#!/bin/sh
# 'ubuntucpmd15' from Ernst Schumacher
# Version 2012-08-04
# make sure we are in /home/$USER
cd /home/$USER
export PATH=.:$PATH
echo 'check the second box "... (universe)",'
echo 'then "close", "close" again'
echo 'and later "Y" when asked to continue'
gksu gksu --desktop /usr/share/applications/software-properties.desktop /usr/bin/software-properties-gtk
sudo apt-get update
sudo apt-get install tcsh make eog gfortran libblas-dev libatlas-base-dev fftw-dev
test -e ./cpmdmake15 || wget chemsoft.ch/downloads/cpmdmake15
test -e ./cpmd-v3_15_1.tgz || wget chemsoft.ch/downloads/cpmd-v3_15_1.tgz
test -e ./cpmd2cube.tar.gz || wget chemsoft.ch/downloads/cpmd2cube.tar.gz
test -e ./cpmd-test.tar.gz || wget chemsoft.ch/downloads/cpmd-test.tar.gz
chmod +x cpmdmake15
./cpmdmake15
exit

export LD_LIBRARY_PATH=/home/$USER/CPMD-3.15.1

test -e ./cpmdmake15 || wget chemsoft.ch/downloads/cpmdmake15
test -e ./cpmd-v3_15_1.tgz || wget chemsoft.ch/downloads/cpmd-v3_15_1.tgz

test -e ./cpmdmake || wget chemsoft.ch/downloads/cpmdmake
#test -e ./cpmd-v3_15_1.tgz || wget chemsoft.ch/downloads/cpmd-v3_15_1.tgz

sudo apt-get update
sudo apt-get install tcsh make eog gfortran libblas-dev libatlas-base-dev fftw-dev

#--------------- Default Configuration for PC-GFORTRAN ---------------
SRC  = .
DEST = .
BIN  = .
FFLAGS = -c -fdefault-real-8 -O2 -fcray-pointer
LFLAGS = -L/usr/lib/atlas -llapack -lblas
CFLAGS = -c -O2 -Wall
CPP = /lib/cpp -P -C -traditional
CPPFLAGS = -D__Linux -D__PGI -D__GNU -DFFT_DEFAULT
NOOPT_FLAG =
CC = gcc
FC = gfortran
LD = gfortran
AR = ar
#----------------------------------------------------------------------------
# Personal Configuration
# My_Conf:
# All arguments:  PC-GFORTRAN
#----------------------------------------------------------------------------
#----------------------------------------------------------------------------
# End of Personal Configuration
#----------------------------------------------------------------------------
CFGDEST = .
CFGMACH = PC-GFORTRAN
CFGQMMM =
#

