diff --git a/_episodes/02-lammps-on-archer2.md b/_episodes/02-lammps-on-archer2.md index 2bfd108..7795d41 100644 --- 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 index 9e6b580..811bc40 100644 --- 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 index f26b922..41e08de 100644 --- 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: >