x no OpenMP threads + +AMOEBA timing breakdown: + Init time: 0.000111932 2.32% + Hal time: 0.00045057 9.33% + Mpole time: 0.00055958 11.59% + Induce time: 0.00238881 49.46% + Polar time: 0.0013042 27.00% + Total time: 0.00482974 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0048575 | 0.0048575 | 0.0048575 | 0.0 | 90.06 +Bond | 9.4036e-05 | 9.4036e-05 | 9.4036e-05 | 0.0 | 1.74 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 1.3435e-05 | 1.3435e-05 | 1.3435e-05 | 0.0 | 0.25 +Output | 0.00034323 | 0.00034323 | 0.00034323 | 0.0 | 6.36 +Modify | 3.5435e-05 | 3.5435e-05 | 3.5435e-05 | 0.0 | 0.66 +Other | | 4.986e-05 | | | 0.92 + +Nlocal: 6 ave 6 max 6 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 15 ave 15 max 15 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 15 +Ave neighs/atom = 2.5 +Ave special neighs/atom = 2 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/amoeba/log.7Jul22.water_dimer.amoeba.g++.4 b/examples/amoeba/log.7Jul22.water_dimer.amoeba.g++.4 new file mode 100644 index 0000000000..f4ec45928d --- /dev/null +++ b/examples/amoeba/log.7Jul22.water_dimer.amoeba.g++.4 @@ -0,0 +1,147 @@ +LAMMPS (23 Jun 2022) +# water dimer with AMOEBA or HIPPO + +units real +boundary s s s + +atom_style amoeba +bond_style class2 +angle_style amoeba +dihedral_style none + +# per-atom properties required by AMOEBA or HIPPO + +fix amtype all property/atom i_amtype ghost yes +fix extra all property/atom i_amgroup d_redID d_pval ghost yes +fix extra2 all property/atom i_polaxe d2_xyzaxis 3 + +# read data file + +read_data data.water_dimer.amoeba fix amtype NULL "Tinker Types" +Reading data file ... + orthogonal box = (-1.463996 -0.756549 -0.009705) to (0.933234 0.75612 2.935934) + 2 by 1 by 2 MPI processor grid + reading atoms ... + 6 atoms + scanning bonds ... + 2 = max bonds/atom + scanning angles ... + 1 = max angles/atom + reading bonds ... + 4 bonds + reading angles ... + 2 angles +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.009 seconds + +# force field + +pair_style amoeba +pair_coeff * * amoeba_water.prm amoeba_water.key +Reading potential file amoeba_water.prm with DATE: 2022-07-05 +Reading potential file amoeba_water.key with DATE: 2022-07-05 + +special_bonds lj/coul 0.5 0.5 0.5 one/five yes +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0.5 0.5 0.5 + special bond factors coul: 0.5 0.5 0.5 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of 1-5 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000 seconds + +# thermo output + +compute virial all pressure NULL virial + +thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*] + +#dump 1 all custom 10 dump.water_dimer id type x y z fx fy fz +#dump_modify 1 sort id + +# dynamics + +fix 1 all nve + +thermo 10 +run 100 +AMOEBA force field settings + hal: cut 10 taper 8 vscale 0 0 1 1 + multipole: cut 10 aewald 0 mscale 0 0 0.4 1 + polar: cut 10 aewald 0 + pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 1 1 1 1 d/u scale 0 1 + precondition: cut 4.5 +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12 + ghost atom cutoff = 12 + binsize = 6, bins = 1 1 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair amoeba, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp: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 0.0160927 on 4 procs for 100 steps with 6 atoms + +Performance: 536.891 ns/day, 0.045 hours/ns, 6214.012 timesteps/s +99.7% CPU use with 4 MPI tasks x no OpenMP threads + +AMOEBA timing breakdown: + Init time: 0.000643833 4.58% + Hal time: 0.000105979 0.75% + Mpole time: 0.00070704 5.03% + Induce time: 0.0115637 82.32% + Polar time: 0.00101148 7.20% + Total time: 0.0140469 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.014163 | 0.014289 | 0.01443 | 0.1 | 88.79 +Bond | 1.3072e-05 | 4.8341e-05 | 8.4206e-05 | 0.0 | 0.30 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.00071242 | 0.00081499 | 0.0010064 | 0.0 | 5.06 +Output | 0.00041395 | 0.00049646 | 0.0005516 | 0.0 | 3.08 +Modify | 2.5768e-05 | 3.3385e-05 | 4.7843e-05 | 0.0 | 0.21 +Other | | 0.0004106 | | | 2.55 + +Nlocal: 1.5 ave 3 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 4.5 ave 6 max 3 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 3.75 ave 12 max 0 min +Histogram: 2 0 1 0 0 0 0 0 0 1 + +Total # of neighbors = 15 +Ave neighs/atom = 2.5 +Ave special neighs/atom = 2 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/amoeba/log.7Jul22.water_dimer.hippo.g++.1 b/examples/amoeba/log.7Jul22.water_dimer.hippo.g++.1 new file mode 100644 index 0000000000..5eaf8cf8a5 --- /dev/null +++ b/examples/amoeba/log.7Jul22.water_dimer.hippo.g++.1 @@ -0,0 +1,151 @@ +LAMMPS (23 Jun 2022) +# water dimer with AMOEBA or HIPPO + +units real +boundary s s s + +atom_style amoeba +bond_style class2 +angle_style amoeba +dihedral_style none + +# per-atom properties required by AMOEBA or HIPPO + +fix amtype all property/atom i_amtype ghost yes +fix extra all property/atom i_amgroup d_redID d_pval ghost yes +fix extra2 all property/atom i_polaxe d2_xyzaxis 3 + +# read data file + +read_data data.water_dimer.hippo fix amtype NULL "Tinker Types" +Reading data file ... + orthogonal box = (-1.463996 -0.756549 -0.009705) to (0.933234 0.75612 2.935934) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 6 atoms + scanning bonds ... + 2 = max bonds/atom + scanning angles ... + 1 = max angles/atom + reading bonds ... + 4 bonds + reading angles ... + 2 angles +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.007 seconds + +# force field + +pair_style hippo +pair_coeff * * hippo_water.prm hippo_water.key +Reading potential file hippo_water.prm with DATE: 2022-07-05 +Reading potential file hippo_water.key with DATE: 2022-07-05 + +special_bonds lj/coul 0.5 0.5 0.5 one/five yes +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0.5 0.5 0.5 + special bond factors coul: 0.5 0.5 0.5 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of 1-5 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000 seconds + +# thermo output + +compute virial all pressure NULL virial + +thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*] + +#dump 1 all custom 10 dump.water_dimer id type x y z fx fy fz +#dump_modify 1 sort id + +# dynamics + +fix 1 all nve + +thermo 10 +run 100 +HIPPO force field settings + repulsion: cut 10 taper 8 rscale 0 0 1 1 + qxfer: cut 10 taper 8 mscale 0 0 0.4 1 + dispersion: cut 10 aewald 0 dspscale 0 0 0.4 1 + multipole: cut 10 aewald 0 mscale 0 0 0.4 1 + polar: cut 10 aewald 0 + pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 0.2 1 1 1 d/u scale 0 1 + precondition: cut 4.5 +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12 + ghost atom cutoff = 12 + binsize = 6, bins = 1 1 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair hippo, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp: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 0.00554871 on 1 procs for 100 steps with 6 atoms + +Performance: 1557.118 ns/day, 0.015 hours/ns, 18022.197 timesteps/s +98.4% CPU use with 1 MPI tasks x no OpenMP threads + +HIPPO timing breakdown: + Init time: 0.000115545 2.34% + Repulse time: 0.000625219 12.67% + Disp time: 0.000296056 6.00% + Mpole time: 0.000954451 19.35% + Induce time: 0.00169706 34.40% + Polar time: 0.001079 21.87% + Qxfer time: 0.000160858 3.26% + Total time: 0.0049333 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0049642 | 0.0049642 | 