ChemWiki - User contributions [en]

Building ML potentials with AML

2023-05-30T16:49:19Z

Yl4619:

This page includes a short tutorial on how to install the AML package on Imperial's cluster and set up all the necessary tools to run it.

[https://github.com/CompPhysVienna/n2p2 n2p2] is the main software used by the AML package to build the neural network potentials, which has to be downloaded and compiled correctly first. However, the compilation requires quite a few tools, and it can be cumbersome to download and install them individually. To make this task easier, we can install CP2K first which comes with a lot of tools that can be used by n2p2, so we don't have to install them manually.

==Installation of CP2K version 8.1==

===Installation of OpenMPI===
The first step is to install OpenMPI. [https://edu.itp.phys.ethz.ch/hs12/programming_techniques/openmpi.pdf Here] is a fantastic tutorial on how to do that. After step 7 in that tutorial, run this command together with the other 2 as well.
<pre>
echo "OMPI_HOME=$HOME/opt/openmpi/" >> ~/.bashrc
</pre>
This should set up OpenMPI correctly. To use OpenMPI (or, to let the system know that you have OpenMPI), run this every time when a new terminal session starts.
<pre>
source ~/.bashrc
</pre>

===Installation of CP2K===
Now we can install CP2K. The first step is to clone the GitHub repository.
<pre>
git clone -b support/v8.1 --recursive https://github.com/cp2k/cp2k.git cp2k
</pre>
Now we have already cloned it into a directory called cp2k, we need to go to that directory and run the following command
<pre>
cd tools/toolchain/
./install_cp2k_toolchain.sh --no-check-certificate --with-elpa=no
</pre>
After these commands there will be instructions (and/or ERRORs) at the end. Follow the instructions, if the above command is successful the instruction will ask you to do something like this
<pre>
source install/setup
cp /install/arch/* ~/cp2k/arch/
cd ~/cp2k
make ARCH=local VERSION="ssmp sdbg psmp pdbg" &> make.log
</pre>

This whole process can take hours so be patient. With CP2K installed and compiled, we can use the tools included to build n2p2.

==Installation of n2p2==
[https://compphysvienna.github.io/n2p2/topics/build.html This documentation] of n2p2 gives some instruction on how to build the software. However, to actually build the software, we will need some of the packages we installed with CP2K. We do this by including the tools in the '''~/.bashrc''' file using the same 'echo' command as before.

For example, when compiling we need the header file '''gsl/gsh_rng.h''', which is located in the CP2K toolchain directory. The path to the folder containing '''gsl/gsl_rng.h''' on my computer is
<pre>
/rds/general/user/yl4619/home/cp2k-8.1/tools/toolchain/install/gsl-2.6/include
</pre>
So I need to add this to the '''CPATH''' variable by doing
<pre>
echo "export CPATH=$CPATH:/rds/general/user/yl4619/home/cp2k-8.1/tools/toolchain/install/gsl-2.6/include" >> $HOME/.bashrc
</pre>

We will need to link several other libraries/binaries/header files too, so just try to compile and read the error message which will tell you which package you are lacking, and search for that in the CP2K toolchain directory and link it using the method above. There will be several types of files that need to linked: use '''$PATH''' to link '''bin''' folders, '''$LIBRARY_PATH''' to link '''lib''' folders, and '''$CPATH''' to link '''include''' folders.

One special one is the OpenBLAS package. Some of the components of n2p2 requires BLAS when compiling and cannot recognise OpenBLAS as a variant of BLAS. So for this we need to manually change the '''makefile''' file in n2p2/src/application: change '''$(PROJECT_LDFLAGS_BLAS)''' in the file to '''-lopenblas -lgslcblas''', which should solve the problem.

All components in the n2p2 package should compile successfully after this. For the compilation of both CP2K and n2p2, the compiled applications might not be usable on specific [https://en.wikipedia.org/wiki/Instruction_set_architecture instruction sets], so make sure when you are submitting jobs you submit to the right queue that uses compatible instruction sets. For example, I compiled on the login node of the cluster which uses '''Rome''', so when submit jobs I specify the CPU type with
<pre>
#PBS cpu_type=rome
</pre>

==Installation of AML==
The AML package can be smoothly installed following the instructions on its [https://github.com/MarsalekGroup/aml GitHub repository]

==Running the AML package==
Follow the example given in the AML package.

Building ML potentials with AML

2023-05-04T12:49:26Z

Yl4619:

This page includes a short tutorial on how to install the AML package and set up all the necessary tools to run it.

[https://github.com/CompPhysVienna/n2p2 n2p2] is the main software used by the AML package to build the neural network potentials, which has to be downloaded and compiled correctly first. However, the compilation requires quite a few tools, and it can be cumbersome to download and install them individually. To make this task easier, we can install CP2K first which comes with a lot of tools that can be used by n2p2, so we don't have to install them manually.

==Installation of CP2K version 8.1==

===Installation of OpenMPI===
The first step is to install OpenMPI. [https://edu.itp.phys.ethz.ch/hs12/programming_techniques/openmpi.pdf Here] is a fantastic tutorial on how to do that. After step 7 in that tutorial, run this command together with the other 2 as well.
<pre>
echo "OMPI_HOME=$HOME/opt/openmpi/" >> ~/.bashrc
</pre>
This should set up OpenMPI correctly. To use OpenMPI (or, to let the system know that you have OpenMPI), run this every time when a new terminal session starts.
<pre>
source ~/.bashrc
</pre>

===Installation of CP2K===
Now we can install CP2K. The first step is to clone the GitHub repository.
<pre>
git clone -b support/v8.1 --recursive https://github.com/cp2k/cp2k.git cp2k
</pre>
Now we have already cloned it into a directory called cp2k, we need to go to that directory and run the following command
<pre>
cd tools/toolchain/
./install_cp2k_toolchain.sh --no-check-certificate --with-elpa=no
</pre>
After these commands there will be instructions (and/or ERRORs) at the end. Follow the instructions, if the above command is successful the instruction will ask you to do something like this
<pre>
source install/setup
cp /install/arch/* ~/cp2k/arch/
cd ~/cp2k
make ARCH=local VERSION="ssmp sdbg psmp pdbg" &> make.log
</pre>

This whole process can take hours so be patient. With CP2K installed and compiled, we can use the tools included to build n2p2.

==Installation of n2p2==
[https://compphysvienna.github.io/n2p2/topics/build.html This documentation] of n2p2 gives some instruction on how to build the software. However, to actually build the software, we will need some of the packages we installed with CP2K. We do this by including the tools in the '''~/.bashrc''' file using the same 'echo' command as before.

For example, when compiling we need the header file '''gsl/gsh_rng.h''', which is located in the CP2K toolchain directory. The path to the folder containing '''gsl/gsl_rng.h''' on my computer is
<pre>
/rds/general/user/yl4619/home/cp2k-8.1/tools/toolchain/install/gsl-2.6/include
</pre>
So I need to add this to the '''CPATH''' variable by doing
<pre>
echo "export CPATH=$CPATH:/rds/general/user/yl4619/home/cp2k-8.1/tools/toolchain/install/gsl-2.6/include" >> $HOME/.bashrc
</pre>

We will need to link several other libraries/binaries/header files too, so just try to compile and read the error message which will tell you which package you are lacking, and search for that in the CP2K toolchain directory and link it using the method above. There will be several types of files that need to linked: use '''$PATH''' to link '''bin''' folders, '''$LIBRARY_PATH''' to link '''lib''' folders, and '''$CPATH''' to link '''include''' folders.

