mirror of https://gitlab.com/scemama/eplf
Improved input files. Work to do
This commit is contained in:
Anthony Scemama
parent
b92517db0b
commit
ba98fcf957
132
configure.ac
132
configure.ac
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@ -34,8 +34,12 @@ AC_PREREQ([2.50])
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AC_INIT([EPLF], [], [scemama@irsamc.ups-tlse.fr],[eplf],[http://eplf.sourceforge.net])
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AC_SYS_LONG_FILE_NAMES
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ROOT=`pwd`
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AC_SUBST([ROOT])
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EPLF_PATH=`pwd`
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AC_SUBST(EPLF_PATH)
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EXE=$EPLF_PATH/bin/eplf
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AC_SUBST(EXE)
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AC_CONFIG_SRCDIR([src/main.irp.f])
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AC_CONFIG_FILES([make.config])
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@ -45,6 +49,103 @@ AC_PROG_LN_S
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AC_PROG_RANLIB
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AC_PROG_CC
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# Check for wget
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AC_CHECK_PROGS([WGET],[wget],[])
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######################################################
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# Define download function
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AC_DEFUN([AC_DOWNLOAD],[{
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# AC_DOWNLOAD ( VARIABLE, name, url )
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WHERE=
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if [[ ! -z $WGET ]] ; then
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echo ""
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echo "**************************"
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echo $2 is not installed
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echo "**************************"
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echo "Do you want to download it?"
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select x in yes no
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do
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if [[ ! -z $x ]] ; then
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break
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fi
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done
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if [[ $x == yes ]] ; then
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if [[ ! -d "Downloads" ]] ; then
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mkdir $EPLF_PATH/Downloads
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fi
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cd $EPLF_PATH/Downloads
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mkdir $EPLF_PATH/Downloads/tmp
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cd $EPLF_PATH/Downloads/tmp
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wget -nc "$3" && WHERE=`ls -tr | tail -1`
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mv * $EPLF_PATH/Downloads
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cd $EPLF_PATH/Downloads
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rm -rf tmp
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cd $EPLF_PATH
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fi
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if [[ ! -z $WHERE ]] ; then
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echo $2 was downloaded to Downloads/$WHERE.
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$1=1
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else
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AC_MSG_ERROR([$2 should be installed. You can download it at
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$3])
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fi
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else
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AC_MSG_ERROR([Please download $2 at
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$3])
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fi
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}])
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######################################################
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# Check for python
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AC_CHECK_PROGS([PYTHON],[python],[])
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if [[ -z $PYTHON ]] ; then
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AC_MSG_ERROR([Python should be installed:
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http://www.python.org])
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fi
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######################################################
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# IRPF90 compiler
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AC_CHECK_PROGS([IRPF90],[irpf90],[])
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if [[ -z $IRPF90 ]] ; then
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AC_DOWNLOAD([IRPF90],[IRPF90],[http://sourceforge.net/projects/irpf90/files/latest])
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AC_MSG_ERROR([Install IRPF90 and run this configure script again.])
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fi
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######################################################
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# EZFIO
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EZFIO=`ls EZFIO*.tar.gz`
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if [[ -z $EZFIO ]] ; then
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AC_DOWNLOAD([EZFIO],[EZFIO],[http://sourceforge.net/projects/ezfio/files/latest])
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if [[ -z $EZFIO ]] ; then
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AC_MSG_ERROR([Download EZFIO.tar.gz into $PWD and run this configure script again.])
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fi
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mv Downloads/EZFIO*.tar.gz .
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fi
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######################################################
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# Check for MPI
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EPLF_HAS_MPI=0
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if [[ -z "$STATIC" ]] ; then
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AC_CHECK_PROGS([MPIRUN],[mpirun mpiexec],[])
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if [[ ! -z $MPIRUN ]] ; then
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MPIRUN=`which $MPIRUN`
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fi
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AC_CHECK_PROGS([MPIFC],[mpif90],[])
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if [[ -z $MPIFC ]] ; then
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echo "**************************"
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echo "Warning: MPI not found. You can get OpenMPI at:"
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echo "http://www.open-mpi.org/software/ompi/v1.4/downloads/openmpi-1.4.1.tar.gz"
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echo "**************************"
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else
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EPLF_HAS_MPI=1
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fi
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fi
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AC_SUBST([EPLF_HAS_MPI])
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# Test if Static zlib is present
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# ------------------------------
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@ -52,15 +153,6 @@ AC_CHECK_LIB([z],[gzclose],[STATIC=1],[STATIC=0],[-static])
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STATIC_LIB="../EZFIO/lib/libezfio_irp.a"
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SHARED_LIB="-L../EZFIO/lib -lezfio"
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# Test IRPF90
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# ------------
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AC_CHECK_PROG([IRPF90],[irpf90],[yes],[no])
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if [[ $IRPF90 = no ]] ; then
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AC_MSG_ERROR([Please install IRPF90:\nhttp://irpf90.sourceforge.net])
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fi
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IRPF90=`which irpf90`
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# Test Fortran
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# ------------
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@ -101,7 +193,7 @@ else
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=====================================================
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Using shared library. Add
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$ROOT/EZFIO/lib/
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$EPLF_PATH/EZFIO/lib/
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to the LD_LIBRARY_PATH environment variable.
