# .bashrc

# Source global definitions
if [ -f /etc/bashrc ]; then
	. /etc/bashrc
fi

# User specific aliases and functions

###################################
# select Intel Compiler Version
#
####INTELCOMPILER=12.0
INTELCOMPILER=11.1
#INTELCOMPILER=10.1
####INTELCOMPILER=9.1

###################################
# select MPI
#
MPI=OpenMPI
####MPI=mpich


###################################
# set mkl version
#
if [ x${INTELCOMPILER} == x"10.1" ]; then
# for Intel Compiler 10.1
	MKLVER=10.1.3
else
# for Intel Compiler 9.1
	MKLVER=9.1
fi

ARCH=`/bin/uname -m`
COMPVER="`echo $INTELCOMPILER |sed 's/\.//'`"

case "$ARCH" in
  ia64)
	FARCH=fc
	CARCH=cc
	MKLARCH=64
	IARCH=ia64
	;;
  i686)
	FARCH=fc
	CARCH=cc
	MKLARCH=32
	IARCH=ia32
	;;
  em64t|x86_64)
	FARCH=fce
	CARCH=cce
	MKLARCH=em64t
	IARCH=intel64
	;;
esac

###################################
# for Intel Compiler and mkl
#
if [ x${INTELCOMPILER} == x"12.0" ]; then
# Intel compiler 12.0 (composer xe 2011)
        if [ -r /opt/intel/composerxe/bin/compilervars.sh ]; then
                . /opt/intel/composerxe/bin/compilervars.sh $IARCH
        fi
elif [ x${INTELCOMPILER} == x"11.1" ]; then
# Intel compiler 11.1
        if [ -r /opt/intel/Compiler/${INTELCOMPILER}/bin/ifortvars.sh ]; then
                . /opt/intel/Compiler/${INTELCOMPILER}/bin/ifortvars.sh $IARCH
        fi
        if [ -r /opt/intel/Compiler/${INTELCOMPILER}/bin/iccvars.sh ]; then
                . /opt/intel/Compiler/${INTELCOMPILER}/bin/iccvars.sh $IARCH
        fi
elif [ x${INTELCOMPILER} ]; then
# Intel Compiler 9.1 and 10.1
	if [ -r /opt/intel/${FARCH}/${INTELCOMPILER}/bin/ifortvars.sh ]; then
		. /opt/intel/${FARCH}/${INTELCOMPILER}/bin/ifortvars.sh
	fi
	if [ -r /opt/intel/${CARCH}/${INTELCOMPILER}/bin/iccvars.sh ]; then
		. /opt/intel/${CARCH}/${INTELCOMPILER}/bin/iccvars.sh
	fi
	if [ -r /opt/intel/mkl/${MKLVER}/tools/environment/mklvars${MKLARCH}.sh ]; then
		. /opt/intel/mkl/${MKLVER}/tools/environment/mklvars${MKLARCH}.sh
	fi
fi

####################################
# for MPICH
#
if [ x${INTELCOMPILER} -a x${MPI} == x"mpich" ]; then
	export PATH=/usr/local/mpich-intel${COMPVER}/bin:$PATH
	export MANPATH=/usr/local/mpich-intel${COMPVER}/man:`man -w`
fi

####################################
# for OpenMPI
#
if [ x${INTELCOMPILER} -a x${MPI} == x"OpenMPI" ]; then
	export PATH=/usr/local/openmpi-intel${COMPVER}/bin:$PATH
	if [ -z "${LD_LIBRARY_PATH}" ]
	then
		export LD_LIBRARY_PATH=/usr/lib64:/usr/local/openmpi-intel${COMPVER}/lib
	else
		export LD_LIBRARY_PATH=/usr/lib64:/usr/local/openmpi-intel${COMPVER}/lib:$LD_LIBRARY_PATH
	fi
	## OpenMPI 1.3 or later, and the environment
	##  OMPI_MCA_pls_rsh_agent OMPI_MCA_mpi_show_handle_leaks
	##   Please comment out.
	# export OMPI_MCA_pls_rsh_agent=/usr/bin/rsh
	# export OMPI_MCA_mpi_show_handle_leaks=1
	export MANPATH=/usr/local/openmpi-intel${COMPVER}/share/man/:`man -w`
fi