0.0049642 | 0.0 | 89.47 +Bond | 8.7687e-05 | 8.7687e-05 | 8.7687e-05 | 0.0 | 1.58 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 1.8012e-05 | 1.8012e-05 | 1.8012e-05 | 0.0 | 0.32 +Output | 0.00037567 | 0.00037567 | 0.00037567 | 0.0 | 6.77 +Modify | 4.1717e-05 | 4.1717e-05 | 4.1717e-05 | 0.0 | 0.75 +Other | | 6.144e-05 | | | 1.11 + +Nlocal: 6 ave 6 max 6 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 15 ave 15 max 15 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 15 +Ave neighs/atom = 2.5 +Ave special neighs/atom = 2 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/amoeba/log.7Jul22.water_dimer.hippo.g++.4 b/examples/amoeba/log.7Jul22.water_dimer.hippo.g++.4 new file mode 100644 index 0000000000..cccd71a5d6 --- /dev/null +++ b/examples/amoeba/log.7Jul22.water_dimer.hippo.g++.4 @@ -0,0 +1,151 @@ +LAMMPS (23 Jun 2022) +# water dimer with AMOEBA or HIPPO + +units real +boundary s s s + +atom_style amoeba +bond_style class2 +angle_style amoeba +dihedral_style none + +# per-atom properties required by AMOEBA or HIPPO + +fix amtype all property/atom i_amtype ghost yes +fix extra all property/atom i_amgroup d_redID d_pval ghost yes +fix extra2 all property/atom i_polaxe d2_xyzaxis 3 + +# read data file + +read_data data.water_dimer.hippo fix amtype NULL "Tinker Types" +Reading data file ... + orthogonal box = (-1.463996 -0.756549 -0.009705) to (0.933234 0.75612 2.935934) + 2 by 1 by 2 MPI processor grid + reading atoms ... + 6 atoms + scanning bonds ... + 2 = max bonds/atom + scanning angles ... + 1 = max angles/atom + reading bonds ... + 4 bonds + reading angles ... + 2 angles +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.008 seconds + +# force field + +pair_style hippo +pair_coeff * * hippo_water.prm hippo_water.key +Reading potential file hippo_water.prm with DATE: 2022-07-05 +Reading potential file hippo_water.key with DATE: 2022-07-05 + +special_bonds lj/coul 0.5 0.5 0.5 one/five yes +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0.5 0.5 0.5 + special bond factors coul: 0.5 0.5 0.5 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of 1-5 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000 seconds + +# thermo output + +compute virial all pressure NULL virial + +thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*] + +#dump 1 all custom 10 dump.water_dimer id type x y z fx fy fz +#dump_modify 1 sort id + +# dynamics + +fix 1 all nve + +thermo 10 +run 100 +HIPPO force field settings + repulsion: cut 10 taper 8 rscale 0 0 1 1 + qxfer: cut 10 taper 8 mscale 0 0 0.4 1 + dispersion: cut 10 aewald 0 dspscale 0 0 0.4 1 + multipole: cut 10 aewald 0 mscale 0 0 0.4 1 + polar: cut 10 aewald 0 + pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 0.2 1 1 1 d/u scale 0 1 + precondition: cut 4.5 +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12 + ghost atom cutoff = 12 + binsize = 6, bins = 1 1 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair hippo, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp: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 0.0121417 on 4 procs for 100 steps with 6 atoms + +Performance: 711.596 ns/day, 0.034 hours/ns, 8236.062 timesteps/s +99.4% CPU use with 4 MPI tasks x no OpenMP threads + +HIPPO timing breakdown: + Init time: 0.000597179 5.89% + Repulse time: 0.000498881 4.92% + Disp time: 8.8931e-05 0.88% + Mpole time: 0.000837487 8.26% + Induce time: 0.00727381 71.77% + Polar time: 0.000785393 7.75% + Qxfer time: 4.87313e-05 0.48% + Total time: 0.0101354 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.010257 | 0.010374 | 0.01049 | 0.1 | 85.44 +Bond | 1.2833e-05 | 4.7018e-05 | 8.6931e-05 | 0.0 | 0.39 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.0006916 | 0.00076578 | 0.00092404 | 0.0 | 6.31 +Output | 0.00040685 | 0.00049547 | 0.00057258 | 0.0 | 4.08 +Modify | 3.3096e-05 | 3.6004e-05 | 4.4046e-05 | 0.0 | 0.30 +Other | | 0.0004238 | | | 3.49 + +Nlocal: 1.5 ave 3 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 4.5 ave 6 max 3 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 3.75 ave 12 max 0 min +Histogram: 2 0 1 0 0 0 0 0 0 1 + +Total # of neighbors = 15 +Ave neighs/atom = 2.5 +Ave special neighs/atom = 2 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/amoeba/log.7Jul22.water_hexamer.amoeba.g++.1 b/examples/amoeba/log.7Jul22.water_hexamer.amoeba.g++.1 new file mode 100644 index 0000000000..ba9d7c5391 --- /dev/null +++ b/examples/amoeba/log.7Jul22.water_hexamer.amoeba.g++.1 @@ -0,0 +1,146 @@ +LAMMPS (23 Jun 2022) +# water hexamer with AMOEBA or HIPPO + +units real +boundary s s s + +atom_style amoeba +bond_style class2 +angle_style amoeba +dihedral_style none + +# per-atom properties required by AMOEBA or HIPPO + +fix amtype all property/atom i_amtype ghost yes +fix extra all property/atom i_amgroup d_redID d_pval ghost yes +fix extra2 all property/atom i_polaxe d2_xyzaxis 3 + +# read data file + +read_data data.water_hexamer.amoeba fix amtype NULL "Tinker Types" +Reading data file ... + orthogonal box = (-2.517835 -1.523041 -1.734766) to (2.675716 2.01883 2.220847) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 18 atoms + scanning bonds ... + 2 = max bonds/atom + scanning angles ... + 1 = max angles/atom + reading bonds ... + 12 bonds + reading angles ... + 6 angles +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.007 seconds + +# force field + +pair_style amoeba +pair_coeff * * amoeba_water.prm amoeba_water.key +Reading potential file amoeba_water.prm with DATE: 2022-07-05 +Reading potential file amoeba_water.key with DATE: 2022-07-05 + +special_bonds lj/coul 0.5 0.5 0.5 one/five yes +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0.5 0.5 0.5 + special bond factors coul: 0.5 0.5 0.5 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of 1-5 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000 seconds + +# thermo output + +compute virial all pressure NULL virial + +thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*] + +#dump 1 all custom 10 dump.water_hexamer id type x y z fx fy fz +#dump_modify 1 sort id + +# dynamics + +fix 1 all nve + +thermo 10 +run 100 +AMOEBA force field settings + hal: cut 10 taper 8 vscale 0 0 1 1 + multipole: cut 10 aewald 0 mscale 0 0 0.4 1 + polar: cut 10 aewald 0 + pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 1 1 1 1 d/u scale 0 1 + precondition: cut 4.5 +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12 + ghost atom cutoff = 12 + binsize = 6, bins = 1 1 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair amoeba, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + AMOEBA 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 0.0418011 on 1 procs for 100 steps with 18 atoms + +Performance: 206.693 ns/day, 0.116 hours/ns, 2392.284 timesteps/s +99.4% CPU use with 1 MPI tasks x no OpenMP threads + +AMOEBA timing breakdown: + Init time: 0.000326312 0.80% + Hal time: 0.0050371 12.28% + Mpole time: 0.00454501 11.08% + Induce time: 0.0200157 48.79% + Polar time: 0.0110863 27.02% + Total time: 0.0410272 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.041065 | 0.041065 | 0.041065 | 0.0 | 98.24 +Bond | 0.00019979 | 0.00019979 | 0.00019979 | 0.0 | 0.48 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 1.5617e-05 | 1.5617e-05 | 1.5617e-05 | 0.0 | 0.04 +Output | 0.00037937 | 0.00037937 | 0.00037937 | 0.0 | 0.91 +Modify | 6.5901e-05 | 6.5901e-05 | 6.5901e-05 | 0.0 | 0.16 +Other | | 7.527e-05 | | | 0.18 + +Nlocal: 18 ave 18 max 18 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 153 ave 153 max 153 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 153 +Ave neighs/atom = 8.5 +Ave special neighs/atom = 2 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/amoeba/log.7Jul22.water_hexamer.amoeba.g++.4 b/examples/amoeba/log.7Jul22.water_hexamer.amoeba.g++.4 new file mode 100644 index 0000000000..1cbc7797e9 --- /dev/null +++ b/examples/amoeba/log.7Jul22.water_hexamer.amoeba.g++.4 @@ -0,0 +1,147 @@ +LAMMPS (23 Jun 2022) +# water hexamer with AMOEBA or HIPPO + +units real +boundary s s s + +atom_style amoeba +bond_style class2 +angle_style amoeba +dihedral_style none + +# per-atom properties required by AMOEBA or HIPPO + +fix amtype all property/atom i_amtype ghost yes +fix extra all property/atom i_amgroup d_redID d_pval ghost yes +fix extra2 all property/atom i_polaxe d2_xyzaxis 3 + +# read data file + +read_data data.water_hexamer.amoeba fix amtype NULL "Tinker Types" +Reading data file ... + orthogonal box = (-2.517835 -1.523041 -1.734766) to (2.675716 2.01883 2.220847) + 2 by 1 by 2 MPI processor grid + reading atoms ... + 18 atoms + scanning bonds ... + 2 = max bonds/atom + scanning angles ... + 1 = max angles/atom + reading bonds ... + 12 bonds + reading angles ... + 6 angles +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.008 seconds + +# force field + +pair_style amoeba +pair_coeff * * amoeba_water.prm amoeba_water.key +Reading potential file amoeba_water.prm with DATE: 2022-07-05 +Reading potential file amoeba_water.key with DATE: 2022-07-05 + +special_bonds lj/coul 0.5 0.5 0.5 one/five yes +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0.5 0.5 0.5 + special bond factors coul: 0.5 0.5 0.5 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of 1-5 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000 seconds + +# thermo output + +compute virial all pressure NULL virial + +thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*] + +#dump 1 all custom 10 dump.water_hexamer id type x y z fx fy fz +#dump_modify 1 sort id + +# dynamics + +fix 1 all nve + +thermo 10 +run 100 +AMOEBA force field settings + hal: cut 10 taper 8 vscale 0 0 1 1 + multipole: cut 10 aewald 0 mscale 0 0 0.4 1 + polar: cut 10 aewald 0 + pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 1 1 1 1 d/u scale 0 1 + precondition: cut 4.5 +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12 + ghost atom cutoff = 12 + binsize = 6, bins = 1 1 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair amoeba, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp: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 0.0397428 on 4 procs for 100 steps with 18 atoms + +Performance: 217.398 ns/day, 0.110 hours/ns, 2516.180 timesteps/s +100.0% CPU use with 4 MPI tasks x no OpenMP threads + +AMOEBA timing breakdown: + Init time: 0.000772875 2.05% + Hal time: 0.00114925 3.04% + Mpole time: 0.00316129 8.37% + Induce time: 0.0278156 73.61% + Polar time: 0.0048762 12.90% + Total time: 0.0377876 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.03793 | 0.038002 | 0.038115 | 0.0 | 95.62 +Bond | 6.3821e-05 | 8.0969e-05 | 9.9652e-05 | 0.0 | 0.20 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.00067584 | 0.00085989 | 0.0009896 | 0.0 | 2.16 +Output | 0.00035407 | 0.00040202 | 0.00051789 | 0.0 | 1.01 +Modify | 3.6589e-05 | 4.0916e-05 | 4.417e-05 | 0.0 | 0.10 +Other | | 0.0003569 | | | 0.90 + +Nlocal: 4.5 ave 6 max 3 min +Histogram: 1 0 0 1 0 0 1 0 0 1 +Nghost: 13.5 ave 15 max 12 min +Histogram: 1 0 0 1 0 0 1 0 0 1 +Neighs: 38.25 ave 77 max 9 min +Histogram: 2 0 0 0 0 0 1 0 0 1 + +Total # of