ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Merge branch 'master' into collected-small-changes

Browse Source
This commit is contained in:
Axel Kohlmeyer
2021-02-08 15:33:22 -05:00
parent ca1a5731e7 a3a84c4493
commit d42a165ccf
10 changed files with 2588 additions and 149 deletions
Download Patch File Download Diff File Expand all files Collapse all files

86
doc/src/fix_bond_react.rst
View File

@ -41,7 +41,7 @@ Syntax
* template-ID(post-reacted) = ID of a molecule template containing post-reaction topology
* map_file = name of file specifying corresponding atom-IDs in the pre- and post-reacted templates
* zero or more individual keyword/value pairs may be appended to each react argument
* individual_keyword = *prob* or *max_rxn* or *stabilize_steps* or *custom_charges*
* individual_keyword = *prob* or *max_rxn* or *stabilize_steps* or *custom_charges* or *molecule* or *modify_create*
.. parsed-literal::
@ -59,6 +59,12 @@ Syntax
off = allow both inter- and intramolecular reactions (default)
inter = search for reactions between molecules with different IDs
intra = search for reactions within the same molecule
*modify_create* keyword values
*fit* value = *all* or *fragmentID*
all = use all eligible atoms for create-atoms fit (default)
fragmentID = ID of molecule fragment used for create-atoms fit
*overlap* value = R
R = only insert atom/molecule if further than R from existing particles (distance units)
Examples
""""""""
@ -89,7 +95,9 @@ documentation. Topology changes are defined in pre- and post-reaction
molecule templates and can include creation and deletion of bonds,
angles, dihedrals, impropers, bond types, angle types, dihedral types,
atom types, or atomic charges. In addition, reaction by-products or
other molecules can be identified and deleted.
other molecules can be identified and deleted. Finally, atoms can be
created and inserted at specific positions relative to the reaction
site.
Fix bond/react does not use quantum mechanical (eg. fix qmmm) or
pairwise bond-order potential (eg. Tersoff or AIREBO) methods to
@ -262,14 +270,14 @@ command page.
The post-reacted molecule template contains a sample of the reaction
site and its surrounding topology after the reaction has occurred. It
must contain the same number of atoms as the pre-reacted template. A
one-to-one correspondence between the atom IDs in the pre- and
post-reacted templates is specified in the map file as described
below. Note that during a reaction, an atom, bond, etc. type may
change to one that was previously not present in the simulation. These
new types must also be defined during the setup of a given simulation.
A discussion of correctly handling this is also provided on the
:doc:`molecule <molecule>` command page.
must contain the same number of atoms as the pre-reacted template
(unless there are created atoms). A one-to-one correspondence between
the atom IDs in the pre- and post-reacted templates is specified in
the map file as described below. Note that during a reaction, an atom,
bond, etc. type may change to one that was previously not present in
the simulation. These new types must also be defined during the setup
of a given simulation. A discussion of correctly handling this is also
provided on the :doc:`molecule <molecule>` command page.
.. note::
@ -283,7 +291,7 @@ A discussion of correctly handling this is also provided on the
The map file is a text document with the following format:
A map file has a header and a body. The header of map file the
contains one mandatory keyword and four optional keywords. The
contains one mandatory keyword and five optional keywords. The
mandatory keyword is 'equivalences':
.. parsed-literal::
@ -296,11 +304,12 @@ The optional keywords are 'edgeIDs', 'deleteIDs', 'chiralIDs' and
.. parsed-literal::
N *edgeIDs* = # of edge atoms N in the pre-reacted molecule template
N *deleteIDs* = # of atoms N that are specified for deletion
N *chiralIDs* = # of specified chiral centers N
N *constraints* = # of specified reaction constraints N
N *deleteIDs* = # of atoms N that are deleted
N *createIDs* = # of atoms N that are created
N *chiralIDs* = # of chiral centers N
N *constraints* = # of reaction constraints N
The body of the map file contains two mandatory sections and four
The body of the map file contains two mandatory sections and five
optional sections. The first mandatory section begins with the keyword
'InitiatorIDs' and lists the two atom IDs of the initiator atom pair
in the pre-reacted molecule template. The second mandatory section
@ -313,8 +322,10 @@ the keyword 'EdgeIDs' and lists the atom IDs of edge atoms in the
pre-reacted molecule template. The second optional section begins with
the keyword 'DeleteIDs' and lists the atom IDs of pre-reaction
template atoms to delete. The third optional section begins with the
keyword 'CreateIDs' and lists the atom IDs of the post-reaction
template atoms to create. The fourth optional section begins with the
keyword 'ChiralIDs' lists the atom IDs of chiral atoms whose
handedness should be enforced. The fourth optional section begins with
handedness should be enforced. The fifth optional section begins with
the keyword 'Constraints' and lists additional criteria that must be
satisfied in order for the reaction to occur. Currently, there are
five types of constraints available, as discussed below: 'distance',
@ -353,6 +364,38 @@ A sample map file is given below:
----------
A user-specified set of atoms can be deleted by listing their
pre-reaction template IDs in the DeleteIDs section. A deleted atom
must still be included in the post-reaction molecule template, in
which it cannot be bonded to an atom that is not deleted. In addition
to deleting unwanted reaction by-products, this feature can be used to
remove specific topologies, such as small rings, that may be otherwise
indistinguishable.
Atoms can be created by listing their post-reaction template IDs in
the CreateIDs section. A created atom should not be included in the
pre-reaction template. The inserted positions of created atoms are
determined by the coordinates of the post-reaction template, after
optimal translation and rotation of the post-reaction template to the
reaction site (using a fit with atoms that are neither created nor
deleted). The *modify_create* keyword can be used to modify the
default behavior when creating atoms. The *modify_create* keyword has
two sub-keywords, *fit* and *overlap*. One or more of the sub-keywords
may be used after the *modify_create* keyword. The *fit* sub-keyword
can be used to specify which post-reaction atoms are used for the
optimal translation and rotation of the post-reaction template. The
*fragmentID* value of the *fit* sub-keyword must be the name of a
molecule fragment defined in the post-reaction :doc:`molecule
<molecule>` template, and only atoms in this fragment are used for the
fit. Atoms are created only if no current atom in the simulation is
within a distance R of any created atom, including the effect of
periodic boundary conditions if applicable. R is defined by the
*overlap* sub-keyword. Note that the default value for R is 0.0, which
will allow atoms to strongly overlap if you are inserting where other
atoms are present. The velocity of each created atom is initialized in
a random direction with a magnitude calculated from the instantaneous
temperature of the reaction site.
The handedness of atoms that are chiral centers can be enforced by
listing their IDs in the ChiralIDs section. A chiral atom must be
bonded to four atoms with mutually different atom types. This feature
@ -528,15 +571,6 @@ the same molecule ID are considered for the reaction.
A few other considerations:
Many reactions result in one or more atoms that are considered
unwanted by-products. Therefore, bond/react provides the option to
delete a user-specified set of atoms. These pre-reaction atoms are
identified in the map file. A deleted atom must still be included in
the post-reaction molecule template, in which it cannot be bonded to
an atom that is not deleted. In addition to deleting unwanted reaction
by-products, this feature can be used to remove specific topologies,
such as small rings, that may be otherwise indistinguishable.
Optionally, you can enforce additional behaviors on reacting atoms.
For example, it may be beneficial to force reacting atoms to remain at
a certain temperature. For this, you can use the internally-created
@ -610,7 +644,7 @@ Default
"""""""
The option defaults are stabilization = no, prob = 1.0, stabilize_steps = 60,
reset_mol_ids = yes, custom_charges = no, molecule = off
reset_mol_ids = yes, custom_charges = no, molecule = off, modify_create = no
----------

66
examples/USER/reaction/create_atoms_polystyrene/grow_styrene.map Normal file
View File

@ -0,0 +1,66 @@
map file: styrene growth
1 edgeIDs
30 equivalences
16 createIDs
InitiatorIDs
4
13
EdgeIDs
30
CreateIDs
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
Equivalences
1 45
2 46
3 44
4 43
5 42
6 41
7 40
8 39
9 38
10 37
11 36
12 35
13 34
14 33
15 32
16 31
17 17
18 18
19 19
20 20
21 21
22 22
23 23
24 24
25 25
26 26
27 27
28 28
29 29
30 30

456
examples/USER/reaction/create_atoms_polystyrene/grow_styrene_post.data_template Executable file
View File

@ -0,0 +1,456 @@
molecule template: end of chain plus polymerized styrene
46 atoms
48 bonds
81 angles
121 dihedrals
35 impropers
1 fragments
Fragments
create_fit 34 44
Types
1 1
2 2
3 1
4 5
5 1
6 2
7 1
8 2
9 1
10 2
11 1
12 2
13 2
14 6
15 2
16 2
17 1
18 2
19 1
20 5
21 1
22 2
23 1
24 2
25 1
26 2
27 1
28 2
29 2
30 6
31 1
32 2
33 1
34 5
35 1
36 2
37 1
38 2
39 1
40 2
41 1
42 2
43 2
44 6
45 2
46 2
Charges
1 -0.129000
2 0.123700
3 0.026600
4 -0.018200
5 -0.129000
6 0.123700
7 -0.173400
8 0.140300
9 -0.113400
10 0.128800
11 -0.173400
12 0.140300
13 0.051600
14 -0.069600
15 0.035400
16 0.035400
17 -0.129000
18 0.123700
19 0.026600
20 -0.018200
21 -0.129000
22 0.123700
23 -0.173400
24 0.140300
25 -0.113400
26 0.128800
27 -0.173400
28 0.140300
29 0.051600
30 -0.069600
31 -0.129000
32 0.123700
33 0.026600
34 -0.018200
35 -0.129000
36 0.123700
37 -0.173400
38 0.140300
39 -0.113400
40 0.128800
41 -0.173400
42 0.140300
43 0.051600
44 -0.069600
45 0.035400
46 0.035400
Coords
1 24.130699 1.043900 -1.309300
2 25.062700 1.582900 -1.309300
3 22.900700 1.753900 -1.309300
4 22.900700 3.253900 -1.309300
5 21.670700 1.043900 -1.309300
6 20.738701 1.582900 -1.309300
7 21.670700 -0.376100 -1.309300
8 20.738701 -0.915100 -1.309300
9 22.900700 -1.086100 -1.309300
10 22.900700 -2.163100 -1.309300
11 24.130699 -0.376100 -1.309300
12 25.062700 -0.915100 -1.309300
13 23.766701 3.658900 -0.952300
14 21.622700 3.802900 -1.871300
15 21.672701 4.544900 -1.970300
16 20.979700 2.979900 -2.165300
17 13.465800 0.682500 -1.658900
18 14.397800 1.221500 -1.658900
19 12.235800 1.392500 -1.658900
20 12.235800 2.892500 -1.658900
21 11.005800 0.682500 -1.658900
22 10.073800 1.221500 -1.658900
23 11.005800 -0.737500 -1.658900
24 10.073800 -1.276500 -1.658900
25 12.235800 -1.447500 -1.658900
26 12.235800 -2.524500 -1.658900
27 13.465800 -0.737500 -1.658900
28 14.397800 -1.276500 -1.658900
29 13.101800 3.297500 -1.301900
30 10.957800 3.441500 -2.220900
31 18.663500 0.855500 -1.372100
32 19.595501 1.394500 -1.372100
33 17.433500 1.565500 -1.372100
34 17.433500 3.065500 -1.372100
35 16.203501 0.855500 -1.372100
36 15.271500 1.394500 -1.372100
37 16.203501 -0.564500 -1.372100
38 15.271500 -1.103500 -1.372100
39 17.433500 -1.274500 -1.372100
40 17.433500 -2.351500 -1.372100
41 18.663500 -0.564500 -1.372100
42 19.595501 -1.103500 -1.372100
43 18.299500 3.470500 -1.015100
44 16.155500 3.614500 -1.934100
45 16.205500 4.356500 -2.033100
46 15.512500 2.791500 -2.228100
Bonds
1 1 1 2
2 2 1 3
3 2 1 11
4 11 3 4
5 2 3 5
6 12 13 4
7 13 4 14
8 1 5 6
9 2 5 7
10 1 7 8
11 2 7 9
12 1 9 10
13 2 9 11
14 1 11 12
15 10 15 14
16 10 16 14
17 9 14 34
18 1 17 18
19 2 17 19
20 2 17 27
21 7 19 20
22 2 19 21
23 8 29 20
24 9 30 20
25 9 44 20
26 1 21 22
27 2 21 23
28 1 23 24
29 2 23 25
30 1 25 26
31 2 25 27
32 1 27 28
33 1 31 32
34 2 31 33
35 2 31 41
36 7 33 34
37 2 33 35
38 8 43 34
39 9 44 34
40 1 35 36
41 2 35 37
42 1 37 38
43 2 37 39
44 1 39 40
45 2 39 41
46 1 41 42
47 10 45 44
48 10 46 44
Angles
1 1 3 1 2
2 1 11 1 2
3 2 3 1 11
4 17 1 3 4
5 2 1 3 5
6 17 5 3 4
7 18 3 4 13
8 19 3 4 14
9 20 13 4 14
10 1 3 5 6
11 2 3 5 7
12 1 7 5 6
13 1 5 7 8
14 2 5 7 9
15 1 9 7 8
16 1 7 9 10
17 2 7 9 11
18 1 11 9 10
19 2 1 11 9
20 1 1 11 12
21 1 9 11 12
22 21 15 14 4
23 21 16 14 4
24 22 4 14 34
25 15 15 14 16
26 14 15 14 34
27 14 16 14 34
28 1 19 17 18
29 1 27 17 18
30 2 19 17 27
31 9 17 19 20
32 2 17 19 21
33 9 21 19 20
34 10 19 20 29
35 11 19 20 30
36 11 19 20 44
37 12 29 20 30
38 12 29 20 44
39 13 30 20 44
40 1 19 21 22
41 2 19 21 23
42 1 23 21 22
43 1 21 23 24
44 2 21 23 25
45 1 25 23 24
46 1 23 25 26
47 2 23 25 27
48 1 27 25 26
49 2 17 27 25
50 1 17 27 28
51 1 25 27 28
52 1 33 31 32
53 1 41 31 32
54 2 33 31 41
55 9 31 33 34
56 2 31 33 35
57 9 35 33 34
58 11 33 34 14
59 12 43 34 14
60 13 14 34 44
61 10 33 34 43
62 11 33 34 44
63 12 43 34 44
64 1 33 35 36
65 2 33 35 37
66 1 37 35 36
67 1 35 37 38
68 2 35 37 39
69 1 39 37 38
70 1 37 39 40
71 2 37 39 41
72 1 41 39 40
73 2 31 41 39
74 1 31 41 42
75 1 39 41 42
76 16 20 44 34
77 14 45 44 20
78 14 46 44 20
79 14 45 44 34
80 14 46 44 34
81 15 45 44 46
Dihedrals
1 20 2 1 3 4
2 2 5 3 1 2
3 21 11 1 3 4
4 4 11 1 3 5
5 2 9 11 1 2
6 5 2 1 11 12
7 4 3 1 11 9
8 2 3 1 11 12
9 22 1 3 4 13
10 23 1 3 4 14
11 22 5 3 4 13
12 23 5 3 4 14
13 2 1 3 5 6
14 4 1 3 5 7
15 20 6 5 3 4
16 21 7 5 3 4
17 24 3 4 14 15
18 24 3 4 14 16
19 25 3 4 14 34
20 26 13 4 14 15
21 26 13 4 14 16
22 27 13 4 14 34
23 2 3 5 7 8
24 4 3 5 7 9
25 5 6 5 7 8
26 2 9 7 5 6
27 2 5 7 9 10
28 4 5 7 9 11
29 5 8 7 9 10
30 2 11 9 7 8
31 4 7 9 11 1
32 2 7 9 11 12
33 2 1 11 9 10
34 5 10 9 11 12
35 28 4 14 34 33
36 29 4 14 34 43
37 30 4 14 34 44
38 31 15 14 34 33
39 32 15 14 34 43
40 33 15 14 34 44
41 31 16 14 34 33
42 32 16 14 34 43
43 33 16 14 34 44
44 10 18 17 19 20
45 2 21 19 17 18
46 11 27 17 19 20
47 4 27 17 19 21
48 2 25 27 17 18
49 5 18 17 27 28
50 4 19 17 27 25
51 2 19 17 27 28
52 12 17 19 20 29
53 13 17 19 20 30
54 13 17 19 20 44
55 12 21 19 20 29
56 13 21 19 20 30
57 13 21 19 20 44
58 2 17 19 21 22
59 4 17 19 21 23
60 10 22 21 19 20
61 11 23 21 19 20
62 34 34 44 20 19
63 31 45 44 20 19
64 31 46 44 20 19
65 35 34 44 20 29
66 32 45 44 20 29
67 32 46 44 20 29
68 36 34 44 20 30
69 33 45 44 20 30
70 33 46 44 20 30
71 2 19 21 23 24
72 4 19 21 23 25
73 5 22 21 23 24
74 2 25 23 21 22
75 2 21 23 25 26
76 4 21 23 25 27
77 5 24 23 25 26
78 2 27 25 23 24
79 4 23 25 27 17
80 2 23 25 27 28
81 2 17 27 25 26
82 5 26 25 27 28
83 10 32 31 33 34
84 2 35 33 31 32
85 11 41 31 33 34
86 4 41 31 33 35
87 2 39 41 31 32
88 5 32 31 41 42
89 4 33 31 41 39
90 2 33 31 41 42
91 13 31 33 34 14
92 12 31 33 34 43
93 13 31 33 34 44
94 13 35 33 34 14
95 12 35 33 34 43
96 13 35 33 34 44
97 2 31 33 35 36
98 4 31 33 35 37
99 10 36 35 33 34
100 11 37 35 33 34
101 36 20 44 34 14
102 33 45 44 34 14
103 33 46 44 34 14
104 34 20 44 34 33
105 31 45 44 34 33
106 31 46 44 34 33
107 35 20 44 34 43
108 32 45 44 34 43
109 32 46 44 34 43
110 2 33 35 37 38
111 4 33 35 37 39
112 5 36 35 37 38
113 2 39 37 35 36
114 2 35 37 39 40
115 4 35 37 39 41
116 5 38 37 39 40
117 2 41 39 37 38
118 4 37 39 41 31
119 2 37 39 41 42
120 2 31 41 39 40
121 5 40 39 41 42
Impropers
1 1 3 1 11 2
2 8 1 3 5 4
3 9 3 4 13 14
4 1 3 5 7 6
5 1 5 7 9 8
6 1 7 9 11 10
7 1 1 11 9 12
8 1 19 17 27 18
9 5 17 19 21 20
10 1 19 21 23 22
11 1 21 23 25 24
12 1 23 25 27 26
13 1 17 27 25 28
14 1 33 31 41 32
15 5 31 33 35 34
16 1 33 35 37 36
17 1 35 37 39 38
18 1 37 39 41 40
19 1 31 41 39 42
20 1 15 14 16 4
21 1 15 14 4 34
22 1 16 14 4 34
23 1 15 14 16 34
24 1 19 20 29 30
25 1 19 20 29 44
26 1 19 20 30 44
27 1 29 20 30 44
28 1 33 34 43 14
29 1 33 34 14 44
30 1 43 34 14 44
31 1 33 34 43 44
32 1 45 44 34 20
33 1 46 44 34 20
34 1 45 44 46 20
35 1 45 44 46 34

