diff --git a/examples/USER/quip/in.gap b/examples/USER/quip/in.gap index 37667e39b94bc041381ab7510f1c0e28a955ecb2..dd049a473704dbef392095746bdc1578e4bec736 100644 --- a/examples/USER/quip/in.gap +++ b/examples/USER/quip/in.gap @@ -17,6 +17,6 @@ fix 1 all nve thermo 10 timestep 0.001 -dump 1 all custom 10 dump.gap id fx fy fz +#dump 1 all custom 10 dump.gap id fx fy fz run 40 diff --git a/examples/USER/quip/in.molecular b/examples/USER/quip/in.molecular index 24d21d6762d8aa010e2edc13708f3ca5d0852c78..4253399d7c7c517160b06061c500c1cd4e1a715c 100644 --- a/examples/USER/quip/in.molecular +++ b/examples/USER/quip/in.molecular @@ -1,7 +1,6 @@ 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 @@ -28,7 +27,7 @@ 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 +pair_coeff * * quip sw_example.xml "IP SW" 14 1 bond_style none angle_style none diff --git a/examples/USER/quip/in.sw b/examples/USER/quip/in.sw index c1367ac8055e2452632dabbc6a3c7b60b0e31483..aaa4217b2ff81f1bff71e86eba7d0fb3138a4c7e 100644 --- a/examples/USER/quip/in.sw +++ b/examples/USER/quip/in.sw @@ -10,6 +10,7 @@ read_data data_sw pair_style quip pair_coeff * * sw_example.xml "IP SW" 14 +velocity all create 10.0 355311 neighbor 0.3 bin neigh_modify delay 10 @@ -17,6 +18,6 @@ fix 1 all nve thermo 10 timestep 0.001 -dump 1 all custom 10 dump.sw id fx fy fz +#dump 1 all custom 10 dump.sw id fx fy fz -run 1 +run 100 diff --git a/examples/USER/quip/log.24Jul17.molecular.g++.1 b/examples/USER/quip/log.24Jul17.molecular.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..28fc63579b8dfb43e02b2cd36152157c12afad0b --- /dev/null +++ b/examples/USER/quip/log.24Jul17.molecular.g++.1 @@ -0,0 +1,130 @@ +LAMMPS (24 Jul 2017) + using 1 OpenMP thread(s) per MPI task +units metal +atom_style full +boundary p p p +timestep 0.0001 # 0.1 fs + +read_data methane-box-8.data + 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 + 4 = max # of 1-2 neighbors + 3 = max # of 1-3 neighbors + 3 = max # of 1-4 neighbors + 4 = max # of special neighbors + +# 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 + 4 = max # of 1-2 neighbors + 3 = max # of 1-3 neighbors + 3 = max # of 1-4 neighbors + 4 = max # of special neighbors + +# 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 sw_example.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 +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 +Per MPI rank memory allocation (min/avg/max) = 8.288 | 8.288 | 8.288 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 0.0537777 on 1 procs for 10 steps with 40 atoms + +Performance: 1.607 ns/day, 14.938 hours/ns, 185.951 timesteps/s +90.3% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.053478 | 0.053478 | 0.053478 | 0.0 | 99.44 +Bond | 1.9073e-06 | 1.9073e-06 | 1.9073e-06 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 7.7724e-05 | 7.7724e-05 | 7.7724e-05 | 0.0 | 0.14 +Output | 0.00018263 | 0.00018263 | 0.00018263 | 0.0 | 0.34 +Modify | 1.5974e-05 | 1.5974e-05 | 1.5974e-05 | 0.0 | 0.03 +Other | | 2.122e-05 | | | 0.04 + +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 diff --git a/examples/USER/quip/log.24Jul17.molecular.g++.4 b/examples/USER/quip/log.24Jul17.molecular.g++.4 new file mode 100644 index 0000000000000000000000000000000000000000..a8be8e77bb4b2452eda764f00f5085d7209dbd53 --- /dev/null +++ b/examples/USER/quip/log.24Jul17.molecular.g++.4 @@ -0,0 +1,130 @@ +LAMMPS (24 Jul 2017) + using 1 OpenMP thread(s) per MPI task +units metal +atom_style full +boundary p p p +timestep 0.0001 # 0.1 fs + +read_data methane-box-8.data + orthogonal box = (-0.499095 -0.270629 0.131683) to (8.4109 8.63937 9.04168) + 1 by 2 by 2 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 + 4 = max # of 1-2 neighbors + 3 = max # of 1-3 neighbors + 3 = max # of 1-4 neighbors + 4 = max # of special neighbors + +# 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 + 4 = max # of 1-2 neighbors + 3 = max # of 1-3 neighbors + 3 = max # of 1-4 neighbors + 4 = max # of special neighbors + +# 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 sw_example.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 +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 +Per MPI rank memory allocation (min/avg/max) = 8.26 | 8.386 | 8.762 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 0.0506847 on 4 procs for 10 steps with 40 atoms + +Performance: 1.705 ns/day, 14.079 hours/ns, 197.298 timesteps/s +94.4% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.04216 | 0.045656 | 0.049349 | 1.2 | 90.08 +Bond | 1.9073e-06 | 2.4438e-06 | 2.861e-06 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.00068545 | 0.004438 | 0.0079191 | 3.9 | 8.76 +Output | 0.00048304 | 0.00053334 | 0.00060964 | 0.0 | 1.05 +Modify | 1.1444e-05 | 1.4424e-05 | 1.9312e-05 | 0.0 | 0.03 +Other | | 4.047e-05 | | | 0.08 + +Nlocal: 10 ave 15 max 6 min +Histogram: 1 0 0 1 1 0 0 0 0 1 +Nghost: 878 ave 948 max 812 min +Histogram: 1 0 1 0 0 0 1 0 0 1 +Neighs: 1192 ave 1764 