Improved input files. Work to do

configure.ac

@@ -34,8 +34,12 @@ AC_PREREQ([2.50])
 AC_INIT([EPLF], [], [scemama@irsamc.ups-tlse.fr],[eplf],[http://eplf.sourceforge.net])
 
 AC_SYS_LONG_FILE_NAMES
-ROOT=`pwd`
+
-AC_SUBST([ROOT])
+EPLF_PATH=`pwd`
+AC_SUBST(EPLF_PATH)
+
+EXE=$EPLF_PATH/bin/eplf
+AC_SUBST(EXE)
 
 AC_CONFIG_SRCDIR([src/main.irp.f])
 AC_CONFIG_FILES([make.config])
@@ -45,6 +49,103 @@ AC_PROG_LN_S
 AC_PROG_RANLIB
 AC_PROG_CC
 
+
+# Check for wget
+AC_CHECK_PROGS([WGET],[wget],[])
+
+######################################################
+# Define download function
+AC_DEFUN([AC_DOWNLOAD],[{
+ # AC_DOWNLOAD ( VARIABLE, name, url )
+ WHERE=
+ if [[ ! -z $WGET ]] ; then
+   echo ""
+   echo "**************************"
+   echo $2 is not installed
+   echo "**************************"
+   echo "Do you want to download it?"
+   select x in yes no
+   do
+    if [[ ! -z $x ]] ; then
+      break
+    fi
+   done
+   if [[ $x == yes ]] ; then
+      if [[ ! -d "Downloads" ]] ; then
+        mkdir $EPLF_PATH/Downloads
+      fi
+      cd $EPLF_PATH/Downloads
+      mkdir $EPLF_PATH/Downloads/tmp
+      cd $EPLF_PATH/Downloads/tmp
+      wget -nc "$3" && WHERE=`ls -tr | tail -1`
+      mv * $EPLF_PATH/Downloads
+      cd $EPLF_PATH/Downloads
+      rm -rf tmp
+      cd $EPLF_PATH
+   fi
+   if [[ ! -z $WHERE ]] ; then
+      echo $2 was downloaded to Downloads/$WHERE.
+      $1=1
+   else
+      AC_MSG_ERROR([$2 should be installed. You can download it at
+    $3])
+   fi
+ else
+    AC_MSG_ERROR([Please download $2 at
+    $3])
+ fi
+}])
+
+######################################################
+# Check for python
+AC_CHECK_PROGS([PYTHON],[python],[])
+if [[ -z $PYTHON ]] ; then
+  AC_MSG_ERROR([Python should be installed:
+  http://www.python.org])
+fi
+
+######################################################
+# IRPF90 compiler
+AC_CHECK_PROGS([IRPF90],[irpf90],[])
+if [[ -z $IRPF90 ]] ; then
+  AC_DOWNLOAD([IRPF90],[IRPF90],[http://sourceforge.net/projects/irpf90/files/latest])
+  AC_MSG_ERROR([Install IRPF90 and run this configure script again.])
+fi
+
+######################################################
+# EZFIO
+EZFIO=`ls EZFIO*.tar.gz`
+if [[ -z $EZFIO ]] ; then
+  AC_DOWNLOAD([EZFIO],[EZFIO],[http://sourceforge.net/projects/ezfio/files/latest])
+  if [[ -z $EZFIO ]] ; then
+    AC_MSG_ERROR([Download EZFIO.tar.gz into $PWD and run this configure script again.])
+  fi
+  mv Downloads/EZFIO*.tar.gz .
+fi
+
+######################################################
+# Check for MPI
+EPLF_HAS_MPI=0
+if [[ -z "$STATIC" ]] ; then
+  AC_CHECK_PROGS([MPIRUN],[mpirun mpiexec],[])
+  if [[ ! -z $MPIRUN ]] ; then
+    MPIRUN=`which $MPIRUN`
+  fi
+
+  AC_CHECK_PROGS([MPIFC],[mpif90],[])
+  if [[ -z $MPIFC ]] ; then
+    echo "**************************"
+    echo "Warning: MPI not found. You can get OpenMPI at:"
+    echo "http://www.open-mpi.org/software/ompi/v1.4/downloads/openmpi-1.4.1.tar.gz"
+    echo "**************************"
+  else
+    EPLF_HAS_MPI=1
+  fi
+fi
+AC_SUBST([EPLF_HAS_MPI])
+
+
+
 # Test if Static zlib is present
 # ------------------------------
 
@@ -52,15 +153,6 @@ AC_CHECK_LIB([z],[gzclose],[STATIC=1],[STATIC=0],[-static])
 STATIC_LIB="../EZFIO/lib/libezfio_irp.a"
 SHARED_LIB="-L../EZFIO/lib -lezfio"
 
-# Test IRPF90
-# ------------
-
-AC_CHECK_PROG([IRPF90],[irpf90],[yes],[no])
-if [[ $IRPF90 = no ]] ; then
-  AC_MSG_ERROR([Please install IRPF90:\nhttp://irpf90.sourceforge.net])
-fi
-IRPF90=`which irpf90`
-
 # Test Fortran
 # ------------
 
@@ -101,7 +193,7 @@ else
 =====================================================
 
   Using shared library. Add
-   $ROOT/EZFIO/lib/
+   $EPLF_PATH/EZFIO/lib/
   to the LD_LIBRARY_PATH environment variable.
 
