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Installation: Setting Up the viewORCA Program and Pre-Requisites Packages

The following webpage describes how to install viewORCA on your computer, as well as all the other programs required by viewORCA.

Pre-requisites

Python 3 and pip3

This program is designed to work with Python 3. This program can only be used with Python 3.7. This is because the CSD Python API can only run using Python 3.7.

To find out if you have Python 3 on your computer and what version you have, type into the terminal

python --version

If you have Python 3 on your computer, you will get the version of python you have on your computer. E.g.

user@computer_name path % python --version
Python 3.7.9

If you have Python 3, you may have pip installed on your computer as well. pip is a python package installation tool that is recommended by Python for installing Python packages. To see if you have pip installed, type into the terminal

pip list
If you get back a list of python packages install on your computer, you have pip installed. E.g.

user@computer_name Documentation % pip3 list
Package                       Version
----------------------------- ---------
alabaster                     0.7.12
asap3                         3.11.10
ase                           3.20.1
Babel                         2.8.0
certifi                       2020.6.20
chardet                       3.0.4
click                         7.1.2
cycler                        0.10.0
docutils                      0.16
Flask                         1.1.2
idna                          2.10
imagesize                     1.2.0
itsdangerous                  1.1.0
Jinja2                        2.11.2
kiwisolver                    1.2.0
MarkupSafe                    1.1.1
matplotlib                    3.3.1
numpy                         1.19.1
packaging                     20.4
Pillow                        7.2.0
pip                           20.2.4
Pygments                      2.7.1
pyparsing                     2.4.7
python-dateutil               2.8.1
pytz                          2020.1
requests                      2.24.0
scipy                         1.5.2
setuptools                    41.2.0
six                           1.15.0
snowballstemmer               2.0.0
Sphinx                        3.2.1
sphinx-pyreverse              0.0.13
sphinx-rtd-theme              0.5.0
sphinx-tabs                   1.3.0
sphinxcontrib-applehelp       1.0.2
sphinxcontrib-devhelp         1.0.2
sphinxcontrib-htmlhelp        1.0.3
sphinxcontrib-jsmath          1.0.1
sphinxcontrib-plantuml        0.18.1
sphinxcontrib-qthelp          1.0.3
sphinxcontrib-serializinghtml 1.1.4
sphinxcontrib-websupport      1.2.4
urllib3                       1.25.10
Werkzeug                      1.0.1
wheel                         0.33.1
xlrd                          1.2.0

If you do not see this, you probably do not have pip installed on your computer. If this is the case, check out PIP Installation.

Note

In most cases, pip and pip3 are synonymous for the Python Installation Package for Python 3. However in some cases, pip will be directed to the Python Installation Package for Python 2 rather than Python 3. To check this, run in the terminal:

pip --version

If the output indicates you this Python Installation Package is for Python 2 and not Python 3, only install packages using the pip3 name.

For the rest of this documentation, pip will be used, however if your computer's pip refers to Python 2 and not Python 3, use pip3 instead of pip.

Packaging

The packaging program is also used in this program to check the versions of ASE that you are using for compatibility issues. The easiest way to install packaging is though pip. Type the following into the terminal:

pip3 install --upgrade --user packaging

Numpy

The numpy program is used in this program to perform matrix calculations, as well as used by ase. The easiest way to install numpy is though pip. Type the following into the terminal:

pip3 install --upgrade --user numpy

Scipy

The scipy program is used by the ase program. The easiest way to install scipy is though pip. Type the following into the terminal:

pip3 install --upgrade --user scipy

Matplotlib

The matplotlib program is used in this program to create the energy profile plots made by the viewORCA neb_snap module. The easiest way to install matplotlib is though pip. Type the following into the terminal:

pip3 install --upgrade --user matplotlib

Atomic Simulation Environment (ASE)

The ACSD program uses the Atomic Simulation Environment (ASE) to read in the crystal data from various file format, to process the crystals, and to save the the crystals to disk. Read more about ASE here.

The installation of ASE can be found on the ASE installation page, however from experience if you are using ASE for the first time, it is best to install ASE using pip, the package manager that is an extension of python to keep all your program easily managed and easy to import into your python.

