Merge pull request #1270 from akohlmey/get-moltemplate-from-web

moltemplate tool :h4,link(moltemplate)

The moltemplate sub-directory contains a Python-based tool for

building molecular systems based on a text-file description, and

creating LAMMPS data files that encode their molecular topology as

lists of bonds, angles, dihedrals, etc.  See the README.TXT file for

more information.

The moltemplate sub-directory contains instructions for installing

moltemplate, a Python-based tool for building molecular systems based

on a text-file description, and creating LAMMPS data files that encode

their molecular topology as lists of bonds, angles, dihedrals, etc.

See the README.txt file for more information.

This tool was written by Andrew Jewett (jewett.aij at gmail.com), who

supports it.  It has its own WWW page at

"http://moltemplate.org"_http://moltemplate.org.

The latest sources can be found "on its GitHub page"_https://github.com/jewettaij/moltemplate/releases

:line

lmp2cfg		       convert LAMMPS output to CFG files for AtomEye viz

matlab		       MatLab scripts for post-processing LAMMPS output

micelle2d	       create a data file of small lipid chains in solvent

moltemplate            Moltemplate builder program

moltemplate            Instructions for installing the Moltemplate builder program

msi2lmp		       use Accelrys Insight code to setup LAMMPS input

phonon                 post-process output of the fix phonon command

polybond               Python tool for programmable polymer bonding

# from https://github.com/github/gitignore/blob/master/Python.gitignore

# Byte-compiled / optimized / DLL files

__pycache__/

*.py[cod]

*$py.class

# C extensions

*.so

# Distribution / packaging

.Python

env/

build/

develop-eggs/

dist/

downloads/

eggs/

.eggs/

lib/

lib64/

parts/

sdist/

var/

wheels/

*.egg-info/

.installed.cfg

*.egg

# PyInstaller

#  Usually these files are written by a python script from a template

#  before PyInstaller builds the exe, so as to inject date/other infos into it.

*.manifest

*.spec

# Installer logs

pip-log.txt

pip-delete-this-directory.txt

# Unit test / coverage reports

htmlcov/

.tox/

.coverage

.coverage.*

.cache

nosetests.xml

coverage.xml

*,cover

.hypothesis/

# Translations

*.mo

*.pot

# Django stuff:

*.log

local_settings.py

# Flask stuff:

instance/

.webassets-cache

# Scrapy stuff:

.scrapy

# Sphinx documentation

docs/_build/

# PyBuilder

target/

# Jupyter Notebook

.ipynb_checkpoints

# pyenv

.python-version

# celery beat schedule file

celerybeat-schedule

# dotenv

.env

# virtualenv

.venv/

venv/

ENV/

# Spyder project settings

.spyderproject

# Rope project settings

.ropeproject

# text-editor temporary files:

*~

# misc rubbish

deleteme*

DELETEME*

######## files specific to moltemplate and lammps ########

# latex/bibtex temporary files for the moltemplate manual:

moltemplate_manual*.aux

moltemplate_manual*.bbl

moltemplate_manual*.blg

moltemplate_manual*.log

moltemplate_manual*.out

moltemplate_manual*.toc

######## files created by running LAMMPS: ########

log.lammps

log.cite

traj*.lammpstrj

######## files generated by running moltemplate: ########

system.data

system.in

system.in.init

system.in.settings

system.in.charges

system.psf

ttree_assignments.txt

output_ttree/

# Sections from the LAMMPS data file generated by moltemplate.sh

"Data Header"*

"Data Atoms"*

"Data Masses"*

"Data Velocities"*

"Data Bonds"*

"Data Bond List"*

"Data Bonds AtomId AtomId"*

"Data Angles"*

"Data Dihedrals"*

"Data Impropers"*

"Data Bond Coeffs"*

"Data Angle Coeffs"*

"Data Dihedral Coeffs"*

"Data Improper Coeffs"*

"Data Pair Coeffs"*

"Data PairIJ Coeffs"*

# interactions-by-type (not id. This is not part of the LAMMPS standard.)

"Data Charge By Bond"*

"Data Bonds By Type"*

"Data Angles By Type"*

"Data Dihedrals By Type"*

"Data Impropers By Type"*

# class2 data sections

"Data BondBond Coeffs"*

"Data BondAngle Coeffs"*

"Data MiddleBondTorsion Coeffs"*

"Data EndBondTorsion Coeffs"*

"Data AngleTorsion Coeffs"*

"Data AngleAngleTorsion Coeffs"*

"Data BondBond13 Coeffs"*

"Data AngleAngle Coeffs"*

# sections for non-point-like particles:

"Data Ellipsoids"*

"Data Lines"*

"Data Triangles"*

# periodic boundary conditions

"Data Boundary"*

# Sections from the LAMMPS input script(s) generated by moltemplate.sh

"In Init"*

"In Settings"*

"In Coords"*

"In Charges"*

#temporary file created by moltemplate.sh for storing coordinates

tmp_atom_coords.dat

Modified BSD License (BSD-3-Clause)

====================

_Copyright © `2012`, `University of California, Santa Barbara`_  

_All rights reserved._

Redistribution and use in source and binary forms, with or without

modification, are permitted provided that the following conditions are met:

1. Redistributions of source code must retain the above copyright

   notice, this list of conditions and the following disclaimer.

2. Redistributions in binary form must reproduce the above copyright

   notice, this list of conditions and the following disclaimer in the

   documentation and/or other materials provided with the distribution.

3. Neither the name of the copyright holders nor the names of its

   contributors may be used to endorse or promote products derived from 

   this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS “AS IS”

AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE

IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE

ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE

LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR

CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF

SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS

INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN

CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)

ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF

THE POSSIBILITY OF SUCH DAMAGE.

