#!/bin/csh
#PBS -l walltime=72:00:00
#  select=<number nodes>,ncpus=<cores/node>,mpiprocs=<MPI procs/node>
#  Total cores requested = <number of nodes> X <MPI procs/node>
#PBS -l select=2:ncpus=8:mpiprocs=8
#PBS -l place=scatter:excl
#PBS -M victor.bermudez@nrl.navy.mil
#PBS -N NEB
#PBS -V
#PBS -M victor.bermudez@nrl.navy.mil
#PBS -m abe
#
set JOBID=`echo $PBS_JOBID | cut -f1 -d.`
set NSLOTS=`wc -l $PBS_NODEFILE | cut -f1 -d " "`
set SYSNAME=SiC+SiOH+HF-NEB
setenv TMPZ /lustre/cmf/scratch/b/bermudez/$JOBID

cd $PBS_O_WORKDIR
if (! -e $TMPZ) mkdir -p $TMPZ
# cp $INPUT $TMPZ || echo "PROBLEM COPYING $INPUT INPUT FILE\!\!\!\!"

# module load adf/2009.01.r23102
# module unload adf
# module load adf/2010.02
module load intel/11.1
module load mk1/11.1.072
module load fftw/3.1.2
module load espresso/4.3.1


setenv SCM_TMPDIR /lustre/cmf/scratch/b/bermudez/$JOBID
setenv SCM_USETMPDIR yes
setenv P4_RSHCOMMAND ssh

set MPI_DSM_DISTRIBUTE
set MPI_USE_IB
set MPI_MEMMAP_OFF

cd $TMPZ
echo "Starting PWscf ($0) at >`date`< on >`hostname`< under userid >`whoami`< in directory >`pwd`<"

# Creates the file to run the NEB calculation
cat > $SYSNAME.in << EOF
BEGIN
BEGIN_PATH_INPUT
&PATH
restart_mode='from_scratch',
string_method='neb',
ds=2.d0,
opt_scheme='broyden',
num_of_images=5,
nstep_path=10,
k_max=0.3d0,
k_min=0.2d0,
CI_scheme='auto'
/
END_PATH_INPUT

BEGIN_ENGINE_INPUT
&CONTROL
title='alpha-SiC; (2x2) slab supercell + OH; NEB for HF on (0001)',
pseudo_dir='/lustre/cmf/scratch/b/bermudez/QE_PP/',
etot_conv_thr=1.0D-4,
forc_conv_thr=1.0D-3,
verbosity='default'
/

&SYSTEM
ibrav=4,
a=6.190, c=53.0,
nat=74,
ntyp=5,
ecutwfc=40.0,
ecutrho=400.0,
occupations='fixed',
nosym_evc=.TRUE.
/

&ELECTRONS
electron_maxstep=100,
conv_thr=1.0D-9,
mixing_mode='plain'
/

ATOMIC_SPECIES
Si  28.0855  Si_pbe-n-van_UPF
C   12.0107  C_pbe-van_ak_UPF
O   15.9994  O_pbe-van_ak_UPF
F   18.9984032 F_pbe-n-van_UPF
H   1.00794  H_pbe-van_ak_UPF

