Package gromacs :: Package analysis :: Package plugins :: Module energy :: Class _Energy

Class _Energy

         object --+        
                  |        
utilities.FileUtils --+    
                      |    
            core.Worker --+
                          |
                         _Energy

Energy worker class.

Gromacs 4-git energy terms

Select the terms you want from the following list by selecting either (part of) the name or the number or a combination. End your selection with an empty line or a zero

 1  Bond             2  Angle            3  Proper-Dih.      4  Ryckaert-Bell.
 5  Improper-Dih.    6  LJ-14            7  Coulomb-14       8  LJ-(SR)
 9  Disper.-corr.   10  Coulomb-(SR)    11  Coul.-recip.    12  Potential
13  Kinetic-En.     14  Total-Energy    15  Temperature     16  Pressure-(bar)
17  Cons.-rmsd-()   18  Box-X           19  Box-Y           20  Box-Z
21  Volume          22  Density-(SI)    23  pV              24  Vir-XX
25  Vir-XY          26  Vir-XZ          27  Vir-YX          28  Vir-YY
29  Vir-YZ          30  Vir-ZX          31  Vir-ZY          32  Vir-ZZ
33  Pres-XX-(bar)   34  Pres-XY-(bar)   35  Pres-XZ-(bar)   36  Pres-YX-(bar)
37  Pres-YY-(bar)   38  Pres-YZ-(bar)   39  Pres-ZX-(bar)   40  Pres-ZY-(bar)
41  Pres-ZZ-(bar)   42  #Surf*SurfTen   43  Mu-X            44  Mu-Y
45  Mu-Z                                46  Coul-SR:SOLVENT-SOLVENT
47  LJ-SR:SOLVENT-SOLVENT               48  Coul-14:SOLVENT-SOLVENT
49  LJ-14:SOLVENT-SOLVENT               50  Coul-SR:SOLVENT-LIPIDS
51  LJ-SR:SOLVENT-LIPIDS                52  Coul-14:SOLVENT-LIPIDS
53  LJ-14:SOLVENT-LIPIDS                54  Coul-SR:SOLVENT-Protein
55  LJ-SR:SOLVENT-Protein               56  Coul-14:SOLVENT-Protein
57  LJ-14:SOLVENT-Protein               58  Coul-SR:LIPIDS-LIPIDS
59  LJ-SR:LIPIDS-LIPIDS                 60  Coul-14:LIPIDS-LIPIDS
61  LJ-14:LIPIDS-LIPIDS                 62  Coul-SR:LIPIDS-Protein
63  LJ-SR:LIPIDS-Protein                64  Coul-14:LIPIDS-Protein
65  LJ-14:LIPIDS-Protein                66  Coul-SR:Protein-Protein
67  LJ-SR:Protein-Protein               68  Coul-14:Protein-Protein
69  LJ-14:Protein-Protein               70  T-SOLVENT
71  T-LIPIDS        72  T-Protein       73  Lamb-SOLVENT    74  Lamb-LIPIDS
75  Lamb-Protein

Instance Methods

[hide private]

__init__(self, **kwargs)
Set up Energy analysis.

source code

_register_hook(self, **kwargs)
Run when registering; requires simulation.

source code

run(self, force=False, **gmxargs)
Analyze trajectory and write energy files.

source code

analyze(self, **kwargs)
Collect output xvg files as :class:`gromacs.formats.XVG` objects.

source code

plot(self, **kwargs)
Plot all results in one graph, labelled by the result keys.

source code

Inherited from core.Worker: figdir, plugindir, savefig, store_xvg, topdir

Inherited from utilities.FileUtils: __repr__, check_file_exists, filename, infix_filename

Inherited from utilities.FileUtils (private): _init_filename

Inherited from object: __delattr__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __setattr__, __str__

Class Variables

[hide private]

terms = ['Potential', 'Kinetic-En.', 'Total-Energy', 'Temperat...

Inherited from utilities.FileUtils: default_extension

Instance Variables

[hide private]

Inherited from core.Worker: plugin, plugin_name

Inherited from utilities.FileUtils: real_filename

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, **kwargs)
(Constructor)

source code

Set up Energy analysis.

This is the worker class; this is where all the real analysis is done.

Overrides: object.__init__

_register_hook(self, **kwargs)

source code

Run when registering; requires simulation.

Overrides: core.Worker._register_hook

run(self, force=False, **gmxargs)

source code

Analyze trajectory and write energy files.

:Arguments:
  - *force*: do analysis and overwrite existing files
  - *gmxargs*: additional keyword arguments for :func:`gromacs.g_energy`

Overrides: core.Worker.run

analyze(self, **kwargs)

source code

Collect output xvg files as :class:`gromacs.formats.XVG` objects.

:Returns:  a dictionary of the results and also sets ``self.results``.

Overrides: core.Worker.analyze

plot(self, **kwargs)

source code

Plot all results in one graph, labelled by the result keys.

Parameters:

figure -
- True: save figures in the given formats
- "name.ext": save figure under this filename (ext -> format)
- False: only show on screen
formats (sequence) - sequence of all formats that should be saved [('png', 'pdf')]
plotargs - keyword arguments for pylab.plot()

Overrides: core.Worker.plot

Class Variable Details

[hide private]

terms

Value:

['Potential', 'Kinetic-En.', 'Total-Energy', 'Temperature', 'Pressure'
, 'Volume', 'Box-X', 'Box-Y', 'Box-Z',]

Class _Energy

__init__(self, **kwargs) (Constructor)

_register_hook(self, **kwargs)

run(self, force=False, **gmxargs)

analyze(self, **kwargs)

plot(self, **kwargs)

terms

init(self, **kwargs)
(Constructor)