[![Build Status](https://travis-ci.org/jewettaij/moltemplate.svg?branch=master)](https://travis-ci.org/jewettaij/moltemplate.svg?branch=master)

Moltemplate

===========

##  Description

Moltemplate is a *general* cross-platform text-based molecule builder for **LAMMPS** and **ESPResSo**.  Moltemplate was intended for building custom coarse-grained molecular models, but it can be used to prepare realistic all-atom simulations as well.  It currently supports the **OPLS**, **COMPASS**, **AMBER**(GAFF,GAFF2), **MARTINI**, **SDK**, **LOPLS**(2015), and **TraPPE**(1998) force fields, and includes approximately 40 examples.  (New force fields and examples are added continually by users.)

This folder used to contain a distribution of Moltemplate, a general purpose,

cross-platform, text-based molecule and topology builder for LAMMPS.

Moltemplate was originally conceived for building custom coarse-grained

molecular models, but it has since been generalized for all-atom simulations

as well.  It currently supports the OPLS, COMPASS, AMBER(GAFF,GAFF2),

MARTINI, SDK, LOPLS(2015), and TraPPE(1998) force fields, and includes

(New force fields and examples are added continually through user

contributions).

Moltemplate is now distributed via the pip python package manager,

or can be downloaded from http://www.moltemplate.org/download.html

or https://github.com/jewettaij/moltemplate/releases

The most up-to-date version is usually available through GitHub

## Typical usage

## INSTALLATION INSTRUCTIONS

This directory should contain 3 folders:

## Download / install via pip

If you have a working installation of "pip" and access to the internet,

you can download and install it into your home directory ($HOME/.local/bin

and the corresponding python package folders) simply by:

   pip install moltemplate --user

If instead, you want a system-wide installation, you need superuser access,

e.g. via:

   sudo pip install moltemplate

Updates to this distribution method are less frequent, than others, so if

you need a more recent version, you can download it as a .tar.gz or .zip

archive from the moltemplate home page or GitHub (see linke above). After

downloading an archive and unpacking it, you should have 3 folders.

    moltemplate/                  <-- source code and force fields

    doc/                          <-- the moltemplate reference manual

    examples/                     <-- examples built with moltemplate

There are two ways to install moltemplate:

From here on, you can use pip to install this downloaded version as well

by issuing the following command from within the top-level directory of

the unpacked source archive:

## Installation using pip

If you are familiar with pip, then run the following command from within the directory where this README file is located:

    pip install . --user

    pip install .

If you want to install into a system folder, then you need to run pip with

superuser priviledges. e.g. with:

If you receive an error regarding permissions, then run pip with the "--user" argument:

    sudo pip install .

    pip install . --user

Make sure that your default pip install bin directory is in your PATH.

This is usually something like ~/.local/bin/ or ~/anaconda3/bin/.

If you have installed anaconda, this will be done for you automatically.

As you can see, this is mostly identical to the direct install with pip.

Make sure that your default pip install bin directory is in your PATH.  (This is usually something like ~/.local/bin/ or ~/anaconda3/bin/.  If you have installed anaconda, this will be done for you automatically.)  Later, you can uninstall moltemplate using:

Later, you can uninstall moltemplate using:

    pip uninstall moltemplate

If you continue to run into difficulty, try installing moltemplate into a temporary virtual environment by installing "*virtualenv*", downloading moltemplate (to "~/moltemplate" in the example below), and running these commands:

If you continue to run into difficulty, try installing moltemplate into

a temporary virtual environment by installing virtualenv, downloading

moltemplate (to "~/moltemplate" in the example below), and running

these commands:

    cd ~/moltemplate

    virtualenv venv

    pip install .

    #(now do something useful with moltemplate...)

(You will have to "run source ~/moltemplate/venv/bin/activate" beforehand every time you want to run moltemplate.

The *virtualenv* tool is

[explained in detail here](http://docs.python-guide.org/en/latest/dev/virtualenvs/))  If all this fails, then try installing moltemplate by manually updating your \$PATH environment variable.  Instructions for doing that are included below.

(You will have to "run source ~/moltemplate/venv/bin/activate" beforehand

every time you want to run moltemplate.

The *virtualenv* tool is explained in detail here:

http://docs.python-guide.org/en/latest/dev/virtualenvs/

If all this fails, then try installing moltemplate by manually updating

your \$PATH environment variable.  Instructions for doing that are included below.

## Manual installation:

Alternatively, you can edit your $PATH environment variable manually to 

include the subdirectory where the "moltemplate.sh" script is located,

as well as the subdirectory where most of the python scripts are located.

Suppose the directory with this README file is named "moltemplate"

Alternatively, after downloading and unpacking the moltemplate source archive,

you can edit your $PATH environment variable manually to include the subdirectory

where the "moltemplate.sh" script is located, as well as the subdirectory where

most of the python scripts are located.

Suppose the top-level directory of the unpacked archive "moltemplate"

and is located in your home directory:

If you use the bash shell, typically you would edit your

### WINDOWS installation suggestions

You can install both moltemplate and LAMMPS in windows, but you will first need to install the BASH shell environment on your computer.  If you are using Windows 10 or later, try installing the "Windows Subsystem for Linux (WSL)"

You can install both moltemplate and LAMMPS in windows, but you will

first need to install the BASH shell environment on your computer.

If you are using Windows 10 or later, try installing the "Windows Subsystem for Linux (WSL)"

https://solarianprogrammer.com/2017/04/15/install-wsl-windows-subsystem-for-linux/

https://msdn.microsoft.com/en-us/commandline/wsl/faq

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/))

## License

Moltemplate is available under the terms of the open-source 3-clause BSD

license.  (See `LICENSE.md`.)