294
examples/USER/reaction/create_atoms_polystyrene/grow_styrene_pre.data_template Normal file
View File

@ -0,0 +1,294 @@
molecule template: end of styrene chain
30 atoms
31 bonds
51 angles
73 dihedrals
21 impropers
Types
1 2
2 2
3 6
4 2
5 2
6 1
7 2
8 1
9 2
10 1
11 2
12 1
13 5
14 1
15 2
16 1
17 1
18 2
19 1
20 5
21 1
22 2
23 1
24 2
25 1
26 2
27 1
28 2
29 2
30 6
Coords
1 59.89981112372972 62.733697275315585 59.09884284578856
2 61.41970248324232 63.42116581894993 59.52874545893742
3 60.864754970096406 62.91724243011892 59.559720865992695
4 62.139819000186826 61.41011937002877 60.81065044071466
5 60.036455711425084 57.160029629288026 60.31958663310848
6 59.734195751174056 58.18706337912225 60.20562410798949
7 57.64574781117771 57.712432799329 59.860109977091554
8 58.37408644866664 58.50134169314242 59.94422053768215
9 56.94300092269842 60.093170109004795 59.5955638127831
10 57.974275786582744 59.85577775892068 59.793714995577716
11 58.63231375134033 61.922969938852454 59.79065033121885
12 58.934573711591355 60.89593618901822 59.904612856337835
13 61.30908151524225 61.68041745837013 60.28316188676589
14 60.29468229868386 60.58165855333751 60.16601625920239
15 61.725768540066994 58.98982945913568 60.51467315154424
16 60.69449367618267 59.2272218092198 60.31652196874961
17 56.90935800040509 62.609851248143706 59.150831390216375
18 57.940632148874506 62.37245957639904 59.3489824055682
19 56.509546622906285 63.96428799226142 59.00032568066915
20 57.52394583946467 65.06304689729403 59.11747130823266
21 55.14943732039887 64.27856630628159 58.738922110361806
22 54.84717807556275 65.30559937777636 58.62495975268562
23 54.18913939539026 63.23840787618404 58.62802424960169
24 53.15786524692084 63.4757995479287 58.42987323424986
25 54.58895077288906 61.88397113206633 58.77852995914891
26 53.86061213540014 61.09506223825291 58.69441939855832
27 55.94906007539648 61.56969281804616 59.039933529456256
28 56.2513193202326 60.54265974655139 59.15389588713244
29 58.35468332440925 64.79274880895268 59.64495986218142
30 57.07961929431883 66.29987186904283 58.394030287459465
Charges
1 0.0354
2 0.0354
3 -0.0696
4 0.0516
5 0.1403
6 -0.1734
7 0.1288
8 -0.1134
9 0.1403
10 -0.1734
11 0.1237
12 -0.129
13 -0.0182
14 0.0266
15 0.1237
16 -0.129
17 -0.129
18 0.1237
19 0.0266
20 -0.0182
21 -0.129
22 0.1237
23 -0.1734
24 0.1403
25 -0.1134
26 0.1288
27 -0.1734
28 0.1403
29 0.0516
30 -0.0696
Bonds
1 10 1 3
2 10 2 3
3 8 4 13
4 1 6 5
5 1 8 7
6 2 8 6
7 1 10 9
8 2 10 8
9 1 12 11
10 2 12 10
11 9 13 3
12 7 14 13
13 2 14 12
14 1 16 15
15 2 16 14
16 2 16 6
17 1 17 18
18 2 17 19
19 2 17 27
20 7 19 20
21 2 19 21
22 9 20 30
23 9 20 3
24 1 21 22
25 2 21 23
26 1 23 24
27 2 23 25
28 1 25 26
29 2 25 27
30 1 27 28
31 8 29 20
Angles
1 16 20 3 13
2 14 2 3 20
3 14 1 3 20
4 14 2 3 13
5 14 1 3 13
6 15 2 3 1
7 2 16 6 8
8 1 16 6 5
9 1 8 6 5
10 1 10 8 7
11 2 10 8 6
12 1 6 8 7
13 1 12 10 9
14 2 12 10 8
15 1 8 10 9
16 1 14 12 11
17 2 14 12 10
18 1 10 12 11
19 10 14 13 4
20 11 14 13 3
21 12 4 13 3
22 9 16 14 13
23 2 16 14 12
24 9 12 14 13
25 1 14 16 15
26 1 6 16 15
27 2 14 16 6
28 1 19 17 18
29 1 27 17 18
30 2 19 17 27
31 9 17 19 20
32 2 17 19 21
33 9 21 19 20
34 10 19 20 29
35 11 19 20 30
36 11 19 20 3
37 12 29 20 30
38 12 29 20 3
39 13 30 20 3
40 1 19 21 22
41 2 19 21 23
42 1 23 21 22
43 1 21 23 24
44 2 21 23 25
45 1 25 23 24
46 1 23 25 26
47 2 23 25 27
48 1 27 25 26
49 2 17 27 25
50 1 17 27 28
51 1 25 27 28
Dihedrals
1 2 8 6 16 15
2 2 16 6 8 7
3 2 6 8 10 9
4 4 10 8 6 16
5 2 10 8 6 5
6 5 7 8 6 5
7 2 8 10 12 11
8 2 12 10 8 7
9 4 12 10 8 6
10 5 9 10 8 7
11 10 11 12 14 13
12 11 10 12 14 13
13 2 14 12 10 9
14 4 14 12 10 8
15 5 11 12 10 9
16 17 14 13 3 20
17 14 14 13 3 2
18 14 14 13 3 1
19 18 4 13 3 20
20 15 4 13 3 2
21 15 4 13 3 1
22 2 12 14 16 15
23 12 16 14 13 4
24 13 16 14 13 3
25 12 12 14 13 4
26 13 12 14 13 3
27 2 16 14 12 11
28 4 16 14 12 10
29 10 15 16 14 13
30 11 6 16 14 13
31 4 6 16 14 12
32 5 15 16 6 5
33 4 14 16 6 8
34 2 14 16 6 5
35 10 18 17 19 20
36 11 27 17 19 20
37 4 27 17 19 21
38 5 18 17 27 28
39 4 19 17 27 25
40 2 19 17 27 28
41 2 21 19 17 18
42 12 17 19 20 29
43 13 17 19 20 30
44 13 17 19 20 3
45 12 21 19 20 29
46 13 21 19 20 30
47 13 21 19 20 3
48 2 17 19 21 22
49 4 17 19 21 23
50 17 19 20 3 13
51 14 19 20 3 2
52 14 19 20 3 1
53 18 29 20 3 13
54 15 29 20 3 2
55 15 29 20 3 1
56 19 30 20 3 13
57 16 30 20 3 2
58 16 30 20 3 1
59 10 22 21 19 20
60 11 23 21 19 20
61 2 19 21 23 24
62 4 19 21 23 25
63 5 22 21 23 24
64 2 25 23 21 22
65 2 21 23 25 26
66 4 21 23 25 27
67 5 24 23 25 26
68 2 27 25 23 24
69 4 23 25 27 17
70 2 23 25 27 28
71 5 26 25 27 28
72 2 25 27 17 18
73 2 17 27 25 26
Impropers
1 1 2 3 13 20
2 1 1 3 13 20
3 1 2 3 1 20
4 1 2 3 1 13
5 1 16 6 8 5
6 1 10 8 6 7
7 1 12 10 8 9
8 1 14 12 10 11
9 7 14 13 4 3
10 5 16 14 12 13
11 1 14 16 6 15
12 1 19 17 27 18
13 5 17 19 21 20
14 1 19 20 29 30
15 1 19 20 29 3
16 1 19 20 30 3
17 1 29 20 30 3
18 1 19 21 23 22
19 1 21 23 25 24
20 1 23 25 27 26
21 1 17 27 25 28

48
examples/USER/reaction/create_atoms_polystyrene/in.grow_styrene Executable file
View File

@ -0,0 +1,48 @@
# use bond/react 'create atoms' feature to add 30 new styrene monomers to chain
units real
boundary p p p
atom_style full
kspace_style pppm 1.0e-4
pair_style lj/class2/coul/long 8.5
angle_style class2
bond_style class2
dihedral_style class2
improper_style class2
variable T equal 530
read_data trimer.data &
extra/bond/per/atom 5 &
extra/angle/per/atom 15 &
extra/dihedral/per/atom 15 &
extra/improper/per/atom 25 &
extra/special/per/atom 25
molecule mol1 grow_styrene_pre.data_template
molecule mol2 grow_styrene_post.data_template
fix myrxns all bond/react stabilization yes statted_grp .03 &
react rxn1 all 1 0 3.0 mol1 mol2 grow_styrene.map &
modify_create fit create_fit overlap 2.0 &
stabilize_steps 100 max_rxn 30
fix 1 statted_grp_REACT nvt temp $T $T 100
fix 4 bond_react_MASTER_group temp/rescale 1 $T $T 1 1
thermo_style custom step temp press density f_myrxns[1]
thermo 100
run 8000
# write_data final.data nofix

196
examples/USER/reaction/create_atoms_polystyrene/log.24Dec20.grow_styrene.g++.1 Normal file
View File