max 731 min +Histogram: 1 0 0 1 1 0 0 0 0 1 +FullNghs: 2384 ave 3527 max 1439 min +Histogram: 1 0 0 1 1 0 0 0 0 1 + +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 diff --git a/examples/USER/quip/log.24Jul17.sw.g++.1 b/examples/USER/quip/log.24Jul17.sw.g++.1 new file mode 100644 index 0000000000000000000000000000000000000000..c8115f4cfc3ecd0d1da9731f213debd007438039 --- /dev/null +++ b/examples/USER/quip/log.24Jul17.sw.g++.1 @@ -0,0 +1,83 @@ +LAMMPS (24 Jul 2017) + using 1 OpenMP thread(s) per MPI task +# Test of SW potential for Si system + +units metal +boundary p p p + +atom_style atomic + +read_data data_sw + orthogonal box = (0 0 0) to (5.431 5.431 5.431) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 8 atoms + +pair_style quip +pair_coeff * * sw_example.xml "IP SW" 14 + +velocity all create 10.0 355311 +neighbor 0.3 bin +neigh_modify delay 10 + +fix 1 all nve +thermo 10 +timestep 0.001 + +#dump 1 all custom 10 dump.sw id fx fy fz + +run 100 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 4.2258 + ghost atom cutoff = 4.2258 + binsize = 2.1129, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair quip, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.684 | 2.684 | 2.684 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 10 -34.68 0 -34.670952 32.206289 + 10 4.5659178 -34.675073 0 -34.670942 46.253731 + 20 1.606683 -34.672391 0 -34.670937 44.736892 + 30 6.7007748 -34.677011 0 -34.670948 16.403049 + 40 5.682757 -34.676087 0 -34.670945 18.696408 + 50 2.2140716 -34.672942 0 -34.670939 37.592282 + 60 5.0475382 -34.675512 0 -34.670944 37.331666 + 70 7.0990979 -34.677369 0 -34.670946 40.533757 + 80 5.7306189 -34.676128 0 -34.670943 47.748813 + 90 5.0895648 -34.675549 0 -34.670944 38.092721 + 100 4.1070919 -34.674659 0 -34.670943 28.737864 +Loop time of 0.384233 on 1 procs for 100 steps with 8 atoms + +Performance: 22.486 ns/day, 1.067 hours/ns, 260.259 timesteps/s +94.6% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.38365 | 0.38365 | 0.38365 | 0.0 | 99.85 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.00017333 | 0.00017333 | 0.00017333 | 0.0 | 0.05 +Output | 0.00014162 | 0.00014162 | 0.00014162 | 0.0 | 0.04 +Modify | 7.081e-05 | 7.081e-05 | 7.081e-05 | 0.0 | 0.02 +Other | | 0.0001957 | | | 0.05 + +Nlocal: 8 ave 8 max 8 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 162 ave 162 max 162 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 128 ave 128 max 128 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 128 +Ave neighs/atom = 16 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/USER/quip/log.24Jul17.sw.g++.4 b/examples/USER/quip/log.24Jul17.sw.g++.4 new file mode 100644 index 0000000000000000000000000000000000000000..d7306c705564395c5f8f820c92190d6e0b6fe12f --- /dev/null +++ b/examples/USER/quip/log.24Jul17.sw.g++.4 @@ -0,0 +1,83 @@ +LAMMPS (24 Jul 2017) + using 1 OpenMP thread(s) per MPI task +# Test of SW potential for Si system + +units metal +boundary p p p + +atom_style atomic + +read_data data_sw + orthogonal box = (0 0 0) to (5.431 5.431 5.431) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 8 atoms + +pair_style quip +pair_coeff * * sw_example.xml "IP SW" 14 + +velocity all create 10.0 355311 +neighbor 0.3 bin +neigh_modify delay 10 + +fix 1 all nve +thermo 10 +timestep 0.001 + +#dump 1 all custom 10 dump.sw id fx fy fz + +run 100 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 4.2258 + ghost atom cutoff = 4.2258 + binsize = 2.1129, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair quip, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.698 | 2.698 | 2.698 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 10 -34.68 0 -34.670952 32.206289 + 10 4.5659178 -34.675073 0 -34.670942 46.253731 + 20 1.606683 -34.672391 0 -34.670937 44.736892 + 30 6.7007748 -34.677011 0 -34.670948 16.403049 + 40 5.682757 -34.676087 0 -34.670945 18.696408 + 50 2.2140716 -34.672942 0 -34.670939 37.592282 + 60 5.0475382 -34.675512 0 -34.670944 37.331666 + 70 7.0990979 -34.677369 0 -34.670946 40.533757 + 80 5.7306189 -34.676128 0 -34.670943 47.748813 + 90 5.0895648 -34.675549 0 -34.670944 38.092721 + 100 4.1070919 -34.674659 0 -34.670943 28.737864 +Loop time of 0.423803 on 4 procs for 100 steps with 8 atoms + +Performance: 20.387 ns/day, 1.177 hours/ns, 235.959 timesteps/s +90.6% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.39332 | 0.40011 | 0.40704 | 0.8 | 94.41 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.015632 | 0.022605 | 0.029425 | 3.3 | 5.33 +Output | 0.00025702 | 0.00028491 | 0.00035429 | 0.0 | 0.07 +Modify | 7.3671e-05 | 8.1897e-05 | 8.9884e-05 | 0.0 | 0.02 +Other | | 0.0007259 | | | 0.17 + +Nlocal: 2 ave 2 max 2 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 113 ave 113 max 113 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 32 ave 32 max 32 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 128 +Ave neighs/atom = 16 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:00