diff --git a/examples/USER/quip/in.molecular b/examples/USER/quip/in.molecular new file mode 100644 index 0000000000000000000000000000000000000000..24d21d6762d8aa010e2edc13708f3ca5d0852c78 --- /dev/null +++ b/examples/USER/quip/in.molecular @@ -0,0 +1,48 @@ +units metal +atom_style full +boundary p p p +processors 1 1 1 +timestep 0.0001 # 0.1 fs + +read_data methane-box-8.data + +# DISCLAIMER: This potential mixes parameters from methane and silane +# potentials and is NOT intended to be a realistic representation of either +# system. It is meant to demonstrate the use of hybrid QUIP/LAMMPS potentials, +# including the use of separate 'special_bonds' settings. + +pair_style hybrid/overlay lj/cut 8.0 quip + +# exclusion setting for quip; cannot be exactly 1.0 1.0 1.0, +# since that would not flag 1-2, 1-3, and 1-4 pairs in lj/cut +special_bonds lj/coul 0.999999999 0.999999999 0.999999999 + +# Intermolecular: OPLS (JACS 118 (45), p. 11225 (1996)) +# Coulomb interactions ommitted for simplicity +pair_coeff 1 1 lj/cut 0.0028619844 3.5 # CT +pair_coeff 2 2 lj/cut 0.0013009018 2.5 # HC +pair_coeff 1 2 lj/cut 0.0019295487 2.95 +pair_modify shift no +# change exclusion settings for lj/cut only: exclude bonded pairs +pair_modify pair lj/cut special lj/coul 0.0 0.0 0.0 + +# Intramolecular +# Tell QUIP to pretend this is silane (which is covered by the parameter file) +pair_coeff * * quip ip.parms.SW.xml "IP SW" 14 1 +bond_style none +angle_style none + +fix 1 all nve + +# Include diagnostics that allow us to compare to a pure QUIP run +compute equip all pair quip +compute evdw all pair lj/cut +compute vir all pressure NULL virial + +thermo_style custom step epair ke etotal temp press c_vir c_evdw c_equip +thermo 1 + +# dump 1 all custom 1 dump.molecular id type x y z fx fy fz +# dump_modify 1 sort id + +run 10 diff --git a/examples/USER/quip/methane-box-8.data b/examples/USER/quip/methane-box-8.data new file mode 100644 index 0000000000000000000000000000000000000000..2a55fcf5517f01000db1654f02e8d20961aafde4 --- /dev/null +++ b/examples/USER/quip/methane-box-8.data @@ -0,0 +1,162 @@ +LAMMPS data file. CGCMM style. atom_style full generated by VMD/TopoTools v1.1 on Sat Oct 22 17:48:43 BST 2016. Original generated with Packmol + 40 atoms + 32 bonds + 48 angles + 0 dihedrals + 0 impropers + 2 atom types + 1 bond types + 1 angle types + 0 dihedral types + 0 improper types + -0.499095 8.410905 xlo xhi + -0.270629 8.639371 ylo yhi + 0.131683 9.041683 zlo zhi + +# Pair Coeffs +# +# 1 CT +# 2 HC + +# Bond Coeffs +# +# 1 CT-HC + +# Angle Coeffs +# +# 1 HC-CT-HC + + Masses + + 1 12.011000 # CT + 2 1.008000 # HC + + Atoms + +1 1 1 -0.240000 3.937038 0.677603 7.362249 # CT +2 1 2 0.060000 4.193022 1.709034 7.595834 # HC +3 1 2 0.060000 2.905136 0.486052 7.649386 # HC +4 1 2 0.060000 4.596317 0.007308 7.909996 # HC +5 1 2 0.060000 4.053670 0.507989 6.293814 # HC +6 2 1 -0.240000 6.131801 2.711096 0.901469 # CT +7 2 2 0.060000 6.787439 1.886720 0.628555 # HC +8 2 2 0.060000 5.728610 3.167652 -0.000171 # HC +9 2 2 0.060000 