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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15327 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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lib/qmmm/example-mc/README Normal file
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This directory contains an example for the mechanic coupling

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lib/qmmm/example-mc/mm-master/data.water Normal file
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LAMMPS data file for water
96 atoms
64 bonds
32 angles
0 dihedrals
0 impropers
2 atom types
1 bond types
1 angle types
0 dihedral types
0 improper types
0.0 9.865 xlo xhi
0.0 9.865 ylo yhi
0.0 9.865 zlo zhi
Masses
1 15.9994
2 1.008
Pair Coeffs
1 0.102 3.188
2 0.000 0.000
Bond Coeffs
1 450 0.9572
Angle Coeffs
1 55.0 104.52
Atoms
1 0 1 -0.83400 -4.943157 4.999555 1.106073
2 0 2 0.41700 -3.989383 5.319684 0.882671
3 0 2 0.41700 -4.970859 4.118886 0.645414
4 0 1 -0.83400 0.087651 3.997966 0.245184
5 0 2 0.41700 -0.189448 3.238564 0.737637
6 0 2 0.41700 0.340165 3.716546 -0.646859
7 0 1 -0.83400 -1.476825 2.573003 3.969964
8 0 2 0.41700 -2.476262 2.342909 3.971242
9 0 2 0.41700 -1.177059 2.137822 4.797386
10 0 1 -0.83400 -2.866718 -2.698567 -5.842805
11 0 2 0.41700 -2.116039 -2.563955 -6.460863
12 0 2 0.41700 -2.633035 -3.566300 -5.365619
13 0 1 -0.83400 4.305354 0.916065 2.310797
14 0 2 0.41700 4.681590 1.456886 1.564890
15 0 2 0.41700 4.477897 -0.001266 2.162118
16 0 1 -0.83400 3.140624 -2.958877 0.699556
17 0 2 0.41700 2.416048 -3.267548 1.282072
18 0 2 0.41700 3.733007 -3.780312 0.657627
19 0 1 -0.83400 -2.702605 -5.503344 -2.185117
20 0 2 0.41700 -2.503651 -6.454759 -1.864686
21 0 2 0.41700 -2.445484 -4.875090 -1.412444
22 0 1 -0.83400 -0.499359 1.396504 -3.109410
23 0 2 0.41700 -0.051681 2.161550 -2.706675
24 0 2 0.41700 -1.148357 1.125379 -2.447316
25 0 1 -0.83400 4.890520 4.325756 3.842052
26 0 2 0.41700 3.893761 4.308535 3.950637
27 0 2 0.41700 4.946166 4.514250 2.851741
28 0 1 -0.83400 5.691644 1.713787 4.310484
29 0 2 0.41700 5.228679 2.581555 4.361998
30 0 2 0.41700 5.119255 1.176301 3.635805
31 0 1 -0.83400 0.560959 0.041910 -5.382932
32 0 2 0.41700 1.221529 -0.722558 -5.312134
33 0 2 0.41700 -0.033504 0.016189 -4.590395
34 0 1 -0.83400 -0.740775 1.579130 1.430754
35 0 2 0.41700 0.200064 1.382700 1.565649
36 0 2 0.41700 -0.918129 1.879209 2.375874
37 0 1 -0.83400 3.602330 -0.138439 -3.581327
38 0 2 0.41700 4.487536 -0.216376 -4.000513
39 0 2 0.41700 3.049262 -0.796203 -4.061640
40 0 1 -0.83400 -2.574131 1.816065 -0.773020
41 0 2 0.41700 -1.984990 1.759512 0.021520
42 0 2 0.41700 -2.623056 0.813950 -0.951715
43 0 1 -0.83400 -0.681860 -2.105217 2.617966
44 0 2 0.41700 0.075591 -2.677482 2.470155
45 0 2 0.41700 -0.381447 -1.260528 3.119035
46 0 1 -0.83400 0.877670 3.520059 -2.346170
47 0 2 0.41700 0.962603 4.130609 -3.093700
48 0 2 0.41700 1.694708 2.956694 -2.260009
49 0 1 -0.83400 4.626681 -5.379887 -3.195904
50 0 2 0.41700 5.384273 -5.281869 -2.664131
51 0 2 0.41700 4.959718 -5.195755 -4.090586