neighbors = 153 +Ave neighs/atom = 8.5 +Ave special neighs/atom = 2 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/amoeba/log.7Jul22.water_hexamer.hippo.g++.1 b/examples/amoeba/log.7Jul22.water_hexamer.hippo.g++.1 new file mode 100644 index 0000000000..b94be8930b --- /dev/null +++ b/examples/amoeba/log.7Jul22.water_hexamer.hippo.g++.1 @@ -0,0 +1,150 @@ +LAMMPS (23 Jun 2022) +# water hexamer with AMOEBA or HIPPO + +units real +boundary s s s + +atom_style amoeba +bond_style class2 +angle_style amoeba +dihedral_style none + +# per-atom properties required by AMOEBA or HIPPO + +fix amtype all property/atom i_amtype ghost yes +fix extra all property/atom i_amgroup d_redID d_pval ghost yes +fix extra2 all property/atom i_polaxe d2_xyzaxis 3 + +# read data file + +read_data data.water_hexamer.hippo fix amtype NULL "Tinker Types" +Reading data file ... + orthogonal box = (-2.517835 -1.523041 -1.734766) to (2.675716 2.01883 2.220847) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 18 atoms + scanning bonds ... + 2 = max bonds/atom + scanning angles ... + 1 = max angles/atom + reading bonds ... + 12 bonds + reading angles ... + 6 angles +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.007 seconds + +# force field + +pair_style hippo +pair_coeff * * hippo_water.prm hippo_water.key +Reading potential file hippo_water.prm with DATE: 2022-07-05 +Reading potential file hippo_water.key with DATE: 2022-07-05 + +special_bonds lj/coul 0.5 0.5 0.5 one/five yes +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0.5 0.5 0.5 + special bond factors coul: 0.5 0.5 0.5 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of 1-5 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000 seconds + +# thermo output + +compute virial all pressure NULL virial + +thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*] + +#dump 1 all custom 10 dump.water_hexamer id type x y z fx fy fz +#dump_modify 1 sort id + +# dynamics + +fix 1 all nve + +thermo 10 +run 100 +HIPPO force field settings + repulsion: cut 10 taper 8 rscale 0 0 1 1 + qxfer: cut 10 taper 8 mscale 0 0 0.4 1 + dispersion: cut 10 aewald 0 dspscale 0 0 0.4 1 + multipole: cut 10 aewald 0 mscale 0 0 0.4 1 + polar: cut 10 aewald 0 + pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 0.2 1 1 1 d/u scale 0 1 + precondition: cut 4.5 +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12 + ghost atom cutoff = 12 + binsize = 6, bins = 1 1 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair hippo, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard + 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 0.0384281 on 1 procs for 100 steps with 18 atoms + +Performance: 224.836 ns/day, 0.107 hours/ns, 2602.266 timesteps/s +99.7% CPU use with 1 MPI tasks x no OpenMP threads + +HIPPO timing breakdown: + Init time: 0.000296169 0.79% + Repulse time: 0.00605807 16.08% + Disp time: 0.00222186 5.90% + Mpole time: 0.00734879 19.51% + Induce time: 0.0128126 34.02% + Polar time: 0.00749189 19.89% + Qxfer time: 0.00142542 3.78% + Total time: 0.0376635 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.037703 | 0.037703 | 0.037703 | 0.0 | 98.11 +Bond | 0.00016755 | 0.00016755 | 0.00016755 | 0.0 | 0.44 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 2.4711e-05 | 2.4711e-05 | 2.4711e-05 | 0.0 | 0.06 +Output | 0.00038288 | 0.00038288 | 0.00038288 | 0.0 | 1.00 +Modify | 6.4863e-05 | 6.4863e-05 | 6.4863e-05 | 0.0 | 0.17 +Other | | 8.521e-05 | | | 0.22 + +Nlocal: 18 ave 18 max 18 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 153 ave 153 max 153 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 153 +Ave neighs/atom = 8.5 +Ave special neighs/atom = 2 