Creating oxygenated amorphous carbon - Revision history

Tigany Zarrouk: /* GCMC in TurboGAP */

2024-11-14T13:22:51Z

GCMC in TurboGAP

Tigany Zarrouk at 14:06, 6 November 2023

2023-11-06T14:06:05Z

Tigany Zarrouk at 10:15, 6 November 2023

2023-11-06T10:15:55Z

Tigany Zarrouk at 10:08, 6 November 2023

2023-11-06T10:08:30Z

Tigany Zarrouk at 10:05, 6 November 2023

2023-11-06T10:05:54Z

Tigany Zarrouk at 09:51, 6 November 2023

2023-11-06T09:51:45Z

Tigany Zarrouk at 14:20, 5 November 2023

2023-11-05T14:20:15Z

Tigany Zarrouk at 14:07, 5 November 2023

2023-11-05T14:07:58Z

Tigany Zarrouk at 14:04, 5 November 2023

2023-11-05T14:04:27Z

Tigany Zarrouk at 14:50, 3 November 2023

2023-11-03T14:50:11Z

@@ Line 293: / Line 293: @@
 mc_move_max = 0.2                        ! Maximum distance for the move of a particular particle
 mc_mu = 0.0                              ! gcmc: Chemical potential [eV], using a large one here
 mc_species = 'O'                         ! gcmc: species to insert / remove
@@ Line 346: / Line 347: @@
 </div>
 <span id="hamiltonian-monte-carlo"></span>
 == Hamiltonian Monte-Carlo ==

@@ Line 93: / Line 93: @@
 * Copy the directory <code>turbogap/tutorials/creating_a-COx</code> to where you want to run.
 * Make sure the python package <code>ase</code> is installed by running <code>pip install ase {--user}</code>.
-* Use the edit the convenience script <code>change_to_local.sh</code> and run.
+* Edit the convenience script <code>change_to_local.sh</code> and run with bash.
 * Change the path environment variable in <code>sample_submit_script.sh</code>.

@@ Line 38: / Line 38: @@
 === For the MLIP workshop ===
-This step is ''not'' necessary if you are at the MLIP workshop. TurboGAP is installed in the path (on Mahti / Puhti)
+If you have a CSC account and can ssh into Mahti/Puhti there is no need to install anything. TurboGAP is installed in the path (on Mahti / Puhti)
 <syntaxhighlight lang="bash">/projappl/project_2008666/turbogap
@@ Line 46: / Line 46: @@
 <syntaxhighlight lang="bash">cd /projappl/project_2008666/turbogap/tutorials/creating_a-COx
 </syntaxhighlight>
-Copy the directory <code>creating_a-COx</code> to wherever you want to do the simulations and then change the project in <code>creating_a-COx/sample_submit_script.sh</code> from
+Copy the directory <code>creating_a-COx</code> to wherever you want to do the simulations and then check the project in <code>creating_a-COx/sample_submit_script.sh</code>, change it from
 <syntaxhighlight lang="bash">#SBATCH --account=project_

@@ Line 361: / Line 361: @@
                                           !   move type
 </pre>
 <span id="npt-using-volume-moves"></span>
 == <math display="inline">NPT</math> using volume moves ==
@@ Line 391: / Line 395: @@
 To run it we do
-<syntaxhighlight lang="bash">cd ../3.volume_mc
+<syntaxhighlight lang="bash">cd ../4.volume_mc
 bash 1.run_volume.sh
 </syntaxhighlight>
 This gives an expansion of the volume.

@@ Line 27: / Line 27: @@
 #* Adaptive time-scale MD (by Uttiyoarnab Saha).
 # Prediction of an arbitrary number of local properties.
-## <u>ML Van der Waals</u> (by prediction of local hirshfeld volumes) using Tkatchenko-Scheffler [https://doi.org/10.1103/PhysRevB.104.054106 Machine learning force fields based on local parametrization of dispersion interactions]
+#* <u>ML Van der Waals</u> (by prediction of local hirshfeld volumes) using Tkatchenko-Scheffler [https://doi.org/10.1103/PhysRevB.104.054106 Machine learning force fields based on local parametrization of dispersion interactions]
-## Heikki Muhli has developed ''Many-Body Dispersion'' capability, with multiple optimisations.
+#* Heikki Muhli has developed ''Many-Body Dispersion'' capability, with multiple optimisations.
-## Max Veit is developing ''electrostatics''.
+#* Max Veit is developing ''electrostatics''.
 # <u>Sneak Peek!</u>: we have added the capability to predict/simulate numerous types of experimental data (ML XPS/XRD) and can allow them to influence simulation. (Talk to Tigany Zarrouk/look out for the papers when they come out on arXiv)!