#!/bin/csh
# Main script for building and installing CPMD
# Ernst Schumacher www.chemsoft.ch April 08 2012
# unpacking cpmd-v3_15_1.tgz and compiling cpmd.x
# unpacking CPMD-test.tar.gz
# unpacking cpmd2cube.tar.gz and compiling cpmd2cube.x
# unpacking and installing vmd-1.8.7
# If the last two archives are not found in /home/$USER the
# test run runme-b2h6.sh just omits using their functions
#
if ( `uname -m` == x86_64 ) then
  set bn = 64
else
  set bn = 32
endif
if (! -e /home/$USER/CPMD/cpmd.x ) then
  if (! -e cpmd-v3_15_1.tgz ) then
    echo Please get 'cpmd-v3_15_1.tgz'
    echo from http://www.cpmd.org
    echo You need a password, obtained by registering,
    echo for downloading the CPMD package
    exit
  endif
# unpack the archive into your home directory
  tar xzvf cpmd-v3_15_1.tgz >& tar.log
  chmod -R 777 CPMD
  cd ~/CPMD/CONFIGURE
  switch ($bn)
    case 32:
      mv PC-GFORTRAN PC-GFORTRAN.junk
      sed 12c\ "LFLAGS='-L/usr/lib/atlas -llapack -lblas'" PC-GFORTRAN.junk > PC-GFORTRAN
      rm -f PC-GFORTRAN.junk
      breaksw
    case 64:
      mv LINUX-x86_64-FEDORA LINUX-x86_64-FEDORA.junk
      sed 13c\ "     LFLAGS='/usr/lib64/libfftw.so.2.0.5 -L/usr/lib64/atlas -llapack -lblas'" LINUX-x86_64-FEDORA.junk > LINUX-x86_64-FEDORA
      rm -f LINUX-x86_64-FEDORA.junk
  endsw
  clear
  echo Building and running cpmd.x
  echo from CPMD on ubuntu V.10.10
  echo cpmdmake script version 2011-08-04
  echo using gfortran v.4.4.3 or higher
  echo " "
  cd ~/CPMD
  switch ($bn)
    case 32:
      ./mkconfig.sh PC-GFORTRAN > Makefile
      breaksw
    case 64:
      ./mkconfig.sh LINUX-x86_64-FEDORA > Makefile
  endsw
  date +"%D %T"
  echo making cpmd.x
  make >& make.log
  date +"%D %T"
  if (! -e cpmd.x ) then
    echo Something went wrong! Look into
    echo ~/CPMD/make.log
    echo to find out what
    exit
  endif
  echo ............. success
  # mv cpmd.x ..
  make clean > /dev/null
  cd /home/$USER
endif
#
if (! -e ~/CPMD-test ) then
  if (! -e cpmd-test.tar.gz ) then
    echo get cpmd-test.tar.gz
    echo from http://www.cpmd.org/downloads/contrib
    echo You need the same password as for CPMD.
    echo Instead of using one of the test input files
    echo you can also compose one of your own
    echo consulting the Manual.
    exit
  else
    tar xzvf cpmd-test.tar.gz >& tar.log
  endif
endif
#
if (! -e ~/cpmd2cube ) then
  if (! -e cpmd2cube.tar.gz ) then
    echo get cpmd2cube.tar.gz
    echo from http://www.cpmd.org/downloads/contrib
    echo if you want to use visualization.
    echo You need the same password as for CPMD
  else
    tar xzvf cpmd2cube.tar.gz >& tar.log
    cd cpmd2cube
    ./Configure -makefile Linux-PC-GFORTRAN-FFTW
    make
    make clean
  endif
endif
if ( -e ~/cpmd2cube/cpmd2cube.x ) then
    cp ~/cpmd2cube/cpmd2cube.x ~/CPMD
endif
#
cd /home/$USER
if (! -e ~/vmd-1.8.7 ) then
  switch ($bn)
    case 32:
      if (! -e vmd-1.8.7.bin.LINUX.opengl.tar.gz ) then
        wget chemsoft.ch/downloads/vmd-1.8.7.bin.LINUX.opengl.tar.gz
      endif
      tar xzvf vmd-1.8.7.bin.LINUX.opengl.tar.gz >& tar.log
      breaksw
    case 64:
      if (! -e vmd-1.8.7.bin.LINUXAMD64.opengl.tar.gz ) then
        wget chemsoft.ch/downloads/vmd-1.8.7.bin.LINUXAMD64.opengl.tar.gz
      endif
      tar xzvf vmd-1.8.7.bin.LINUXAMD64.opengl.tar.gz >& tar.log
  endsw
  cd vmd-1.8.7
  ./configure
  cd src
  sudo make install
  setenv PATH $PATH\:\/usr\/local\/bin\/vmd
endif
#
cd /home/$USER
rm -f *tar.gz
cd ~/CPMD-test/properties
cp *.inp *.psp *.vmd *.xyz *.sh ~/CPMD
cd ~/CPMD
# get rid of arch
mv runme-b2h6.sh runme-b2h6.junk
sed 's/.`arch`//g' runme-b2h6.junk > runme-b2h6.sh
rm -f runme-b2h6.junk

# need cutoff 96.0 for AMD64
mv b2h6-wf.inp b2h6-wf.junk
sed 's/90.0/96.0/' b2h6-wf.junk > b2h6-wf.inp
rm -f b2h6-wf.junk
mv b2h6-prop.inp b2h6-prop.junk
sed 's/90.0/96.0/' b2h6-prop.junk > b2h6-prop.inp
rm -f b2h6-prop.junk
mv b2h6-ks.inp b2h6-ks.junk
sed 's/90.0/96.0/' b2h6-ks.junk > b2h6-ks.inp
rm -f b2h6-ks.junk
mv b2h6-ksorbs.inp b2h6-ksorbs.junk
sed 's/90.0/96.0/' b2h6-ksorbs.junk > b2h6-ksorbs.inp
rm -f b2h6-ksorbs.junk
# need to separate LOCALIZE from other property calcs
cp b2h6-prop.inp b2h6-propnl.inp
mv b2h6-prop.inp b2h6-proploc.inp

mv b2h6-propnl.inp b2h6-propnl.junk
sed 11D b2h6-propnl.junk > b2h6-propnl.inp
rm -f b2h6-propnl.junk

mv b2h6-proploc.inp b2h6-proploc.junk
sed 12,19D b2h6-proploc.junk > b2h6-proploc.inp
rm -f b2h6-proploc.junk
# adjust runme for changed properties calculation
mv runme-b2h6.sh runme-b2h6.junk
sed -e 49c\ '\.\/cpmd.x b2h6-propnl.inp . > b2h6-propnl.out' \
    -e 50i\ '\.\/cpmd.x b2h6-proploc.inp . > b2h6.proploc.out' runme-b2h6.junk > runme-b2h6.sh
rm -f runme-b2h6.junk
chmod +x runme-b2h6.sh

echo " "
echo Now, run all jobs from CPMD-test/properties,
echo optimizing the wavefunctions of B2H6
echo and obtaining several properties.
echo This takes 8 to 15 min