One special one is the OpenBLAS package. Some of the components of n2p2 requires BLAS when compiling and cannot recognise OpenBLAS as a variant of BLAS. So for this we need to manually change the '''makefile''' file in n2p2/src/application: change '''$(PROJECT_LDFLAGS_BLAS)''' in the file to '''-lopenblas -lgslcblas''', which should solve the problem.

All components in the n2p2 package should compile successfully after this. For the compilation of both CP2K and n2p2, the compiled applications might not be usable on specific [https://en.wikipedia.org/wiki/Instruction_set_architecture instruction sets], so make sure when you are submitting jobs you submit to the right queue that uses compatible instruction sets. For example, I compiled on the login node of the cluster which uses '''Rome''', so when submit jobs I specify the CPU type with
<pre>
#PBS cpu_type=rome
</pre>

==Installation of AML==
The AML package can be smoothly installed following the instructions on its [https://github.com/MarsalekGroup/aml GitHub repository]

==Running the AML package==
Follow the example given in the AML package.

Building ML potentials with AML

2023-05-04T12:48:18Z

Yl4619: /* Installation of n2p2 */

Building ML potentials with AML

2023-05-04T12:48:07Z

Yl4619:

This page includes a short tutorial on how to install the AML package and set up all the necessary tools to run it.

[https://github.com/CompPhysVienna/n2p2 n2p2] is the main software used by the AML package to build the neural network potentials, which has to be downloaded and compiled correctly first. However, the compilation requires quite a few tools, and it can be cumbersome to download and install them individually. To make this task easier, we can install CP2K first which comes with a lot of tools that can be used by n2p2, so we don't have to install them manually.

==Installation of CP2K version 8.1==

===Installation of OpenMPI===
The first step is to install OpenMPI. [https://edu.itp.phys.ethz.ch/hs12/programming_techniques/openmpi.pdf Here] is a fantastic tutorial on how to do that. After step 7 in that tutorial, run this command together with the other 2 as well.
<pre>
echo "OMPI_HOME=$HOME/opt/openmpi/" >> ~/.bashrc
</pre>
This should set up OpenMPI correctly. To use OpenMPI (or, to let the system know that you have OpenMPI), run this every time when a new terminal session starts.
<pre>
source ~/.bashrc
</pre>

===Installation of CP2K===
Now we can install CP2K. The first step is to clone the GitHub repository.
<pre>
git clone -b support/v8.1 --recursive https://github.com/cp2k/cp2k.git cp2k
</pre>
Now we have already cloned it into a directory called cp2k, we need to go to that directory and run the following command
<pre>
cd tools/toolchain/
./install_cp2k_toolchain.sh --no-check-certificate --with-elpa=no
</pre>
After these commands there will be instructions (and/or ERRORs) at the end. Follow the instructions, if the above command is successful the instruction will ask you to do something like this
<pre>
source install/setup
cp /install/arch/* ~/cp2k/arch/
cd ~/cp2k
make ARCH=local VERSION="ssmp sdbg psmp pdbg" &> make.log
</pre>

This whole process can take hours so be patient. With CP2K installed and compiled, we can use the tools included to build n2p2.

==Installation of n2p2==
[https://compphysvienna.github.io/n2p2/topics/build.html This documentation] of n2p2 gives some instruction on how to build the software. However, to actually build the software, we will need some of the packages we installed with CP2K. We do this by including the tools in the '''~/.bashrc''' file using the same 'echo' command as before.

For example, when compiling we need the header file '''gsl/gsh_rng.h''', which is located in the CP2K toolchain directory. The path to the folder containing '''gsl/gsl_rng.h''' on my computer is
<pre>
/rds/general/user/yl4619/home/cp2k-8.1/tools/toolchain/install/gsl-2.6/include
</pre>
So I need to add this to the '''CPATH''' variable by doing
<pre>
echo "export CPATH=$CPATH:/rds/general/user/yl4619/home/cp2k-8.1/tools/toolchain/install/gsl-2.6/include" >> $HOME/.bashrc
</pre>

We will need to link several other libraries/binaries/header files too, so just try to compile and read the error message which will tell you which package you are lacking, and search for that in the CP2K toolchain directory and link it using the method above. There will be several types of files that need to linked: use '''$PATH''' to link '''bin''' folders, '''$LIBRARY_PATH''' to link '''lib''' folders, and '''$CPATH''' to link '''include''' folders.

One special one is the OpenBLAS package. Some of the components of n2p2 requires BLAS when compiling and cannot recognise OpenBLAS as a variant of BLAS. So for this we need to manually change the '''makefile''' file in n2p2/src/application: change '''$(PROJECT_LDFLAGS_BLAS)''' in the file to '''-lopenblas -lgslcblas''', which should solve the problem.

All components in the n2p2 package should compile successfully after this. For the compilation of both CP2K and n2p2, the compiled applications might not be usable on specific [https://en.wikipedia.org/wiki/Instruction_set_architecture instruction sets], so make sure when you are submitting jobs you submit to the right queue that uses compatible instruction sets. For example, I compiled on the login node of the cluster which uses '''Rome''', so when submit jobs I specify the CPU type with
<pre>
#PBS cpu_type=rome
<\pre>

==Installation of AML==
The AML package can be smoothly installed following the instructions on its [https://github.com/MarsalekGroup/aml GitHub repository]

Building ML potentials with AML

2023-05-04T12:38:26Z

Yl4619: /* Installation of AML */

This page includes a short tutorial on how to install the AML package and set up all the necessary tools to run it.

[https://github.com/CompPhysVienna/n2p2 n2p2] is the main software used by the AML package to build the neural network potentials, which has to be downloaded and compiled correctly first. However, the compilation requires quite a few tools, and it can be cumbersome to download and install them individually. To make this task easier, we can install CP2K first which comes with a lot of tools that can be used by n2p2, so we don't have to install them manually.

==Installation of CP2K version 8.1==

===Installation of OpenMPI===
The first step is to install OpenMPI. [https://edu.itp.phys.ethz.ch/hs12/programming_techniques/openmpi.pdf Here] is a fantastic tutorial on how to do that. After step 7 in that tutorial, run this command together with the other 2 as well.
<pre>
echo "OMPI_HOME=$HOME/opt/openmpi/" >> ~/.bashrc
</pre>
This should set up OpenMPI correctly. To use OpenMPI (or, to let the system know that you have OpenMPI), run this every time when a new terminal session starts.
<pre>
source ~/.bashrc
</pre>

===Installation of CP2K===
Now we can install CP2K. The first step is to clone the GitHub repository.
<pre>
git clone -b support/v8.1 --recursive https://github.com/cp2k/cp2k.git cp2k
</pre>
Now we have already cloned it into a directory called cp2k, we need to go to that directory and run the following command
<pre>
cd tools/toolchain/
./install_cp2k_toolchain.sh --no-check-certificate --with-elpa=no
</pre>
After these commands there will be instructions (and/or ERRORs) at the end. Follow the instructions, if the above command is successful the instruction will ask you to do something like this
<pre>
source install/setup
cp /install/arch/* ~/cp2k/arch/
cd ~/cp2k
make ARCH=local VERSION="ssmp sdbg psmp pdbg" &> make.log
</pre>

This whole process can take hours so be patient. With CP2K installed and compiled, we can use the tools included to build n2p2.