@@ Line 7: / Line 7: @@
 # Create an amorphous carbon structure using molecular dynamics, via a melt-quench procedure.
 # Perform a standard GCMC calculation to populate the structure with oxygen.
-# Perform a hybrid Monte-Carlo/MD simulation, to relax the volume.
+# Perform a hybrid Monte-Carlo/MD simulations, to relax the system.
 <span id="introduction"></span>
@@ Line 24: / Line 24: @@
 #* <u>GPU implementation</u> in progress (with CSC support too).
 # It can perform not just typical molecular statics (with/without box relaxation) and dynamics (<math display="inline">NVT</math> / <math display="inline">NPT</math>), it can perform ''Grand-Canonical Monte-Carlo'' simulations.
-#* Grand-Canonical Monte Carlo (<math display="inline">\mu VT</math>), with (<math display="inline">NVT</math>) / (<math display="inline">NPT</math>) move types available:
+#* Grand-Canonical Monte Carlo (<math display="inline">\mu VT</math>), with (<math display="inline">NVT</math>) / (<math display="inline">NPT</math>) move types available.
-# <u>ML Van der Waals</u> (by prediction of local hirshfeld volumes) using Tkatchenko-Scheffler [https://doi.org/10.1103/PhysRevB.104.054106 Machine learning force fields based on local parametrization of dispersion interactions]
+#* Adaptive time-scale MD (by Uttiyoarnab Saha).
 # Prediction of an arbitrary number of local properties.
 # <u>Sneak Peek!</u>: we have added the capability to predict/simulate numerous types of experimental data (ML XPS/XRD) and can allow them to influence simulation. (Talk to Tigany Zarrouk/look out for the papers when they come out on arXiv)!
@@ Line 36: / Line 38: @@
 === For the MLIP workshop ===
-This step is ''not'' necessary if you are at the MLIP workshop. TurboGAP is installed in the path (on Mahti)
+This step is ''not'' necessary if you are at the MLIP workshop. TurboGAP is installed in the path (on Mahti / Puhti)
 <syntaxhighlight lang="bash">/projappl/project_2008666/turbogap
@@ Line 52: / Line 54: @@
 <syntaxhighlight lang="bash">#SBATCH --account=project_2008666
 </syntaxhighlight>
 <span id="installation"></span>
 === Installation ===
@@ Line 58: / Line 67: @@
 <syntaxhighlight lang="bash">git clone --recursive http://github.com/mcaroba/turbogap.git /your/turbogap/source/directory
 </syntaxhighlight>
 Where /your/turbogap/source/directory is the directory where you're putting the TurboGAP source code. To build the TurboGAP binary and library, you need to select the options that best match your architecture, by editing this line in the Makefile with one of the names of the corresponding makefiles in turbogap/makefiles:
@@ Line 80: / Line 84: @@
 * Change <code>sample_submit_script.sh</code> to reflect the type of job scheduler you use (here, it's slurm), the modules you've loaded for <code>turbogap</code> and python, and change the <code>PATH</code> environment variable to where you've installed <code>turbogap/bin</code>.
 * Make sure the project account is correct!
 * Change the <code>srun turbogap</code> commands in the <code>script_*.sh</code> files to the standard for your cluster (e.g. <code>mpirun -np $N turbogap</code>).
 * In each of the directories enumerated with &quot;1.,2., etc&quot;, run the scripts in order after the preceding job has finished. They are enumerated with &quot;1.,2., etc&quot; with bash, e.g. <code>bash 1.run_randomise.sh</code>.
@@ Line 87: / Line 92: @@
 * Copy the directory <code>turbogap/tutorials/creating_a-COx</code> to where you want to run.
 * Use the edit the convenience script <code>change_to_local.sh</code> and run.
 * Change the path environment variable in <code>sample_submit_script.sh</code>.
@@ Line 297: / Line 303: @@
 <syntaxhighlight lang="bash">srun turbogap mc
 </syntaxhighlight>
-Which can be done by To run these calculations, do
+To run these calculations, do
 <syntaxhighlight lang="bash">cd ../2.standard_gcmc
@@ Line 339: / Line 345: @@
 </div>
 <span id="npt-using-volume-moves"></span>
 == <math display="inline">NPT</math> using volume moves ==

@@ Line 240: / Line 240: @@
 and using your atom viewer of choice.
-At the end, you should have a structure which is similar to this. [[File:amorphous_carbon.png]]
+At the end, you should have a structure which is similar to this.
 You can look at the local energies predicted by the GAP (here I use <code>ovito</code>).

@@ Line 1: / Line 1: @@
 This tutorial will focus on using molecular dynamics and Grand-Canonical Monte-Carlo (GCMC) simulations to determine equilibrium structures of oxygenated amorphous carbon using '''TurboGAP'''.
-This tutorial is found on the *TurboGAP^ wiki: turbogap.fi (-&gt; tutorials -&gt; Creating oxygenated amorphous carbon)
+This tutorial is found on the '''TurboGAP''' wiki: <u>turbogap.fi</u> (-&gt; tutorials -&gt; Creating oxygenated amorphous carbon) https://turbogap.fi/wiki/index.php/Creating_oxygenated_amorphous_carbon.
 The structure of this tutorial as as follows:
@@ Line 149: / Line 147: @@
 cp diamond.xyz $input_atoms
 </syntaxhighlight>
-<u>Note:</u> In <code>create_diamond.py</code> we make 1000 atoms. We can change this to a smaller number, if you want things to run faster.
+<u>Note:</u> In <code>create_diamond.py</code> we make 1000 atoms. You can change this to a smaller number, if you want things to run faster.
 <syntaxhighlight lang="python">atoms *= (3,3,3)

@@ Line 284: / Line 284: @@
 mc_min_dist = 0.1                        ! gcmc: minimum distance between particles for insertion
 </pre>
 To run it, we run '''TurboGAP''' in <code>mc</code> mode:
@@ Line 330: / Line 332: @@
 </div>
 <span id="npt-using-volume-moves"></span>
 == <math display="inline">NPT</math> using volume moves ==