export MKL_NUM_THREADS=1
export OMP_NUM_THREADS=1

alias ifort='ifort -assume buffered_io '
alias icc='icc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE '

export FORT_BUFFERED=y
export GXX_ROOT=`LANG=C gcc --print-search-dir | grep ^install | awk '{print $2}' | sed 's/\/$//'`

ulimit -s unlimited

#------------------------------------------------------------------------
# this is for XCRYSDEN 1.5.21; added by XCRYSDEN installation on
#------------------------------------------------------------------------
XCRYSDEN_TOPDIR=/usr/local/XCrySDen-1.5.21
XCRYSDEN_SCRATCH=$HOME/xcrys_tmp
export XCRYSDEN_TOPDIR XCRYSDEN_SCRATCH
PATH="$XCRYSDEN_TOPDIR:$PATH:$XCRYSDEN_TOPDIR/scripts:$XCRYSDEN_TOPDIR/util"

###################
# for gromacs 4.5.5

. /usr/local/gromacs/gromacs-4.5.5/bin/GMXRC.bash

###################
# for gromacs 4.0.7
#. /usr/local/gromacs/gromacs-4.0.7/bin/GMXRC.bash

###################
# for gromacs 3.3.3
#. /usr/local/gromacs/gromacs-3.3.3/bin/GMXRC.bash

###################
# for Amber12

export AMBERHOME=/usr/local/amber12
export PATH=$AMBERHOME/bin:$PATH

alias pmdout=/home/mabiao/bin/process_mdout.perl
###################
# for Autodock

#export PATH=/usr/local/autodocksuite-4.2.3/bin:$PATH
#. /usr/local/autodocksuite-4.2.3/bin/mglenv.sh
#. /usr/local/autodocksuite-4.2.3/bin/initMGLtools.sh

###################
# for Gaussian09c01
export g09root=/usr/local/gaussian09c01
export GAUSS_SCRDIR=/scr
. $g09root/g09/bsd/g09.profile

###################
# for Icm
#
export PATH=/home/mabiao/bin/:$PATH
export ICMHOME=/usr/icm

###################
# for paics
#
export PAICS_ROOT=/home/ishi/paics-dev/paics_20121031-1

###################
# for BBQ
#export PATH=$PATH:/usr/java/jre1.7.0_03/bin
CLASSPATH=$CLASSPATH:/home/mabiao/bin/BBQ:/home/mabiao/bin/BBQ/jbcl.jar
export CLASSPATH 

###################
# for MMTSB
export MMTSBDIR=/misc/home/mabiao/bin/mmtsb
export PATH=$PATH:$MMTSBDIR/perl:$MMTSBDIR/bin

###################
# for myself
alias resid=/home/mabiao/bin/reset_resid.sh
alias cl='clear'
alias lt='lsload|sort'
alias ls='ls --color=auto'
alias lr='ls -lhrt'
alias ngramber=/home/mabiao/bin/nagara_cmd/amber_run.sh
alias prpinput=/home/mabiao/bin/nagara_cmd/input_maker.sh
#export PYTHONPATH=/usr/local/bin:$PATH
export PATH=/home/mabiao/bin/pymol:$PATH
# for mgltools
export ADT_ROOT=/home/mabiao/bin/MGLTools-1.5.6/MGLToolsPckgs/AutoDockTools/
export PATH=$PATH:$ADT_ROOT/Utilities24

#for pythonbrew
[[ -s "$HOME/.pythonbrew/etc/bashrc" ]] && source "$HOME/.pythonbrew/etc/bashrc"