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=====================================================
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@ -109,6 +201,22 @@ else
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fi
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AC_SUBST([LIB])
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cd $EPLF_PATH
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echo "export EPLF_PATH=$EPLF_PATH" > $HOME/.eplfrc
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echo "export LD_LIBRARY_PATH=\$EPLF_PATH/EZFIO/lib/:\$LD_LIBRARY_PATH" >> $HOME/.qmcchemrc
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echo "export PATH=\$PATH:\$EPLF_PATH/bin/" >> $HOME/.eplfrc
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echo "export PATH=\$PATH:\$EPLF_PATH/scripts/" >> $HOME/.eplfrc
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echo "export EPLF_HAS_MPI=$EPLF_HAS_MPI" >> $HOME/.eplfrc
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echo "export EPLF_MPIRUN=$MPIRUN" >> $HOME/.eplfrc
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echo "************************************"
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echo "To finish the installation:"
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echo "1) Add the following line to your $HOME/.basrhc file:"
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echo ". $HOME/.eplfrc"
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echo "2) Execute"
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echo ". $HOME/.eplfrc"
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echo "make"
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echo "************************************"
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AC_OUTPUT
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@ -53,6 +53,7 @@ grid_data
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density_lapl real (grid_num_x,grid_num_y,grid_num_z)
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compute
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nproc integer
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eplf logical
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eplf_grad logical
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eplf_lapl logical
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@ -39,8 +39,6 @@ class GeometryEditor(Editor):
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print >>file, "# Geometry : %s"%(inp.name)
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print >>file, "###########################"
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print >>file, ""
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has_fitcusp = False
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has_label = False
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fields = "Charge X Y Z"
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format = "%10.1f "+"%10.6f "*3
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fields = fields.split()
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@ -66,9 +64,76 @@ class GeometryEditor(Editor):
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coord[2].append(float(line[-1]))
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inp.coord = coord
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class GridEditor(Editor):
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def action(self):
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self.origin= self.inp.origin
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self.opposite = self.inp.opposite
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self.step_size = self.inp.step_size
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self.point_num = self.inp.point_num
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if self.origin is None:
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self.origin = [ 0., 0., 0. ]
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for l in xrange(3):
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self.origin[l] = self.inp.nucl_coord[l][1]
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for i in self.inp.nucl_coord[l]:
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self.origin[l] = min(self.origin[l],i)
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self.origin[l] -= 4.
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if self.opposite is None:
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self.opposite = [ 0., 0., 0. ]
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for l in xrange(3):
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self.opposite[l] = self.inp.nucl_coord[l][1]
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for i in self.inp.nucl_coord[l]:
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self.opposite[l] = max(self.opposite[l],i)
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self.opposite[l] += 4.