52 0 1 -0.83400 -2.975363 -0.549128 -4.157351
53 0 2 0.41700 -3.005586 -1.347160 -4.749504
54 0 2 0.41700 -3.484397 0.188753 -4.601707
55 0 1 -0.83400 -1.784475 4.961314 -4.576682
56 0 2 0.41700 -1.799259 4.090209 -5.083548
57 0 2 0.41700 -2.115771 4.808141 -3.667451
58 0 1 -0.83400 3.259544 2.452140 -2.230180
59 0 2 0.41700 3.323170 1.530411 -2.542184
60 0 2 0.41700 3.802574 3.049282 -2.844435
61 0 1 -0.83400 1.201227 -3.873074 1.979232
62 0 2 0.41700 0.666072 -4.403011 1.263244
63 0 2 0.41700 1.518668 -4.606497 2.643697
64 0 1 -0.83400 1.656255 1.671444 2.585800
65 0 2 0.41700 2.558345 1.396868 2.334225
66 0 2 0.41700 1.332188 1.089240 3.372965
67 0 1 -0.83400 2.403906 -1.938370 -5.265845
68 0 2 0.41700 2.088628 -2.761173 -4.852894
69 0 2 0.41700 3.112550 -2.143084 -5.990367
70 0 1 -0.83400 6.671015 -0.695457 -1.582148
71 0 2 0.41700 5.710948 -0.796794 -1.184378
72 0 2 0.41700 6.545527 -0.771012 -2.574381
73 0 1 -0.83400 -5.424609 -1.825624 2.814190
74 0 2 0.41700 -4.617447 -2.210882 3.171264
75 0 2 0.41700 -5.776719 -2.412234 2.075929
76 0 1 -0.83400 1.150487 -4.096740 5.844391
77 0 2 0.41700 1.076286 -3.915393 6.837958
78 0 2 0.41700 0.183470 -4.044319 5.594055
79 0 1 -0.83400 2.061664 4.194185 3.777119
80 0 2 0.41700 1.882571 3.326557 3.243961
81 0 2 0.41700 1.683407 4.114458 4.646069
82 0 1 -0.83400 -2.311755 -4.122312 0.194948
83 0 2 0.41700 -1.444386 -4.631613 0.333538
84 0 2 0.41700 -2.118545 -3.162947 0.233986
85 0 1 -0.83400 1.118351 -3.252459 -1.395623
86 0 2 0.41700 0.435993 -2.622296 -1.064746
87 0 2 0.41700 1.972678 -3.141898 -0.956755
88 0 1 -0.83400 4.038733 -0.963636 -0.898121
89 0 2 0.41700 3.616635 -1.752805 -0.471089
90 0 2 0.41700 3.665491 -0.726014 -1.803310
91 0 1 -0.83400 -0.910973 -1.540333 -0.388194
92 0 2 0.41700 -1.741083 -1.200928 -0.798897
93 0 2 0.41700 -0.901836 -1.451834 0.541945
94 0 1 -0.83400 4.850315 2.494782 0.151704
95 0 2 0.41700 4.126910 2.456315 -0.566034
96 0 2 0.41700 5.642328 2.128654 -0.307363
Bonds
1 1 1 2
2 1 1 3
3 1 4 5
4 1 4 6
5 1 7 8
6 1 7 9
7 1 10 11
8 1 10 12
9 1 13 14
10 1 13 15
11 1 16 17
12 1 16 18
13 1 19 20
14 1 19 21
15 1 22 23
16 1 22 24
17 1 25 26
18 1 25 27
19 1 28 29
20 1 28 30
21 1 31 32
22 1 31 33
23 1 34 35
24 1 34 36
25 1 37 38
26 1 37 39
27 1 40 41
28 1 40 42
29 1 43 44
30 1 43 45
31 1 46 47
32 1 46 48
33 1 49 50
34 1 49 51
35 1 52 53
36 1 52 54
37 1 55 56
38 1 55 57
39 1 58 59
40 1 58 60
41 1 61 62
42 1 61 63
43 1 64 65
44 1 64 66
45 1 67 68
46 1 67 69
47 1 70 71
48 1 70 72
49 1 73 74
50 1 73 75
51 1 76 77
52 1 76 78
53 1 79 80
54 1 79 81
55 1 82 83
56 1 82 84
57 1 85 86
58 1 85 87
59 1 88 89
60 1 88 90
61 1 91 92
62 1 91 93
63 1 94 95
64 1 94 96
Angles
1 1 2 1 3
2 1 5 4 6
3 1 8 7 9
4 1 11 10 12
5 1 14 13 15
6 1 17 16 18
7 1 20 19 21
8 1 23 22 24
9 1 26 25 27
10 1 29 28 30
11 1 32 31 33
12 1 35 34 36
13 1 38 37 39
14 1 41 40 42
15 1 44 43 45
16 1 47 46 48
17 1 50 49 51
18 1 53 52 54
19 1 56 55 57
20 1 59 58 60
21 1 62 61 63
22 1 65 64 66
23 1 68 67 69
24 1 71 70 72
25 1 74 73 75
26 1 77 76 78
27 1 80 79 81
28 1 83 82 84
29 1 86 85 87
30 1 89 88 90
31 1 92 91 93
32 1 95 94 96

