Commit 1ddace4d authored by sjplimp's avatar sjplimp Committed by GitHub
Browse files

Merge pull request #595 from libAtoms/idces2quip 

Add a (contrived) molecular example for USER-QUIP
parents af3d0ca3 1afab981

examples/USER/quip/in.molecular

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+48 −0
Original line number Diff line number Diff line 
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

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

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+162 −0
Original line number Diff line number Diff line 
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

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Original line number Diff line number Diff line 
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

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