==Installation of n2p2==
[https://compphysvienna.github.io/n2p2/topics/build.html This documentation] of n2p2 gives some instruction on how to build the software. However, to actually build the software, we will need some of the packages we installed with CP2K. We do this by including the tools in the '''~/.bashrc''' file using the same 'echo' command as before.

For example, when compiling we need the header file '''gsl/gsh_rng.h''', which is located in the CP2K toolchain directory. The path to the folder containing '''gsl/gsl_rng.h''' on my computer is
<pre>
/rds/general/user/yl4619/home/cp2k-8.1/tools/toolchain/install/gsl-2.6/include
</pre>
So I need to add this to the '''CPATH''' variable by doing
<pre>
echo "export CPATH=$CPATH:/rds/general/user/yl4619/home/cp2k-8.1/tools/toolchain/install/gsl-2.6/include" >> $HOME/.bashrc
</pre>

We will need to link several other libraries/binaries/header files too, so just try to compile and read the error message which will tell you which package you are lacking, and search for that in the CP2K toolchain directory and link it using the method above. There will be several types of files that need to linked: use '''$PATH''' to link '''bin''' folders, '''$LIBRARY_PATH''' to link '''lib''' folders, and '''$CPATH''' to link '''include''' folders.

One special one is the OpenBLAS package. Some of the components of n2p2 requires BLAS when compiling and cannot recognise OpenBLAS as a variant of BLAS. So for this we need to manually change the '''makefile''' file in n2p2/src/application: change '''$(PROJECT_LDFLAGS_BLAS)''' in the file to '''-lopenblas -lgslcblas''', which should solve the problem.

All components in the n2p2 package should compile successfully after this.

==Installation of AML==
The AML package can be smoothly installed following the instructions on its [https://github.com/MarsalekGroup/aml GitHub repository]

Building ML potentials with AML

2023-05-04T12:37:15Z

Yl4619:

Building ML potentials with AML

2023-05-04T12:36:48Z

Yl4619: /* Installation of n2p2 */

Building ML potentials with AML

2023-05-04T12:36:10Z

Yl4619: /* Installation of n2p2 */

Building ML potentials with AML

2023-05-04T12:35:51Z

Yl4619: /* Installation of n2p2 */

Building ML potentials with AML

2023-05-04T12:16:37Z

Yl4619: /* Installation of n2p2 */

This page includes a short tutorial on how to install the AML package and set up all the necessary tools to run it.

[https://github.com/CompPhysVienna/n2p2 n2p2] is the main software used by the AML package to build the neural network potentials, which has to be downloaded and compiled correctly first. However, the compilation requires quite a few tools, and it can be cumbersome to download and install them individually. To make this task easier, we can install CP2K first which comes with a lot of tools that can be used by n2p2, so we don't have to install them manually.

==Installation of CP2K version 8.1==

===Installation of OpenMPI===
The first step is to install OpenMPI. [https://edu.itp.phys.ethz.ch/hs12/programming_techniques/openmpi.pdf Here] is a fantastic tutorial on how to do that. After step 7 in that tutorial, run this command together with the other 2 as well.
<pre>
echo "OMPI_HOME=$HOME/opt/openmpi/" >> ~/.bashrc
</pre>
This should set up OpenMPI correctly. To use OpenMPI (or, to let the system know that you have OpenMPI), run this every time when a new terminal session starts.
<pre>
source ~/.bashrc
</pre>

===Installation of CP2K===
Now we can install CP2K. The first step is to clone the GitHub repository.
<pre>
git clone -b support/v8.1 --recursive https://github.com/cp2k/cp2k.git cp2k
</pre>
Now we have already cloned it into a directory called cp2k, we need to go to that directory and run the following command
<pre>
cd tools/toolchain/
./install_cp2k_toolchain.sh --no-check-certificate --with-elpa=no
</pre>
After these commands there will be instructions (and/or ERRORs) at the end. Follow the instructions, if the above command is successful the instruction will ask you to do something like this
<pre>
source install/setup
cp /install/arch/* ~/cp2k/arch/
cd ~/cp2k
make ARCH=local VERSION="ssmp sdbg psmp pdbg" &> make.log
</pre>

This whole process can take hours so be patient. With CP2K installed and compiled, we can use the tools included to build n2p2.

==Installation of n2p2==
[https://compphysvienna.github.io/n2p2/topics/build.html This documentation] of n2p2 gives some instruction on how to build the software. However, to actually build the software, we will need some of the packages we installed with CP2K. We do this by including the tools in the '''~/.bashrc''' file using the same 'echo' command as before.

For example, when compiling we need the header file '''gsl/gsh_rng.h''', which is located in the CP2K toolchain directory. The path to the folder containing '''gsl/gsl_rng.h''' on my computer is
<pre>
/rds/general/user/yl4619/home/cp2k-8.1/tools/toolchain/install/gsl-2.6/include
</pre>
So I need to add this to the '''CPATH''' variable by doing
<pre>
echo "export CPATH=$CPATH:/rds/general/user/yl4619/home/cp2k-8.1/tools/toolchain/install/gsl-2.6/include" >> $HOME/.bashrc
</pre>

We will need to link several other libraries/binaries/header files too, so just try to compile and read the error message which will tell you which package you are lacking, and search for that in the CP2K toolchain directory and link it using the method above. There will be several types of files that need to linked: use '''$PATH''' to link '''bin''' folders, '''$LIBRARY_PATH''' to link '''lib''' folders, and '''$CPATH''' to link '''include''' folders.

One special one is the OpenBLAS package. The installation of n2p2 requires BLAS and cannot recognise OpenBLAS as a variant of BLAS. So for this we need to manually change the '''makefile''' file

Building ML potentials with AML

2023-05-04T12:15:19Z

Yl4619: /* Installation of n2p2 */

This page includes a short tutorial on how to install the AML package and set up all the necessary tools to run it.

[https://github.com/CompPhysVienna/n2p2 n2p2] is the main software used by the AML package to build the neural network potentials, which has to be downloaded and compiled correctly first. However, the compilation requires quite a few tools, and it can be cumbersome to download and install them individually. To make this task easier, we can install CP2K first which comes with a lot of tools that can be used by n2p2, so we don't have to install them manually.

