Merge pull request #11 from RuiApostolo/gh-pages

Small fixes
EPCCed · Dec 9, 2024 · 9c2a84b · 9c2a84b
2 parents 4d17690 + 74653d9
commit 9c2a84b
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diff --git a/_episodes/02-lammps-on-archer2.md b/_episodes/02-lammps-on-archer2.md
@@ -133,7 +133,7 @@ You can either download these by either:
 ### Using `git`
 
 ```bash
-git clone https://github.com/EPCCed/archer2-intro-to-lammps
+git clone https://github.com/EPCCed/archer2-intro-to-lammps.git
 ```
 
 and then navigating to the `exercises folder` with:
@@ -193,12 +193,13 @@ This will help us to understand what our simulation is doing, and where we can s
 Running:
 
 ```bash
-tail -n 27 log.64_cpus
+tail -n 28 log.64_cpus
 ```
 
 will output the following:
 
 ```
+Performance: 12.825 ns/day, 1.871 hours/ns, 148.442 timesteps/s
 100.0% CPU use with 64 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:

diff --git a/_episodes/05-advanced-input-and-output-commands.md b/_episodes/05-advanced-input-and-output-commands.md
@@ -136,9 +136,9 @@ Our `fix ave/time` has the following parameters:
    - `Nrepeat` is how many sets of values we want to average over (number of samples)
    - `Nevery` is how many time-steps in between samples.
    - `Nfreq` must be a multiple of `Nevery`, and `Nevery` must be non-zero even if `Nrepeat = 1`.
-   - So, for example, an `Nevery` of 2, with `Nrepeat` of 3, and `Nfreq` of 100 100 means that at every time-step multiple of 100,
-     there will be an average written to file, that was calculated by taking 3 samples, 2 time-steps apart.
-     Time-steps 96, 98, and 100 are averaged, and the average is written to file.
+   - So, for example, an `Nevery` of 2, with `Nrepeat` of 3, and `Nfreq` of 100: at every time-step multiple of 100 (`Nfreq`),
+     there will be an average written to file, that was calculated by taking 3 samples (`Nrepeat`), 2 time-steps apart (`Nevery`).
+     So, time-steps 96, 98, and 100 are averaged, and the average is written to file.
      Likewise at time-steps 196, 198, and 200, etc.
    - In this case, we take a sample every 25 time-steps, 100 times, and output at time-step number 5000
      -- so from time-step 2500 to 5000, sampling every 25 time-steps.
@@ -204,7 +204,7 @@ For this command, the file looks something like this:
 ### Mean-squared diplacement (MSD)
 
 The mean-squared displacement (MSD) is a measure of the average displacement that particles travel from their origin position at some given time.
-The slope of the RDF is directly proportional to the diffusion coefficient of the system.
+The slope of the MSD is directly proportional to the diffusion coefficient of the system.
 As with the RDF, we will require a `compute` command and a `fix` command to call that `compute`:
 
 ```

diff --git a/_episodes/08-creating-topology.md b/_episodes/08-creating-topology.md
@@ -93,7 +93,7 @@ In the next section, we will use **VMD** to automatically create the bonds, angl
 
 > ## Tip
 >
-> To solvate large molecules/particles (for example, polymers), it is considerably faster to do multi-stop packing, with different input files, one per molecule type, and using the `fixed` constraint for the topology with the already packed molecules.
+> To solvate large molecules/particles (for example, polymers), it is considerably faster to do multi-step packing, with different input files, one per molecule type, and using the `fixed` constraint for the topology with the already packed molecules.
 >
 > Example:
 >