To install ASE using pip, perform the following in your terminal.

pip3 install --user --upgrade numpy scipy matplotlib
pip3 install --user --upgrade ase

Installing using pip ensures that ASE is being installed to be used by Python 3, and not Python 2. Installing ASE like this will also install all the requisite program needed for ASE. This installation includes the use of features such as viewing the xyz files of structure and looking at ase databases through a website. These should be already assessible, which you can test by entering into the terminal:

ase gui

This should show a GUI with nothing in it, as shown below:

ase_gui_blank.png
This is a blank ase gui screen that you would see if enter ase gui into the terminal.

However, in the case that this does not work, we need to manually add a path to your ~/.bashrc so you can use the ASE features externally outside python. Do the following; first enter the following into the terminal:

pip show ase

This will give a bunch of information, including the location of ase on your computer. For example, when I do this I get:

user@computer_name docs % pip show ase
Name: ase
Version: 3.20.1
Summary: Atomic Simulation Environment
Home-page: https://wiki.fysik.dtu.dk/ase
Author: None
Author-email: None
License: LGPLv2.1+
Location: /Users/geoffreyweal/Library/Python/3.7/lib/python/site-packages
Requires: matplotlib, scipy, numpy
Required-by:

Copy the Location line. If we remove the lib/python/site-packages bit and replace it with bin, this gives us the location of useful ASE programs. The example below is for Python 3.7. 

/Users/geoffreyweal/Library/Python/3.7/bin

Next, add this to your ~/.bashrc file as below:

############################################################
# For ASE
export PATH=/Users/geoffreyweal/Library/Python/3.7/bin:$PATH
############################################################

Write source ~/.bashrc in the terminal and press enter. Once you have done this, try to run ase gui in the terminal. This will hopefully show the ase gui and allow you to access the useful ASE programs through the terminal.

Setting up the viewORCA Program

There are three ways to install viewORCA on your system. These ways are described below:

Install viewORCA through pip3

To install the viewORCA program using pip3, perform the following in your terminal.

pip3 install --upgrade --user viewORCA

The website for viewORCA on pip3 can be found by clicking here.

Tip

This is the recommended way of installing viewORCA on your computer.

Install ACSD through conda

You can install the viewORCA program on conda through pip. Click here to see more information about installing viewORCA through conda.

Install Development Version of viewORCA

If you would like to test the development version of viewORCA from Github, there are two ways to do this:

Warning

This is not recommended as this version of viewORCA may be unstable.

1. Install viewORCA from Github through pip3

You can install viewORCA from Github through pip3 by performing the following in your terminal.

pip3 install --upgrade --user git+https://github.com/geoffreyweal/viewORCA.git

2. Install viewORCA Manually from Github

To install the viewORCA program manually onto your computer, do the following:

  1. Open the terminal and cd into the path that you want to download the programs into.

    cd /Users/USERNAME

  2. Download viewORCA to your computer by typing the following commands into the terminal:

    git clone https://github.com/geoffreyweal/viewORCA.git

  3. Change the permissions of the newly downloded viewORCA folder to 777:

    chmod -R 777 viewORCA

  4. Add the following to your ~bashrc by typing the following into the terminal:

    echo '#############################################
# For the viewORCA Program
export PATH_TO_viewORCA='$PWD'/viewORCA
export PYTHONPATH="$PATH_TO_viewORCA":$PYTHONPATH
export PATH="$PATH_TO_viewORCA"/bin:$PATH
#############################################' >> ~/.bashrc

    This should add the following to your ~/.bashrc file:

    #############################################
# For the ORCA Mechanism Procedure
export PATH_TO_viewORCA="YOUR_PWD_PATH/viewORCA"
export PYTHONPATH="$PATH_TO_viewORCA":$PYTHONPATH
export PATH="$PATH_TO_viewORCA"/bin:$PATH
#############################################

    Tip

    Make sure that the path given to PATH_TO_ACSD is the correct path to the ACSD folder.

    An example of what the PATH_TO_viewORCA path should look like is shown below:

    # An example of:
export PATH_TO_viewORCA="YOUR_PWD_PATH/viewORCA"
# is shown below
export PATH_TO_viewORCA=/Users/USERNAME/viewORCA

  5. Source the ~bashrc file:

    source ~/.bashrc

  6. Check that your computer recognises the programs by typing the following into the terminal

    which viewORCA

    If this has worked, the terminal should give you the path to the viewORCA program. For example

    USERNAME@computer USERNAME % which viewORCA
/Users/USERNAME/viewORCA/bin/viewORCA

    Warning

    If you get the message below, check that the path you gave for PATH_TO_ORCA_Mechanism_Procedure is pointing to the correct folder path. 

    /usr/bin/which: no viewORCA in ...