==Installation of CP2K version 8.1==

===Installation of OpenMPI===
The first step is to install OpenMPI. [https://edu.itp.phys.ethz.ch/hs12/programming_techniques/openmpi.pdf Here] is a fantastic tutorial on how to do that. After step 7 in that tutorial, run this command together with the other 2 as well.
<pre>
echo "OMPI_HOME=$HOME/opt/openmpi/" >> ~/.bashrc
</pre>
This should set up OpenMPI correctly. To use OpenMPI (or, to let the system know that you have OpenMPI), run this every time when a new terminal session starts.
<pre>
source ~/.bashrc
</pre>

===Installation of CP2K===
Now we can install CP2K. The first step is to clone the GitHub repository.
<pre>
git clone -b support/v8.1 --recursive https://github.com/cp2k/cp2k.git cp2k
</pre>
Now we have already cloned it into a directory called cp2k, we need to go to that directory and run the following command
<pre>
cd tools/toolchain/
./install_cp2k_toolchain.sh --no-check-certificate --with-elpa=no
</pre>
After these commands there will be instructions (and/or ERRORs) at the end. Follow the instructions, if the above command is successful the instruction will ask you to do something like this
<pre>
source install/setup
cp /install/arch/* ~/cp2k/arch/
cd ~/cp2k
make ARCH=local VERSION="ssmp sdbg psmp pdbg" &> make.log
</pre>

This whole process can take hours so be patient. With CP2K installed and compiled, we can use the tools included to build n2p2.

==Installation of n2p2==
[https://compphysvienna.github.io/n2p2/topics/build.html This documentation] of n2p2 gives some instruction on how to build the software. However, to actually build the software, we will need some of the packages we installed with CP2K. We do this by including the tools in the '''~/.bashrc''' file using the same 'echo' command as before.

For example, when compiling we need the header file '''gsl/gsh_rng.h''', which is located in the CP2K toolchain directory. The path to the folder containing '''gsl/gsl_rng.h''' on my computer is
<pre>
/rds/general/user/yl4619/home/cp2k-8.1/tools/toolchain/install/gsl-2.6/include
</pre>
So I need to add this to the 'CPATH' variable by doing
<pre>
echo "export CPATH=$CPATH:/rds/general/user/yl4619/home/cp2k-8.1/tools/toolchain/install/gsl-2.6/include" >> $HOME/.bashrc
</pre>

We will need to link several other libraries/binaries/header files too, so just try to compile and read the error message which will tell you which package you are lacking, and search for that in the CP2K toolchain directory and link it using the method above. There will be several types of files that need to linked: use $PATH to link 'bin' folders, $LIBRARY_PATH to link 'lib' folders, and $CPATH to link 'include' folders.

One special one is the OpenBLAS package. The installation of n2p2 requires BLAS and cannot recognise OpenBLAS as a variant of BLAS. So for this we need to manually change the 'makefile' file

Building ML potentials with AML

2023-05-04T12:14:55Z

Yl4619: /* Installation of n2p2 */

This page includes a short tutorial on how to install the AML package and set up all the necessary tools to run it.

[https://github.com/CompPhysVienna/n2p2 n2p2] is the main software used by the AML package to build the neural network potentials, which has to be downloaded and compiled correctly first. However, the compilation requires quite a few tools, and it can be cumbersome to download and install them individually. To make this task easier, we can install CP2K first which comes with a lot of tools that can be used by n2p2, so we don't have to install them manually.

==Installation of CP2K version 8.1==

===Installation of OpenMPI===
The first step is to install OpenMPI. [https://edu.itp.phys.ethz.ch/hs12/programming_techniques/openmpi.pdf Here] is a fantastic tutorial on how to do that. After step 7 in that tutorial, run this command together with the other 2 as well.
<pre>
echo "OMPI_HOME=$HOME/opt/openmpi/" >> ~/.bashrc
</pre>
This should set up OpenMPI correctly. To use OpenMPI (or, to let the system know that you have OpenMPI), run this every time when a new terminal session starts.
<pre>
source ~/.bashrc
</pre>

===Installation of CP2K===
Now we can install CP2K. The first step is to clone the GitHub repository.
<pre>
git clone -b support/v8.1 --recursive https://github.com/cp2k/cp2k.git cp2k
</pre>
Now we have already cloned it into a directory called cp2k, we need to go to that directory and run the following command
<pre>
cd tools/toolchain/
./install_cp2k_toolchain.sh --no-check-certificate --with-elpa=no
</pre>
After these commands there will be instructions (and/or ERRORs) at the end. Follow the instructions, if the above command is successful the instruction will ask you to do something like this
<pre>
source install/setup
cp /install/arch/* ~/cp2k/arch/
cd ~/cp2k
make ARCH=local VERSION="ssmp sdbg psmp pdbg" &> make.log
</pre>

This whole process can take hours so be patient. With CP2K installed and compiled, we can use the tools included to build n2p2.

==Installation of n2p2==
[https://compphysvienna.github.io/n2p2/topics/build.html This documentation] of n2p2 gives some instruction on how to build the software. However, to actually build the software, we will need some of the packages we installed with CP2K. We do this by including the tools in the '''~/.bashrc''' file using the same 'echo' command as before.

For example, when compiling we need the header file 'gsl/gsh_rng.h', which is located in the CP2K toolchain directory. The path to the folder containing 'gsl/gsl_rng.h' on my computer is
<pre>
/rds/general/user/yl4619/home/cp2k-8.1/tools/toolchain/install/gsl-2.6/include
</pre>
So I need to add this to the 'CPATH' variable by doing
<pre>
echo "export CPATH=$CPATH:/rds/general/user/yl4619/home/cp2k-8.1/tools/toolchain/install/gsl-2.6/include" >> $HOME/.bashrc
</pre>

We will need to link several other libraries/binaries/header files too, so just try to compile and read the error message which will tell you which package you are lacking, and search for that in the CP2K toolchain directory and link it using the method above. There will be several types of files that need to linked: use $PATH to link 'bin' folders, $LIBRARY_PATH to link 'lib' folders, and $CPATH to link 'include' folders.

One special one is the OpenBLAS package. The installation of n2p2 requires BLAS and cannot recognise OpenBLAS as a variant of BLAS. So for this we need to manually change the 'makefile' file

Building ML potentials with AML

2023-05-04T12:12:35Z

Yl4619: /* Installation of n2p2 */

This page includes a short tutorial on how to install the AML package and set up all the necessary tools to run it.

[https://github.com/CompPhysVienna/n2p2 n2p2] is the main software used by the AML package to build the neural network potentials, which has to be downloaded and compiled correctly first. However, the compilation requires quite a few tools, and it can be cumbersome to download and install them individually. To make this task easier, we can install CP2K first which comes with a lot of tools that can be used by n2p2, so we don't have to install them manually.