./runme-b2h6.sh
if ( -e b2h6-wf.out ) cat b2h6-wf.out
if ( -e b2h6-ksorb-6.tga ) eog b2h6-ksorb-6.tga
exit

#!/bin/sh
#PBS -l walltime=2:00:00
#

if [ "$PBS_ENVIRONMENT" = "PBS_BATCH" ]
then
  cd $PBS_O_WORKDIR
fi

# for this script to work, you need to have
# cpmd.x and cpmd2cube.x executables in the current working directory
# and vmd version 1.8.2 in your searchpath
cdx=0
c2c=0
vmd=0

test -e ./cpmd.x      && cdx=1
test -e ./cpmd2cube.x && c2c=1
hash vmd 2> /dev/null && vmd=1

test $cdx -eq 1 || echo WARNING: cpmd.x is NOT available
test $c2c -eq 1 || echo WARNING: cpmd2cube is NOT available
test $vmd -eq 1 || echo WARNING: vmd is NOT available

# no point in continuing without cpmd.x
test $cdx -eq 1 || exit 666

# redirect stdout and stderr to a file
exec 1> runme-b2h6.log
exec 2>&1

# turn on verbose shell execution
set -vx

# first clean up the mess from the last run.
rm -f RESTART* DENSITY* EL* LATEST GEOMETRY* GSHELL *.tga\
    *.cube *.pdb IONS+CENTER* WANNIER* OVERLAP WFNCOEF

# optimize the wf and get a first set of 'DENSITY' format files...
./cpmd.x b2h6-wf.inp . > b2h6-wf.out
if [ $c2c ]
then
  ./cpmd2cube.x -o b2h6-elf   -rho -halfmesh  ELF
  ./cpmd2cube.x -o b2h6-dens  -rho -halfmesh  DENSITY
  ./cpmd2cube.x -o b2h6-elpot -rho -halfmesh  ELPOT
fi

# and calculate lots of properties
./cpmd.x b2h6-propnl.inp . > b2h6-propnl.out
./cpmd.x b2h6-proploc.inp . > b2h6.proploc.out
if [ $c2c ]
then
  ./cpmd2cube.x -o b2h6-local- -psi -halfmesh WANNIER_1.[0-9]*
fi
mv RHO_TOT.cube b2h6-rho.cube
mv IONS+CENTERS.xyz b2h6-wc.xyz

# diagonalize the remaining KS orbitals...
./cpmd.x b2h6-ks.inp . > b2h6-ks.out

# now get some KS orbitals
./cpmd.x b2h6-ksorbs.inp . > b2h6-ksorbs.out

# rename the next batch of outputs.
for f in 01 02 03 04 05 06 07 08 09 10 11 12 13 14
do
  test -f PSI.0$f.cube && mv PSI.0$f.cube b2h6-orb-$f.cube
done

# use vmd to generate a picture gallery.
if [ $vmd ]
then
  vmd -dispdev none -size 600 400 -e b2h6-wannier.vmd
  if [ $c2c ]
  then
    vmd -dispdev none -size 600 400 -e b2h6-dens.vmd
    vmd -dispdev none -size 600 400 -e b2h6-elpot.vmd
    vmd -dispdev none -size 600 400 -e b2h6-elf.vmd
    vmd -dispdev none -size 600 400 -e b2h6-local-orbs.vmd
  fi
  vmd -dispdev none -size 600 400 -e b2h6-rho.vmd
  vmd -dispdev none -size 600 400 -e b2h6-ksorb-1.vmd
  vmd -dispdev none -size 600 400 -e b2h6-ksorb-6.vmd
  vmd -dispdev none -size 600 400 -e b2h6-ksorb-7.vmd
  vmd -dispdev none -size 600 400 -e b2h6-ksorb-8.vmd
fi

# clean up the mess from this run.
rm -f RESTART* DENSITY* EL* LATEST GEOMETRY* GSHELL \
    *.pdb WANNIER* OVERLAP WFNCOEF
exit 0

12Â¥: Originally posted by Ò»Éù̾Ϣ010 at 2013-05-07 08:45:26
Linux Deepin 12.06 32λ DELL 5100 ̨ʽ»ú
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/home/administrator/CPMD-3.15.3/make.log
to find out what
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