Add a (contrived) molecular example for USER-QUIP

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.

examples/USER/quip/in.molecular

+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

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

+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
+

examples/USER/quip/out.molecular

+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