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Modulegraph

PLUMED Version 2.11

PLUMED is a composed of a modules that contain a variety of different functionalities but that share a common basic syntax. You can find all the modules that are available within PLUMED in the following graph. The graph also shows the interdependencies between the various modules. If you click on the modules in the graph module-specific information will open. The colors of the nodes in the graph below indicate whether the module is always compiled (blue), on by default (green) or off by default (red). If you need a feature from a module that is by default off you need to explicitly tell PLUMED to include it during the configure stage by using:

./configure --enable-module=module-name

Each module contains implementations of a number of actions. You can find a list of all the actions implemented in in PLUMED here.

You can view the information about the modules in the graph above in a table by following the following link. 


%%{init: {"flowchart": {"defaultRenderer": "elk"}} }%%
flowchart TD
subgraph g0 [ ]
0("bias")
style 0 fill:green
1("generic")
style 1 fill:green
6("annfunc")
style 6 fill:red
42("pytorch")
style 42 fill:red
0~~~42;
19("pathbias")
style 19 fill:red
1~~~19;
end
12("function")
style 12 fill:green
12--> g0;
subgraph g2 [ ]
33("membranefusion")
style 33 fill:red
2("mapping")
style 2 fill:red
4("secondarystructure")
style 4 fill:green
8("volumes")
style 8 fill:red
33~~~8;
40("pines")
style 40 fill:red
2~~~40;
41("piv")
style 41 fill:red
4~~~41;
43("s2cm")
style 43 fill:red
8~~~43;
45("sizeshape")
style 45 fill:red
40~~~45;
14("crystdistrib")
style 14 fill:red
41~~~14;
17("landmarks")
style 17 fill:red
43~~~17;
end
5("colvar")
style 5 fill:green
5--> g2;
subgraph g3 [ ]
11("isdb")
style 11 fill:green
32("funnel")
style 32 fill:red
3("multicolvar")
style 3 fill:green
38("maze")
style 38 fill:red
11~~~38;
end
0--> g3;
5--> g3;
subgraph g10 [ ]
34("pamm")
style 34 fill:red
10("symfunc")
style 10 fill:red
16("clusters")
style 16 fill:red
20("gridtools")
style 20 fill:green
34~~~20;
28("envsim")
style 28 fill:red
10~~~28;
29("liquid_crystal")
style 29 fill:green
16~~~29;
end
3--> g10;
subgraph g13 [ ]
35("kenref")
style 35 fill:red
37("logmfd")
style 37 fill:red
13("ves")
style 13 fill:red
47("ttsketch")
style 47 fill:red
35~~~47;
25("drr")
style 25 fill:red
37~~~25;
26("opes")
style 26 fill:red
13~~~26;
27("eds")
style 27 fill:red
47~~~27;
30("fisst")
style 30 fill:red
25~~~30;
end
0--> g13;
subgraph g23 [ ]
48("wham")
style 48 fill:red
31("fourier")
style 31 fill:red
23("contour")
style 23 fill:red
end
20--> g23;
subgraph g36 [ ]
36("setup")
style 36 fill:green
44("sasa")
style 44 fill:red
39("metatomic")
style 39 fill:red
end
24("core")
style 24 fill:blue
24--> g36;
1-->7;
1-->18;
1-->21;
2-->9;
5-->7;
7("vatom")
style 7 fill:green
7-->5;
9("dimred")
style 9 fill:red
12-->15;
15("adjmat")
style 15 fill:red
15-->21;
17-->9;
18("valtools")
style 18 fill:blue
18-->12;
18-->15;
20-->9;
21("matrixtools")
style 21 fill:green
21-->15;
21-->22;
21-->46;
22("refdist")
style 22 fill:green
22-->5;
24-->12;
24-->18;
46("sprint")
style 46 fill:red
46-->49;
49("xsprint")
style 49 fill:red
click 0 "../module_bias" "PLUMED's suite of command line tools[Authors:The PLUMED core developers]"
click 1 "../module_generic" "PLUMED's suite of command line tools[Authors:The PLUMED core developers]"
click 2 "../module_mapping" "PLUMED's suite of command line tools[Authors:The PLUMED core developers]"
click 3 "../module_multicolvar" "PLUMED's suite of command line tools[Authors:The PLUMED core developers]"
click 4 "../module_secondarystructure" "PLUMED's suite of command line tools[Authors:The PLUMED core developers]"
click 5 "../module_colvar" "PLUMED's suite of command line tools[Authors:The PLUMED core developers]"
click 6 "../module_annfunc" "PLUMED's suite of command line tools[Authors:The PLUMED core developers]"
click 7 "../module_vatom" "PLUMED's suite of command line tools[Authors:The PLUMED core developers]"
click 8 "../module_volumes" "PLUMED's suite of command line tools[Authors:The PLUMED core developers]"