6.696346 3.453106 1.462433 # HC +10 2 2 0.060000 5.314820 2.336948 1.515051 # HC +11 3 1 -0.240000 5.723143 6.225007 1.430856 # CT +12 3 2 0.060000 5.585279 6.712817 2.393651 # HC +13 3 2 0.060000 5.584847 6.951755 0.632938 # HC +14 3 2 0.060000 4.994507 5.424203 1.322354 # HC +15 3 2 0.060000 6.727906 5.811248 1.374455 # HC +16 4 1 -0.240000 5.573754 5.038579 4.999124 # CT +17 4 2 0.060000 4.512787 5.184293 5.191620 # HC +18 4 2 0.060000 6.006150 5.966299 4.629893 # HC +19 4 2 0.060000 5.703088 4.256326 4.253924 # HC +20 4 2 0.060000 6.073008 4.747398 5.921016 # HC +21 5 1 -0.240000 2.108870 2.623461 3.348534 # CT +22 5 2 0.060000 2.886488 2.470897 2.602897 # HC +23 5 2 0.060000 1.382727 3.341833 2.973541 # HC +24 5 2 0.060000 2.554989 3.003606 4.265288 # HC +25 5 2 0.060000 1.611274 1.677549 3.552431 # HC +26 6 1 -0.240000 6.106165 2.015183 5.526875 # CT +27 6 2 0.060000 6.075817 2.038391 4.439456 # HC +28 6 2 0.060000 6.076127 0.982573 5.868599 # HC +29 6 2 0.060000 5.248943 2.554122 5.925227 # HC +30 6 2 0.060000 7.023739 2.485633 5.874240 # HC +31 7 1 -0.240000 0.644265 2.699668 7.212713 # CT +32 7 2 0.060000 0.403413 2.521819 6.166625 # HC +33 7 2 0.060000 0.098429 1.993976 7.835627 # HC +34 7 2 0.060000 0.361861 3.715309 7.482326 # HC +35 7 2 0.060000 1.713326 2.567585 7.366300 # HC +36 8 1 -0.240000 0.588072 6.428183 7.473536 # CT +37 8 2 0.060000 0.540903 6.363141 6.388417 # HC +38 8 2 0.060000 -0.008121 5.629967 7.910991 # HC +39 8 2 0.060000 0.197701 7.391140 7.796481 # HC +40 8 2 0.060000 1.621770 6.328495 7.798280 # HC + + Bonds + +1 1 1 3 +2 1 1 5 +3 1 1 2 +4 1 1 4 +5 1 6 7 +6 1 6 9 +7 1 6 8 +8 1 6 10 +9 1 11 14 +10 1 11 13 +11 1 11 12 +12 1 11 15 +13 1 16 17 +14 1 16 18 +15 1 16 19 +16 1 16 20 +17 1 21 22 +18 1 21 24 +19 1 21 25 +20 1 21 23 +21 1 26 27 +22 1 26 28 +23 1 26 29 +24 1 26 30 +25 1 31 33 +26 1 31 32 +27 1 31 34 +28 1 31 35 +29 1 36 38 +30 1 36 37 +31 1 36 39 +32 1 36 40 + + Angles + +1 1 3 1 5 +2 1 2 1 3 +3 1 3 1 4 +4 1 2 1 5 +5 1 4 1 5 +6 1 2 1 4 +7 1 7 6 9 +8 1 7 6 8 +9 1 7 6 10 +10 1 8 6 9 +11 1 9 6 10 +12 1 8 6 10 +13 1 13 11 14 +14 1 12 11 14 +15 1 14 11 15 +16 1 12 11 13 +17 1 13 11 15 +18 1 12 11 15 +19 1 17 16 18 +20 1 17 16 19 +21 1 17 16 20 +22 1 18 16 19 +23 1 18 16 20 +24 1 19 16 20 +25 1 22 21 24 +26 1 22 21 25 +27 1 22 21 23 +28 1 24 21 25 +29 1 23 21 24 +30 1 23 21 25 +31 1 27 26 28 +32 1 27 26 29 +33 1 27 26 30 +34 1 28 26 29 +35 1 28 26 30 +36 1 29 26 30 +37 1 32 31 33 +38 1 33 31 34 +39 1 33 31 35 +40 1 32 31 34 +41 1 32 31 35 +42 1 34 31 35 +43 1 37 36 38 +44 1 38 36 39 +45 1 38 36 40 +46 1 37 36 39 +47 1 37 36 40 +48 1 39 36 40 + diff --git a/examples/USER/quip/out.molecular b/examples/USER/quip/out.molecular new file mode 100644 index 0000000000000000000000000000000000000000..0e8d07d389360f6715cc4d40063264f1ab9473b6 --- /dev/null +++ b/examples/USER/quip/out.molecular @@ -0,0 +1,93 @@ +LAMMPS (6 Jul 2017) +Reading data file ... + orthogonal box = (-0.499095 -0.270629 0.131683) to (8.4109 8.63937 9.04168) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 