@ -0,0 +1,196 @@
LAMMPS (24 Dec 2020)
Reading data file ...
orthogonal box = (50.000000 50.000000 50.000000) to (250.00000 250.00000 250.00000)
1 by 1 by 1 MPI processor grid
reading atoms ...
48 atoms
reading velocities ...
48 velocities
scanning bonds ...
8 = max bonds/atom
scanning angles ...
21 = max angles/atom
scanning dihedrals ...
33 = max dihedrals/atom
scanning impropers ...
29 = max impropers/atom
reading bonds ...
50 bonds
reading angles ...
84 angles
reading dihedrals ...
127 dihedrals
reading impropers ...
36 impropers
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
8 = max # of 1-3 neighbors
17 = max # of 1-4 neighbors
46 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.077 seconds
Read molecule template mol1:
1 molecules
30 atoms with max type 6
31 bonds with max type 10
51 angles with max type 16
73 dihedrals with max type 19
21 impropers with max type 7
Read molecule template mol2:
1 molecules
46 atoms with max type 6
48 bonds with max type 13
81 angles with max type 22
121 dihedrals with max type 36
35 impropers with max type 9
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined
PPPM initialization ...
WARNING: System is not charge neutral, net charge = -0.00060000000 (../kspace.cpp:324)
using 12-bit tables for long-range coulomb (../kspace.cpp:339)
G vector (1/distance) = 0.20144813
grid = 45 45 45
stencil order = 5
estimated absolute RMS force accuracy = 0.00053712952
estimated relative force accuracy = 1.6175496e-06
using double precision KISS FFT
3d grid and FFT values/proc = 125000 91125
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 39 39 39
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair lj/class2/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix bond/react, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 1
Per MPI rank memory allocation (min/avg/max) = 48.02 | 48.02 | 48.02 Mbytes
Step Temp Press Density f_myrxns[1]
0 496.23742 0.9983211 6.4856516e-05 0
100 534.05394 -0.76952227 6.4856516e-05 0
200 552.2225 -0.55375493 6.4856516e-05 0
300 857.52834 -0.4272061 8.6475354e-05 1
400 714.10681 1.5004615 8.6475354e-05 1
500 678.19171 0.21965471 8.6475354e-05 1
600 572.3234 0.87879933 8.6475354e-05 1
700 996.17398 -0.24269717 0.00010809419 2
800 904.50395 1.3662054 0.00010809419 2
900 1097.1568 -2.2909907 0.00012971303 3
1000 954.08892 1.7705672 0.00012971303 3
1100 1102.0377 -1.7018446 0.00015133187 4
1200 1239.785 -0.30442903 0.00015133187 4
1300 1388.4127 1.3301175 0.00017295071 5
1400 1559.3853 1.6709729 0.00017295071 5
1500 1471.8623 0.8268427 0.00017295071 5
1600 1543.6793 2.1987908 0.00019456955 6
1700 1694.5595 0.48852817 0.00019456955 6
1800 1632.7737 -1.4617692 0.00021618839 7
1900 1922.6502 1.1664257 0.00021618839 7
2000 2223.503 -0.95799878 0.00023780722 8
2100 2142.6035 0.88444463 0.00025942606 9
2200 2298.8636 3.4239313 0.00025942606 9
2300 2252.4355 0.82167302 0.00025942606 9
2400 2321.0788 1.7499714 0.00025942606 9
2500 2095.6715 0.55288444 0.00025942606 9
2600 2136.0316 -3.833114 0.00025942606 9
2700 2466.3134 -2.2519511 0.00025942606 9
2800 2294.3454 1.0637304 0.00025942606 9
2900 2340.3891 1.3997049 0.0002810449 10
3000 2272.0013 -0.27591886 0.0002810449 10
3100 2333.9696 -0.11772138 0.0002810449 10
3200 2409.0946 -1.025473 0.0002810449 10
3300 2148.023 1.6752329 0.0002810449 10
3400 2267.636 -0.45297583 0.0002810449 10
3500 2457.622 0.35627297 0.0002810449 10
3600 2288.008 -15.516626 0.00030266374 11
3700 2458.2681 1.4571773 0.00030266374 11
3800 2566.7623 -29.140553 0.00032428258 12
3900 2839.4062 0.64583638 0.00032428258 12
4000 2893.9852 -52.954497 0.00034590142 13
4100 3021.3611 -65.03731 0.00036752025 14
4200 3002.7136 1.5750081 0.00036752025 14
4300 3218.6248 -120.74039 0.00038913909 15
4400 3345.1482 -0.96545269 0.00038913909 15
4500 3603.2429 1.2438833 0.00038913909 15
4600 3129.8814 -249.91806 0.00041075793 16
4700 3769.052 -289.24351 0.00043237677 17
4800 3560.4714 -3.1655406 0.00043237677 17
4900 3452.2717 -2.1270765 0.00043237677 17
5000 3594.3247 -523.48506 0.00045399561 18
5100 3578.4199 1.0009097 0.00045399561 18
5200 3822.1566 1.0526914 0.00047561445 19
5300 3901.8883 -0.14607602 0.00047561445 19
5400 4059.3644 -1.7789927 0.00049723329 20
5500 4163.6847 1.0240127 0.00049723329 20
5600 4109.1649 0.80199787 0.00049723329 20
5700 4391.2091 2.8730036 0.00049723329 20
5800 4279.6579 -0.36499822 0.00051885212 21
5900 4296.2695 -1.3064528 0.00051885212 21
6000 4065.3758 -2.0483224 0.00051885212 21
6100 4772.5362 -2.6814694 0.00054047096 22
6200 4627.029 2.999215 0.0005620898 23
6300 5120.7881 0.65372968 0.00058370864 24
6400 4588.9559 3.7570705 0.00058370864 24
6500 5008.7814 2.3595833 0.00060532748 25
6600 5195.0053 1.4641612 0.00060532748 25
6700 5622.293 -0.33396047 0.00062694632 26
6800 5515.1957 -4.234874 0.00062694632 26
6900 5156.7455 0.40171954 0.00064856516 27
7000 5120.1639 -1.6065245 0.00064856516 27
7100 5650.0327 0.94436323 0.00067018399 28
7200 5985.1115 -3.8940347 0.00069180283 29
7300 5983.197 0.5293568 0.00069180283 29
7400 6001.1559 -0.13712834 0.00071342167 30
7500 5889.2134 0.17230892 0.00071342167 30
7600 5797.31 2.0920058 0.00071342167 30
7700 5865.2783 -0.18556395 0.00071342167 30
7800 6207.0659 -5.6237083 0.00071342167 30
7900 5627.5108 -2.3718942 0.00071342167 30
8000 5823.9502 -0.85418578 0.00071342167 30
Loop time of 184.87 on 1 procs for 8000 steps with 528 atoms
Performance: 3.739 ns/day, 6.419 hours/ns, 43.274 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.3043 | 3.3043 | 3.3043 | 0.0 | 1.79
Bond | 8.0003 | 8.0003 | 8.0003 | 0.0 | 4.33
Kspace | 168.33 | 168.33 | 168.33 | 0.0 | 91.05
Neigh | 4.6322 | 4.6322 | 4.6322 | 0.0 | 2.51
Comm | 0.077927 | 0.077927 | 0.077927 | 0.0 | 0.04
Output | 0.0020548 | 0.0020548 | 0.0020548 | 0.0 | 0.00
Modify | 0.5005 | 0.5005 | 0.5005 | 0.0 | 0.27
Other | | 0.02483 | | | 0.01
Nlocal: 528.000 ave 528 max 528 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 341.000 ave 341 max 341 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 35111.0 ave 35111 max 35111 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 35111
Ave neighs/atom = 66.498106
Ave special neighs/atom = 11.409091
Neighbor list builds = 8000
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:03:05

196
examples/USER/reaction/create_atoms_polystyrene/log.24Dec20.grow_styrene.g++.4 Normal file
View File

@ -0,0 +1,196 @@
LAMMPS (24 Dec 2020)
Reading data file ...
orthogonal box = (50.000000 50.000000 50.000000) to (250.00000 250.00000 250.00000)
1 by 2 by 2 MPI processor grid
reading atoms ...
48 atoms
reading velocities ...
48 velocities
scanning bonds ...
8 = max bonds/atom
scanning angles ...
21 = max angles/atom
scanning dihedrals ...
33 = max dihedrals/atom
scanning impropers ...
29 = max impropers/atom
reading bonds ...
50 bonds
reading angles ...
84 angles
reading dihedrals ...
127 dihedrals
reading impropers ...
36 impropers
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
8 = max # of 1-3 neighbors
17 = max # of 1-4 neighbors
46 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.007 seconds
Read molecule template mol1:
1 molecules
30 atoms with max type 6
31 bonds with max type 10
51 angles with max type 16
73 dihedrals with max type 19
21 impropers with max type 7
Read molecule template mol2:
1 molecules
46 atoms with max type 6
48 bonds with max type 13
81 angles with max type 22
121 dihedrals with max type 36
35 impropers with max type 9
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined
PPPM initialization ...
WARNING: System is not charge neutral, net charge = -0.00060000000 (../kspace.cpp:324)
using 12-bit tables for long-range coulomb (../kspace.cpp:339)
G vector (1/distance) = 0.20144813
grid = 45 45 45
stencil order = 5
estimated absolute RMS force accuracy = 0.00053712952
estimated relative force accuracy = 1.6175496e-06
using double precision KISS FFT
3d grid and FFT values/proc = 39200 24300
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 39 39 39
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair lj/class2/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix bond/react, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 1
Per MPI rank memory allocation (min/avg/max) = 38.70 | 38.92 | 39.43 Mbytes
Step Temp Press Density f_myrxns[1]
0 496.23742 0.9983211 6.4856516e-05 0
100 534.05394 -0.76952227 6.4856516e-05 0
200 552.2225 -0.55375493 6.4856516e-05 0
300 857.52834 -0.4272061 8.6475354e-05 1
400 714.10681 1.5004615 8.6475354e-05 1
500 678.19171 0.21965471 8.6475354e-05 1
600 572.3234 0.87879933 8.6475354e-05 1
700 996.17398 -0.24269717 0.00010809419 2
800 904.50395 1.3662054 0.00010809419 2
900 1097.1568 -2.2909907 0.00012971303 3
1000 954.08892 1.7705672 0.00012971303 3
1100 1102.0377 -1.7018446 0.00015133187 4
1200 1239.785 -0.30442903 0.00015133187 4
1300 1388.4127 1.3301175 0.00017295071 5
1400 1559.3853 1.6709729 0.00017295071 5
1500 1471.8623 0.8268427 0.00017295071 5
1600 1543.6793 2.1987908 0.00019456955 6
1700 1694.5595 0.48852817 0.00019456955 6
1800 1632.7737 -1.4617692 0.00021618839 7
1900 1922.6502 1.1664257 0.00021618839 7
2000 2223.503 -0.95799878 0.00023780722 8
2100 2142.6035 0.88444463 0.00025942606 9
2200 2298.8636 3.4239313 0.00025942606 9
2300 2252.4355 0.82167302 0.00025942606 9
2400 2321.0788 1.7499714 0.00025942606 9
2500 2095.6715 0.55288444 0.00025942606 9
2600 2136.0316 -3.833114 0.00025942606 9
2700 2466.3134 -2.2519511 0.00025942606 9
2800 2294.3454 1.0637304 0.00025942606 9
2900 2340.3891 1.3997049 0.0002810449 10
3000 2272.0013 -0.27591886 0.0002810449 10
3100 2333.9696 -0.11772138 0.0002810449 10
3200 2409.0946 -1.025473 0.0002810449 10
3300 2148.023 1.6752329 0.0002810449 10
3400 2267.636 -0.45297583 0.0002810449 10
3500 2457.622 0.35627297 0.0002810449 10
3600 2288.008 -15.516626 0.00030266374 11
3700 2458.2681 1.4571773 0.00030266374 11
3800 2566.7623 -29.140553 0.00032428258 12
3900 2839.4062 0.64583638 0.00032428258 12
4000 2893.2204 -53.187892 0.00034590142 13
4100 3024.6375 -65.068146 0.00036752025 14
4200 3004.6784 1.4155214 0.00036752025 14
4300 3033.1895 1.8572273 0.00036752025 14
4400 3157.2542 -0.92462977 0.00036752025 14
4500 3557.7137 -194.46498 0.00038913909 15
4600 3096.485 -1.830492 0.00038913909 15
4700 3488.088 -286.81055 0.00041075793 16
4800 3390.5493 -372.77818 0.00043237677 17
4900 3773.7226 -446.58574 0.00045399561 18
5000 3703.0159 -0.81188551 0.00045399561 18
5100 4051.3067 1.2567439 0.00045399561 18
5200 3813.3682 0.92945737 0.00047561445 19
5300 4036.0078 -2.5336258 0.00049723329 20
5400 4219.803 -0.96928261 0.00049723329 20
5500 4433.7447 -0.026762463 0.00051885212 21
5600 4477.4505 -1.417316 0.00054047096 22
5700 4500.0306 -1.0551443 0.00054047096 22
5800 4600.3507 -4.9580056 0.00054047096 22
5900 4765.4978 -2.2546941 0.0005620898 23
6000 5442.6193 0.91161284 0.00058370864 24
6100 5086.8047 -0.9875332 0.00060532748 25
6200 5485.3437 -2.8296626 0.00062694632 26
6300 4988.0396 -0.15179023 0.00064856516 27
6400 5597.3703 4.2941885 0.00067018399 28
6500 5677.0263 -2.8611595 0.00069180283 29
6600 6058.0009 1.4111778 0.00071342167 30
6700 5859.0817 -2.5782466 0.00071342167 30
6800 5879.3941 -4.5681807 0.00071342167 30
6900 6398.288 2.5259412 0.00071342167 30
7000 6250.1096 -2.6049627 0.00071342167 30
7100 5849.651 -0.44062578 0.00071342167 30
7200 5778.6532 -0.27299118 0.00071342167 30
7300 5977.6661 4.2483639 0.00071342167 30
7400 5862.4231 1.0289519 0.00071342167 30
7500 6482.376 7.5412373 0.00071342167 30
7600 5810.4325 1.0343075 0.00071342167 30
7700 5916.7304 2.304302 0.00071342167 30
7800 5869.9504 -0.5946555 0.00071342167 30
7900 5804.0522 -4.1207689 0.00071342167 30
8000 6077.1704 0.52211243 0.00071342167 30
Loop time of 60.5603 on 4 procs for 8000 steps with 528 atoms
Performance: 11.413 ns/day, 2.103 hours/ns, 132.100 timesteps/s
99.9% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0041695 | 0.90113 | 2.3423 | 102.8 | 1.49
Bond | 0.011606 | 2.1188 | 5.8107 | 163.9 | 3.50
Kspace | 47.987 | 52.817 | 55.679 | 43.7 | 87.21
Neigh | 3.5961 | 3.6262 | 3.6496 | 1.2 | 5.99
Comm | 0.11097 | 0.16569 | 0.26369 | 15.3 | 0.27
Output | 0.0020366 | 0.0023427 | 0.0032469 | 1.1 | 0.00
Modify | 0.62302 | 0.91659 | 1.1227 | 21.5 | 1.51
Other | | 0.0126 | | | 0.02
Nlocal: 132.000 ave 295 max 0 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Nghost: 133.000 ave 349 max 0 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Neighs: 8383.50 ave 20143 max 0 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Total # of neighbors = 33534
Ave neighs/atom = 63.511364
Ave special neighs/atom = 11.409091
Neighbor list builds = 8000
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:01:00

796
examples/USER/reaction/create_atoms_polystyrene/trimer.data Normal file
View File

@ -0,0 +1,796 @@
polystyrene trimer
48 atoms
7 atom types
50 bonds
13 bond types
84 angles
22 angle types
127 dihedrals
36 dihedral types
36 impropers
9 improper types
50 250 xlo xhi
50 250 ylo yhi
50 250 zlo zhi
Masses
1 12.0112
2 1.00797
3 12.0112
4 12.0112
5 12.0112
6 12.0112
7 12.0112
Pair Coeffs # lj/class2/coul/long
1 0.064 4.01
2 0.02 2.7
3 0.064 4.01
4 0.064 3.9
5 0.054 4.01
6 0.054 4.01
7 0.054 4.01
Bond Coeffs # class2
1 1.0982 372.825 -803.453 894.317
2 1.417 470.836 -627.618 1327.63
3 1.501 321.902 -521.821 572.163
4 1.0883 365.768 -725.54 781.662
5 1.34 543.99 -1238.2 1644.03
6 1.0883 365.768 -725.54 781.662
7 1.501 321.902 -521.821 572.163
8 1.101 345 -691.89 844.6
9 1.53 299.67 -501.77 679.81
10 1.101 345 -691.89 844.6
11 1.501 321.902 -521.821 572.163
12 1.101 345 -691.89 844.6
13 1.53 299.67 -501.77 679.81
Angle Coeffs # class2
1 117.94 35.1558 -12.4682 0
2 118.9 61.0226 -34.9931 0
3 120.05 44.7148 -22.7352 0
4 111 44.3234 -9.4454 0
5 108.4 43.9594 -8.3924 -9.3379
6 124.88 35.2766 -17.774 -1.6215
7 124.88 35.2766 -17.774 -1.6215
8 115.49 29.6363 -12.4853 -6.2218
9 120.05 44.7148 -22.7352 0
10 111 44.3234 -9.4454 0
11 108.4 43.9594 -8.3924 -9.3379
12 110.77 41.453 -10.604 5.129
13 112.67 39.516 -7.443 -9.5583
14 110.77 41.453 -10.604 5.129
15 107.66 39.641 -12.921 -2.4318
16 112.67 39.516 -7.443 -9.5583
17 120.05 44.7148 -22.7352 0
18 111 44.3234 -9.4454 0
19 108.4 43.9594 -8.3924 -9.3379
20 110.77 41.453 -10.604 5.129
21 110.77 41.453 -10.604 5.129
22 112.67 39.516 -7.443 -9.5583
BondBond Coeffs
1 1.0795 1.417 1.0982
2 68.2856 1.417 1.417
3 12.0676 1.417 1.501
4 2.9168 1.501 1.0883
5 0 1.501 1.34
6 10.1047 1.0883 1.34
7 10.1047 1.0883 1.34
8 4.8506 1.0883 1.0883
9 12.0676 1.417 1.501
10 2.9168 1.501 1.101
11 0 1.501 1.53
12 3.3872 1.101 1.53
13 0 1.53 1.53
14 3.3872 1.101 1.53
15 5.3316 1.101 1.101
16 0 1.53 1.53
17 12.0676 1.417 1.501
18 2.9168 1.501 1.101
19 0 1.501 1.53
20 3.3872 1.101 1.53
21 3.3872 1.101 1.53
22 0 1.53 1.53
BondAngle Coeffs
1 20.0033 24.2183 1.417 1.0982
2 28.8708 28.8708 1.417 1.417
3 31.0771 47.0579 1.417 1.501
4 26.4608 11.7717 1.501 1.0883
5 0 0 1.501 1.34
6 19.0592 23.3588 1.0883 1.34
7 19.0592 23.3588 1.0883 1.34
8 17.9795 17.9795 1.0883 1.0883
9 31.0771 47.0579 1.417 1.501
10 26.4608 11.7717 1.501 1.101
11 0 0 1.501 1.53
12 11.421 20.754 1.101 1.53
13 8.016 8.016 1.53 1.53
14 11.421 20.754 1.101 1.53
15 18.103 18.103 1.101 1.101
16 8.016 8.016 1.53 1.53
17 31.0771 47.0579 1.417 1.501
18 26.4608 11.7717 1.501 1.101
19 0 0 1.501 1.53
20 11.421 20.754 1.101 1.53
21 11.421 20.754 1.101 1.53
22 8.016 8.016 1.53 1.53
Dihedral Coeffs # class2
1 0 0 1.559 0 0 0
2 0 0 3.9661 0 0 0
3 0 0 4.4072 0 0 0
4 8.3667 0 1.1932 0 0 0
5 0 0 1.8769 0 0 0
6 0 0 0 0 0 0
7 0 0 0 0 0 0
8 0 0 0 0 0 0
9 0 0 4.8974 0 0 0
10 0 0 1.559 0 0 0
11 0 0 4.4072 0 0 0
12 -0.2801 0 -0.0678 0 -0.0122 0
13 -0.2802 0 -0.0678 0 -0.0122 0
14 -0.0228 0 0.028 0 -0.1863 0
15 -0.1432 0 0.0617 0 -0.1083 0
16 0 0 0.0316 0 -0.1681 0
17 0 0 0 0 0 0
18 0 0 0.0316 0 -0.1681 0
19 0 0 0.0514 0 -0.143 0
20 0 0 1.559 0 0 0
21 0 0 4.4072 0 0 0
22 -0.2801 0 -0.0678 0 -0.0122 0
23 -0.2802 0 -0.0678 0 -0.0122 0
24 -0.0228 0 0.028 0 -0.1863 0
25 0 0 0 0 0 0
26 -0.1432 0 0.0617 0 -0.1083 0
27 0 0 0.0316 0 -0.1681 0
28 0 0 0 0 0 0
29 0 0 0.0316 0 -0.1681 0
30 0 0 0.0514 0 -0.143 0
31 -0.0228 0 0.028 0 -0.1863 0
32 -0.1432 0 0.0617 0 -0.1083 0
33 0 0 0.0316 0 -0.1681 0
34 0 0 0 0 0 0
35 0 0 0.0316 0 -0.1681 0
36 0 0 0.0514 0 -0.143 0
AngleAngleTorsion Coeffs
1 4.4444 117.94 120.05
2 -4.8141 118.9 117.94
3 -14.4097 118.9 120.05
4 0 118.9 118.9
5 0.3598 117.94 117.94
6 0 120.05 111
7 0 120.05 108.4
8 0 108.4 124.88
9 -7.0058 124.88 124.88
10 4.4444 117.94 120.05
11 -14.4097 118.9 120.05
12 -5.8888 120.05 111
13 0 120.05 108.4
14 0 108.4 110.77
15 -12.564 110.77 110.77
16 -16.164 112.67 110.77
17 0 108.4 112.67
18 -16.164 110.77 112.67
19 -22.045 112.67 112.67
20 4.4444 117.94 120.05
21 -14.4097 118.9 120.05
22 -5.8888 120.05 111
23 0 120.05 108.4
24 0 108.4 110.77
25 0 108.4 112.67
26 -12.564 110.77 110.77
27 -16.164 110.77 112.67
28 0 112.67 108.4
29 -16.164 112.67 110.77
30 -22.045 112.67 112.67
31 0 110.77 108.4
32 -12.564 110.77 110.77
33 -16.164 110.77 112.67
34 0 112.67 108.4
35 -16.164 112.67 110.77
36 -22.045 112.67 112.67
EndBondTorsion Coeffs
1 0 -0.4879 0 0 -1.797 0 1.0982 1.501
2 0 -6.8958 0 0 -0.4669 0 1.417 1.0982
3 0 -0.6918 0 0 0.2421 0 1.417 1.501
4 -0.1185 6.3204 0 -0.1185 6.3204 0 1.417 1.417
5 0 -0.689 0 0 -0.689 0 1.0982 1.0982
6 0 0 0 0 0 0 1.417 1.0883
7 0 0 0 0 0 0 1.417 1.34
8 0 0 0 0 0 0 1.501 1.0883
9 0.7129 0.5161 0 0.7129 0.5161 0 1.0883 1.0883
10 0 -0.4879 0 0 -1.797 0 1.0982 1.501
11 0 -0.6918 0 0 0.2421 0 1.417 1.501
12 -0.5835 1.122 0.3978 1.3997 0.7756 0 1.417 1.101
13 0 0 0 0 0 0 1.417 1.53
14 0 0 0 0 0 0 1.501 1.101
15 0.213 0.312 0.0777 0.213 0.312 0.0777 1.101 1.101
16 0.2486 0.2422 -0.0925 0.0814 0.0591 0.2219 1.53 1.101
17 0 0 0 0 0 0 1.501 1.53
18 0.0814 0.0591 0.2219 0.2486 0.2422 -0.0925 1.101 1.53
19 -0.0732 0 0 -0.0732 0 0 1.53 1.53
20 0 -0.4879 0 0 -1.797 0 1.0982 1.501
21 0 -0.6918 0 0 0.2421 0 1.417 1.501
22 -0.5835 1.122 0.3978 1.3997 0.7756 0 1.417 1.101
23 0 0 0 0 0 0 1.417 1.53
24 0 0 0 0 0 0 1.501 1.101
25 0 0 0 0 0 0 1.501 1.53
26 0.213 0.312 0.0777 0.213 0.312 0.0777 1.101 1.101
27 0.0814 0.0591 0.2219 0.2486 0.2422 -0.0925 1.101 1.53
28 0 0 0 0 0 0 1.53 1.501
29 0.2486 0.2422 -0.0925 0.0814 0.0591 0.2219 1.53 1.101
30 -0.0732 0 0 -0.0732 0 0 1.53 1.53
31 0 0 0 0 0 0 1.101 1.501
32 0.213 0.312 0.0777 0.213 0.312 0.0777 1.101 1.101
33 0.0814 0.0591 0.2219 0.2486 0.2422 -0.0925 1.101 1.53
34 0 0 0 0 0 0 1.53 1.501
35 0.2486 0.2422 -0.0925 0.0814 0.0591 0.2219 1.53 1.101
36 -0.0732 0 0 -0.0732 0 0 1.53 1.53
MiddleBondTorsion Coeffs
1 0 3.9421 0 1.417
2 0 -1.1521 0 1.417
3 0 9.1792 0 1.417
4 27.5989 -2.312 0 1.417
5 0 4.8228 0 1.417
6 0 0 0 1.501
7 0 0 0 1.501
8 0 0 0 1.34
9 0.8558 6.3911 0 1.34
10 0 3.9421 0 1.417
11 0 9.1792 0 1.417
12 -5.5679 1.4083 0.301 1.501
13 0 0 0 1.501
14 0 0 0 1.53
15 -14.261 -0.5322 -0.4864 1.53
16 -14.879 -3.6581 -0.3138 1.53
17 0 0 0 1.53
18 -14.879 -3.6581 -0.3138 1.53
19 -17.787 -7.1877 0 1.53
20 0 3.9421 0 1.417
21 0 9.1792 0 1.417
22 -5.5679 1.4083 0.301 1.501
23 0 0 0 1.501
24 0 0 0 1.53
25 0 0 0 1.53
26 -14.261 -0.5322 -0.4864 1.53
27 -14.879 -3.6581 -0.3138 1.53
28 0 0 0 1.53
29 -14.879 -3.6581 -0.3138 1.53
30 -17.787 -7.1877 0 1.53
31 0 0 0 1.53
32 -14.261 -0.5322 -0.4864 1.53
33 -14.879 -3.6581 -0.3138 1.53
34 0 0 0 1.53
35 -14.879 -3.6581 -0.3138 1.53
36 -17.787 -7.1877 0 1.53
BondBond13 Coeffs
1 0.8743 1.0982 1.501
2 -6.2741 1.417 1.0982
3 2.5085 1.417 1.501
4 53 1.417 1.417
5 -1.7077 1.0982 1.0982
6 0 1.417 1.0883
7 0 1.417 1.34
8 0 1.501 1.0883
9 0 1.0883 1.0883
10 0.8743 1.0982 1.501
11 2.5085 1.417 1.501
12 -3.4826 1.417 1.101
13 0 1.417 1.53
14 0 1.501 1.101
15 0 1.101 1.101
16 0 1.53 1.101
17 0 1.501 1.53
18 0 1.101 1.53
19 0 1.53 1.53
20 0.8743 1.0982 1.501
21 2.5085 1.417 1.501
22 -3.4826 1.417 1.101
23 0 1.417 1.53
24 0 1.501 1.101
25 0 1.501 1.53
26 0 1.101 1.101
27 0 1.101 1.53
28 0 1.53 1.501
29 0 1.53 1.101
30 0 1.53 1.53
31 0 1.101 1.501
32 0 1.101 1.101
33 0 1.101 1.53
34 0 1.53 1.501
35 0 1.53 1.101
36 0 1.53 1.53
AngleTorsion Coeffs
1 0 3.4601 0 0 -0.1242 0 117.94 120.05
2 0 2.5014 0 0 2.7147 0 118.9 117.94
3 0 3.8987 0 0 -4.4683 0 118.9 120.05
4 1.9767 1.0239 0 1.9767 1.0239 0 118.9 118.9
5 0 2.4501 0 0 2.4501 0 117.94 117.94
6 0 0 0 0 0 0 120.05 111
7 0 0 0 0 0 0 120.05 108.4
8 0 0 0 0 0 0 108.4 124.88
9 -1.8911 3.254 0 -1.8911 3.254 0 124.88 124.88
10 0 3.4601 0 0 -0.1242 0 117.94 120.05
11 0 3.8987 0 0 -4.4683 0 118.9 120.05
12 0.2251 0.6548 0.1237 4.6266 0.1632 0.0461 120.05 111
13 0 0 0 0 0 0 120.05 108.4
14 0 0 0 0 0 0 108.4 110.77
15 -0.8085 0.5569 -0.2466 -0.8085 0.5569 -0.2466 110.77 110.77
16 -0.2454 0 -0.1136 0.3113 0.4516 -0.1988 112.67 110.77
17 0 0 0 0 0 0 108.4 112.67
18 0.3113 0.4516 -0.1988 -0.2454 0 -0.1136 110.77 112.67
19 0.3886 -0.3139 0.1389 0.3886 -0.3139 0.1389 112.67 112.67
20 0 3.4601 0 0 -0.1242 0 117.94 120.05
21 0 3.8987 0 0 -4.4683 0 118.9 120.05
22 0.2251 0.6548 0.1237 4.6266 0.1632 0.0461 120.05 111
23 0 0 0 0 0 0 120.05 108.4
24 0 0 0 0 0 0 108.4 110.77
25 0 0 0 0 0 0 108.4 112.67
26 -0.8085 0.5569 -0.2466 -0.8085 0.5569 -0.2466 110.77 110.77
27 0.3113 0.4516 -0.1988 -0.2454 0 -0.1136 110.77 112.67
28 0 0 0 0 0 0 112.67 108.4
29 -0.2454 0 -0.1136 0.3113 0.4516 -0.1988 112.67 110.77
30 0.3886 -0.3139 0.1389 0.3886 -0.3139 0.1389 112.67 112.67
31 0 0 0 0 0 0 110.77 108.4
32 -0.8085 0.5569 -0.2466 -0.8085 0.5569 -0.2466 110.77 110.77
33 0.3113 0.4516 -0.1988 -0.2454 0 -0.1136 110.77 112.67
34 0 0 0 0 0 0 112.67 108.4
35 -0.2454 0 -0.1136 0.3113 0.4516 -0.1988 112.67 110.77
36 0.3886 -0.3139 0.1389 0.3886 -0.3139 0.1389 112.67 112.67
Improper Coeffs # class2
1 4.8912 0
2 7.8153 0
3 0 0
4 2.8561 0
5 7.8153 0
6 0 0
7 0 0
8 7.8153 0
9 0 0
AngleAngle Coeffs
1 0 0 0 118.9 117.94 117.94
2 0 0 0 118.9 120.05 120.05
3 0 0 0 111 124.88 108.4
4 0 0 0 115.49 124.88 124.88
5 0 0 0 118.9 120.05 120.05
6 0 0 0 107.66 110.77 110.77
7 0 0 0 111 110.77 108.4
8 0 0 0 118.9 120.05 120.05
9 0 0 0 111 110.77 108.4
Atoms # full
44 1 2 3.5400000000000001e-02 6.1476397222913839e+01 8.2376490601205234e+01 6.0906939115836181e+01
45 1276 2 3.5400000000000001e-02 5.8398688202244472e+01 8.0172948526664996e+01 6.2115536813582672e+01
46 1276 6 -6.9599999999999995e-02 5.9489073989392523e+01 8.0264057167571636e+01 6.1984002598976552e+01
48 1276 2 3.5400000000000001e-02 5.9675170230342431e+01 8.0048052449390738e+01 6.0920159395372401e+01
47 1276 2 1.2370000000000000e-01 5.9297455513100488e+01 8.3187777608476154e+01 5.9645157256520122e+01
18 1 5 -1.8200000000000001e-02 6.2426251430535707e+01 8.2055473568260709e+01 6.2971661388612958e+01
19 1 6 -6.9599999999999995e-02 6.1399255844467369e+01 8.1794665295860213e+01 6.1821819828185660e+01
21 1 1 -1.2900000000000000e-01 6.4032918371445831e+01 8.0190179089286701e+01 6.3021564712316334e+01
22 1 1 2.6599999999999999e-02 6.3672975135915053e+01 8.1418558650051665e+01 6.2448012627881994e+01
23 1 2 3.5400000000000001e-02 6.1545198223694939e+01 8.0836309422842305e+01 6.1349823957467130e+01
27 1276 2 5.1600000000000000e-02 5.9809503696580933e+01 8.1831265916389881e+01 6.3253745193271065e+01
28 1276 5 -1.8200000000000001e-02 5.9900307947967441e+01 8.1677453781363639e+01 6.2190757403657820e+01
31 1276 2 1.2370000000000000e-01 5.8050043823867973e+01 8.2698312265456622e+01 6.3667111329534436e+01
38 1 2 1.2370000000000000e-01 6.3754126973935612e+01 7.9931147303963002e+01 6.4022259163067275e+01
20 1 2 1.2370000000000000e-01 6.4070158368422781e+01 8.2950071388392274e+01 6.1042631212883315e+01
24 1 1 -1.2900000000000000e-01 6.4337973861569580e+01 8.1916618276489871e+01 6.1387866780102470e+01
37 1 2 1.4030000000000001e-01 6.5360115866618415e+01 7.8586112104863830e+01 6.3004997314380716e+01
39 1 1 -1.7340000000000000e-01 6.5018338085325610e+01 7.9478260591306125e+01 6.2440745569712817e+01
40 1 1 -1.1340000000000000e-01 6.5628759887796605e+01 7.9941156332165264e+01 6.1248476296558067e+01
41 1 1 -1.7340000000000000e-01 6.5247995680260402e+01 8.1172439250598345e+01 6.0753045571239831e+01
42 1 2 1.2880000000000000e-01 6.6569600059599281e+01 7.9514748976494360e+01 6.0810611807135601e+01
43 1 2 1.4030000000000001e-01 6.5780165393063371e+01 8.1570974991007958e+01 5.9850915261812396e+01
9 1276 2 1.2880000000000000e-01 5.5651795605743445e+01 8.5074472139235127e+01 6.1094480497979262e+01
30 1276 2 1.4030000000000001e-01 5.6082982679196888e+01 8.3912863624076010e+01 6.3351889697403472e+01
33 1276 1 -1.7340000000000000e-01 5.6718133911388506e+01 8.3758479063002000e+01 6.2493293749545209e+01
34 1276 1 -1.1340000000000000e-01 5.6498352105218459e+01 8.4426576393179090e+01 6.1290147608586011e+01
6 3822 1 -1.7340000000000000e-01 6.3308103537340351e+01 8.7713509787622499e+01 6.4643082313868433e+01
7 3822 1 -1.2900000000000000e-01 6.3010291684764312e+01 8.6423650045069493e+01 6.4252844241495922e+01
8 3822 2 1.2370000000000000e-01 6.2089199187020355e+01 8.6309198636296912e+01 6.3711263099850854e+01
10 1276 2 1.4030000000000001e-01 5.7266131308654970e+01 8.4599328362003035e+01 5.9281511478144402e+01
11 3822 2 3.5400000000000001e-02 6.1694306618059791e+01 8.3823470438280594e+01 6.3778953909925114e+01
12 3822 5 -1.8200000000000001e-02 6.3814926998838651e+01 8.3900077798460728e+01 6.4108991789590448e+01
13 3822 6 -6.9599999999999995e-02 6.2604540882379787e+01 8.3491998603381077e+01 6.3249610918984622e+01
14 3822 2 1.2370000000000000e-01 6.5739253131027880e+01 8.4813736128157771e+01 6.5351692111169555e+01
15 3822 1 -1.2900000000000000e-01 6.5071144269009466e+01 8.5646783550482454e+01 6.5086813218945636e+01
16 3822 1 2.6599999999999999e-02 6.3957099792282079e+01 8.5375816595044753e+01 6.4385073943729708e+01
17 1 2 5.1600000000000000e-02 6.2256484483973310e+01 8.1576962161157596e+01 6.3963984654065122e+01
26 3822 2 5.1600000000000000e-02 6.4196825763126355e+01 8.3291442832977836e+01 6.4907094488854057e+01
29 1276 1 2.6599999999999999e-02 5.8784742332505303e+01 8.2766055380197670e+01 6.1667239692876961e+01
32 1276 1 -1.2900000000000000e-01 5.7836199787435064e+01 8.3005060229118428e+01 6.2669788306756018e+01
35 1276 1 -1.2900000000000000e-01 5.8572661840325132e+01 8.3404075689965083e+01 6.0443288532625175e+01
36 1276 1 -1.7340000000000000e-01 5.7380616699226330e+01 8.4134680429976896e+01 6.0248710539932475e+01
25 3822 2 3.5400000000000001e-02 6.2750675036816460e+01 8.3891633300878468e+01 6.2249429178485677e+01
5 3822 2 1.4030000000000001e-01 6.2626160082050376e+01 8.8416565740835182e+01 6.4093918967496805e+01
1 3822 2 1.2880000000000000e-01 6.4863557606529355e+01 8.9096029197548390e+01 6.5342927535537825e+01
2 3822 1 -1.1340000000000000e-01 6.4627442641031166e+01 8.8047381925321190e+01 6.5138073202291650e+01
3 3822 2 1.4030000000000001e-01 6.6470254992065406e+01 8.6991893750821745e+01 6.5857474890608984e+01
4 3822 1 -1.7340000000000000e-01 6.5416488888088338e+01 8.6963894801200169e+01 6.5357641085394278e+01
Velocities
44 -1.1274099342391698e-02 2.8614364731871914e-02 7.8116535486555949e-03
45 2.3164382404151666e-03 3.9815732957733160e-03 -2.9971878581527899e-02
46 -7.1653099619954563e-03 4.5491360587300133e-04 4.9898614093692017e-03
48 9.8069086061434527e-03 4.0008139512159270e-03 6.2934259772882122e-03
47 2.2646445306743783e-03 1.3029071608409702e-03 4.2232440120174040e-02
18 7.0040064100195757e-03 3.2877451206009701e-03 -3.5376010407568422e-04
19 -1.3998188760009689e-02 7.2238210565990146e-03 7.7956220633332383e-03
21 3.1954292320462373e-03 -2.9717583309420764e-03 -3.1753395094325522e-03
22 5.2997643939121201e-03 -2.9646963088534335e-03 -4.1351926198204894e-03
23 7.6443400078766528e-03 4.0358953976530103e-02 -2.6684706183248367e-02
27 1.9261652416455359e-03 -1.1632914130150688e-02 1.0061732021630769e-02
28 -8.2251676802878315e-03 -1.5111873066969876e-04 1.3808893565582731e-02
31 5.2475840572179860e-03 1.8266996572138715e-02 2.3453280610166885e-03
38 -2.0343905130199073e-02 3.2815536859276281e-02 3.6511922534330152e-03
20 2.2914549087537126e-02 1.4424503744223915e-02 2.1708279654645496e-03
24 -2.4717233344142471e-03 1.2966123098719246e-02 8.1261459853411936e-03
37 -2.4547379584186218e-02 -3.0213966592845171e-02 -3.1437442951939183e-02
39 2.5476117829076835e-03 1.2743160680987653e-03 1.8775880208113892e-03
40 -6.9216508143939990e-03 1.0986173624795060e-02 8.4543093049661480e-03
41 -6.9641432145561661e-03 3.4497795547843439e-03 -6.5914679936187716e-03
42 -1.6682931637687005e-02 -7.9952140358728052e-03 -5.4993265930488526e-02
43 -1.2747392921213267e-03 -8.9033092043203244e-03 -1.4285400545629027e-02
9 -4.6235166357676289e-03 -1.3071850427027999e-02 -1.4097407987100977e-02
30 -1.0949617396609294e-02 2.8255703113196974e-03 1.7171748232322353e-02
33 -6.1375812469323665e-03 -2.4748644899411924e-03 -9.4761978149296138e-03
34 1.3676079846441525e-03 5.6076140293943458e-03 4.3217204641336267e-03
6 -1.0264635053701928e-02 6.5278337056107680e-03 7.0056151148588212e-04
7 -8.7519451205145676e-03 -4.6476440106580945e-03 2.5970484253527112e-03
8 2.1377395557690311e-02 -3.3261274153819453e-03 -1.0112266596677577e-02
10 -3.5793767912309253e-02 -4.7139872292323019e-02 -1.6709528481405608e-02
11 8.5071485795589590e-03 9.9402848610678270e-03 -3.8088596341056854e-03
12 -7.1678159384257103e-04 -6.9164463557228907e-04 -6.4073519808107186e-03
13 -4.8443902657902991e-03 -1.1919190682985097e-03 6.3946846087726637e-03
14 1.4810157483257907e-02 1.9829623839419017e-03 -2.7393844990063056e-02
15 2.4171850935506777e-03 8.5003135180758520e-03 -1.4373227798951704e-03
16 2.7567342910947553e-03 4.7168484476890456e-03 -5.5131873288712992e-03
17 -3.8456662730386774e-02 2.0220106671151108e-02 -1.3822049134399602e-02
26 2.7415414728694614e-02 1.4392155257037418e-03 -6.7281635499082748e-03
29 2.8284983560440745e-03 2.8809942505517976e-03 -9.0489583066552114e-04
32 -3.8543634697614316e-03 4.6751647301899795e-03 4.2171867397204537e-03
35 -8.6957974827209118e-03 -4.4615282666186267e-04 -2.6571026120482824e-03
36 9.4881057996863086e-04 -7.5665878069688429e-03 2.0333670960646154e-03
25 1.8105924111310519e-02 -8.6933495274689535e-03 -1.9695291360338044e-04
5 -5.0447438383189585e-03 -4.5665146331657552e-02 1.0653751333175230e-02
1 -1.7372868398038824e-02 -2.3625357536259349e-03 1.2220266128368908e-02
2 3.7050246021929395e-03 -1.0236943515935205e-03 7.2206774682170580e-03
3 2.3669435799326944e-02 2.7891427939155597e-02 -6.7091036888174346e-03
4 3.4910623999263577e-03 2.6370880132825258e-03 -6.4694788112864129e-03
Bonds
1 10 44 19
2 10 45 46
3 10 48 46
4 9 19 18
5 1 21 38
6 2 21 22
7 2 21 39
8 7 22 18
9 2 22 24
10 10 23 19
11 8 27 28
12 9 28 46
13 9 28 19
14 1 24 20
15 2 24 41
16 1 39 37
17 1 40 42
18 2 40 39
19 1 41 43
20 2 41 40
21 1 33 30
22 1 34 9
23 2 34 33
24 1 6 5
25 2 6 2
26 1 7 8
27 2 7 6
28 10 11 13
29 13 12 13
30 9 13 18
31 1 15 14
32 2 15 16
33 2 15 4
34 11 16 12
35 2 16 7
36 8 17 18
37 12 26 12
38 7 29 28
39 2 29 35
40 1 32 31
41 2 32 29
42 2 32 33
43 1 35 47
44 2 35 36
45 1 36 10
46 2 36 34
47 10 25 13
48 1 2 1
49 2 2 4
50 1 4 3
Angles
1 14 45 46 28
2 14 48 46 28
3 15 45 46 48
4 11 22 18 13
5 12 17 18 13
6 13 13 18 19
7 10 22 18 17
8 11 22 18 19
9 12 17 18 19
10 16 28 19 18
11 14 44 19 28
12 14 23 19 28
13 14 44 19 18
14 14 23 19 18
15 15 44 19 23
16 1 22 21 38
17 1 39 21 38
18 2 22 21 39
19 9 21 22 18
20 2 21 22 24
21 9 24 22 18
22 10 29 28 27
23 11 29 28 46
24 11 29 28 19
25 12 27 28 46
26 12 27 28 19
27 13 46 28 19
28 1 22 24 20
29 2 22 24 41
30 1 41 24 20
31 2 21 39 40
32 1 21 39 37
33 1 40 39 37
34 1 41 40 42
35 2 41 40 39
36 1 39 40 42
37 1 24 41 43
38 2 24 41 40
39 1 40 41 43
40 2 32 33 34
41 1 32 33 30
42 1 34 33 30
43 1 36 34 9
44 2 36 34 33
45 1 33 34 9
46 1 7 6 5
47 2 7 6 2
48 1 2 6 5
49 1 16 7 8
50 2 16 7 6
51 1 6 7 8
52 18 16 12 26
53 19 16 12 13
54 20 26 12 13
55 21 25 13 12
56 21 11 13 12
57 22 12 13 18
58 15 25 13 11
59 14 25 13 18
60 14 11 13 18
61 1 16 15 14
62 1 4 15 14
63 2 16 15 4
64 17 15 16 12
65 2 15 16 7
66 17 7 16 12
67 9 32 29 28
68 2 32 29 35
69 9 35 29 28
70 1 29 32 31
71 1 33 32 31
72 2 29 32 33
73 1 29 35 47
74 2 29 35 36
75 1 36 35 47
76 1 35 36 10
77 2 35 36 34
78 1 34 36 10
79 1 6 2 1
80 2 6 2 4
81 1 4 2 1
82 2 15 4 2
83 1 15 4 3
84 1 2 4 3
Dihedrals
1 34 18 19 28 29
2 31 44 19 28 29
3 31 23 19 28 29
4 35 18 19 28 27
5 32 44 19 28 27
6 32 23 19 28 27
7 36 18 19 28 46
8 33 44 19 28 46
9 33 23 19 28 46
10 36 28 19 18 13
11 33 44 19 18 13
12 33 23 19 18 13
13 34 28 19 18 22
14 31 44 19 18 22
15 31 23 19 18 22
16 35 28 19 18 17
17 32 44 19 18 17
18 32 23 19 18 17
19 10 38 21 22 18
20 11 39 21 22 18
21 4 39 21 22 24
22 5 38 21 39 37
23 4 22 21 39 40
24 2 22 21 39 37
25 2 24 22 21 38
26 13 21 22 18 13
27 12 21 22 18 17
28 13 21 22 18 19
29 13 24 22 18 13
30 12 24 22 18 17
31 13 24 22 18 19
32 2 21 22 24 20
33 4 21 22 24 41
34 14 29 28 46 45
35 14 29 28 46 48
36 15 27 28 46 45
37 15 27 28 46 48
38 16 19 28 46 45
39 16 19 28 46 48
40 10 20 24 22 18
41 11 41 24 22 18
42 2 22 24 41 43
43 4 22 24 41 40
44 5 20 24 41 43
45 2 40 39 21 38
46 2 21 39 40 42
47 2 39 40 41 43
48 4 41 40 39 21
49 2 41 40 39 37
50 5 42 40 39 37
51 2 40 41 24 20
52 2 24 41 40 42
53 4 24 41 40 39
54 5 43 41 40 42
55 2 34 33 32 31
56 2 32 33 34 9
57 2 33 34 36 10
58 4 36 34 33 32
59 2 36 34 33 30
60 5 9 34 33 30
61 2 2 6 7 8
62 2 7 6 2 1
63 4 7 6 2 4
64 5 5 6 2 1
65 20 8 7 16 12
66 21 6 7 16 12
67 2 16 7 6 5
68 4 16 7 6 2
69 5 8 7 6 5
70 24 16 12 13 25
71 24 16 12 13 11
72 25 16 12 13 18
73 26 26 12 13 25
74 26 26 12 13 11
75 27 26 12 13 18
76 28 12 13 18 22
77 29 12 13 18 17
78 30 12 13 18 19
79 31 25 13 18 22
80 32 25 13 18 17
81 33 25 13 18 19
82 31 11 13 18 22
83 32 11 13 18 17
84 33 11 13 18 19
85 20 14 15 16 12
86 21 4 15 16 12
87 4 4 15 16 7
88 5 14 15 4 3
89 4 16 15 4 2
90 2 16 15 4 3
91 2 7 16 15 14
92 22 15 16 12 26
93 23 15 16 12 13
94 22 7 16 12 26
95 23 7 16 12 13
96 2 15 16 7 8
97 4 15 16 7 6
98 2 35 29 32 31
99 12 32 29 28 27
100 13 32 29 28 46
101 13 32 29 28 19
102 12 35 29 28 27
103 13 35 29 28 46
104 13 35 29 28 19
105 2 32 29 35 47
106 4 32 29 35 36
107 10 31 32 29 28
108 11 33 32 29 28
109 4 33 32 29 35
110 5 31 32 33 30
111 4 29 32 33 34
112 2 29 32 33 30
113 10 47 35 29 28
114 11 36 35 29 28
115 2 29 35 36 10
116 4 29 35 36 34
117 5 47 35 36 10
118 2 34 36 35 47
119 2 35 36 34 9
120 4 35 36 34 33
121 5 10 36 34 9
122 2 4 2 6 5
123 4 6 2 4 15
124 2 6 2 4 3
125 5 1 2 4 3
126 2 2 4 15 14
127 2 15 4 2 1
Impropers
1 6 45 46 48 28
2 1 22 18 17 13
3 1 22 18 13 19
4 1 17 18 13 19
5 1 22 18 17 19
6 1 44 19 18 28
7 1 23 19 18 28
8 1 44 19 23 28
9 1 44 19 23 18
10 1 22 21 39 38
11 5 21 22 24 18
12 1 29 28 27 46
13 1 29 28 27 19
14 1 29 28 46 19
15 1 27 28 46 19
16 1 22 24 41 20
17 1 21 39 40 37
18 1 41 40 39 42
19 1 24 41 40 43
20 1 32 33 34 30
21 1 36 34 33 9
22 1 7 6 2 5
23 1 16 7 6 8
24 9 16 12 26 13
25 1 25 13 11 12
26 1 25 13 12 18
27 1 11 13 12 18
28 1 25 13 11 18
29 1 16 15 4 14
30 8 15 16 7 12
31 5 32 29 35 28
32 1 29 32 33 31
33 1 29 35 36 47
34 1 35 36 34 10
35 1 6 2 4 1
36 1 15 4 2 3