==Installation of CP2K version 8.1==

===Installation of OpenMPI===
The first step is to install OpenMPI. [https://edu.itp.phys.ethz.ch/hs12/programming_techniques/openmpi.pdf Here] is a fantastic tutorial on how to do that. After step 7 in that tutorial, run this command together with the other 2 as well.
<pre>
echo "OMPI_HOME=$HOME/opt/openmpi/" >> ~/.bashrc
</pre>
This should set up OpenMPI correctly. To use OpenMPI (or, to let the system know that you have OpenMPI), run this every time when a new terminal session starts.
<pre>
source ~/.bashrc
</pre>

===Installation of CP2K===
Now we can install CP2K. The first step is to clone the GitHub repository.
<pre>
git clone -b support/v8.1 --recursive https://github.com/cp2k/cp2k.git cp2k
</pre>
Now we have already cloned it into a directory called cp2k, we need to go to that directory and run the following command
<pre>
cd tools/toolchain/
./install_cp2k_toolchain.sh --no-check-certificate --with-elpa=no
</pre>
After these commands there will be instructions (and/or ERRORs) at the end. Follow the instructions, if the above command is successful the instruction will ask you to do something like this
<pre>
source install/setup
cp /install/arch/* ~/cp2k/arch/
cd ~/cp2k
make ARCH=local VERSION="ssmp sdbg psmp pdbg" &> make.log
</pre>

This whole process can take hours so be patient. With CP2K installed and compiled, we can use the tools included to build n2p2.

==Installation of n2p2==
[https://compphysvienna.github.io/n2p2/topics/build.html This documentation] of n2p2 gives some instruction on how to build the software. However, to actually build the software, we will need some of the packages we installed with CP2K. We do this by including the tools in the ~/.bashrc file using the same 'echo' command as before.

For example, when compiling we need the header file 'gsl/gsh_rng.h', which is located in the CP2K toolchain directory. The path to the folder containing 'gsl/gsl_rng.h' on my computer is
<pre>
/rds/general/user/yl4619/home/cp2k-8.1/tools/toolchain/install/gsl-2.6/include
</pre>
So I need to add this to the 'CPATH' variable by doing
<pre>
echo "export CPATH=$CPATH:/rds/general/user/yl4619/home/cp2k-8.1/tools/toolchain/install/gsl-2.6/include" >> $HOME/.bashrc
</pre>

We will need to link several other libraries/binaries/header files too, so just try to compile and read the error message which will tell you which package you are lacking, and search for that in the CP2K toolchain directory and link it using the method above. There will be several types of files that need to linked: use $PATH to link 'bin' folders, $LIBRARY_PATH to link 'lib' folders, and $CPATH to link 'include' folders.

One special one is the OpenBLAS package. The installation of n2p2 requires BLAS and cannot recognise OpenBLAS as a variant of BLAS. So for this we need to manually change the 'makefile' file

Building ML potentials with AML

2023-05-04T11:48:10Z

Yl4619: /* Installation of n2p2 */

This page includes a short tutorial on how to install the AML package and set up all the necessary tools to run it.

[https://github.com/CompPhysVienna/n2p2 n2p2] is the main software used by the AML package to build the neural network potentials, which has to be downloaded and compiled correctly first. However, the compilation requires quite a few tools, and it can be cumbersome to download and install them individually. To make this task easier, we can install CP2K first which comes with a lot of tools that can be used by n2p2, so we don't have to install them manually.

==Installation of CP2K version 8.1==

===Installation of OpenMPI===
The first step is to install OpenMPI. [https://edu.itp.phys.ethz.ch/hs12/programming_techniques/openmpi.pdf Here] is a fantastic tutorial on how to do that. After step 7 in that tutorial, run this command together with the other 2 as well.
<pre>
echo "OMPI_HOME=$HOME/opt/openmpi/" >> ~/.bashrc
</pre>
This should set up OpenMPI correctly. To use OpenMPI (or, to let the system know that you have OpenMPI), run this every time when a new terminal session starts.
<pre>
source ~/.bashrc
</pre>

===Installation of CP2K===
Now we can install CP2K. The first step is to clone the GitHub repository.
<pre>
git clone -b support/v8.1 --recursive https://github.com/cp2k/cp2k.git cp2k
</pre>
Now we have already cloned it into a directory called cp2k, we need to go to that directory and run the following command
<pre>
cd tools/toolchain/
./install_cp2k_toolchain.sh --no-check-certificate --with-elpa=no
</pre>
After these commands there will be instructions (and/or ERRORs) at the end. Follow the instructions, if the above command is successful the instruction will ask you to do something like this
<pre>
source install/setup
cp /install/arch/* ~/cp2k/arch/
cd ~/cp2k
make ARCH=local VERSION="ssmp sdbg psmp pdbg" &> make.log
</pre>

This whole process can take hours so be patient. With CP2K installed and compiled, we can use the tools included to build n2p2.

==Installation of n2p2==
[https://compphysvienna.github.io/n2p2/topics/build.html This documentation] of n2p2 gives some instruction on how to build the software. However, to actually build the software, we will need some of the packages we installed with CP2K. We do this by including the tools in the ~/.bashrc file using the same 'echo' command as before.

For example, when compiling we need the header file 'gsl/gsh_rng.h', which is located in the CP2K toolchain directory. The path to the folder containing 'gsl/gsl_rng.h' on my computer is
<pre>
/rds/general/user/yl4619/home/cp2k-8.1/tools/toolchain/install/gsl-2.6/include
</pre>
So I need to add this to the 'CPATH' variable by doing
<pre>
echo "export CPATH=$CPATH:/rds/general/user/yl4619/home/cp2k-8.1/tools/toolchain/install/gsl-2.6/include" >> $HOME/.bashrc
</pre>

We will need to link several other libraries/binaries/header files too, so just try to compile and read the error message which will tell you which package you are lacking, and just search for that in the CP2K toolchain directory and link it using the method above. There will be several types of files that need to linked: use $PATH to link 'bin' folders, $LIBRARY_PATH to link 'lib' folders, and $CPATH to link 'include' folders.

Building ML potentials with AML

2023-05-04T11:47:58Z

Yl4619: /* Installation of n2p2 */

This page includes a short tutorial on how to install the AML package and set up all the necessary tools to run it.

[https://github.com/CompPhysVienna/n2p2 n2p2] is the main software used by the AML package to build the neural network potentials, which has to be downloaded and compiled correctly first. However, the compilation requires quite a few tools, and it can be cumbersome to download and install them individually. To make this task easier, we can install CP2K first which comes with a lot of tools that can be used by n2p2, so we don't have to install them manually.

==Installation of CP2K version 8.1==

===Installation of OpenMPI===
The first step is to install OpenMPI. [https://edu.itp.phys.ethz.ch/hs12/programming_techniques/openmpi.pdf Here] is a fantastic tutorial on how to do that. After step 7 in that tutorial, run this command together with the other 2 as well.
<pre>
echo "OMPI_HOME=$HOME/opt/openmpi/" >> ~/.bashrc
</pre>
This should set up OpenMPI correctly. To use OpenMPI (or, to let the system know that you have OpenMPI), run this every time when a new terminal session starts.
<pre>
source ~/.bashrc
</pre>

===Installation of CP2K===
Now we can install CP2K. The first step is to clone the GitHub repository.
<pre>
git clone -b support/v8.1 --recursive https://github.com/cp2k/cp2k.git cp2k
</pre>
Now we have already cloned it into a directory called cp2k, we need to go to that directory and run the following command
<pre>
cd tools/toolchain/
./install_cp2k_toolchain.sh --no-check-certificate --with-elpa=no
</pre>
After these commands there will be instructions (and/or ERRORs) at the end. Follow the instructions, if the above command is successful the instruction will ask you to do something like this
<pre>
source install/setup
cp /install/arch/* ~/cp2k/arch/
cd ~/cp2k
make ARCH=local VERSION="ssmp sdbg psmp pdbg" &> make.log
</pre>

This whole process can take hours so be patient. With CP2K installed and compiled, we can use the tools included to build n2p2.