BEGIN_POSITIONS
FIRST_IMAGE
ATOMIC_POSITIONS {angstrom} 
F        0.18074       2.01770      13.17017
H       -0.20072       1.10600      12.84627
H       -1.547439879   1.632467590  10.028926390
H        0.000000000  -1.047888843  10.028918514
H        1.547439879   1.632467590  10.028926390
H        3.095000000  -1.047831477  10.028897607
O       -1.547517433   0.761151390   9.578652072
O        0.000000000  -1.919221528   9.578637156
O        1.547517433   0.761151390   9.578652072
O        3.095000000  -1.919136263   9.578665947
Si      -1.547500469   0.883507378   7.912663375
Si       0.000000000  -1.796849881   7.912661591
Si       1.547500469   0.883507378   7.912663375
Si       3.095000000  -1.796830922   7.912663063
C        1.547493018  -0.895584792   7.300879759
C        0.000000000   1.784771526   7.300887869
C       -1.547493018  -0.895584792   7.300879759
C       -3.095000000   1.784758317   7.300867301
Si       1.547498354  -0.888576483   5.397824990
Si       0.000000000   1.791775876   5.397829969
Si      -1.547498354  -0.888576483   5.397824990
Si      -3.095000000   1.791769286   5.397819797
C       -1.547495639   0.898281224   4.759500809
C        0.000000000  -1.782071820   4.759498846
C        1.547495639   0.898281224   4.759500809
C        3.095000000  -1.782066781   4.759498676
Si      -1.547499373   0.897851758   2.858416625
Si       0.000000000  -1.782496390   2.858415125
Si       1.547499373   0.897851758   2.858416625
Si       3.095000000  -1.782499466   2.858415020
C        1.547502710  -0.889212539   2.220903911
C        0.000000000   1.791131724   2.220899422
C       -1.547502710  -0.889212539   2.220903911
C       -3.095000000   1.791134577   2.220905665
Si       1.547501475  -0.890989759   0.319865793
Si       0.000000000   1.789357696   0.319863771
Si      -1.547501475  -0.890989759   0.319865793
Si      -3.095000000   1.789359429   0.319866860
C       -1.547500391   0.895657677  -0.317833664
C        0.000000000  -1.784690258  -0.317832617
C        1.547500391   0.895657677  -0.317833664
C        3.095000000  -1.784693971  -0.317835861
Si      -1.547501482   0.893769500  -2.219092154
Si       0.000000000  -1.786578236  -2.219090372
Si       1.547501482   0.893769500  -2.219092154
Si       3.095000000  -1.786581273  -2.219092389
C        1.547500654  -0.893383735  -2.856895718
C        0.000000000   1.786964119  -2.856897166
C       -1.547500654  -0.893383735  -2.856895718
C       -3.095000000   1.786969583  -2.856901884
Si       1.547500000  -0.893449542  -4.758474000    0   0   0
Si       0.000000000   1.786899083  -4.758474000    0   0   0
Si      -1.547500000  -0.893449542  -4.758474000    0   0   0
Si      -3.095000000   1.786899083  -4.758474000    0   0   0
C       -1.547500000   0.893449542  -5.387526000    0   0   0
C        0.000000000  -1.786899083  -5.387526000    0   0   0
C        1.547500000   0.893449542  -5.387526000    0   0   0
C        3.095000000  -1.786899083  -5.387526000    0   0   0
Si      -1.547500000   0.893449542  -7.294974000    0   0   0
Si       0.000000000  -1.786899083  -7.294974000    0   0   0
Si       1.547500000   0.893449542  -7.294974000    0   0   0
Si       3.095000000  -1.786899083  -7.294974000    0   0   0
C        1.547500000  -0.893449542  -7.924026000    0   0   0
C        0.000000000   1.786899083  -7.924026000    0   0   0
C       -1.547500000  -0.893449542  -7.924026000    0   0   0
C       -3.095000000   1.786899083  -7.924026000    0   0   0
O        1.547516425  -0.791736626  -9.402414591    0   0   0
O        0.000000000   1.888690968  -9.402412000    0   0   0
O       -1.547516425  -0.791736626  -9.402414591    0   0   0
O       -3.095000000   1.888666993  -9.402405868    0   0   0
H        1.547540357  -1.707577441  -9.760908882    0   0   0
H        0.000000000   0.972838260  -9.760971076    0   0   0
H       -1.547540357  -1.707577441  -9.760908882    0   0   0
H       -3.095000000   0.972810044  -9.760959216    0   0   0