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lib/qmmm/example-mc/mm-master/water.in Normal file
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units real
neigh_modify delay 0 every 1 check yes
atom_style full
bond_style harmonic
angle_style harmonic
pair_style lj/cut/coul/long 10.0
pair_modify mix arithmetic
kspace_style pppm 1e-4
special_bonds amber
#atom_modify sort 0.0 0
read_data data.water
timestep 1.0
dump 1 all custom 1 dump.lammpstrj id element xu yu zu
dump_modify 1 element O H
thermo_style multi
thermo 1
group wat id 25:27
fix 1 wat qmmm
fix 2 all nvt temp 300.0 300.0 70.0

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lib/qmmm/example-mc/mm-slave/data.single_water Normal file
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LAMMPS data file for water
3 atoms
2 bonds
1 angles
2 atom types
1 bond types
1 angle types
0.0 9.865 xlo xhi
0.0 9.865 ylo yhi
0.0 9.865 zlo zhi
Masses
1 15.9994
2 1.008
Pair Coeffs
1 0.102 3.188
2 0.000 0.000
Bond Coeffs
1 450 0.9572
Angle Coeffs
1 55.0 104.52
Atoms
1 0 1 -0.8340 4.890520 4.325756 3.842052
2 0 2 0.41700 3.893761 4.308535 3.950637
3 0 2 0.41700 4.946166 4.514250 2.851741
Bonds
1 1 1 2
2 1 1 3
Angles
1 1 2 1 3

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lib/qmmm/example-mc/mm-slave/water_single.in Normal file
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units real
neigh_modify delay 0 every 1 check yes
atom_style full
bond_style harmonic
angle_style harmonic
pair_style lj/cut/coul/long 10.0
pair_modify mix arithmetic
kspace_style pppm 1e-4
special_bonds amber
#atom_modify sort 0.0 0
read_data data.single_water
timestep 1.0
thermo_style multi
thermo 1
fix 1 all qmmm

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lib/qmmm/example-mc/qm-pw/pseudo/H.pbe-van_ak.UPF Normal file
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lib/qmmm/example-mc/qm-pw/pseudo/O.pbe-van_bm.UPF Normal file
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lib/qmmm/example-mc/qm-pw/water.in Normal file
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&CONTROL
title="QMMM"
calculation='md',
restart_mode = 'from_scratch',
tprnfor=.t.,
prefix='ms2',
pseudo_dir='pseudo'
nstep = 2000,
tqmmm = .true.
/
&SYSTEM
ibrav = 1,
celldm(1) = 18.642155649244,
nat = 3,
ntyp = 2,
ecutwfc = 25.0 ,
ecutrho = 250.0 ,
/
&ELECTRONS
conv_thr = 1.D-8,
/
&IONS
ion_positions = 'default'
/
ATOMIC_SPECIES
O 16.0000 O.pbe-van_bm.UPF
H 1.0000 H.pbe-van_ak.UPF
ATOMIC_POSITIONS angstrom
O 4.890520 4.325756 3.842052
H 3.893761 4.308535 3.950637
H 4.946166 4.514250 2.851741
K_POINTS gamma

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lib/qmmm/example-mc/qmmm.inp Normal file
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# configuration file for QMMM wrapper
mode mech # coupling choices: o(ff), m(echanical), e(lectrostatic)
#mode elec # coupling choices: o(ff), m(echanical), e(lectrostatic)
handle qmmm # name of sysv shmem handle
steps 100 # number of QM/MM (MD) steps
verbose 1
restart water.restart # checkpoint/restart file to write out at end
# QM system config
qmdir qm-pw # directory to run QM system in
qminp water.in # input file for QM code
qmout NULL # output file for QM code (or NULL to print to screen)
# MM master config
madir mm-master # directory to run MM master in
mainp water.in # input file for MM master
maout water.out # output file for MM master (or NULL to print to screen)
# MM slave config
sldir mm-slave # directory to run MM slave in
slinp water_single.in # input file for MM slave
slout water_single.out # output file for MM slave (or NULL to print to screen)