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Add a (contrived) molecular example for USER-QUIP

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This example showcases the use of different 'special_bonds' settings for
different pair styles, so quip gets all the bonded neighbours but lj can
exclude them if it needs to.

The results have been checked against a pure quip implementation of the
potential; the expected lammps output is included.

DISCLAIMER: This example mixes parameters for methane and silane and is
NOT intended to be a realistic representation of either system.
This commit is contained in:
Max Veit
2017-07-22 01:33:15 +01:00
parent 52a1c54d50
commit 4e0a249e27
3 changed files with 293 additions and 0 deletions
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examples/USER/quip/in.molecular Normal file
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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
pair_style hybrid/overlay lj/cut 8.0 quip
special_bonds lj/coul 0.999999999 0.999999999 0.999999999 # for quip
# Intermolecular: OPLS (JACS 118 (45), p. 11225 (1996))
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
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

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examples/USER/quip/methane-box-8.data Normal file
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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

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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