LAST_IMAGE
ATOMIC_POSITIONS {angstrom}
H       -2.64339       5.42872      13.43893
O       -3.24147       4.78880      12.99927
H       -2.66427       4.03082      12.76998
H        0.000000000  -1.047888843  10.028918514
H        1.547439879   1.632467590  10.028926390
H        3.095000000  -1.047831477  10.028897607
F       -1.54750       0.88351       9.74266
O        0.000000000  -1.919221528   9.578637156
O        1.547517433   0.761151390   9.578652072
O        3.095000000  -1.919136263   9.578665947
Si      -1.547500469   0.883507378   7.912663375
Si       0.000000000  -1.796849881   7.912661591
Si       1.547500469   0.883507378   7.912663375
Si       3.095000000  -1.796830922   7.912663063
C        1.547493018  -0.895584792   7.300879759
C        0.000000000   1.784771526   7.300887869
C       -1.547493018  -0.895584792   7.300879759
C       -3.095000000   1.784758317   7.300867301
Si       1.547498354  -0.888576483   5.397824990
Si       0.000000000   1.791775876   5.397829969
Si      -1.547498354  -0.888576483   5.397824990
Si      -3.095000000   1.791769286   5.397819797
C       -1.547495639   0.898281224   4.759500809
C        0.000000000  -1.782071820   4.759498846
C        1.547495639   0.898281224   4.759500809
C        3.095000000  -1.782066781   4.759498676
Si      -1.547499373   0.897851758   2.858416625
Si       0.000000000  -1.782496390   2.858415125
Si       1.547499373   0.897851758   2.858416625
Si       3.095000000  -1.782499466   2.858415020
C        1.547502710  -0.889212539   2.220903911
C        0.000000000   1.791131724   2.220899422
C       -1.547502710  -0.889212539   2.220903911
C       -3.095000000   1.791134577   2.220905665
Si       1.547501475  -0.890989759   0.319865793
Si       0.000000000   1.789357696   0.319863771
Si      -1.547501475  -0.890989759   0.319865793
Si      -3.095000000   1.789359429   0.319866860
C       -1.547500391   0.895657677  -0.317833664
C        0.000000000  -1.784690258  -0.317832617
C        1.547500391   0.895657677  -0.317833664
C        3.095000000  -1.784693971  -0.317835861
Si      -1.547501482   0.893769500  -2.219092154
Si       0.000000000  -1.786578236  -2.219090372
Si       1.547501482   0.893769500  -2.219092154
Si       3.095000000  -1.786581273  -2.219092389
C        1.547500654  -0.893383735  -2.856895718
C        0.000000000   1.786964119  -2.856897166
C       -1.547500654  -0.893383735  -2.856895718
C       -3.095000000   1.786969583  -2.856901884
Si       1.547500000  -0.893449542  -4.758474000    0   0   0
Si       0.000000000   1.786899083  -4.758474000    0   0   0
Si      -1.547500000  -0.893449542  -4.758474000    0   0   0
Si      -3.095000000   1.786899083  -4.758474000    0   0   0
C       -1.547500000   0.893449542  -5.387526000    0   0   0
C        0.000000000  -1.786899083  -5.387526000    0   0   0
C        1.547500000   0.893449542  -5.387526000    0   0   0
C        3.095000000  -1.786899083  -5.387526000    0   0   0
Si      -1.547500000   0.893449542  -7.294974000    0   0   0
Si       0.000000000  -1.786899083  -7.294974000    0   0   0
Si       1.547500000   0.893449542  -7.294974000    0   0   0
Si       3.095000000  -1.786899083  -7.294974000    0   0   0
C        1.547500000  -0.893449542  -7.924026000    0   0   0
C        0.000000000   1.786899083  -7.924026000    0   0   0
C       -1.547500000  -0.893449542  -7.924026000    0   0   0
C       -3.095000000   1.786899083  -7.924026000    0   0   0
O        1.547516425  -0.791736626  -9.402414591    0   0   0
O        0.000000000   1.888690968  -9.402412000    0   0   0
O       -1.547516425  -0.791736626  -9.402414591    0   0   0
O       -3.095000000   1.888666993  -9.402405868    0   0   0
H        1.547540357  -1.707577441  -9.760908882    0   0   0
H        0.000000000   0.972838260  -9.760971076    0   0   0
H       -1.547540357  -1.707577441  -9.760908882    0   0   0
H       -3.095000000   0.972810044  -9.760959216    0   0   0

END_POSITIONS

K_POINTS {automatic}
6 6 1 0 0 0

END_ENGINE_INPUT
END
EOF

mpiexec /lustre/cmf/scratch/p/petccm/x86_64/espresso-4.3.1/bin/neb.x -n $NSLOTS -inp $SYSNAME.in > $SYSNAME.out

#date
echo "Ending PWscf ($0) at >`date`< on >`hostname`< under userid >`whoami`< in directory >`pwd`<"
exit 0