click 9 "../module_dimred" "PLUMED's suite of command line tools[Authors:The PLUMED core developers]"
click 10 "../module_symfunc" "PLUMED's suite of command line tools[Authors:The PLUMED core developers]"
click 11 "../module_isdb" "PLUMED's suite of command line tools[Authors:The PLUMED core developers]"
click 12 "../module_function" "PLUMED's suite of command line tools[Authors:The PLUMED core developers]"
click 13 "../module_ves" "PLUMED's suite of command line tools[Authors:The PLUMED core developers]"
click 14 "../module_crystdistrib" "PLUMED's suite of command line tools[Authors:The PLUMED core developers]"
click 15 "../module_adjmat" "PLUMED's suite of command line tools[Authors:The PLUMED core developers]"
click 16 "../module_clusters" "PLUMED's suite of command line tools[Authors:The PLUMED core developers]"
click 17 "../module_landmarks" "PLUMED's suite of command line tools[Authors:The PLUMED core developers]"
click 18 "../module_valtools" "PLUMED's suite of command line tools[Authors:The PLUMED core developers]"
click 19 "../module_pathbias" "PLUMED's suite of command line tools[Authors:The PLUMED core developers]"
click 20 "../module_gridtools" "PLUMED's suite of command line tools[Authors:The PLUMED core developers]"
click 21 "../module_matrixtools" "PLUMED's suite of command line tools[Authors:The PLUMED core developers]"
click 22 "../module_refdist" "PLUMED's suite of command line tools[Authors:The PLUMED core developers]"
click 23 "../module_contour" "PLUMED's suite of command line tools[Authors:The PLUMED core developers]"
click 24 "../module_core" "PLUMED's suite of command line tools[Authors:The PLUMED core developers]"
click 25 "../module_drr" "PLUMED's suite of command line tools[Authors:The PLUMED core developers]"
click 26 "../module_opes" "PLUMED's suite of command line tools[Authors:The PLUMED core developers]"
click 27 "../module_eds" "PLUMED's suite of command line tools[Authors:The PLUMED core developers]"
click 28 "../module_envsim" "PLUMED's suite of command line tools[Authors:The PLUMED core developers]"
click 29 "../module_liquid_crystal" "PLUMED's suite of command line tools[Authors:The PLUMED core developers]"
click 30 "../module_fisst" "PLUMED's suite of command line tools[Authors:The PLUMED core developers]"
click 31 "../module_fourier" "PLUMED's suite of command line tools[Authors:The PLUMED core developers]"
click 32 "../module_funnel" "PLUMED's suite of command line tools[Authors:The PLUMED core developers]"
click 33 "../module_membranefusion" "PLUMED's suite of command line tools[Authors:The PLUMED core developers]"
click 34 "../module_pamm" "PLUMED's suite of command line tools[Authors:The PLUMED core developers]"
click 35 "../module_kenref" "PLUMED's suite of command line tools[Authors:The PLUMED core developers]"
click 36 "../module_setup" "PLUMED's suite of command line tools[Authors:The PLUMED core developers]"
click 37 "../module_logmfd" "PLUMED's suite of command line tools[Authors:The PLUMED core developers]"
click 38 "../module_maze" "PLUMED's suite of command line tools[Authors:The PLUMED core developers]"
click 39 "../module_metatomic" "PLUMED's suite of command line tools[Authors:The PLUMED core developers]"
click 40 "../module_pines" "PLUMED's suite of command line tools[Authors:The PLUMED core developers]"
click 41 "../module_piv" "PLUMED's suite of command line tools[Authors:The PLUMED core developers]"
click 42 "../module_pytorch" "PLUMED's suite of command line tools[Authors:The PLUMED core developers]"
click 43 "../module_s2cm" "PLUMED's suite of command line tools[Authors:The PLUMED core developers]"
click 44 "../module_sasa" "PLUMED's suite of command line tools[Authors:The PLUMED core developers]"
click 45 "../module_sizeshape" "PLUMED's suite of command line tools[Authors:The PLUMED core developers]"
click 46 "../module_sprint" "PLUMED's suite of command line tools[Authors:The PLUMED core developers]"
click 47 "../module_ttsketch" "PLUMED's suite of command line tools[Authors:The PLUMED core developers]"
click 48 "../module_wham" "PLUMED's suite of command line tools[Authors:The PLUMED core developers]"
click 49 "../module_xsprint" "PLUMED's suite of command line tools[Authors:The PLUMED core developers]"