Merge pull request #308 from aproeme/master

Update for cp2/2023.2 install

docs/software-packages/cp2k.md

@@ -14,79 +14,54 @@ state optimisation using NEB or dimer method.
 
 ## Useful Links
 
-- [CP2K Reference Manual](https://manual.cp2k.org/#gsc.tab=0)
+- [CP2K Reference Manual](https://manual.cp2k.org)
 - [CP2K HOWTOs](https://www.cp2k.org/howto)
 - [CP2K FAQs](https://www.cp2k.org/faq)
 
 ## Using CP2K on Cirrus
 
-CP2K is available through the `cp2k` module. MPI only `cp2k.popt` and
-MPI/OpenMP Hybrid `cp2k.psmp` binaries are available.
+CP2K is available through the `cp2k` module. Loading this module
+provides access to the MPI/OpenMP hybrid `cp2k.psmp` executable.
 
-## Running parallel CP2K jobs - MPI Only
+To run CP2K after loading this module you should also source the
+environment setup script that was generated by CP2K's toolchain (see
+example job script below)
 
-To run CP2K using MPI only, load the `cp2k` module and use the
-`cp2k.popt` executable.
-
-For example, the following script will run a CP2K job using 4 nodes (144
-cores):
-
-     #!/bin/bash
-
-     # Slurm job options (name, compute nodes, job time)
-     #SBATCH --job-name=CP2K_test
-     #SBATCH --time=0:20:0
-     #SBATCH --exclusive
-     #SBATCH --nodes=4
-     #SBATCH --tasks-per-node=36 
-     #SBATCH --cpus-per-task=1
-
-     # Replace [budget code] below with your budget code (e.g. t01)
-     #SBATCH --account=[budget code]
-     # Replace [partition name] below with your partition name (e.g. standard,gpu)
-     #SBATCH --partition=[partition name]
-     # Replace [qos name] below with your qos name (e.g. standard,long,gpu)
-     #SBATCH --qos=[qos name]
-
-     # Load CP2K
-     module load cp2k
-
-     #Ensure that no libraries are inadvertently using threading
-     export OMP_NUM_THREADS=1
-
-     # Run using input in test.inp
-     srun cp2k.popt -i test.inp
 
 ## Running Parallel CP2K Jobs - MPI/OpenMP Hybrid Mode
 
 To run CP2K using MPI and OpenMP, load the `cp2k` module and use the
-`cp2k.psmp` executable.
+`cp2k.psmp` executable. 
 
 For example, the following script will run a CP2K job using 8 nodes,
 with 2 OpenMP threads per MPI process:
 
-     #!/bin/bash
+    #!/bin/bash
+
+    # Slurm job options (name, compute nodes, job time)
+    #SBATCH --job-name=CP2K_test
+    #SBATCH --time=0:20:0
+    #SBATCH --exclusive
+    #SBATCH --nodes=8
+    #SBATCH --tasks-per-node=18
+    #SBATCH --cpus-per-task=2
+
+    # Replace [budget code] below with your budget code (e.g. t01)
+    #SBATCH --account=[budget code]
+    # Replace [partition name] below with your partition name (e.g. standard,gpu)
+    #SBATCH --partition=[partition name]
+    # Replace [qos name] below with your qos name (e.g. standard,long,gpu)
+    #SBATCH --qos=[qos name]
 
-     # Slurm job options (name, compute nodes, job time)
-     #SBATCH --job-name=CP2K_test
-     #SBATCH --time=0:20:0
-     #SBATCH --exclusive
-     #SBATCH --nodes=8
-     #SBATCH --tasks-per-node=18
-     #SBATCH --cpus-per-task=2
+    # Load CP2K
+    module load cp2k
 
-     # Replace [budget code] below with your budget code (e.g. t01)
-     #SBATCH --account=[budget code]
-     # Replace [partition name] below with your partition name (e.g. standard,gpu)
-     #SBATCH --partition=[partition name]
-     # Replace [qos name] below with your qos name (e.g. standard,long,gpu)
-     #SBATCH --qos=[qos name]
+    # Source the environment setup script generated by CP2K's install toolchain
+    source $CP2K/tools/toolchain/install/setup
 
-     # Load CP2K
-     module load cp2k
+    # Set the number of threads to the value specified for --cpus-per-task above
+    export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
 
-     # Set the number of threads to 2
-     export OMP_NUM_THREADS=2
+    # Run using input in test.inp
+    srun cp2k.psmp -i test.inp
 
-     # Run using input in test.inp
-     srun cp2k.psmp -i test.inp