Commit a515ed9d authored by Éamonn Murray's avatar Éamonn Murray

More minor text fixes

parent d743caf1
......@@ -90,8 +90,8 @@ this calculation for a methane molecule.
[`01_CH4_scf.in`](CH4/01_CH4_scf.in). You'll see that we have set this up as
usual. We have specified both the `prefix = CH4` and `outdir = './out'` as
this calculation generates many intermediate files, so it will be easier to
keep them all together. We have also set the positions such that C atom is
at the centre of the cell. This will make some subsequent visualization a
keep them all together. We have also set the positions such that the C atom
is at the centre of the cell. This will make some subsequent visualization a
little easier.
- Run `pw.x` with this input file and examine the output to ensure it worked
as expected.
......@@ -147,10 +147,11 @@ this calculation for a methane molecule.
Take a look at the file `CH4.plot_chi.dat` now. You'll see the file is not
really amenable for plotting.
- First we can extract the oscillator strength with the following awk command:
```bash
awk '/S\(E\)=/{print $2, $3}' CH4.plot_chi.dat > ostrength.dat
awk '/S\(E\)=/{print $2, $3}' CH4.plot_chi.dat > ostrength.dat
```
This will print the second and third character on every line containing the
text `S(E)=` (we need to use a `\` to escape the parentheses). This extracts
......@@ -167,14 +168,14 @@ alone is sufficient. This is a complex number, and we should look at both
the real and imaginary parts.
- Parse the energy, the real and the imaginary part of the susceptibility
(from the 11 component of chi in the `plot_chi.dat` file) and plot the real
and imaginary parts together in gnuplot.
(from the 11 component of chi in the `plot_chi.dat` file) and plot both the
real and imaginary parts together in gnuplot.
- If you parse this to a file with three columns: x, y1, y2, you can plot
them together in gnuplot as
`plot "file" with lines, "file" using 1:3 with lines`.
- You can plot several plots together by separating them with commas, and
you can use the keyword `using` to specify the columns to plot (it is
`1:2` by default.
`1:2` by default).
Charge Density Response
-----------------------
......@@ -216,9 +217,9 @@ Then we have added an addition section `LR_POST`, which is needed whenever
hopefully work correctly.
Run `turbo_lanczos.x` with this input file. It'll take a couple of minutes to
finish. Once completed you'll see either a pair of files named
finish. Once completed you'll see *either* a pair of files named
`CH4-absorbtive-pol1.cube` and `CH4-dispersive-pol1.cube` have been created,
or a single file named `CH4-summed-rho-pol1.cube`. The former are generated
*or* a single file named `CH4-summed-rho-pol1.cube`. The former are generated
where the code determines the energy `omeg` (including the broadening `epsil`)
you are calculating at corresponds to a resonance where there is a peak in the
spectrum, and the latter is output otherwise. In our case we should be within
......@@ -230,9 +231,11 @@ this to open one of the generated files by navigating through File -> Open
Structure -> Gaussian98 Cube File, and selecting the file. You can look at the
regions where the charge density is increased and decreased in response to the
oscillating electric field of the photon by going to Tools -> Data Grid, click
OK. Then select an appropriate Isovalue in the menu that appears (you can
repeat this process with different values till you see something interesting),
tick the `Render +/- isovalue` box, and click `Submit`.
OK. Then select an appropriate Isovalue in the menu that appears, tick the
`Render +/- isovalue` box, and click `Submit`. To find a good isovalue you can
repeat this process with different values within the listed maximum and
minimum on the grid till you see something interesting; the menu will stay
visible after you click submit.
Convergence
-----------
......
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