581
src/USER-REACTION/fix_bond_react.cpp
View File

@ -88,6 +88,9 @@ enum{ATOM,FRAG};
// keyword values that accept variables as input
enum{NEVERY,RMIN,RMAX,PROB};
// flag for one-proc vs shared reaction sites
enum{LOCAL,GLOBAL};
// values for molecule_keyword
enum{OFF,INTER,INTRA};
@ -208,6 +211,9 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
memory->create(limit_duration,nreacts,"bond/react:limit_duration");
memory->create(stabilize_steps_flag,nreacts,"bond/react:stabilize_steps_flag");
memory->create(custom_charges_fragid,nreacts,"bond/react:custom_charges_fragid");
memory->create(create_atoms_flag,nreacts,"bond/react:create_atoms_flag");
memory->create(modify_create_fragid,nreacts,"bond/react:modify_create_fragid");
memory->create(overlapsq,nreacts,"bond/react:overlapsq");
memory->create(molecule_keyword,nreacts,"bond/react:molecule_keyword");
memory->create(nconstraints,nreacts,"bond/react:nconstraints");
memory->create(constraintstr,nreacts,MAXLINE,"bond/react:constraintstr");
@ -231,6 +237,9 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
max_rxn[i] = INT_MAX;
stabilize_steps_flag[i] = 0;
custom_charges_fragid[i] = -1;
create_atoms_flag[i] = 0;
modify_create_fragid[i] = -1;
overlapsq[i] = 0;
molecule_keyword[i] = OFF;
nconstraints[i] = 0;
// set default limit duration to 60 timesteps
@ -396,6 +405,28 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
else if (strcmp(arg[iarg+1],"intra") == 0) molecule_keyword[rxn] = INTRA;
else error->one(FLERR,"Bond/react: Illegal option for 'molecule' keyword");
iarg += 2;
} else if (strcmp(arg[iarg],"modify_create") == 0) {
if (iarg++ > narg) error->all(FLERR,"Illegal fix bond/react command: "
"'modify_create' has too few arguments");
while (iarg < narg && strcmp(arg[iarg],"react") != 0 ) {
if (strcmp(arg[iarg],"fit") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix bond/react command: "
"'modify_create' has too few arguments");
if (strcmp(arg[iarg+1],"all") == 0) modify_create_fragid[rxn] = -1; //default
else {
modify_create_fragid[rxn] = atom->molecules[reacted_mol[rxn]]->findfragment(arg[iarg+1]);
if (modify_create_fragid[rxn] < 0) error->one(FLERR,"Bond/react: Molecule fragment for "
"'modify_create' keyword does not exist");
}
iarg += 2;
} else if (strcmp(arg[iarg],"overlap") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix bond/react command: "
"'modify_create' has too few arguments");
overlapsq[rxn] = utils::numeric(FLERR,arg[iarg+1],false,lmp);
overlapsq[rxn] *= overlapsq[rxn];
iarg += 2;
} else break;
}
} else error->all(FLERR,"Illegal fix bond/react command: unknown keyword");
}
}
@ -412,6 +443,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
memory->create(landlocked_atoms,max_natoms,nreacts,"bond/react:landlocked_atoms");
memory->create(custom_charges,max_natoms,nreacts,"bond/react:custom_charges");
memory->create(delete_atoms,max_natoms,nreacts,"bond/react:delete_atoms");
memory->create(create_atoms,max_natoms,nreacts,"bond/react:create_atoms");
memory->create(chiral_atoms,max_natoms,6,nreacts,"bond/react:chiral_atoms");
for (int j = 0; j < nreacts; j++)
@ -419,9 +451,15 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
edge[i][j] = 0;
custom_charges[i][j] = 1; // update all partial charges by default
delete_atoms[i][j] = 0;
create_atoms[i][j] = 0;
for (int k = 0; k < 6; k++) {
chiral_atoms[i][k][j] = 0;
}
// default equivalences to their own mol index
// all but created atoms will be updated
for (int m = 0; m < 2; m++) {
equivalences[i][m][j] = i+1;
}
}
// read all map files afterward
@ -431,11 +469,13 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
twomol = atom->molecules[reacted_mol[i]];
onemol->check_attributes(0);
twomol->check_attributes(0);
if (onemol->natoms != twomol->natoms)
error->all(FLERR,"Bond/react: Reaction templates must contain the same number of atoms");
get_molxspecials();
read(i);
fclose(fp);
if (ncreate == 0 && onemol->natoms != twomol->natoms)
error->all(FLERR,"Bond/react: Reaction templates must contain the same number of atoms");
else if (ncreate > 0 && onemol->natoms + ncreate != twomol->natoms)
error->all(FLERR,"Bond/react: Incorrect number of created atoms");
iatomtype[i] = onemol->type[ibonding[i]-1];
jatomtype[i] = onemol->type[jbonding[i]-1];
find_landlocked_atoms(i);
@ -498,10 +538,10 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
partner = finalpartner = nullptr;
distsq = nullptr;
probability = nullptr;
maxcreate = 0;
created = nullptr;
ncreate = nullptr;
allncreate = 0;
maxattempt = 0;
attempt = nullptr;
nattempt = nullptr;
allnattempt = 0;
local_num_mega = 0;
ghostly_num_mega = 0;
restore = nullptr;
@ -543,18 +583,20 @@ FixBondReact::~FixBondReact()
memory->destroy(partner);
memory->destroy(finalpartner);
memory->destroy(ncreate);
memory->destroy(nattempt);
memory->destroy(distsq);
memory->destroy(probability);
memory->destroy(created);
memory->destroy(attempt);
memory->destroy(edge);
memory->destroy(equivalences);
memory->destroy(reverse_equiv);
memory->destroy(landlocked_atoms);
memory->destroy(custom_charges);
memory->destroy(delete_atoms);
memory->destroy(create_atoms);
memory->destroy(chiral_atoms);
memory->destroy(rxn_name);
memory->destroy(nevery);
memory->destroy(cutsq);
memory->destroy(unreacted_mol);
@ -572,7 +614,10 @@ FixBondReact::~FixBondReact()
memory->destroy(molecule_keyword);
memory->destroy(constraints);
memory->destroy(nconstraints);
// need to delete rxn_name and constraintstr
memory->destroy(constraintstr);
memory->destroy(create_atoms_flag);
memory->destroy(modify_create_fragid);
memory->destroy(overlapsq);
memory->destroy(iatomtype);
memory->destroy(jatomtype);
@ -777,7 +822,7 @@ void FixBondReact::init()
// check cutoff for iatomtype,jatomtype
for (int i = 0; i < nreacts; i++) {
if (closeneigh[i] == -1) // indicates will search for non-bonded bonding atoms
if (!utils::strmatch(force->pair_style,"^hybrid"))
if (force->pair == nullptr || cutsq[i][1] > force->pair->cutsq[iatomtype[i]][jatomtype[i]])
error->all(FLERR,"Bond/react: Fix bond/react cutoff is longer than pairwise cutoff");
}
@ -844,19 +889,19 @@ void FixBondReact::post_integrate()
memory->destroy(partner);
memory->destroy(finalpartner);
memory->destroy(distsq);
memory->destroy(ncreate);
memory->destroy(nattempt);
memory->destroy(probability);
nmax = atom->nmax;
memory->create(partner,nmax,"bond/react:partner");
memory->create(finalpartner,nmax,"bond/react:finalpartner");
memory->create(distsq,nmax,2,"bond/react:distsq");
memory->create(ncreate,nreacts,"bond/react:ncreate");
memory->create(nattempt,nreacts,"bond/react:nattempt");
memory->create(probability,nmax,"bond/react:probability");
}
// reset create counts
for (int i = 0; i < nreacts; i++) {
ncreate[i] = 0;
nattempt[i] = 0;
}
int nlocal = atom->nlocal;
@ -938,7 +983,7 @@ void FixBondReact::post_integrate()
// and probability constraint is satisfied
// if other atom is owned by another proc, it should do same thing
int temp_ncreate = 0;
int temp_nattempt = 0;
for (int i = 0; i < nlocal; i++) {
if (partner[i] == 0) {
continue;
@ -959,17 +1004,17 @@ void FixBondReact::post_integrate()
}
}
// store final created bond partners and count the rxn possibility once
// store final bond partners and count the rxn possibility once
finalpartner[i] = tag[j];
finalpartner[j] = tag[i];
if (tag[i] < tag[j]) temp_ncreate++;
if (tag[i] < tag[j]) temp_nattempt++;
}
// cycle loop if no even eligible bonding atoms were found (on any proc)
int some_chance;
MPI_Allreduce(&temp_ncreate,&some_chance,1,MPI_INT,MPI_SUM,world);
MPI_Allreduce(&temp_nattempt,&some_chance,1,MPI_INT,MPI_SUM,world);
if (!some_chance) continue;
// communicate final partner
@ -977,7 +1022,7 @@ void FixBondReact::post_integrate()
commflag = 3;
comm->forward_comm_fix(this);
// add instance to 'created' only if this processor
// add instance to 'attempt' only if this processor
// owns the atoms with smaller global ID
// NOTE: we no longer care about ghost-ghost instances as bond/create did
// this is because we take care of updating topology later (and differently)
@ -988,21 +1033,21 @@ void FixBondReact::post_integrate()
j = atom->map(finalpartner[i]);
// if (j < 0 || tag[i] < tag[j]) {
if (tag[i] < tag[j]) { //atom->map(std::min(tag[i],tag[j])) <= nlocal &&
if (ncreate[rxnID] == maxcreate) {
maxcreate += DELTA;
// third column of 'created': bond/react integer ID
memory->grow(created,maxcreate,2,nreacts,"bond/react:created");
if (nattempt[rxnID] == maxattempt) {
maxattempt += DELTA;
// third column of 'attempt': bond/react integer ID
memory->grow(attempt,maxattempt,2,nreacts,"bond/react:attempt");
}
// to ensure types remain in same order
// unnecessary now taken from reaction map file
if (iatomtype[rxnID] == type[i]) {
created[ncreate[rxnID]][0][rxnID] = tag[i];
created[ncreate[rxnID]][1][rxnID] = finalpartner[i];
attempt[nattempt[rxnID]][0][rxnID] = tag[i];
attempt[nattempt[rxnID]][1][rxnID] = finalpartner[i];
} else {
created[ncreate[rxnID]][0][rxnID] = finalpartner[i];
created[ncreate[rxnID]][1][rxnID] = tag[i];
attempt[nattempt[rxnID]][0][rxnID] = finalpartner[i];
attempt[nattempt[rxnID]][1][rxnID] = tag[i];
}
ncreate[rxnID]++;
nattempt[rxnID]++;
}
}
}
@ -1010,11 +1055,11 @@ void FixBondReact::post_integrate()
// break loop if no even eligible bonding atoms were found (on any proc)
int some_chance;
allncreate = 0;
allnattempt = 0;
for (int i = 0; i < nreacts; i++)
allncreate += ncreate[i];
allnattempt += nattempt[i];
MPI_Allreduce(&allncreate,&some_chance,1,MPI_INT,MPI_SUM,world);
MPI_Allreduce(&allnattempt,&some_chance,1,MPI_INT,MPI_SUM,world);
if (!some_chance) {
unlimit_bond();
return;
@ -1242,13 +1287,13 @@ void FixBondReact::superimpose_algorithm()
memory->create(restore_pt,MAXGUESS,4,"bond/react:restore_pt");
memory->create(pioneers,max_natoms,"bond/react:pioneers");
memory->create(restore,max_natoms,MAXGUESS*4,"bond/react:restore");
memory->create(local_mega_glove,max_natoms+1,allncreate,"bond/react:local_mega_glove");
memory->create(ghostly_mega_glove,max_natoms+1,allncreate,"bond/react:ghostly_mega_glove");
memory->create(local_mega_glove,max_natoms+1,allnattempt,"bond/react:local_mega_glove");
memory->create(ghostly_mega_glove,max_natoms+1,allnattempt,"bond/react:ghostly_mega_glove");
attempted_rxn = 1;
for (int i = 0; i < max_natoms+1; i++) {
for (int j = 0; j < allncreate; j++) {
for (int j = 0; j < allnattempt; j++) {
local_mega_glove[i][j] = 0;
ghostly_mega_glove[i][j] = 0;
}
@ -1256,7 +1301,7 @@ void FixBondReact::superimpose_algorithm()
// let's finally begin the superimpose loop
for (rxnID = 0; rxnID < nreacts; rxnID++) {
for (lcl_inst = 0; lcl_inst < ncreate[rxnID]; lcl_inst++) {
for (lcl_inst = 0; lcl_inst < nattempt[rxnID]; lcl_inst++) {
onemol = atom->molecules[unreacted_mol[rxnID]];
twomol = atom->molecules[reacted_mol[rxnID]];
@ -1279,10 +1324,10 @@ void FixBondReact::superimpose_algorithm()
int myjbonding = jbonding[rxnID];
glove[myibonding-1][0] = myibonding;
glove[myibonding-1][1] = created[lcl_inst][0][rxnID];
glove[myibonding-1][1] = attempt[lcl_inst][0][rxnID];
glove_counter++;
glove[myjbonding-1][0] = myjbonding;
glove[myjbonding-1][1] = created[lcl_inst][1][rxnID];
glove[myjbonding-1][1] = attempt[lcl_inst][1][rxnID];
glove_counter++;
// special case, only two atoms in reaction templates
@ -1353,7 +1398,7 @@ void FixBondReact::superimpose_algorithm()
global_megasize = 0;
ghost_glovecast(); // consolidate all mega_gloves to all processors
dedup_mega_gloves(0); // make sure atoms aren't added to more than one reaction
dedup_mega_gloves(LOCAL); // make sure atoms aren't added to more than one reaction
MPI_Allreduce(&local_rxn_count[0],&reaction_count[0],nreacts,MPI_INT,MPI_SUM,world);
@ -1405,8 +1450,8 @@ void FixBondReact::superimpose_algorithm()
next_reneighbor = update->ntimestep;
// call limit_bond in 'global_mega_glove mode.' oh, and local mode
limit_bond(0); // add reacting atoms to nve/limit
limit_bond(1);
limit_bond(LOCAL); // add reacting atoms to nve/limit
limit_bond(GLOBAL);
update_everything(); // change topology
}
@ -1912,7 +1957,7 @@ int FixBondReact::check_constraints()
}
if (ANDgate != 1) satisfied[i] = 0;
} else if (constraints[i][rxnID].type == ARRHENIUS) {
t = get_temperature();
t = get_temperature(glove,0,1);
prrhob = constraints[i][rxnID].par[1]*pow(t,constraints[i][rxnID].par[2])*
exp(-constraints[i][rxnID].par[3]/(force->boltz*t));
if (prrhob < rrhandom[(int) constraints[i][rxnID].par[0]]->uniform()) satisfied[i] = 0;
@ -2044,7 +2089,7 @@ void FixBondReact::get_IDcoords(int mode, int myID, double *center)
compute local temperature: average over all atoms in reaction template
------------------------------------------------------------------------- */
double FixBondReact::get_temperature()
double FixBondReact::get_temperature(tagint **myglove, int row_offset, int col)
{
int i,ilocal;
double adof = domain->dimension;
@ -2058,13 +2103,13 @@ double FixBondReact::get_temperature()
if (rmass) {
for (i = 0; i < onemol->natoms; i++) {
ilocal = atom->map(glove[i][1]);
ilocal = atom->map(myglove[i+row_offset][col]);
t += (v[ilocal][0]*v[ilocal][0] + v[ilocal][1]*v[ilocal][1] +
v[ilocal][2]*v[ilocal][2]) * rmass[ilocal];
}
} else {
for (i = 0; i < onemol->natoms; i++) {
ilocal = atom->map(glove[i][1]);
ilocal = atom->map(myglove[i+row_offset][col]);
t += (v[ilocal][0]*v[ilocal][0] + v[ilocal][1]*v[ilocal][1] +
v[ilocal][2]*v[ilocal][2]) * mass[type[ilocal]];
}
@ -2169,7 +2214,8 @@ void FixBondReact::find_landlocked_atoms(int myrxn)
// always remove edge atoms from landlocked list
for (int i = 0; i < twomol->natoms; i++) {
if (edge[equivalences[i][1][myrxn]-1][myrxn] == 1) landlocked_atoms[i][myrxn] = 0;
if (create_atoms[i][myrxn] == 0 && edge[equivalences[i][1][myrxn]-1][myrxn] == 1)
landlocked_atoms[i][myrxn] = 0;
else landlocked_atoms[i][myrxn] = 1;
}
int nspecial_limit = -1;
@ -2193,44 +2239,48 @@ void FixBondReact::find_landlocked_atoms(int myrxn)
// bad molecule templates check
// if atoms change types, but aren't landlocked, that's bad
for (int i = 0; i < twomol->natoms; i++) {
if (twomol->type[i] != onemol->type[equivalences[i][1][myrxn]-1] && landlocked_atoms[i][myrxn] == 0) {
char str[128];
snprintf(str,128,"Bond/react: Atom type affected by reaction %s too close to template edge",rxn_name[myrxn]);
error->all(FLERR,str);
if (create_atoms[i][myrxn] == 0) {
if (twomol->type[i] != onemol->type[equivalences[i][1][myrxn]-1] && landlocked_atoms[i][myrxn] == 0) {
char str[128];
snprintf(str,128,"Bond/react: Atom type affected by reaction %s too close to template edge",rxn_name[myrxn]);
error->all(FLERR,str);
}
}
}
// additionally, if a bond changes type, but neither involved atom is landlocked, bad
// would someone want to change an angle type but not bond or atom types? (etc.) ...hopefully not yet
for (int i = 0; i < twomol->natoms; i++) {
if (landlocked_atoms[i][myrxn] == 0) {
for (int j = 0; j < twomol->num_bond[i]; j++) {
int twomol_atomj = twomol->bond_atom[i][j];
if (landlocked_atoms[twomol_atomj-1][myrxn] == 0) {
int onemol_atomi = equivalences[i][1][myrxn];
int onemol_batom;
for (int m = 0; m < onemol->num_bond[onemol_atomi-1]; m++) {
onemol_batom = onemol->bond_atom[onemol_atomi-1][m];
if (onemol_batom == equivalences[twomol_atomj-1][1][myrxn]) {
if (twomol->bond_type[i][j] != onemol->bond_type[onemol_atomi-1][m]) {
char str[128];
snprintf(str,128,"Bond/react: Bond type affected by reaction %s too close to template edge",rxn_name[myrxn]);
error->all(FLERR,str);
}
}
}
if (newton_bond) {
int onemol_atomj = equivalences[twomol_atomj-1][1][myrxn];
for (int m = 0; m < onemol->num_bond[onemol_atomj-1]; m++) {
onemol_batom = onemol->bond_atom[onemol_atomj-1][m];
if (onemol_batom == equivalences[i][1][myrxn]) {
if (twomol->bond_type[i][j] != onemol->bond_type[onemol_atomj-1][m]) {
if (create_atoms[i][myrxn] == 0) {
if (landlocked_atoms[i][myrxn] == 0) {
for (int j = 0; j < twomol->num_bond[i]; j++) {
int twomol_atomj = twomol->bond_atom[i][j];
if (landlocked_atoms[twomol_atomj-1][myrxn] == 0) {
int onemol_atomi = equivalences[i][1][myrxn];
int onemol_batom;
for (int m = 0; m < onemol->num_bond[onemol_atomi-1]; m++) {
onemol_batom = onemol->bond_atom[onemol_atomi-1][m];
if (onemol_batom == equivalences[twomol_atomj-1][1][myrxn]) {
if (twomol->bond_type[i][j] != onemol->bond_type[onemol_atomi-1][m]) {
char str[128];
snprintf(str,128,"Bond/react: Bond type affected by reaction %s too close to template edge",rxn_name[myrxn]);
error->all(FLERR,str);
}
}
}
if (newton_bond) {
int onemol_atomj = equivalences[twomol_atomj-1][1][myrxn];
for (int m = 0; m < onemol->num_bond[onemol_atomj-1]; m++) {
onemol_batom = onemol->bond_atom[onemol_atomj-1][m];
if (onemol_batom == equivalences[i][1][myrxn]) {
if (twomol->bond_type[i][j] != onemol->bond_type[onemol_atomj-1][m]) {
char str[128];
snprintf(str,128,"Bond/react: Bond type affected by reaction %s too close to template edge",rxn_name[myrxn]);
error->all(FLERR,str);
}
}
}
}
}
}
}
@ -2252,13 +2302,22 @@ void FixBondReact::find_landlocked_atoms(int myrxn)
// also, if atoms change number of bonds, but aren't landlocked, that could be bad
if (me == 0)
for (int i = 0; i < twomol->natoms; i++) {
if (twomol_nxspecial[i][0] != onemol_nxspecial[equivalences[i][1][myrxn]-1][0] && landlocked_atoms[i][myrxn] == 0) {
char str[128];