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if self.step_size is None:
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self.step_size = [ 0., 0., 0. ]
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for l in xrange(3):
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self.step_size[l] = (self.opposite[l] - self.origin[l])/float(self.point_num[l])
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self.inp.point_num = self.point_num
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self.inp.origin = self.origin
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self.inp.opposite = self.opposite
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self.inp.step_size = self.step_size
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edit_temp_file(self.inp,self.write_grid_file,self.read_grid_file)
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def write_grid_file(self,file,inp):
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print >>file, "###########################"
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print >>file, "# Grid : %s"%(inp.name)
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print >>file, "###########################"
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print >>file, ""
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print >>file, "# Number of points along x, y, z"
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print >>file, "%d %d %d"%tuple(self.point_num)
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print >>file, ""
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print >>file, "# Coordinates of the origin (x,y,z)"
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print >>file, "%f %f %f"%tuple(self.origin)
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print >>file, ""
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print >>file, "# Coordinates of the opposite point (x,y,z)"
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print >>file, "%f %f %f"%tuple(self.opposite)
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print >>file, ""
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print >>file, "# Step sizes (x,y,z)"
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print >>file, "%f %f %f"%tuple(self.step_size)
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def read_grid_file(self,file,inp):
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lines = file.readlines()
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lines = filter(lambda x: len(x.strip())>0,lines)
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lines = filter(lambda x: not x.startswith("#"),lines)
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buffer = lines.pop(0).split()
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self.inp.point_num = map(int,buffer)
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buffer = lines.pop(0).split()
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self.inp.origin = map(float,buffer)
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buffer = lines.pop(0).split()
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self.inp.opposite = map(float,buffer)
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buffer = lines.pop(0).split()
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self.inp.step_size = self.step_size
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def edit(x,inp):
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d = { "geometry": GeometryEditor,
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"grid_parameters": GridEditor,
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}
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d[x](inp,x.replace("_"," ")).edit()
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@ -139,6 +204,28 @@ def edit_temp_file(input_file,write_file,read_file,saved_file=None):
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os.remove(filename)
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def build_script(inp):
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grid = "${EPLF_PATH}/bin/to_cube %s"%(inp.name)
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run_script = "run_"+inp.name
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file = open(run_script,'w')
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buffer = """
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#!/bin/bash
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source ${HOME}/.eplfrc
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$RUNCOMMAND
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$RUNGRID
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""".lstrip()
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command = "${EPLF_PATH}/bin/eplf %s"%(inp.name)
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if inp.has_mpi:
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command = "${MPIRUN} -np %d "%(inp.nproc)+command
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grid = "${MPIRUN} -np 1 "+command
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buffer = buffer.replace("$RUNCOMMAND",command)
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buffer = buffer.replace("$RUNGRID",grid)
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print >>file, buffer
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file.close()
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os.chmod(run_script,0744)
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def main():
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if len(sys.argv) not in [2,3]:
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print "Syntax : %s <EZFIO_File> [input_file]"%(sys.argv[0])
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@ -149,5 +236,6 @@ def main():
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else:
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saved_file = None
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edit_temp_file(inp,write_main_file,read_main_file,saved_file)
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build_script(inp)
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main()
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@ -6,10 +6,10 @@ import os
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geom_data = """
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nucl_charge nucl_coord
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""".split()
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ro_data = """det_num nucl_num mo_num ao_num
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ro_data = """det_num nucl_num mo_num ao_num has_mpi
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""".split()
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rw_data = """
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point_num step_size origin opposite
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point_num step_size origin opposite nproc
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compute_elf compute_eplf compute_density
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compute_elf_grad compute_eplf_grad compute_density_grad
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compute_elf_lapl compute_eplf_lapl compute_density_lapl
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@ -60,9 +60,18 @@ class InputFile(object):
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raise InputFileExn("This directory is not a EZFIO file.")
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os.chdir(wd)
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ezfio.set_filename(name)
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self.name = name
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l = len(name)
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while name[l-1] == '/':
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l -= 1
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self.name = name[:l]
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# Read-only values
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def get_has_mpi(self):
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if os.getenv("EPLF_HAS_MPI","1") == "1":
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return True
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else:
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return False
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def get_det_num(self):
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if ezfio.has_determinants_det_num():
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return ezfio.get_determinants_det_num()
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@ -168,10 +177,9 @@ class InputFile(object):
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if len(value) != 3:
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raise InputFileExn("Wrong type")
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for i in value:
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if not isinstance(i,list):
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if not isinstance(i,float):
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raise InputFileExn("Wrong type")
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for i in value:
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for j in i:
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for j in value:
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try:
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float(j)
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except:
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@ -191,16 +199,28 @@ class InputFile(object):
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if len(value) != 3:
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raise InputFileExn("Wrong type")
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for i in value:
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if not isinstance(i,list):
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if not isinstance(i,float):
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raise InputFileExn("Wrong type")
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for i in value:
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for j in i:
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for j in value:
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try:
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float(j)
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except:
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raise InputFileExn("Wrong type")
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ezfio.set_grid_opposite(value)
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def get_nproc(self):
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if ezfio.has_compute_nproc():
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return ezfio.get_compute_nproc()
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else:
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return 1
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def set_nproc(self,value):
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if not isinstance(value,int):
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raise InputFileExn("Wrong type")
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if value < 1:
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raise InputFileExn("Wrong type")
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ezfio.set_compute_nproc(value)
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def get_compute_elf(self):
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if ezfio.has_compute_elf():
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return ezfio.get_compute_elf()
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