Minor editorial changes of the documentation text

Doc/pages/H_conv.rst

@@ -1,12 +1,12 @@
 Converged Results
 =================
-In MD a large number of settings must be chosen to ensure
+In MD, a large number of settings must be chosen correctly to ensure that
 high quality results are obtained. Some of these include the size of the MD
 box, the time step and the simulation length. The choice of these settings
-also depend on the analysis calculation, for example, the dynamics coherent
-structure factor is much more difficult to obtain converged results
+also depends on the type of intended analysis; for example, the dynamic
+coherent structure factor is much more difficult to converge
 when compared to the dynamics incoherent structure factor. In this section
-we will show how the calculations results change with different MD settings
+we will show how the calculation results change with different MD settings
 for a simple liquid argon system.
 
 
@@ -17,7 +17,7 @@ Pair Distribution Function
 --------------------------
 Here we run a liquid argon trajectory with four different simulation box
 sizes: 1.146, 2.292, 4.584 and 9.168 nm. The same atom density,
-temperature, time step and simulation length is used for all cases. We
+temperature, time step and simulation length are used for all cases. We
 calculate the pair distribution function for all trajectories.
 
 .. _figure-pdf:
@@ -34,8 +34,8 @@ calculate the pair distribution function for all trajectories.
 
 In :numref:`figure-pdf` we show the results for the PDF plotted to half
 the box size. Our smallest box size 1.146 nm (blue in :numref:`figure-pdf`)
-is small enough for the periodic image of the argon atoms to have an
-significant affect on itself. Compared to our largest system size, the
+is small enough for the periodic image of the argon atoms to have a
+significant effect on itself. Compared to our largest system size, the
 first peak is shifted to a slightly longer distance, is too high and too broad.
 
 
@@ -44,12 +44,12 @@ Simulation Length
 
 Dynamic Coherent Structure Factor
 ---------------------------------
-For analysis calculations which calculate a correlation function,
+For analysis types which calculate a correlation function,
 a balance between the length of your correlation function and the number of
-configurations that you average over for each time step must be made.
+configurations that you average over for each time step must be reached.
 Here we run dynamic coherent structure factor calculations using
 the liquid argon trajectory with the 4.584 nm box size, ideal
-instrument resolutions and two different correlation frames settings.
+instrument resolution and two different correlation frames settings.
 
 .. _figure-coh-fqt:
 
@@ -74,39 +74,39 @@ instrument resolutions and two different correlation frames settings.
    using a 240 ps and 12 ns MD simulation of liquid argon plotted in blue
    and orange respectively.
 
-In the first calculation (blue in :numref:`figure-coh-fqt` and :numref:`figure-coh-sqw`) we
-use a correlation frames setting of (0, 2000, 1, 1000). So that the first
+In the first calculation (blue in :numref:`figure-coh-fqt` and :numref:`figure-coh-sqw`), we
+use a correlation frames setting of (0, 2000, 1, 1000). The first
 and last frames will be 0 and 2000 and the number of time
 steps of the correlation function will be 1000. This will mean that for
 this calculation each time step of the correlation function will be
 averaged over 1001 = 2000 -- 1000 + 1 configurations. For the blue plot in
-:numref:`figure-coh-fqt` we can see :math:`F(q, t)` oscillate around zero,
+:numref:`figure-coh-fqt` we can see :math:`F(q, t)` oscillate around zero;
 after Fourier transforming we obtain a noisy :math:`S(q, f)` which is
 especially poor around zero energy.
 
-In the second calculation (orange in :numref:`figure-coh-fqt` and :numref:`figure-coh-sqw`)
-we use a correlation frames setting of (0, 100000, 1, 1000). So that each time
+In the second calculation (orange in :numref:`figure-coh-fqt` and :numref:`figure-coh-sqw`),
+we use a correlation frames setting of (0, 100000, 1, 1000). It means that each time
 step of the correlation function will be averaged over 99001 = 100000 -- 1000 + 1
-configurations but will be same length of the first calculation. Visually
-we can see that :math:`F(q, t)` decay and stay closer to zero, after Fourier
+configurations, but will still be the same length as the first calculation. Visually,
+we can see that :math:`F(q, t)` decay and stay closer to zero, and after Fourier
 transforming we obtain a much smoother :math:`S(q, f)`. There is still
-some noise perhaps an even longer trajectory would be required. Clearly for dynamic
+some noise; perhaps an even longer trajectory would be required. Clearly for dynamic
 coherent structure factor calculations, to obtain high quality results longer
 trajectories are needed so that a larger number of configurations are used per
 time step of the correlation function.
 
