#! /bin/bash

# This script installs mylammps automatically in an invidual user's home directory. It is specially designed to work for Ubuntu. It should theoretically work for Ubuntu of other version. 

## It is assumed that fftw3 and mpich2 are already properly installed
 
# This script will create a folder mylamps in ~/ (home directory of current user).
# Choose either scp from www2 (not current version) or git (current/latest version) or wget. By default, wget is used.
# Make sure you have git installed, or yum install git.x86_64 as root, if you wish to download with git clone (instead of scp)


######### begin downloading ###########################
cd ~/

# Use either Option 1 or Option 2, but not both to download the mylammps. By default, Option 2 is used. Option 2 is faster but it does not contains the lastest version of mylammps. Option 1 is slower but it downloads directly the latest version from the source in the web.

## Option 1. Uncomment if want to use this option.
# git clone http://git.icms.temple.edu/lammps-ro.git mylammps 
## End of Option 1

## Option 2. Default option.
wget -r -l1 --no-parent -A.tar.gz http://www2.fizik.usm.my/configrepo/howto/mylammps/
cp www2.fizik.usm.my/configrepo/howto/mylammps/*.tar.gz .

mv lammps-* mylammps.tar.gz
tar -zxvf mylammps.tar.gz
mv lammps-* mylammps
rm -rf www2.fizik.usm.my mylammps.tar.gz 
#mkdir mylammps
## End of Option 2
 

 
####### begin installation ####################################################

# atc #
cd ~/mylammps
cd lib
cd atc
wget http://www2.fizik.usm.my/configrepo/howto/mylammps/Makefile.g++.atc.ubuntu
mv Makefile.g++ Makefile.g++.bk
cp Makefile.g++.atc.ubuntu Makefile.g++
make -f Makefile.g++

# linalg #
cd ~/mylammps/lib
cd linalg
make -f Makefile.gfortran

# mean #
cd ~/mylammps/lib
cd meam  
wget http://www2.fizik.usm.my/configrepo/howto/mylammps/Makefile.lammps.ubuntu
mv Makefile.lammps Makefile.lammps.orig
mv Makefile.lammps.ubuntu Makefile.lammps 
make -f Makefile.gfortran

# reax #
cd ~/mylammps/lib
cd reax  
wget http://www2.fizik.usm.my/configrepo/howto/mylammps/Makefile.lammps.ubuntu
mv Makefile.lammps Makefile.lammps.orig
mv Makefile.lammps.ubuntu Makefile.lammps 
make -f Makefile.gfortran

# peom #
cd ~/mylammps/lib
cd poems
make -f Makefile.g++

# Now exit /lib 
cd ~/mylammps/src/MAKE

wget http://www2.fizik.usm.my/configrepo/howto/mylammps/Makefile.g++.src.MAKE.ubuntu
cp Makefile.g++ Makefile.g++.bk
cp Makefile.g++.src.MAKE.ubuntu Makefile.g++
cd  ~/mylammps/src/
make yes-all
make no-user-cuda
make no-gpu
make no-user-awpmd
make no-kim
make g++

### Post-installation ####

### Add the following aliases into ~/.bashrc
echo 'alias mmpiexec="/opt/mpich2/gnu/bin/mpiexec"' >> ~/.bashrc
echo 'alias lg++="~/mylammps/src/lmp_g++"' >> ~/.bashrc
### End of Post-installation ####

# To run an mylammps calclation, you must prepare an input file named as 'in.XXXX'. For example, to run the calculation 'colloid', which is kept in the folder ~/mylammps/examples/in.colloid, issue the command:
# 'mmpiexec -f ~/hosts -np NP lg++ < ~/mylammps/examples/in.colloid'
# where NP = number of processors, NP = 1, 2, 3, ...

# Note that the executable 'mmpiexec', 'lg++' must be ready before issuing the above command. 'mmpiexec' and 'lg++' are aliases that are to be defined in ~/.bashrc. 

# Nota also that to run lammps in mpi mode, a ~/hosts file must be created. It should contain the list of nodes to be used to run a lammps calculation, e.g.,

#anicca.usm.my
#compute-0-0
#compute-0-1
#compute-0-2
# ...

# Alternatively, you can also specify the node's using their private IP addresses, e.g.,
# 10.1.1.1
# 10.1.255.245 
# 10.1.255.246 
# 10.1.255.247
# ...
# To check the private IP address of the nodes, just issue the command '/sbin/ifconfig'


# How to set the number of 'NP':

# anicca.usm.my, is a Rocks 5.4.3 cluster comprised of 30 nodes, where each node contains 4 cores. So the total number of cores available is 4 x 30. If the list as appear in ~/hosts contains only 20 nodes, then NP = 20 x 4 = 80 is the optimal number to use. If NP is set to be more than 80, non-optimal mpi performance may result. To run only a calculation in a single machine, set NP = 4, and list only 1 node in ~/hosts.