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nMOLDYN autostart files

The nMOLDYN autostart files (extension .py) are Python scripts that can be direclty run without an explicit call to nMOLDYN. To run such a file, just type:
`./file.py` on unix
or
`file.py` on Windows
where `file.py` is the name of the nMOLDYN autostart file.

A nMOLDYN autostart file must have the following format:
1. `#!path_to_your_python_executable`
2. `from nMOLDYN.Analysis.Template import analysis_name`
3. `parameters = {}`
4. `parameters["version"] = "nmoldyn_version"`
5. `parameters["estimate"] = "no"`
6. `parameters["name1"] = value1`
7. `parameters["nameN"] = valueN`
8. `analysis = analysis_name(parameters)`
9. `analysis.runAnalysis()` some explanations are necessary about the structure of this file:

- Line 1.: path_to_your_python_executable is the path to the Python executable of the Python distribution where nMOLDYN is installed. This line is optional on Windows.
- Line 2.: analysis_name is the nMOLDYN internal name of the analysis to run. A comprehensive list of the nMOLDYN analysis internal names associated to each analysis is showed in Tab. 5.1.
- Line 3.: this line initalizes the dictionnary that will stores the analysis input parameters.
- Line 4.: nmoldyn_version is the version number of nMOLDYN. This line is optional.
- Line 5.: if set to "yes" instead of "no". the analysis will be run in estimate mode (see Section 4.2.3 for details). If "no" the full analysis will be run. If this parameter is omitted, the full analysis will be run.
- Line 6.: name1 is the name in lower case of the first parameters of the analysis with value equal to value1. Idem for Line 7.. The order in which the parameters appear is not relevant. A comprehensive list of the parameters names and expected values associated to each analysis can be found using the right column of Tab. 5.1.
- Line 8.: analysis_name is the same that in Line 2..
- Line 9.: this line runs the analysis.

The figure 5.1 shows an example of an autostart file for the MSD analysis. It was direclty generated from nMOLDYN GUI. Saving an autostart file from the GUI (see Section 4.2.3) is often the easiest way to get such file. This file providing then a convenient starting point for customization.

Figure 5.1: Example of a nMOLDYN autostart file derived for a MSD analysis.

Table 5.1: List of the nMOLDYN analysis internal names.
Analysis | nMOLDYN internal name | Section
Mean-Square Displacement | MeanSquareDisplacement_serial | 4.2.4.1
Root Mean-Square Deviation | RootMeanSquareDeviation_serial | 4.2.4.2
Radius of gyration | RadiusOfGyration_serial | 4.2.4.3
Angular Correlation | AngularCorrelation_serial | 4.2.4.4
Velocity Autocorrelation Function | CartesianVelocityAutoCorrelationFunction_serial | 4.2.4.5
Density Of States | CartesianDensityOfStates_serial | 4.2.4.6
Pass-Band Filtered Trajectory | PassBandFilteredTrajectory_serial | 4.2.4.7
Global Motion Filtered Trajectory | GlobalMotionFilteredTrajectory_serial | 4.2.4.8
Rigid-Body Trajectory | RigidBodyTrajectory_serial | 4.2.4.9
Center Of Mass Trajectory | CenterOfMassTrajectory_serial | 4.2.4.10
Auto-Regressive Analysis | AutoRegressiveAnalysis_serial | 4.2.4.11
Quasi Harmonic Analysis | QuasiHarmonicAnalysis_serial | 4.2.4.12
Reorientational Correlation Function | ReorientationalCorrelationFunction_serial | 4.2.4.13
Angular Velocity AutoCorrelation Function | AngularVelocityAutoCorrelationFunction_serial | 4.2.4.14
Angular Density Of States | AngularDensityOfStates_serial | 4.2.4.15
Dynamic Coherent Structure Factor | DynamicCoherentStructureFactor_serial | 4.2.5.2
Dynamic Coherent Structure Factor (AR Model) | DynamicCoherentStructureFactorAR_serial | 4.2.5.3
Dynamic Incoherent Structure Factor | DynamicIncoherentStructureFactor_serial | 4.2.5.4
Dynamic Incoherent Structure Factor (AR Model) | DynamicIncoherentStructureFactorAR_serial | 4.2.5.5
Dynamic Incoherent Structure Factor (Gaussian Approximation) | DynamicIncoherentStructureFactorGaussian_serial | 4.2.5.6
Elastic Incoherent Structure Factor | ElasticIncoherentStructureFactor_serial | 4.2.5.7
Static Coherent Structure Factor | StaticCoherentStructureFactor_serial | 4.2.5.8
Smoothed Static Coherent Structure Factor | SmoothedStaticCoherentStructureFactor_serial | 4.2.5.9
Pair Distribution Function | PairDistributionFunction_serial | 4.2.6.1
Coordination number | CoordinationNumber_serial | 4.2.6.2
Spatial Density | SpatialDensity_serial | 4.2.6.3
ScrewFit analysis | ScrewFitAnalysis_serial | 4.2.6.4
Order Parameter | OrderParameter_serial | 4.2.7.1
Order Parameter (Contact Model) | OrderParameterContactModel_serial | 4.2.7.2

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