forked from lijiext/lammps
143 lines
5.8 KiB
Plaintext
143 lines
5.8 KiB
Plaintext
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Moltemplate
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===========
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## Description
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This folder used to contain a distribution of Moltemplate, a general purpose,
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cross-platform, text-based molecule and topology builder for LAMMPS.
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Moltemplate was originally conceived for building custom coarse-grained
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molecular models, but it has since been generalized for all-atom simulations
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as well. It currently supports the OPLS, COMPASS, AMBER(GAFF,GAFF2),
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MARTINI, SDK, LOPLS(2015), and TraPPE(1998) force fields, and includes
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(New force fields and examples are added continually through user
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contributions).
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Moltemplate is now distributed via the pip python package manager,
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or can be downloaded from http://www.moltemplate.org/download.html
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or https://github.com/jewettaij/moltemplate/releases
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The most up-to-date version is usually available through GitHub
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## Typical usage
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moltemplate.sh [-atomstyle style] [-pdb/-xyz coord_file] [-vmd] system.lt
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## Web page
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Documentation, examples, and supporting code can be downloaded at:
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http://www.moltemplate.org
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## Requirements
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Moltemplate requires the Bourne-shell, and a recent version of python
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(2.7, 3.0 or higher), and can run on OS X, linux, or windows. (...if a
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suitable shell environment has been installed. See below.)
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## INSTALLATION INSTRUCTIONS
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## Download / install via pip
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If you have a working installation of "pip" and access to the internet,
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you can download and install it into your home directory ($HOME/.local/bin
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and the corresponding python package folders) simply by:
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pip install moltemplate --user
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If instead, you want a system-wide installation, you need superuser access,
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e.g. via:
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sudo pip install moltemplate
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Updates to this distribution method are less frequent, than others, so if
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you need a more recent version, you can download it as a .tar.gz or .zip
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archive from the moltemplate home page or GitHub (see link above). After
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downloading an archive and unpacking it, you should have 3 folders.
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moltemplate/ <-- source code and force fields
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doc/ <-- the moltemplate reference manual
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examples/ <-- examples built with moltemplate
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From here on, you can use pip to install this downloaded version as well
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by issuing the following command from within the top-level directory of
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the unpacked source archive:
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pip install . --user
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If you want to install into a system folder, then you need to run pip with
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superuser privileges. e.g. with:
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sudo pip install .
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Make sure that your default pip install bin directory is in your PATH.
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This is usually something like ~/.local/bin/ or ~/anaconda3/bin/.
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If you have installed anaconda, this will be done for you automatically.
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As you can see, this is mostly identical to the direct install with pip.
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Later, you can uninstall moltemplate using:
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pip uninstall moltemplate
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If you continue to run into difficulty, try installing moltemplate into
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a temporary virtual environment by installing virtualenv, downloading
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moltemplate (to "~/moltemplate" in the example below), and running
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these commands:
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cd ~/moltemplate
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virtualenv venv
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source venv/bin/activate
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pip install .
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#(now do something useful with moltemplate...)
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(You will have to "run source ~/moltemplate/venv/bin/activate" beforehand
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every time you want to run moltemplate.
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The *virtualenv* tool is explained in detail here:
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http://docs.python-guide.org/en/latest/dev/virtualenvs/
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If all this fails, then try installing moltemplate by manually updating
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your \$PATH environment variable. Instructions for doing that are included below.
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## Manual installation:
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Alternatively, after downloading and unpacking the moltemplate source archive,
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you can edit your $PATH environment variable manually to include the subdirectory
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where the "moltemplate.sh" script is located, as well as the subdirectory where
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most of the python scripts are located.
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Suppose the top-level directory of the unpacked archive "moltemplate"
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and is located in your home directory:
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If you use the bash shell, typically you would edit your
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`~/.profile`, `~/.bash_profile` or `~/.bashrc` files
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to contain the following lines:
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export PATH="$PATH:$HOME/moltemplate/moltemplate"
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export PATH="$PATH:$HOME/moltemplate/moltemplate/scripts"
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If you use the tcsh shell, typically you would edit your
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`~/.login`, `~/.cshrc`, or `~/.tcshrc` files to contain the following lines:
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setenv PATH "$PATH:$HOME/moltemplate/moltemplate"
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setenv PATH "$PATH:$HOME/moltemplate/moltemplate/scripts"
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After making these changes, you may need to start a new terminal (shell) for the changes to take effect. If you do not know what a `PATH` environment variable is and are curious, read:
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http://www.linfo.org/path_env_var.html
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(I receive this question often.)
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### WINDOWS installation suggestions
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You can install both moltemplate and LAMMPS in windows, but you will
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first need to install the BASH shell environment on your computer.
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If you are using Windows 10 or later, try installing the "Windows Subsystem for Linux (WSL)"
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https://solarianprogrammer.com/2017/04/15/install-wsl-windows-subsystem-for-linux/
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https://msdn.microsoft.com/en-us/commandline/wsl/faq
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If you are using an older version of windows, try following the tutorial written by Yanqing Fu instead:
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https://sourceforge.net/p/lammps/mailman/message/32599824/
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To use LAMMPS and moltemplate, You will also need to install (and learn how to use) a text editor. (Word, Wordpad, and Notepad will not work.) Popular free text editors which you can safely install and run from within the WSL terminal include: **nano**, **ne**, **emacs**, **vim**, and **jove**. (Unfortunately, as of 2017-5-17, [graphical unix-friendly text editors such as Atom, VSCode, Notepad++, and sublime won't work with WSL, and may cause file system corruption. Avoid these editors for now.](https://www.reddit.com/r/bashonubuntuonwindows/comments/6bu1d1/since_we_shouldnt_edit_files_stored_in_wsl_with/))
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