snprintf(str,128,"Bond/react: Atom affected by reaction %s too close to template edge",rxn_name[myrxn]);
error->warning(FLERR,str);
break;
if (create_atoms[i][myrxn] == 0) {
if (twomol_nxspecial[i][0] != onemol_nxspecial[equivalences[i][1][myrxn]-1][0] && landlocked_atoms[i][myrxn] == 0) {
char str[128];
snprintf(str,128,"Bond/react: Atom affected by reaction %s too close to template edge",rxn_name[myrxn]);
error->warning(FLERR,str);
break;
}
}
}
// finally, if a created atom is not landlocked, bad!
for (int i = 0; i < twomol->natoms; i++) {
if (create_atoms[i][myrxn] == 1 && landlocked_atoms[i][myrxn] == 0) {
error->one(FLERR,"Bond/react: Created atom too close to template edge");
}
}
}
/* ----------------------------------------------------------------------
@ -2268,30 +2327,30 @@ allows for same site undergoing different pathways, in parallel
void FixBondReact::dedup_mega_gloves(int dedup_mode)
{
// dedup_mode == 0 for local_dedup
// dedup_mode == 1 for global_mega_glove
// dedup_mode == LOCAL for local_dedup
// dedup_mode == GLOBAL for global_mega_glove
for (int i = 0; i < nreacts; i++) {
if (dedup_mode == 0) local_rxn_count[i] = 0;
if (dedup_mode == 1) ghostly_rxn_count[i] = 0;
if (dedup_mode == LOCAL) local_rxn_count[i] = 0;
if (dedup_mode == GLOBAL) ghostly_rxn_count[i] = 0;
}
int dedup_size = 0;
if (dedup_mode == 0) {
if (dedup_mode == LOCAL) {
dedup_size = local_num_mega;
} else if (dedup_mode == 1) {
} else if (dedup_mode == GLOBAL) {
dedup_size = global_megasize;
}
tagint **dedup_glove;
memory->create(dedup_glove,max_natoms+1,dedup_size,"bond/react:dedup_glove");
if (dedup_mode == 0) {
if (dedup_mode == LOCAL) {
for (int i = 0; i < dedup_size; i++) {
for (int j = 0; j < max_natoms+1; j++) {
dedup_glove[j][i] = local_mega_glove[j][i];
}
}
} else if (dedup_mode == 1) {
} else if (dedup_mode == GLOBAL) {
for (int i = 0; i < dedup_size; i++) {
for (int j = 0; j < max_natoms+1; j++) {
dedup_glove[j][i] = global_mega_glove[j][i];
@ -2371,7 +2430,7 @@ void FixBondReact::dedup_mega_gloves(int dedup_mode)
// we must update local_mega_glove and local_megasize
// we can simply overwrite local_mega_glove column by column
if (dedup_mode == 0) {
if (dedup_mode == LOCAL) {
int new_local_megasize = 0;
for (int i = 0; i < local_num_mega; i++) {
if (dedup_mask[i] == 0) {
@ -2388,7 +2447,7 @@ void FixBondReact::dedup_mega_gloves(int dedup_mode)
// we must update global_mega_glove and global_megasize
// we can simply overwrite global_mega_glove column by column
if (dedup_mode == 1) {
if (dedup_mode == GLOBAL) {
int new_global_megasize = 0;
for (int i = 0; i < global_megasize; i++) {
if (dedup_mask[i] == 0) {
@ -2425,7 +2484,7 @@ void FixBondReact::limit_bond(int limit_bond_mode)
int nlocal = atom->nlocal;
int temp_limit_num = 0;
tagint *temp_limit_glove;
if (limit_bond_mode == 0) {
if (limit_bond_mode == LOCAL) {
int max_temp = local_num_mega * (max_natoms + 1);
temp_limit_glove = new tagint[max_temp];
for (int j = 0; j < local_num_mega; j++) {
@ -2436,7 +2495,7 @@ void FixBondReact::limit_bond(int limit_bond_mode)
}
}
} else if (limit_bond_mode == 1) {
} else if (limit_bond_mode == GLOBAL) {
int max_temp = global_megasize * (max_natoms + 1);
temp_limit_glove = new tagint[max_temp];
for (int j = 0; j < global_megasize; j++) {
@ -2532,11 +2591,15 @@ void FixBondReact::glove_ghostcheck()
int ghostly = 0;
#if !defined(MPI_STUBS)
if (comm->style == 0) {
for (int i = 0; i < onemol->natoms; i++) {
int ilocal = atom->map(glove[i][1]);
if (ilocal >= atom->nlocal || localsendlist[ilocal] == 1) {
ghostly = 1;
break;
if (create_atoms_flag[rxnID] == 1) {
ghostly = 1;
} else {
for (int i = 0; i < onemol->natoms; i++) {
int ilocal = atom->map(glove[i][1]);
if (ilocal >= atom->nlocal || localsendlist[ilocal] == 1) {
ghostly = 1;
break;
}
}
}
} else {
@ -2624,7 +2687,7 @@ void FixBondReact::ghost_glovecast()
column, 0, world);
}
if (me == 0) dedup_mega_gloves(1); // global_mega_glove mode
if (me == 0) dedup_mega_gloves(GLOBAL); // global_mega_glove mode
MPI_Bcast(&global_megasize,1,MPI_INT,0,world);
MPI_Bcast(&(global_mega_glove[0][0]), global_megasize, column, 0, world);
@ -2642,9 +2705,8 @@ update molecule IDs, charges, types, special lists and all topology
void FixBondReact::update_everything()
{
int nlocal; // must be defined after create_atoms
int *type = atom->type;
int nlocal = atom->nlocal;
int **nspecial = atom->nspecial;
tagint **special = atom->special;
@ -2654,8 +2716,7 @@ void FixBondReact::update_everything()
// used when deleting atoms
int ndel,ndelone;
int *mark = new int[nlocal];
for (int i = 0; i < nlocal; i++) mark[i] = 0;
int *mark;
tagint *tag = atom->tag;
AtomVec *avec = atom->avec;
@ -2694,6 +2755,20 @@ void FixBondReact::update_everything()
rxnID = global_mega_glove[0][i];
// reactions already shuffled from dedup procedure, so can skip first N
if (iskip[rxnID]++ < nghostlyskips[rxnID]) continue;
// we can insert atoms here, now that reactions are finalized
// can't do it any earlier, due to skipped reactions (max_rxn)
// reactions that create atoms are always treated as 'global'
if (create_atoms_flag[rxnID] == 1) {
onemol = atom->molecules[unreacted_mol[rxnID]];
twomol = atom->molecules[reacted_mol[rxnID]];
if (insert_atoms(global_mega_glove,i))
; else { // create aborted
reaction_count_total[rxnID]--;
continue;
}
}
for (int j = 0; j < max_natoms+1; j++)
update_mega_glove[j][update_num_mega] = global_mega_glove[j][i];
update_num_mega++;
@ -2702,6 +2777,9 @@ void FixBondReact::update_everything()
delete [] iskip;
// mark to-delete atoms
nlocal = atom->nlocal;
mark = new int[nlocal];
for (int i = 0; i < nlocal; i++) mark[i] = 0;
for (int i = 0; i < update_num_mega; i++) {
rxnID = update_mega_glove[0][i];
onemol = atom->molecules[unreacted_mol[rxnID]];
@ -2731,25 +2809,6 @@ void FixBondReact::update_everything()
}
}
//maybe add check that all 1-3 neighbors of a local atoms are at least ghosts -> unneeded --jg
//okay, here goes:
for (int i = 0; i < update_num_mega; i++) {
rxnID = update_mega_glove[0][i];
twomol = atom->molecules[reacted_mol[rxnID]];
for (int j = 0; j < twomol->natoms; j++) {
int jj = equivalences[j][1][rxnID]-1;
if (atom->map(update_mega_glove[jj+1][i]) < nlocal && atom->map(update_mega_glove[jj+1][i]) >= 0) {
if (landlocked_atoms[j][rxnID] == 1) {
for (int k = 0; k < nspecial[atom->map(update_mega_glove[jj+1][i])][2]; k++) {
if (atom->map(special[atom->map(update_mega_glove[jj+1][i])][k]) < 0) {
error->all(FLERR,"Bond/react: Fix bond/react needs ghost atoms from further away - most likely too many processors");
}
}
}
}
}
}
int insert_num;
// very nice and easy to completely overwrite special bond info for landlocked atoms
for (int i = 0; i < update_num_mega; i++) {
@ -3205,6 +3264,279 @@ void FixBondReact::update_everything()
}
}
/* ----------------------------------------------------------------------
insert created atoms
------------------------------------------------------------------------- */
int FixBondReact::insert_atoms(tagint **my_mega_glove, int iupdate)
{
// inserting atoms based off fix_deposit->pre_exchange
int flag;
imageint *imageflags;
double **coords,lamda[3],rotmat[3][3],vnew[3];
double *newcoord;
double **v = atom->v;
double t,delx,dely,delz,rsq;
memory->create(coords,twomol->natoms,3,"bond/react:coords");
memory->create(imageflags,twomol->natoms,"bond/react:imageflags");
double *sublo,*subhi;
if (domain->triclinic == 0) {
sublo = domain->sublo;
subhi = domain->subhi;
} else {
sublo = domain->sublo_lamda;
subhi = domain->subhi_lamda;
}
// find current max atom and molecule IDs
tagint *tag = atom->tag;
double **x = atom->x;
tagint *molecule = atom->molecule;
int nlocal = atom->nlocal;
tagint maxtag_all,maxmol_all;
tagint max = 0;
for (int i = 0; i < nlocal; i++) max = MAX(max,tag[i]);
MPI_Allreduce(&max,&maxtag_all,1,MPI_LMP_TAGINT,MPI_MAX,world);
max = 0;
for (int i = 0; i < nlocal; i++) max = MAX(max,molecule[i]);
MPI_Allreduce(&max,&maxmol_all,1,MPI_LMP_TAGINT,MPI_MAX,world);
int dimension = domain->dimension;
// only proc that owns reacting atom (use ibonding),
// fits post-reaction template to reaction site, for creating atoms
int n2superpose = 0;
for (int j = 0; j < twomol->natoms; j++) {
if (modify_create_fragid[rxnID] >= 0)
if (!twomol->fragmentmask[modify_create_fragid[rxnID]][j]) continue;
if (!create_atoms[j][rxnID] && !delete_atoms[equivalences[j][1][rxnID]][rxnID])
n2superpose++;
}
int ifit = atom->map(my_mega_glove[ibonding[rxnID]+1][iupdate]); // use this local ID to find fitting proc
Superpose3D<double, double **> superposer(n2superpose);
int fitroot = 0;
if (ifit >= 0 && ifit < atom->nlocal) {
fitroot = me;
// get 'temperatere' averaged over site, used for created atoms' vels
t = get_temperature(my_mega_glove,1,iupdate);
double **xfrozen; // coordinates for the "frozen" target molecule
double **xmobile; // coordinates for the "mobile" molecule
memory->create(xfrozen,n2superpose,3,"bond/react:xfrozen");
memory->create(xmobile,n2superpose,3,"bond/react:xmobile");
tagint iatom;
tagint iref = -1; // choose first atom as reference
int fit_incr = 0;
for (int j = 0; j < twomol->natoms; j++) {
if (modify_create_fragid[rxnID] >= 0)
if (!twomol->fragmentmask[modify_create_fragid[rxnID]][j]) continue;
int ipre = equivalences[j][1][rxnID]-1; // equiv pre-reaction template index
if (!create_atoms[j][rxnID] && !delete_atoms[ipre][rxnID]) {
if (atom->map(my_mega_glove[ipre+1][iupdate]) < 0) {
printf("WARNING: eligible atoms skipped for created-atoms fit on %d\n",me);
continue;
}
iatom = atom->map(my_mega_glove[ipre+1][iupdate]);
if (iref == -1) iref = iatom;
iatom = domain->closest_image(iref,iatom);
for (int k = 0; k < 3; k++) {
xfrozen[fit_incr][k] = x[iatom][k];
xmobile[fit_incr][k] = twomol->x[j][k];
}
fit_incr++;
}
}
double rmsd = superposer.Superpose(xfrozen, xmobile);
for (int i = 0; i < 3; i++)
for (int j = 0; j < 3; j++)
rotmat[i][j] = superposer.R[i][j];
memory->destroy(xfrozen);
memory->destroy(xmobile);
}
MPI_Allreduce(MPI_IN_PLACE,&fitroot,1,MPI_INT,MPI_SUM,world);
MPI_Bcast(&t,1,MPI_DOUBLE,fitroot,world);
// get coordinates and image flags
for (int m = 0; m < twomol->natoms; m++) {
if (create_atoms[m][rxnID] == 1) {
// apply optimal rotation/translation for created atom coords
// also map coords back into simulation box
if (fitroot == me) {
MathExtra::matvec(rotmat,twomol->x[m],coords[m]);
for (int i = 0; i < 3; i++) coords[m][i] += superposer.T[i];
imageflags[m] = atom->image[ifit];
domain->remap(coords[m],imageflags[m]);
}
MPI_Bcast(&imageflags[m],1,MPI_LMP_IMAGEINT,fitroot,world);
MPI_Bcast(coords[m],3,MPI_DOUBLE,fitroot,world);
}
}
// check distance between any existing atom and inserted atom
// if less than near, abort
if (overlapsq[rxnID] > 0) {
int abortflag = 0;
for (int m = 0; m < twomol->natoms; m++) {
if (create_atoms[m][rxnID] == 1) {
for (int i = 0; i < nlocal; i++) {
delx = coords[m][0] - x[i][0];
dely = coords[m][1] - x[i][1];
delz = coords[m][2] - x[i][2];
domain->minimum_image(delx,dely,delz);
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < overlapsq[rxnID]) {
abortflag = 1;
break;
}
}
if (abortflag) break;
}
}
MPI_Allreduce(MPI_IN_PLACE,&abortflag,1,MPI_INT,MPI_MAX,world);
if (abortflag) {
memory->destroy(coords);
memory->destroy(imageflags);
return 0;
}
}
// clear ghost count and any ghost bonus data internal to AtomVec
// same logic as beginning of Comm::exchange()
// do it now b/c inserting atoms will overwrite ghost atoms
atom->nghost = 0;
atom->avec->clear_bonus();
// check if new atoms are in my sub-box or above it if I am highest proc
// if so, add atom to my list via create_atom()
// initialize additional info about the atoms
// set group mask to "all" plus fix group
int preID; // new equivalences index
int add_count = 0;
for (int m = 0; m < twomol->natoms; m++) {
if (create_atoms[m][rxnID] == 1) {
// increase atom count
add_count++;
preID = onemol->natoms+add_count;
if (domain->triclinic) {
domain->x2lamda(coords[m],lamda);
newcoord = lamda;
} else newcoord = coords[m];
flag = 0;
if (newcoord[0] >= sublo[0] && newcoord[0] < subhi[0] &&
newcoord[1] >= sublo[1] && newcoord[1] < subhi[1] &&
newcoord[2] >= sublo[2] && newcoord[2] < subhi[2]) flag = 1;
else if (dimension == 3 && newcoord[2] >= domain->boxhi[2]) {
if (comm->layout != Comm::LAYOUT_TILED) {
if (comm->myloc[2] == comm->procgrid[2]-1 &&
newcoord[0] >= sublo[0] && newcoord[0] < subhi[0] &&
newcoord[1] >= sublo[1] && newcoord[1] < subhi[1]) flag = 1;
} else {
if (comm->mysplit[2][1] == 1.0 &&
newcoord[0] >= sublo[0] && newcoord[0] < subhi[0] &&
newcoord[1] >= sublo[1] && newcoord[1] < subhi[1]) flag = 1;
}
} else if (dimension == 2 && newcoord[1] >= domain->boxhi[1]) {
if (comm->layout != Comm::LAYOUT_TILED) {
if (comm->myloc[1] == comm->procgrid[1]-1 &&
newcoord[0] >= sublo[0] && newcoord[0] < subhi[0]) flag = 1;
} else {
if (comm->mysplit[1][1] == 1.0 &&
newcoord[0] >= sublo[0] && newcoord[0] < subhi[0]) flag = 1;
}
}
int root = 0;
if (flag) {
root = me;
atom->avec->create_atom(twomol->type[m],coords[m]);
int n = atom->nlocal - 1;
atom->tag[n] = maxtag_all + add_count;
// locally update mega_glove
my_mega_glove[preID][iupdate] = atom->tag[n];
if (atom->molecule_flag) {
if (twomol->moleculeflag) {
atom->molecule[n] = maxmol_all + twomol->molecule[m];
} else {
atom->molecule[n] = maxmol_all + 1;
}
}
atom->mask[n] = 1 | groupbit;
atom->image[n] = imageflags[m];
// guess a somewhat reasonable initial velocity based on reaction site
// further control is possible using bond_react_MASTER_group
// compute |velocity| corresponding to a given temperature t, using specific atom's mass
double vtnorm = sqrt(t / (force->mvv2e / (dimension * force->boltz)) / atom->mass[twomol->type[m]]);
v[n][0] = random[rxnID]->uniform();
v[n][1] = random[rxnID]->uniform();
v[n][2] = random[rxnID]->uniform();
double vnorm = sqrt(v[n][0]*v[n][0] + v[n][1]*v[n][1] + v[n][2]*v[n][2]);
v[n][0] = v[n][0]/vnorm*vtnorm;
v[n][1] = v[n][1]/vnorm*vtnorm;
v[n][2] = v[n][2]/vnorm*vtnorm;
modify->create_attribute(n);
// initialize group statuses
// why aren't these more global...
int flag;
int index1 = atom->find_custom("limit_tags",flag);
int *i_limit_tags = atom->ivector[index1];
int *i_statted_tags;
if (stabilization_flag == 1) {
int index2 = atom->find_custom(statted_id,flag);
i_statted_tags = atom->ivector[index2];
}
int index3 = atom->find_custom("react_tags",flag);
int *i_react_tags = atom->ivector[index3];
i_limit_tags[n] = update->ntimestep + 1;
if (stabilization_flag == 1) i_statted_tags[n] = 0;
i_react_tags[n] = rxnID;
}
// globally update mega_glove and equivalences
MPI_Allreduce(MPI_IN_PLACE,&root,1,MPI_INT,MPI_SUM,world);
MPI_Bcast(&my_mega_glove[preID][iupdate],1,MPI_LMP_TAGINT,root,world);
equivalences[m][0][rxnID] = m+1;
equivalences[m][1][rxnID] = preID;
reverse_equiv[preID-1][0][rxnID] = preID;
reverse_equiv[preID-1][1][rxnID] = m+1;
}
}
// reset global natoms
// if global map exists, reset it now instead of waiting for comm
// since other pre-exchange fixes may use it
// invoke map_init() b/c atom count has grown
atom->natoms += add_count;
if (atom->natoms < 0)
error->all(FLERR,"Too many total atoms");
maxtag_all += add_count;
if (maxtag_all >= MAXTAGINT)
error->all(FLERR,"New atom IDs exceed maximum allowed ID");
if (atom->map_style != Atom::MAP_NONE) {
atom->map_init();
atom->map_set();
}
// atom creation successful
memory->destroy(coords);
memory->destroy(imageflags);
return 1;
}
/* ----------------------------------------------------------------------
read superimpose file
------------------------------------------------------------------------- */
@ -3222,6 +3554,7 @@ void FixBondReact::read(int myrxn)
// skip blank lines or lines that start with "#"
// stop when read an unrecognized line
ncreate = 0;
while (1) {
readline(line);
@ -3240,6 +3573,7 @@ void FixBondReact::read(int myrxn)
"equal number of atoms in reaction templates");
}
else if (strstr(line,"deleteIDs")) sscanf(line,"%d",&ndelete);
else if (strstr(line,"createIDs")) sscanf(line,"%d",&ncreate);
else if (strstr(line,"chiralIDs")) sscanf(line,"%d",&nchiral);
else if (strstr(line,"constraints")) {
sscanf(line,"%d",&nconstraints[myrxn]);
@ -3276,6 +3610,8 @@ void FixBondReact::read(int myrxn)
Equivalences(line, myrxn);
} else if (strcmp(keyword,"DeleteIDs") == 0) {
DeleteAtoms(line, myrxn);
} else if (strcmp(keyword,"CreateIDs") == 0) {
CreateAtoms(line, myrxn);
} else if (strcmp(keyword,"ChiralIDs") == 0) {
ChiralCenters(line, myrxn);
} else if (strcmp(keyword,"Constraints") == 0) {
@ -3312,7 +3648,7 @@ void FixBondReact::Equivalences(char *line, int myrxn)
for (int i = 0; i < nequivalent; i++) {
readline(line);
sscanf(line,"%d %d",&tmp1,&tmp2);
if (tmp1 > onemol->natoms || tmp2 > onemol->natoms)
if (tmp1 > onemol->natoms || tmp2 > twomol->natoms)
error->one(FLERR,"Bond/react: Invalid template atom ID in map file");
//equivalences is-> clmn 1: post-reacted, clmn 2: pre-reacted
equivalences[tmp2-1][0][myrxn] = tmp2;
@ -3335,6 +3671,17 @@ void FixBondReact::DeleteAtoms(char *line, int myrxn)
}
}
void FixBondReact::CreateAtoms(char *line, int myrxn)
{
create_atoms_flag[myrxn] = 1;
int tmp;
for (int i = 0; i < ncreate; i++) {
readline(line);
sscanf(line,"%d",&tmp);
create_atoms[tmp-1][myrxn] = 1;
}
}
void FixBondReact::CustomCharges(int ifragment, int myrxn)
{
for (int i = 0; i < onemol->natoms; i++)