-In both calculation the correlation function time steps was set to 1000 which
+In both calculations the number of correlation function time steps was set to 1000, which
 corresponds to a time of 120 ps. From the :math:`F(q, t)`, we can see that
-this is a sufficiently long to ensure that the correlation function decays
-to zero, we can see that it does not change significantly beyond 30 ps or so.
-For other calculations or systems this might not have be the case and a
-more careful choice for the correlation frames maybe required.
+this is sufficiently long to ensure that the correlation function decays
+to zero. We can see that it does not change significantly beyond 30 ps or so.
+For other calculations or systems this might not be the case and a
+more careful choice for the correlation frames may be required.
 
 Dynamic Incoherent Structure Factor
 -----------------------------------
 Here we run the dynamic incoherent structure factor calculations using the same
-liquid argon system and correlation frames settings as the dynamic coherent
-structure factor calculations for the dynamic coherent structure factor above.
+liquid argon system and correlation frames settings as in the dynamic coherent
+structure factor calculations above.
 
 .. _figure-inc-fqt:
 
@@ -135,15 +135,15 @@ In contrast to the coherent calculations, there
 are only minor differences between calculations with the (0, 2000, 1, 1000) and
 (0, 100000, 1, 1000) correlation frames settings, results shown in blue
 and orange in :numref:`figure-inc-fqt` and :numref:`figure-inc-sqw` respectively.
-We can see the the incoherent calculation requires a much smaller number of
+We can see that the incoherent calculation requires a much smaller number of
 configurations per time step to approach convergence.
 
 Static Structure Factor
 -----------------------
 Unlike the previous two calculations, the static structure factor does
 not require the calculations of a correlation function. The quality of
-your results will depend on the length of your trajectory among and number
-of other things but obviously there will not be a correlation frames
+your results will depend on the length of your trajectory (among a number
+of other things) but obviously there will not be a correlation frames
 setting to specify.
 
 .. _figure-ssf-conv:
@@ -153,16 +153,16 @@ setting to specify.
    :width: 11.748cm
    :height: 9.393cm
 
-   The static structure factor using a single frame of a MD simulation
+   The static structure factor using a single frame of an MD simulation
    and a 12 ns MD simulation of liquid argon plotted in blue and orange
    respectively.
 
 In :numref:`figure-ssf-conv` we plot the static structure factor
-calculated from a single frame of a MD simulation and a 12 ns MD
-simulation. We can see the even when we use a single frame the SSF is
+calculated from a single frame of an MD simulation and a 12 ns MD
+simulation. We can see that even when we use a single frame, the SSF is
 quite close to the results from the 12 ns MD simulation. This occurs
 since converged results can be obtained for large system sizes or
 long trajectories. The argon trajectory used contain a total of 2048
-atoms which appears to be large enough to obtain enough statistics for
-good static structure factor results so that only a short MD
+atoms which appears to be sufficient to obtain enough statistics for
+good static structure factor results, so that only a short MD
 simulation would be required.

Doc/pages/files.rst

@@ -22,8 +22,13 @@ is built on top of HDF5. Using
 HDF5 ensures platform independence, efficient data storage, and 
 self-contained information within trajectory files.
 
-Furthermore, users can used MDANSE to convert trajectories from
-other formats to the MDT format required perform analysis calculations.
+Trajectories have to be converted to the MDT format before
+MDANSE can perform analysis calculations. Multiple converters
+are available in MDANSE to convert outputs of different MD engines
+to the MDT format.
+
+The results of MDANSE analysis runs are saved in MDA files.
+Contents of the MDA files can be viewed and plotted in the MDANSE GUI.
 
 .. _text_output: