.. include:: .colors.rst How To Install =============== This page will explain how to install all the packages you need for this project step by step. .. _installation: Requirement ----------- This package requires a C++ compiler". Environments under intel 19.1.2 were tested Install libraly code (MolStrucClassifier) -------------------------------------------- Copy the repository ^^^^^^^^^^^^^^^^^^^ You can copy the repository by typing the following command: .. code:: console git clone https://github.com/rogalj/MolStrucClassifier.git If you already installed the repository, you can update it by typing: .. code:: console git pull If you are an editor, check the following command as well. If you make any changes and want to add directories/files to the GitHub repository, you can upload them by typing: .. code:: console git add name_of_folder/file The following command can check the status of the local repository. This command will show all the files that you added, deleted or modified which are not yet reflected to the local repository. .. code:: console git status When you upload the directories/files, you can also add a comment as following: .. code:: console git commit -m "WHATEVER THE COMMENT YOU WANT" This process will add to your local repository. If you want to add them to the global repository, type: .. code:: console git push At this point, your work will be on the GitHub repository. If you made a mistake and added an unnecessary file, type: .. code:: console git reset to cancel the command you were working on. Install LAMMPS code ------------------- In order to run the libraly programs in LAMMPS, you need to have the LAMMPS code. If you don't need to connect with LAMMPS, you can skip this section. If you already have LAMMPS, make sure you connect the libraly and have the appropriate packages shown in Step 4. Step 1 ^^^^^^ Go to the directory where you want to store the lammps code. I use mylammps as an example. Run the following command at mylammps directory to install LAMMPS from github. Run the following command .. code:: console git clone -b release https://github.com/lammps/lammps.git mylammps If you want to add files (such as fix, compute files), add them in the src directory. You can also add directories in the src directory. Step 2 ^^^^^^ The Next step is to get an appropriate module into your system: .. code:: console module load intel/19.1.2 module load openmpi/intel/4.1.1 module load gcc/10.2.0 We also tested with Intel 17.0.0.098 and OpenMPI 2.1.6. After you load modules, update files in the src directory by typing: .. code:: console make mpi Step 3 ^^^^^^ The next step is to run the LAMMPS code using symbolic links and soft links. (which enable you to run the program from different directories) On GREENE, people usually make a link in a bin directory. Let's make a bin directory if you don't have one. (first go to /home/username/bin). .. code:: console ln -s /home/username/mylammps/src/lmp_mpi lammps Make another softlink that connects the LAMMPS code and the libraly files. Make a file in the libraly directory like `Dafed_DK.inc`. In this file you should have two things to connect the file. When you make this file, make sure to change the path to the appropriate name for your case. .. code:: console DAFED_LOAD= /home/drk354/MolStrucClassifier/MolStrucClassifier/molvec_lib/ver2.0/libcv_nn.so -ldl DAFED_DEPENDENCIES = /home/drk354/MolStrucClassifier/MolStrucClassifier/molvec_lib/ver2.0/libcv_nn.so After this, go to the parent directory and type the following commands: .. code:: console ln -s /home/drk354/MolStrucClassifier/MolStrucClassifier/molvec_lib/ver2.0/Dafed_DK.inc Dafed.inc ln -s /home/drk354/MolStrucClassifier/MolStrucClassifier/molvec_lib/ver2.0/dafed_link.h Dafed.h Step 4 ^^^^^^ You are almost there! The next step is to install some additional LAMMPS packages at the source directory. You will need the following packages: .. table:: :align: left +---------------+ |name_of_package| +===============+ | KSPACE | +---------------+ | MANYBODY | +---------------+ | MOLECULE | +---------------+ |EXTRA-MOLECULE | +---------------+ If you use the old LAMMPS from 2019 or before, you also need to add package called 'OPT'. The command you need to type to get these additional packages is as folows: .. code:: console make yes-name_of_package You can check the status from typing: .. code:: console make pi Open ``Makefile.package`` and add the following to connect the source directory to the libraly directories: .. code:: console PKG_LIB = $(DAFED_LOAD) Open ``Makefile.package.setting`` and add the following line at the end of the file: .. code:: console include ../../Dafed.inc Install moltemplate ------------------- In order to run the libraly programs in LAMMPS, you need to have specific data file called .data. If you cannot find the dataset online, check the following section to create one. If you have a .data file with missing critical information (such as bonds, angles, dihedrals, improper angles information), you can use moltemplate to fill these. If you do not have .data file, refer to :doc:`How_to_use` for more information. Step 1 ^^^^^^ Run the following command to install Moltemplate: .. code:: console git clone https://github.com/jewettaij/moltemplate moltemplate Step 2 ^^^^^^ To create a symbolic link, navigate to the bin directory (/home/username/bin), as shown in Step 3 of Installing LAMMPS. .. code:: console git clone https://github.com/jewettaij/moltemplate moltemplate Step 3 ^^^^^^ Python3.7.2 or above is required to use for this program. On Greene, we have python 3.8.6 and you have to load this module as follows: .. code:: console module load python/intel/3.8.6 Step 4 ^^^^^^ Navigate to the Moltemplate directory and finish the installation: .. code:: console pip3 install . Install Ogre ------------ Ogre is a computational tool to create a surface with a vacuum region. In this project, I used this code to create surfaces. Step 1 ^^^^^^ If you want to download the code, go to `Ogre webpage `_ and choose Ogre2.0. Step 2 ^^^^^^ After downloading the program, make some minor changes if the code does not work. Go to ``/Ogre-master/ogre/utils`` and remove the following two lines: .. code:: console from ogre.utils.surface_energy import convergence_plots from ogre.utils.unique_planes import UniquePlanes Next, go to ``/Ogre-master/ogre/utils`` and remove the following two lines: .. code:: console from ogre.utils.surface_energy import convergence_plots from ogre.utils.unique_planes import UniquePlanes Go to ``/Ogre-master/ibslib/io`` and open ``check.py`` and change line 22 from: .. code:: console extension2format = ase_extension2format` to: .. code:: console extension2format = deepcopy(ase_extension2format) Using NYU GREENE ----------------- We will use NYU's high-performance computer, GREENE, as an example. If you do not have access to the account, visit the `NYU HPC account page `_ to request access or download the appropriate softwares on your computer.