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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:

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.
\includegraphics[width=10cm]{Figures/msd_autostart_file.eps}

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



next up previous contents
Next: nMOLDYN input files Up: Using nMOLDYN from the Previous: Using nMOLDYN from the   Contents
pellegrini eric 2009-10-06