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/amoeba/log.7Jul22.water_hexamer.hippo.g++.4 b/examples/amoeba/log.7Jul22.water_hexamer.hippo.g++.4 new file mode 100644 index 0000000000..aeb3bd7420 --- /dev/null +++ b/examples/amoeba/log.7Jul22.water_hexamer.hippo.g++.4 @@ -0,0 +1,151 @@ +LAMMPS (23 Jun 2022) +# water hexamer with AMOEBA or HIPPO + +units real +boundary s s s + +atom_style amoeba +bond_style class2 +angle_style amoeba +dihedral_style none + +# per-atom properties required by AMOEBA or HIPPO + +fix amtype all property/atom i_amtype ghost yes +fix extra all property/atom i_amgroup d_redID d_pval ghost yes +fix extra2 all property/atom i_polaxe d2_xyzaxis 3 + +# read data file + +read_data data.water_hexamer.hippo fix amtype NULL "Tinker Types" +Reading data file ... + orthogonal box = (-2.517835 -1.523041 -1.734766) to (2.675716 2.01883 2.220847) + 2 by 1 by 2 MPI processor grid + reading atoms ... + 18 atoms + scanning bonds ... + 2 = max bonds/atom + scanning angles ... + 1 = max angles/atom + reading bonds ... + 12 bonds + reading angles ... + 6 angles +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.008 seconds + +# force field + +pair_style hippo +pair_coeff * * hippo_water.prm hippo_water.key +Reading potential file hippo_water.prm with DATE: 2022-07-05 +Reading potential file hippo_water.key with DATE: 2022-07-05 + +special_bonds lj/coul 0.5 0.5 0.5 one/five yes +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0.5 0.5 0.5 + special bond factors coul: 0.5 0.5 0.5 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of 1-5 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.001 seconds + +# thermo output + +compute virial all pressure NULL virial + +thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*] + +#dump 1 all custom 10 dump.water_hexamer id type x y z fx fy fz +#dump_modify 1 sort id + +# dynamics + +fix 1 all nve + +thermo 10 +run 100 +HIPPO force field settings + repulsion: cut 10 taper 8 rscale 0 0 1 1 + qxfer: cut 10 taper 8 mscale 0 0 0.4 1 + dispersion: cut 10 aewald 0 dspscale 0 0 0.4 1 + multipole: cut 10 aewald 0 mscale 0 0 0.4 1 + polar: cut 10 aewald 0 + pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 0.2 1 1 1 d/u scale 0 1 + precondition: cut 4.5 +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12 + ghost atom cutoff = 12 + binsize = 6, bins = 1 1 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair hippo, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp: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 0.0332539 on 4 procs for 100 steps with 18 atoms + +Performance: 259.819 ns/day, 0.092 hours/ns, 3007.165 timesteps/s +99.4% CPU use with 4 MPI tasks x no OpenMP threads + +HIPPO timing breakdown: + Init time: 0.000776397 2.52% + Repulse time: 0.00298646 9.69% + Disp time: 0.000570048 1.85% + Mpole time: 0.00370735 12.02% + Induce time: 0.0186844 60.59% + Polar time: 0.00372843 12.09% + Qxfer time: 0.000377474 1.22% + Total time: 0.0308356 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.030832 | 0.031056 | 0.031379 | 0.1 | 93.39 +Bond | 7.9467e-05 | 9.2634e-05 | 0.00010651 | 0.0 | 0.28 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.00073586 | 0.0011119 | 0.001379 | 0.8 | 3.34 +Output | 0.00045718 | 0.00052546 | 0.00061508 | 0.0 | 1.58 +Modify | 3.7723e-05 | 5.1869e-05 | 6.5238e-05 | 0.0 | 0.16 +Other | | 0.000416 | | | 1.25 + +Nlocal: 4.5 ave 6 max 3 min +Histogram: 1 0 0 1 0 0 1 0 0 1 +Nghost: 13.5 ave 15 max 12 min +Histogram: 1 0 0 1 0 0 1 0 0 1 +Neighs: 38.25 ave 77 max 9 min +Histogram: 2 0 0 0 0 0 1 0 0 1 + +Total # of neighbors = 153 +Ave neighs/atom = 8.5 +Ave special neighs/atom = 2 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:00