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Update tutorial 1 to include the new GUI options #21

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53 changes: 34 additions & 19 deletions tutorials/tutorial1-phase-transition/README.md
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Expand Up @@ -107,6 +107,10 @@ contain this information. Here we used the
which required us to use the *electron* unit system. Another
crucial detail is the size of the simulation time step.
You can also find it in the LAMMPS script (and it set to 0.2).
Since the frames are numbered in the LAMMPS output, the converter
uses the time step of the simulation, and calculates the time
step of the trajectory (which may include only a subset of all
the frames) based on the frame numbers.

Go to the 'Converters' tab in the GUI, and pick the LAMMPS
converter. Now you have to pass the correct inputs to the
Expand All @@ -127,7 +131,7 @@ name `mdanse_outputs/converted_trajectory.mdt`.
If some of the fields are not filled out correctly, the
GUI will try to make it clear
by disabling the 'RUN!' button and highlighting the
wrong entries.
invalid entries.

<p align="center">
<img width="800" src="pictures/gui_converter_errors.png"/>
Expand All @@ -153,7 +157,16 @@ from mdanse_inputs as the working directory.

## Load the trajectory

Go to the 'Trajectories' tab and load the trajectory created
Once the conversion of the trajectory has completed, the
trajectory will be loaded automatically. You can see it in
the 'Trajectories' tab. (If you switch off the GUI and start it
again, none of the trajectories will be loaded initially,
but you can load them again using the top menu File -> Open
Recent Trajectory File. Otherwise you can go to the 'Trajectories'
tab and click 'Load .MDT Trajectories' to load one or more
trajectories manually.)

Go to the 'Trajectories' tab and select the trajectory created
by the converter in the previous step. You should see the first
frame of the trajectory in the 3D viewer. Also, basic information
about the trajectory will be displayed in the bottom-left
Expand Down Expand Up @@ -205,13 +218,14 @@ You can plot the calculated temperature by going to the
<img width="800" src="pictures/gui_plot_creator.png"/>
</p>

Load the analysis result using the
'Load .MDA results' button. Now, unfold the contents
tree in the data view below, and click on the 'temperature'
dataset. It will appear in the box on the right.
Since we only have one curve to plot, you can just click
the 'Plot Data' button. The curve will be plotted in
the current plot in the 'Plot Holder' tab.
Once the temperature calculation has ended, the results will
be loaded into the 'Plot Creator' tab.
(If you switched off the GUI after the calculation and started
it again, you can quickly load the results again using the
File -> Open Recent Results File. You can also load one or more
result files using the 'Load .MDA results' button in the
'Plot Creator' tab.) In the 'Plot Creator' tab, double-click
the file name to create the plot.

Go to the 'Plot Holder' tab and have a look at the results.
Most likely the first and last values of the temperature
Expand All @@ -238,19 +252,17 @@ Same as in the previous part of the tutorial,
make sure that the trajectory has been loaded into the GUI.

In the Actions tab, go to
'Analysis -> Structure -> RootMeanSquareDeviation'.
'Analysis -> Dynamics -> RootMeanSquareDeviation'.
The default values of the input fields should work well
in this example; the only thing that needs to be set
is the output filename. In the script we used
the destination `mdanse_outputs/root_mean_square_displacement.mda`.

Again, you can observe the progress of the analysis in the
'Running Jobs' tab. Once the calculation has finished,
go to the 'Plot Creator' tab. On the right side, 'Clear'
the table of data and create a 'New Plot'. Then, load the
output file you just created, and select the dataset
'rmsd_all'. On the right, click 'Plot Data' and go
to the Plot Holder tab. You will see the calculated
go to the 'Plot Creator' tab. Double-click the
name of the new file and go
to the 'Plot Holder' tab. You will see the calculated
root mean square displacement of atoms from the
reference position (which in our analysis was
the initial position).
Expand Down Expand Up @@ -278,10 +290,13 @@ set frames to 700, 900, 1, change the output file name to
and click 'RUN!' again. (The script that will do the same thing
for you outside of the GUI 'script4_pdf.py')

In the Plot Creator tab click 'Clear', 'New Plot', and load
both the output files you just created. Add 'pdf_total'
data set from each of the two files to the plot and click
'Plot Data'. In the Plot Holder tab you should now
In the 'Plot Creator' tab, we will overplot the results of the
two Pair Distribution Function calculations. Click 'Clear',
then 'New Plot', and finally unfold the data tree of each
of the two files. You will see several data groups ('pdf', 'rdf',
and 'tcf'). You can add datasets to the current plot selection
by clicking their names. From each file pick the 'pdf/total' dataset,
then click 'Plot Data'. In the 'Plot Holder' tab you should now
see a plot like this one:

<p align="center">
Expand Down