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Action for reading masses and charges from a PDB file #1087

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merged 4 commits into from
Sep 3, 2024
Merged

Action for reading masses and charges from a PDB file #1087

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b300e57
Added action that allows you to set the masses and charges from a PDB…
Jun 13, 2024
24fe95a
Fixed manual for MassChangeInput action
Jun 13, 2024
765d075
Changed name of READ_MASS_CHARGE to READMASSCHARGE to be consistent w…
Jun 14, 2024
9398658
Added functionality to READMASSCHARGE so that you can read masses and…
Jun 14, 2024
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1 change: 1 addition & 0 deletions regtest/basic/rt-readmasscharge/Makefile
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include ../../scripts/test.make
4 changes: 4 additions & 0 deletions regtest/basic/rt-readmasscharge/config
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type=driver
# this is to test a different name
arg="--plumed=plumed.dat --timestep=0.05 --ixyz trajectory.xyz"
extra_files="../../trajectories/trajectory.xyz"
109 changes: 109 additions & 0 deletions regtest/basic/rt-readmasscharge/mc.reference
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#! FIELDS index mass charge
0 1 1
1 2 0
2 3 1
3 2 0
4 1 1
5 2 0
6 3 1
7 2 0
8 1 10
9 2 0
10 3 20
11 1 1
12 1 1
13 1 1
14 1 1
15 1 1
16 1 1
17 1 1
18 1 1
19 1 1
20 1 1
21 1 1
22 1 1
23 1 1
24 1 1
25 1 1
26 1 1
27 1 1
28 1 1
29 1 1
30 1 1
31 1 1
32 1 1
33 1 1
34 1 1
35 1 1
36 1 1
37 1 1
38 1 1
39 1 1
40 1 1
41 1 1
42 1 1
43 1 1
44 1 1
45 1 1
46 1 1
47 1 1
48 1 1
49 1 1
50 1 1
51 1 1
52 1 1
53 1 1
54 1 1
55 1 1
56 1 1
57 1 1
58 1 1
59 1 1
60 1 1
61 1 1
62 1 1
63 1 1
64 1 1
65 1 1
66 1 1
67 1 1
68 1 1
69 1 1
70 1 1
71 1 1
72 1 1
73 1 1
74 1 1
75 1 1
76 1 1
77 1 1
78 1 1
79 1 1
80 1 1
81 1 1
82 1 1
83 1 1
84 1 1
85 1 1
86 1 1
87 1 1
88 1 1
89 1 1
90 1 1
91 1 1
92 1 1
93 1 1
94 1 1
95 1 1
96 1 1
97 1 1
98 1 1
99 1 1
100 1 1
101 1 1
102 1 1
103 1 1
104 1 1
105 1 1
106 1 1
107 1 10
3 changes: 3 additions & 0 deletions regtest/basic/rt-readmasscharge/plumed.dat
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mq: READMASSCHARGE PDBFILE=test.pdb
DUMPMASSCHARGE FILE=mc

108 changes: 108 additions & 0 deletions regtest/basic/rt-readmasscharge/test.pdb
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ATOM 1 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 2 Ar 0.000 0.000 0.000 2.00 0.00
ATOM 3 Ar 0.000 0.000 0.000 3.00 1.00
ATOM 4 Ar 0.000 0.000 0.000 2.00 0.00
ATOM 5 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 6 Ar 0.000 0.000 0.000 2.00 0.00
ATOM 7 Ar 0.000 0.000 0.000 3.00 1.00
ATOM 8 Ar 0.000 0.000 0.000 2.00 0.00
ATOM 9 Ar 0.000 0.000 0.000 1.00 10.00
ATOM 10 Ar 0.000 0.000 0.000 2.00 0.00
ATOM 11 Ar 0.000 0.000 0.000 3.00 20.00
ATOM 12 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 13 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 14 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 15 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 16 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 17 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 18 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 19 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 20 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 21 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 22 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 23 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 24 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 25 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 26 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 27 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 28 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 29 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 30 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 31 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 32 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 33 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 34 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 35 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 36 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 37 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 38 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 39 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 40 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 41 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 42 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 43 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 44 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 45 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 46 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 47 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 48 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 49 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 50 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 51 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 52 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 53 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 54 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 55 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 56 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 57 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 58 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 59 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 60 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 61 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 62 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 63 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 64 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 65 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 66 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 67 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 68 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 69 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 70 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 71 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 72 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 73 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 74 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 75 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 76 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 77 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 78 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 79 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 80 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 81 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 82 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 83 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 84 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 85 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 86 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 87 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 88 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 89 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 90 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 91 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 92 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 93 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 94 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 95 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 96 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 97 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 98 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 99 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 100 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 101 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 102 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 103 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 104 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 105 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 106 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 107 Ar 0.000 0.000 0.000 1.00 1.00
ATOM 108 Ar 0.000 0.000 0.000 1.00 10.00
1 change: 1 addition & 0 deletions regtest/basic/rt-readmasscharge2/Makefile
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include ../../scripts/test.make
4 changes: 4 additions & 0 deletions regtest/basic/rt-readmasscharge2/config
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Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
type=driver
# this is to test a different name
arg="--plumed=plumed.dat --timestep=0.05 --ixyz trajectory.xyz"
extra_files="../../trajectories/trajectory.xyz"
109 changes: 109 additions & 0 deletions regtest/basic/rt-readmasscharge2/mc.reference
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Original file line number Diff line number Diff line change
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#! FIELDS index mass charge
0 1 1
1 2 0
2 3 1
3 2 0
4 1 1
5 2 0
6 3 1
7 2 0
8 1 10
9 2 0
10 3 20
11 1 1
12 1 1
13 1 1
14 1 1
15 1 1
16 1 1
17 1 1
18 1 1
19 1 1
20 1 1
21 1 1
22 1 1
23 1 1
24 1 1
25 1 1
26 1 1
27 1 1
28 1 1
29 1 1
30 1 1
31 1 1
32 1 1
33 1 1
34 1 1
35 1 1
36 1 1
37 1 1
38 1 1
39 1 1
40 1 1
41 1 1
42 1 1
43 1 1
44 1 1
45 1 1
46 1 1
47 1 1
48 1 1
49 1 1
50 1 1
51 1 1
52 1 1
53 1 1
54 1 1
55 1 1
56 1 1
57 1 1
58 1 1
59 1 1
60 1 1
61 1 1
62 1 1
63 1 1
64 1 1
65 1 1
66 1 1
67 1 1
68 1 1
69 1 1
70 1 1
71 1 1
72 1 1
73 1 1
74 1 1
75 1 1
76 1 1
77 1 1
78 1 1
79 1 1
80 1 1
81 1 1
82 1 1
83 1 1
84 1 1
85 1 1
86 1 1
87 1 1
88 1 1
89 1 1
90 1 1
91 1 1
92 1 1
93 1 1
94 1 1
95 1 1
96 1 1
97 1 1
98 1 1
99 1 1
100 1 1
101 1 1
102 1 1
103 1 1
104 1 1
105 1 1
106 1 1
107 1 10
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