40 atoms + scanning bonds ... + 4 = max bonds/atom + scanning angles ... + 6 = max angles/atom + reading bonds ... + 32 bonds + reading angles ... + 48 angles +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 + 3 = max # of 1-3 neighbors + 3 = max # of 1-4 neighbors + 4 = max # of special neighbors +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 1 1 1 + special bond factors coul: 1 1 1 + 4 = max # of 1-2 neighbors + 3 = max # of 1-3 neighbors + 3 = max # of 1-4 neighbors + 4 = max # of special neighbors +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10 + ghost atom cutoff = 10 + binsize = 5, bins = 2 2 2 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair lj/cut, perpetual, half/full from (2) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (2) pair quip, perpetual + attributes: full, newton on + pair build: full/bin + stencil: full/bin/3d + bin: standard +Setting up Verlet run ... + Unit style : metal + Current step : 0 + Time step : 0.0001 +Per MPI rank memory allocation (min/avg/max) = 9.543 | 9.543 | 9.543 Mbytes +Step E_pair KinEng TotEng Temp Press c_vir c_evdw c_equip + 0 -5.3530213 0 -5.3530213 0 518847.56 518847.56 -0.10904079 -5.2439805 + 1 -5.9384459 0.58384822 -5.3545977 115.81657 517370.5 516488.87 -0.10783656 -5.8306093 + 2 -7.669616 2.3104051 -5.3592109 458.30954 512986.36 509497.58 -0.10422283 -7.5653932 + 3 -10.473314 5.1069211 -5.3663924 1013.0477 505833.04 498121.43 -0.098049469 -10.375264 + 4 -14.234705 8.859182 -5.3755227 1757.3747 496127.44 482749.79 -0.089147485 -14.145557 + 5 -18.806851 13.420941 -5.3859098 2662.28 484148.76 463882.72 -0.077305196 -18.729546 + 6 -24.021727 18.625147 -5.3965797 3694.6259 470219.95 442095.39 -0.06194509 -23.959782 + 7 -29.702647 24.295529 -5.4071176 4819.446 454683.57 417996.56 -0.042859727 -29.659787 + 8 -35.67405 30.257258 -5.4167913 6002.0599 437887.03 392197.62 -0.019248651 -35.654801 + 9 -41.771047 36.345757 -5.4252893 7209.8209 420163.51 365280.27 0.0096063065 -41.780653 + 10 -47.845522 42.413161 -5.4323614 8413.3973 401821.91 337776.7 0.044743702 -47.890266 +Loop time of 0.131692 on 1 procs for 10 steps with 40 atoms + +Performance: 0.656 ns/day, 36.581 hours/ns, 75.935 timesteps/s +97.2% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.12961 | 0.12961 | 0.12961 | 0.0 | 98.42 +Bond | 7.391e-06 | 7.391e-06 | 7.391e-06 | 0.0 | 0.01 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.00013185 | 0.00013185 | 0.00013185 | 0.0 | 0.10 +Output | 0.0018771 | 0.0018771 | 0.0018771 | 0.0 | 1.43 +Modify | 2.5988e-05 | 2.5988e-05 | 2.5988e-05 | 0.0 | 0.02 +Other | | 4.268e-05 | | | 0.03 + +Nlocal: 40 ave 40 max 40 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1175 ave 1175 max 1175 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 4768 ave 4768 max 4768 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 9536 ave 9536 max 9536 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 9536 +Ave neighs/atom = 238.4 +Ave special neighs/atom = 4 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:00