18
src/USER-REACTION/fix_bond_react.h
View File

@ -67,6 +67,9 @@ class FixBondReact : public Fix {
int custom_exclude_flag;
int *stabilize_steps_flag;
int *custom_charges_fragid;
int *create_atoms_flag;
int *modify_create_fragid;
double *overlapsq;
int *molecule_keyword;
int maxnconstraints;
int *nconstraints;
@ -84,10 +87,10 @@ class FixBondReact : public Fix {
int max_natoms; // max natoms in a molecule template
tagint *partner,*finalpartner;
double **distsq,*probability;
int *ncreate;
int maxcreate;
int allncreate;
tagint ***created;
int *nattempt;
int maxattempt;
int allnattempt;
tagint ***attempt;
class Molecule *onemol; // pre-reacted molecule template
class Molecule *twomol; // post-reacted molecule template
@ -117,7 +120,7 @@ class FixBondReact : public Fix {
int *ibonding,*jbonding;
int *closeneigh; // indicates if bonding atoms of a rxn are 1-2, 1-3, or 1-4 neighbors
int nedge,nequivalent,ndelete,nchiral; // # edge, equivalent atoms in mapping file
int nedge,nequivalent,ndelete,ncreate,nchiral; // # edge, equivalent atoms in mapping file
int attempted_rxn; // there was an attempt!
int *local_rxn_count;
int *ghostly_rxn_count;
@ -133,6 +136,7 @@ class FixBondReact : public Fix {
int **landlocked_atoms; // all atoms at least three bonds away from edge atoms
int **custom_charges; // atoms whose charge should be updated
int **delete_atoms; // atoms in pre-reacted templates to delete
int **create_atoms; // atoms in post-reacted templates to create
int ***chiral_atoms; // pre-react chiral atoms. 1) flag 2) orientation 3-4) ordered atom types
int **nxspecial,**onemol_nxspecial,**twomol_nxspecial; // full number of 1-4 neighbors
@ -156,6 +160,7 @@ class FixBondReact : public Fix {
void EdgeIDs(char *, int);
void Equivalences(char *, int);
void DeleteAtoms(char *, int);
void CreateAtoms(char *,int);
void CustomCharges(int, int);
void ChiralCenters(char *, int);
void ReadConstraints(char *, int);
@ -169,7 +174,7 @@ class FixBondReact : public Fix {
void ring_check();
int check_constraints();
void get_IDcoords(int, int, double *);
double get_temperature();
double get_temperature(tagint **, int, int);
int get_chirality(double[12]); // get handedness given an ordered set of coordinates
void open(char *);
@ -185,6 +190,7 @@ class FixBondReact : public Fix {
void glove_ghostcheck();
void ghost_glovecast();
void update_everything();
int insert_atoms(tagint **, int);
void unlimit_bond();
void limit_bond(int);
void dedup_mega_gloves(int); //dedup global mega_glove