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Commit 85120842 authored by Axel Kohlmeyer's avatar Axel Kohlmeyer
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update QUIP examples to closer match typical LAMMPS examples

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examples/USER/quip/in.gap
+ 1
− 1
View file @ 85120842
......@@ -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
examples/USER/quip/in.molecular
+ 1
− 2
View file @ 85120842
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
......
examples/USER/quip/in.sw
+ 3
− 2
View file @ 85120842
......@@ -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
examples/USER/quip/log.24Jul17.molecular.g++.1 0 → 100644
+ 130
− 0
View file @ 85120842
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
examples/USER/quip/log.24Jul17.molecular.g++.4 0 → 100644
+ 130
− 0
View file @ 85120842
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
examples/USER/quip/log.24Jul17.sw.g++.1 0 → 100644
+ 83
− 0
View file @ 85120842
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
examples/USER/quip/log.24Jul17.sw.g++.4 0 → 100644
+ 83
− 0
View file @ 85120842
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
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