==Installation of n2p2==
[https://compphysvienna.github.io/n2p2/topics/build.html This documentation] of n2p2 gives some instruction on how to build the software. However, to actually build the software, we will need some of the packages we installed with CP2K. We do this by including the tools in the ~/.bashrc file using the same 'echo' command as before.

For example, when compiling we need the header file 'gsl/gsh_rng.h', which is located in the CP2K toolchain directory. The path to the folder containing 'gsl/gsl_rng.h' on my computer is
<pre>
/rds/general/user/yl4619/home/cp2k-8.1/tools/toolchain/install/gsl-2.6/include
</pre>
So I need to add this to the 'CPATH' variable by doing
<pre>
echo "export CPATH=$CPATH:/rds/general/user/yl4619/home/cp2k-8.1/tools/toolchain/install/gsl-2.6/include" >> $HOME/.bashrc
</pre>

We will need to link several other libraries/binaries/header files too, so just try to compile and read the error message which will tell you which package you are lacking, and just search for that in the CP2K toolchain directory and link it using the method above. There will be several types of files that need to linked: use $PATH to link 'bin' folders, $LIBRARY_PATH to link 'lib' folders, and CPATH to link 'include' folders.

Building ML potentials with AML

2023-05-04T11:45:07Z

Yl4619: /* Installation of n2p2 */

Building ML potentials with AML

2023-05-04T11:42:52Z

Yl4619: /* Installation of n2p2 */

Building ML potentials with AML

2023-05-04T11:42:14Z

Yl4619: /* Installation of n2p2 */

Building ML potentials with AML

2023-05-04T11:42:07Z

Yl4619: /* Installation of n2p2 */

Building ML potentials with AML

2023-05-04T11:39:21Z

Yl4619: /* Installation of n2p2 */

Building ML potentials with AML

2023-05-04T11:39:13Z

Yl4619: /* Installation of n2p2 */

Building ML potentials with AML

2023-05-04T10:08:03Z

Yl4619: /* Installation of n2p2 */

Building ML potentials with AML

2023-05-04T10:07:24Z

Yl4619: /* Installation of n2p2 */

Building ML potentials with AML

2023-05-04T10:06:01Z

Yl4619: /* Installation of n2p2 */

Building ML potentials with AML

2023-05-04T09:56:23Z

Yl4619: /* Installation of n2p2 */

Building ML potentials with AML

2023-05-04T09:42:32Z

Yl4619:

Building ML potentials with AML

2023-05-04T09:42:12Z

Yl4619: /* Installation of CP2K */

Building ML potentials with AML

2023-05-04T09:41:52Z

Yl4619:

Building ML potentials with AML

2023-05-04T09:40:38Z

Yl4619: /* Installation of CP2K */

Building ML potentials with AML

2023-05-04T09:40:24Z

Yl4619: /* Installation of CP2K */

Building ML potentials with AML

2023-05-04T09:40:10Z

Yl4619: /* Installation of CP2K */

Building ML potentials with AML

2023-05-04T09:33:01Z

Yl4619:

Building ML potentials with AML

2023-05-04T09:31:21Z

Yl4619:

Building ML potentials with AML

2023-05-04T09:26:24Z

Yl4619:

Building ML potentials with AML

2023-05-04T09:23:38Z

Yl4619:

Building ML potentials with AML

2023-05-04T09:21:09Z

Yl4619:

Building ML potentials with AML

2023-05-04T09:16:56Z

Yl4619:

Building ML potentials with AML

2023-05-04T09:14:59Z

Yl4619:

Building ML potentials with AML

2023-05-04T09:13:05Z

Yl4619:

Building ML potentials with AML

2023-05-04T09:12:55Z

Yl4619: /* Installation of CP2K version 8.1 */

Building ML potentials with AML

2023-05-04T09:06:47Z

Yl4619:

Building ML potentials with AML

2023-05-04T09:04:38Z

Yl4619:

Building ML potentials with AML

2023-05-04T09:01:25Z

Yl4619:

Building ML potentials with AML

2023-05-04T08:58:38Z

Yl4619:

This page includes a short tutorial on how to install the AML package and set up all the necessary tools to run it.

[https://github.com/CompPhysVienna/n2p2 n2p2]
==Installation of CP2K version 8.1==

Building ML potentials with AML

2023-05-04T08:55:15Z

Yl4619: /* Installation of CP2K version 8.1 */

This page includes a short tutorial on how to install the AML package and set up all the necessary tools to run it.

==Installation of CP2K version 8.1==

Building ML potentials with AML

2023-05-04T08:55:02Z

Yl4619:

This page includes a short tutorial on how to install the AML package and set up all the necessary tools to run it.

=Installation of CP2K version 8.1=

Building ML potentials with AML

2023-05-03T14:07:30Z

Yl4619:

This page includes a short tutorial on how to install the AML package and set up all the necessary tools to run it.

Building ML potentials with AML

2023-05-03T14:01:06Z

Yl4619: Created page with "Hi this is the page"

Hi this is the page

Nano Electrochemistry Group

2023-05-03T14:00:44Z

Yl4619: /* Building ML potentials with AML */

<div style="padding: 10px; background: #87adde; border: 1px solid #FFAA99; font-family: Trebuchet MS, sans-serif; font-size: 95%;">

<div style="border:1px solid #90C0FF; background:#ffffff; width:90%; padding:4px">
This page provides a series of tutorials designed to help with the computational modelling of electrochemical system; their aim is to provide general workflows and useful tip to model fundamental components and properties of electrochemical systems. The tutorials have been designed by the researchers of the Computational NanoElectrochemistry Group led by Dr Clotilde Cucinotta [link to group page] and collaborators.
Several simulation packages (CP2K, LAMMPS, QuantumEspresso, etc.), as well as other tools, such as molecular visualisers or programming languages, are described in these tutorials; links to the relevant manuals are provided at the bottom of the page.
Script and programs written by the components of the research group are also described in each tutorial; these tools have been devised to help with running calculations and with data analysis and can be found in the linked GitLub repository [https://gitlab.doc.ic.ac.uk/rgc].

==Running in a Cluster Tutorials==

===[[How to run on ARCHER 2]]===
Written by:[[Contributors#Songyuan| Songyuan]]

===[[Imperial CX1: Instructions and basic concepts of parallel computing]]===
Written by:[[Contributors| Huanyu]]

A collection of useful resources and brief introductions to the basic concepts of parallel computing for beginners to use the high-performance computing service at Imperial.

===[[Run CRYSTALs on Imperial CX1]]===
Written by:[[Contributors| Huanyu ]]

Intructions on how to submit a CRYSTAL job on CX1

==Reaction Dynamics==
===[[Lammps and plumed|Lammps and plumed]]===
Written by:[[Contributors| Frederik]]

Tutorial on how to use the PLUMED software package to perform biased molecular dynamics simulations in LAMMPS.

===[[Converging magnetic systems in CP2K]]===
Written by:[[Contributors| Chris]]

* Contents:
** MULTIPLICITY keyword to calculate magnetic systems
** &BS section and MAGNETIZATION keyword to improve convergence
* System: Metallic bulk Ni and slab in vacuum
* Computational package: CP2K.

===[[Optimization of metallic surfaces parameters|Optimizing parameters for metallic surfaces]]===
Written by:[[Contributors| Margherita]]

* Contents:
** Tutorials on how to define the appropriate set of parameters needed to model a metallic system: Basis set, CUTOFF and '''k'''-points grid;
** Tutorials on how to calculate relevant quantities of metallic surfaces: work function, equilibrium lattice parameter and electronic structure;
* System: metallic surfaces (Platinum slab used as example);
* Computational package: CP2K.

===Surface analysis===
Written by:[[Contributors| Songyuan]]

===[[Dimers in gas phase|Dimers in gas phase]]===
Written by:[[Contributors| Fredrik]]

Tutorial for optimising dimers in the gas phase using gaussian.

===[[Calculation of radial average|Calculation of radial average]]===
Written by:[[Contributors| Kalman]]

Tutorial for calculating the radial average ?.

===[[Adsorption of molecule on surfaces|Adsorption of molecule on surfaces]]===
Written by:[[Contributors| Paolo]]

Tutorial for calculating the adsorption energy of a molecule (or, more in general, any particle) over a specific surface.

===[[Memristors|Simulation of Memristors]]===
Written by:[[Contributors| Felix]]

Tutorial for optimising parameters for memristors using QuantumEspresso.

===[[Hard_carbon|Simulation of Hard Carbons]]===
Written by:[[Contributors| Luke]]

Tutorial for the simulation of hard carbon?

===[[Solving 1D Poisson equation |Solving 1D Poisson equation]]===
Written by:[[Contributors| Remi Khatib ]]

Tutorial for the solution of the 1D Poisson equations given a distribution of point charges

===[[TrendsCatalyticActivity|Trends in catalytic Activity]]===
Tutorial for a computational experiment about trends in catalytic activity for hydrogen evolution. This experiment is part of the third year computational chemistry lab.

written by [[Contributors| Clotilde Cucinotta]]

===[[Building structure with Pymatgen]]===
Written by:[[Contributors| Fei ]]

===[[Analysing AIMD runs with MATLAB in-house suit]]===
Written by:[[Contributors| Rashid ]]

Tutorial for generating crystal structure and surface with Python.

</div>

<div style="border:1px solid #90C0FF; background:#ffffff; width:90%; padding:4px">
==General DFT tutorials==
===[[Convergence test of critical parameters by CRYSTAL]]===
Written by:[[Contributors| Huanyu ]]

A tutorial for performing convergence tests with LCAO-GTO DFT code, CRYSTAL.

</div>

<div style="border:1px solid #90C0FF; background:#ffffff; width:90%; padding:4px">

==Machine Learning Potentials==

===[[Building ML potentials with AML|Building ML potentials with AML]]===
Written by:[[Contributors#Anthony| Anthony]]

Tutorial for building ML potentials with AML.
</div>

<div style="border:1px solid #90C0FF; background:#ffffff; width:90%; padding:4px">

== Becoming an Efficient Research Scientist ==

===[[Writing a Project Proposal]]===
Written by:[[Contributors| Nicholas Harrison ]]

</div>

<div style="border:1px solid #90C0FF; background:#ffffff; width:90%; padding:4px">

==Computational Tools==

===[https://www.cp2k.org/about CP2K]===
*[[CP2K_Tutorial|CP2K TUTORIAL]];
*[https://github.com/cp2k/cp2k/blob/master/INSTALL.md Download and install CP2K ];
*[https://manual.cp2k.org/#gsc.tab=0 Manual];
*[https://www.cp2k.org/howto Useful HOWTOs];
*Reading inputs and outputs (commented files and examples);

===[https://www.quantum-espresso.org/ QUANTUM ESPRESSO]===
*[https://www.quantum-espresso.org/download Download and install QUANTUM ESPRESSO];
*[https://www.quantum-espresso.org/resources/tutorials Useful Tutorials];
*Reading inputs and outputs (commented files and examples);

===[https://www.lammps.org/ LAMMPS]===
*[https://www.lammps.org/download.html Download LAMMPS];
*[https://docs.lammps.org/Manual.html Manual];
*[https://www.lammps.org/tutorials.html Tutorials];

===[https://www.crystal.unito.it/index.html CRYSTAL]===
* [https://tutorials.crystalsolutions.eu/ CRYSTAL Tutorial Project]
* [https://www.crystal.unito.it/basis_sets.html CRYSTAL basis set database for solid state calculations]
* [https://www.basissetexchange.org/ Basis Set Exchange]
Note this site usually contains very diffuse basis sets for quantum chemmistry, which might cause problems for solid state calculations.
* [https://vallico.net/mike_towler/crystal.html Mike Towler's basis set - parameterized around early 2000s]
* [http://crysplot.crystalsolutions.eu/ CRYSPLOT: A web-based visualisation tool]
* [https://gitlab.com/bmgcsc/dl-visualize-v3 DLV3: Visualization tool]
* [https://github.com/crystal-code-tools/CRYSTALpytools CRYSTALpytools: A python-based toolbox for CRYSTAL outputs]
More information is available in [https://www.crystal.unito.it/documentation.html CRYSTAL23 official site].

===[https://www.tcd.ie/Physics/Smeagol/SmeagolAbout.htm Smeagol]===

===others===
</div>

<div style="border:1px solid #90C0FF; background:#ffffff; width:90%; padding:4px">

==Molecular visualizers==
*[http://www.ks.uiuc.edu/Research/vmd/ VMD]
*[http://www.xcrysden.org/ Xcrysden]
*[https://jp-minerals.org/vesta/en/ VESTA]

===Others===
</div>

<div style="border:1px solid #90C0FF; background:#ffffff; width:90%; padding:4px">

==Useful programming languages and environments==

*[http://www-eio.upc.edu/lceio/manuals/Fortran95-manual.pdf Fortran]
*[https://docs.python.org/3/ Python]
*[https://wiki.fysik.dtu.dk/ase/ ASE]
*[https://pymatgen.org/ Pymatgen]

===others===

</div>

[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Main_Page info]

</div>

Nano Electrochemistry Group

2023-05-03T13:59:29Z

Yl4619: /* Building ML potentials with AML */

<div style="padding: 10px; background: #87adde; border: 1px solid #FFAA99; font-family: Trebuchet MS, sans-serif; font-size: 95%;">

<div style="border:1px solid #90C0FF; background:#ffffff; width:90%; padding:4px">
This page provides a series of tutorials designed to help with the computational modelling of electrochemical system; their aim is to provide general workflows and useful tip to model fundamental components and properties of electrochemical systems. The tutorials have been designed by the researchers of the Computational NanoElectrochemistry Group led by Dr Clotilde Cucinotta [link to group page] and collaborators.
Several simulation packages (CP2K, LAMMPS, QuantumEspresso, etc.), as well as other tools, such as molecular visualisers or programming languages, are described in these tutorials; links to the relevant manuals are provided at the bottom of the page.
Script and programs written by the components of the research group are also described in each tutorial; these tools have been devised to help with running calculations and with data analysis and can be found in the linked GitLub repository [https://gitlab.doc.ic.ac.uk/rgc].

==Running in a Cluster Tutorials==

===[[How to run on ARCHER 2]]===
Written by:[[Contributors#Songyuan| Songyuan]]

===[[Imperial CX1: Instructions and basic concepts of parallel computing]]===
Written by:[[Contributors| Huanyu]]

A collection of useful resources and brief introductions to the basic concepts of parallel computing for beginners to use the high-performance computing service at Imperial.

===[[Run CRYSTALs on Imperial CX1]]===
Written by:[[Contributors| Huanyu ]]

Intructions on how to submit a CRYSTAL job on CX1

==Reaction Dynamics==
===[[Lammps and plumed|Lammps and plumed]]===
Written by:[[Contributors| Frederik]]

Tutorial on how to use the PLUMED software package to perform biased molecular dynamics simulations in LAMMPS.

===[[Converging magnetic systems in CP2K]]===
Written by:[[Contributors| Chris]]

* Contents:
** MULTIPLICITY keyword to calculate magnetic systems
** &BS section and MAGNETIZATION keyword to improve convergence
* System: Metallic bulk Ni and slab in vacuum
* Computational package: CP2K.

===[[Optimization of metallic surfaces parameters|Optimizing parameters for metallic surfaces]]===
Written by:[[Contributors| Margherita]]

* Contents:
** Tutorials on how to define the appropriate set of parameters needed to model a metallic system: Basis set, CUTOFF and '''k'''-points grid;
** Tutorials on how to calculate relevant quantities of metallic surfaces: work function, equilibrium lattice parameter and electronic structure;
* System: metallic surfaces (Platinum slab used as example);
* Computational package: CP2K.

===Surface analysis===
Written by:[[Contributors| Songyuan]]

===[[Dimers in gas phase|Dimers in gas phase]]===
Written by:[[Contributors| Fredrik]]

Tutorial for optimising dimers in the gas phase using gaussian.

===[[Calculation of radial average|Calculation of radial average]]===
Written by:[[Contributors| Kalman]]

Tutorial for calculating the radial average ?.

===[[Adsorption of molecule on surfaces|Adsorption of molecule on surfaces]]===
Written by:[[Contributors| Paolo]]

Tutorial for calculating the adsorption energy of a molecule (or, more in general, any particle) over a specific surface.

===[[Memristors|Simulation of Memristors]]===
Written by:[[Contributors| Felix]]

Tutorial for optimising parameters for memristors using QuantumEspresso.

===[[Hard_carbon|Simulation of Hard Carbons]]===
Written by:[[Contributors| Luke]]

Tutorial for the simulation of hard carbon?

===[[Solving 1D Poisson equation |Solving 1D Poisson equation]]===
Written by:[[Contributors| Remi Khatib ]]

Tutorial for the solution of the 1D Poisson equations given a distribution of point charges

===[[TrendsCatalyticActivity|Trends in catalytic Activity]]===
Tutorial for a computational experiment about trends in catalytic activity for hydrogen evolution. This experiment is part of the third year computational chemistry lab.

written by [[Contributors| Clotilde Cucinotta]]

===[[Building structure with Pymatgen]]===
Written by:[[Contributors| Fei ]]

===[[Analysing AIMD runs with MATLAB in-house suit]]===
Written by:[[Contributors| Rashid ]]

Tutorial for generating crystal structure and surface with Python.

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==General DFT tutorials==
===[[Convergence test of critical parameters by CRYSTAL]]===
Written by:[[Contributors| Huanyu ]]

A tutorial for performing convergence tests with LCAO-GTO DFT code, CRYSTAL.

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==Machine Learning Potentials==

===Building ML potentials with AML===
Written by:[[Contributors#Anthony| Anthony]]

Tutorial for building ML potentials with AML.
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== Becoming an Efficient Research Scientist ==

===[[Writing a Project Proposal]]===
Written by:[[Contributors| Nicholas Harrison ]]

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==Computational Tools==

===[https://www.cp2k.org/about CP2K]===
*[[CP2K_Tutorial|CP2K TUTORIAL]];
*[https://github.com/cp2k/cp2k/blob/master/INSTALL.md Download and install CP2K ];
*[https://manual.cp2k.org/#gsc.tab=0 Manual];
*[https://www.cp2k.org/howto Useful HOWTOs];
*Reading inputs and outputs (commented files and examples);

===[https://www.quantum-espresso.org/ QUANTUM ESPRESSO]===
*[https://www.quantum-espresso.org/download Download and install QUANTUM ESPRESSO];
*[https://www.quantum-espresso.org/resources/tutorials Useful Tutorials];
*Reading inputs and outputs (commented files and examples);

===[https://www.lammps.org/ LAMMPS]===
*[https://www.lammps.org/download.html Download LAMMPS];
*[https://docs.lammps.org/Manual.html Manual];
*[https://www.lammps.org/tutorials.html Tutorials];

===[https://www.crystal.unito.it/index.html CRYSTAL]===
* [https://tutorials.crystalsolutions.eu/ CRYSTAL Tutorial Project]
* [https://www.crystal.unito.it/basis_sets.html CRYSTAL basis set database for solid state calculations]
* [https://www.basissetexchange.org/ Basis Set Exchange]
Note this site usually contains very diffuse basis sets for quantum chemmistry, which might cause problems for solid state calculations.
* [https://vallico.net/mike_towler/crystal.html Mike Towler's basis set - parameterized around early 2000s]
* [http://crysplot.crystalsolutions.eu/ CRYSPLOT: A web-based visualisation tool]
* [https://gitlab.com/bmgcsc/dl-visualize-v3 DLV3: Visualization tool]
* [https://github.com/crystal-code-tools/CRYSTALpytools CRYSTALpytools: A python-based toolbox for CRYSTAL outputs]
More information is available in [https://www.crystal.unito.it/documentation.html CRYSTAL23 official site].

===[https://www.tcd.ie/Physics/Smeagol/SmeagolAbout.htm Smeagol]===

===others===
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==Molecular visualizers==
*[http://www.ks.uiuc.edu/Research/vmd/ VMD]
*[http://www.xcrysden.org/ Xcrysden]
*[https://jp-minerals.org/vesta/en/ VESTA]

===Others===
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==Useful programming languages and environments==

*[http://www-eio.upc.edu/lceio/manuals/Fortran95-manual.pdf Fortran]
*[https://docs.python.org/3/ Python]
*[https://wiki.fysik.dtu.dk/ase/ ASE]
*[https://pymatgen.org/ Pymatgen]

===others===

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[https://wiki.ch.ic.ac.uk/wiki/index.php?title=Main_Page info]

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