remove old moltemplate version

Author: Andrew Jewett, Shea Group, http://www.chem.ucsb.edu/~sheagroup/

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   --  Description:  --

Moltemplate is a cross-platform text-based molecule builder for LAMMPS. 

   --  Typical usage:  --

moltemplate.sh [-atomstyle style] [-pdb/-xyz coord_file] [-vmd]  system.lt

   --  Web page:  --

Documentation, examples, and supporting code can be downloaded at:

    http://www.moltemplate.org

The most up-to-date version of moltemplate can be downloaded here.

(After download, you can unpack the archive using:

    tar xzf moltemplate_2012-3-31.tar.gz

The date will vary from version to version.)

----------------------------------------------------

----------  INSTALLATION INSTRUCTIONS:  ------------

----------------------------------------------------

This directory should contain two folders:

    src/       <-- location of all python and bash scripts

    common/    <-- location of shared force fields and molecules 

The ``moltemplate.sh'' script and the python scripts that it invokes are 

located in the ``src/'' subdirectory.  You should update your PATH environment 

variable to include this directory.  

If you do not know what a PATH environment variable is, read:

    http://www.linfo.org/path_env_var.html

(I receive this question often.)

It is also a good idea to set your MOLTEMPLATE_PATH environment variable to 

point to the ``common/'' subdirectory.

(Force fields and commonly used molecules will eventually be located here.)

   --  Installation example ---

Suppose the directory with this README.TXT file is located at ~/moltemplate.

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

~/.profile, ~/.bash_profile or ~/.bashrc files to contain the following lines:

    export PATH="$PATH:$HOME/moltemplate/src"

    export MOLTEMPLATE_PATH="$HOME/moltemplate/common"

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

~/.login, ~/.cshrc, or ~/.tcshrc files to contain the following lines:

    setenv PATH "$PATH:$HOME/moltemplate/src"

    setenv MOLTEMPLATE_PATH "$HOME/moltemplate/common"

   --  Requirements:  --

Moltemplate requires the Bourne-shell, and a recent version of python 

(2.7, 3.0 or higher), and can run on OS X, linux, or windows (if a 

suitable shell environment has been installed).

   --  License:  --

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

license.  (See LICENSE.TXT.)

These are examples for the "moltemplate" molecule builder for LAMMPS.

http://www.moltemplate.org

Each directory contains one or more examples.

Each example directory contains:

   images/              This folder has pictures of the molecules in the system

   moltemplate_files/   This folder contains LT files and other auxiliary files

   README_setup.sh      Instructions for how to use moltemplate (executable)

   README_visualize.txt Instructions for viewing in DATA/DUMP files in VMD

     ...and one or more LAMMPS input scripts with names like

   run.in.min

   run.in.npt

   run.in.nvt         

You can run these scripts using

      lmp_linux -i run.in.npt

(The name of your lammps binary, "lmp_linux" in this example, may vary. 

 Sometimes, these scripts must be run in a certain order.  For example

 it may be necessary to run run.in.min to minimize the system before you can use run.in.npt, and later run.in.nvt.  The README_run.sh file in each subdirectory

 specifies indicates the order.  These files have not been optimized.)

# -------- REQUIREMENTS: ---------

# 1) This example requires the "MANYBODY" package.

#    As of 2012-9, it is included by default, but this may change in the future.

#    If lammps complains of a missing pair style enter "make yes-MANYBODY"

#    into the shell before compiling lammps.  For details see:

#   http://lammps.sandia.gov/doc/Section_start.html#start_3

This is a relatively complex example containing two different types of

molecules, and a hybrid of Lennard-Jones and 3-body SW "pair" styles.

The cyclododecane molecule uses the 

TraPPE force field for hydrocarbon chains.  

The parameters for the TraPPE force field are

in a file named "trappe1998.lt" which should be

located in the MOLTEMPLATE_PATH.

(See moltemplate installation instructions.)

The water solvent is implemented using the 3-body single-particle 

coarse-grained "mW" water model:

Molinero, V. and Moore, E.B., J. Phys. Chem. B 2009, 113, 4008-4016

More detailed instructions on how to build LAMMPS input files and 

run a short simulation are provided in other README files.

step 1)

README_setup.sh

step 2)

README_run.sh

# --- Running LAMMPS ---

#  -- Prerequisites: --

# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS 

# input scripts which link to the input scripts and data files

# you hopefully have created earlier with moltemplate.sh:

#   system.in.init, system.in.settings, system.data, system.in.sw

# If not, carry out the instructions in "README_setup.sh".

#

#  -- Instructions: --

# If "lmp_mpi" is the name of the command you use to invoke lammps,

# then you would run lammps on these files this way:

lmp_mpi -i run.in.npt  # minimization and simulation at constant pressure

lmp_mpi -i run.in.nvt  # minimization and simulation at constant volume

#(Note: The constant volume simulation lacks pressure equilibration. These are

#       completely separate simulations. The results of the constant pressure

#       simulation are ignored when beginning the simulation at constant volume.

#       This can be fixed.  Read "run.in.nvt" for equilibration instructions.)

# If you have compiled the MPI version of lammps, you can run lammps in parallel

#mpirun -np 4 lmp_mpi -i run.in.npt

#mpirun -np 4 lmp_mpi -i run.in.nvt

# (assuming you have 4 processors available)