 =====================================================
@@ -109,6 +201,22 @@ else
 fi
 AC_SUBST([LIB])
 
+cd $EPLF_PATH
+echo "export EPLF_PATH=$EPLF_PATH" > $HOME/.eplfrc
+echo "export LD_LIBRARY_PATH=\$EPLF_PATH/EZFIO/lib/:\$LD_LIBRARY_PATH" >> $HOME/.qmcchemrc
+echo "export PATH=\$PATH:\$EPLF_PATH/bin/" >> $HOME/.eplfrc
+echo "export PATH=\$PATH:\$EPLF_PATH/scripts/" >> $HOME/.eplfrc
+echo "export EPLF_HAS_MPI=$EPLF_HAS_MPI" >> $HOME/.eplfrc
+echo "export EPLF_MPIRUN=$MPIRUN" >> $HOME/.eplfrc
+echo "************************************"
+echo "To finish the installation:"
+echo "1) Add the following line to your $HOME/.basrhc file:"
+echo ". $HOME/.eplfrc"
+echo "2) Execute"
+echo ". $HOME/.eplfrc"
+echo "make"
+echo "************************************"
+
 AC_OUTPUT
 
 

eplf.config

@@ -53,6 +53,7 @@ grid_data
  density_lapl        real (grid_num_x,grid_num_y,grid_num_z)
 
 compute
+ nproc               integer
  eplf                logical
  eplf_grad           logical
  eplf_lapl           logical

scripts/eplf_edit.py

@@ -39,8 +39,6 @@ class GeometryEditor(Editor):
     print >>file, "# Geometry : %s"%(inp.name)
     print >>file, "###########################"
     print >>file, ""
-    has_fitcusp = False
-    has_label   = False
     fields = "Charge X Y Z"
     format = "%10.1f "+"%10.6f "*3
     fields = fields.split()
@@ -66,9 +64,76 @@ class GeometryEditor(Editor):
       coord[2].append(float(line[-1]))
     inp.coord = coord
       
+class GridEditor(Editor):
+  def action(self):
+    self.origin= self.inp.origin
+    self.opposite = self.inp.opposite
+    self.step_size = self.inp.step_size
+    self.point_num = self.inp.point_num
+    if self.origin is None:
+      self.origin = [ 0., 0., 0. ]
+      for l in xrange(3): 
+        self.origin[l] = self.inp.nucl_coord[l][1]
+        for i in self.inp.nucl_coord[l]:
+          self.origin[l] = min(self.origin[l],i)
+        self.origin[l] -= 4.
+    if self.opposite is None:
+      self.opposite = [ 0., 0., 0. ]
+      for l in xrange(3): 
+        self.opposite[l] = self.inp.nucl_coord[l][1]
+        for i in self.inp.nucl_coord[l]:
+          self.opposite[l] = max(self.opposite[l],i)
+        self.opposite[l] += 4.
+    if self.step_size is None:
+      self.step_size = [ 0., 0., 0. ]
+      for l in xrange(3): 
+        self.step_size[l] = (self.opposite[l] - self.origin[l])/float(self.point_num[l])
+
+    self.inp.point_num = self.point_num
+    self.inp.origin = self.origin
+    self.inp.opposite = self.opposite
+    self.inp.step_size = self.step_size
+    edit_temp_file(self.inp,self.write_grid_file,self.read_grid_file)
+
+  def write_grid_file(self,file,inp):
+    print >>file, "###########################"
+    print >>file, "# Grid : %s"%(inp.name)
+    print >>file, "###########################"
+    print >>file, ""
+    print >>file, "# Number of points along x, y, z"
+    print >>file, "%d %d %d"%tuple(self.point_num)
+    print >>file, ""
+    print >>file, "# Coordinates of the origin (x,y,z)"
+    print >>file, "%f %f %f"%tuple(self.origin)
+    print >>file, ""
+    print >>file, "# Coordinates of the opposite point (x,y,z)"
+    print >>file, "%f %f %f"%tuple(self.opposite)
+    print >>file, ""
+    print >>file, "# Step sizes (x,y,z)"
+    print >>file, "%f %f %f"%tuple(self.step_size)
+
+  def read_grid_file(self,file,inp):
+    lines = file.readlines()
+    lines = filter(lambda x: len(x.strip())>0,lines)
+    lines = filter(lambda x: not x.startswith("#"),lines)
+
+    buffer = lines.pop(0).split()
+    self.inp.point_num = map(int,buffer)
+
+    buffer = lines.pop(0).split()
+    self.inp.origin = map(float,buffer)
+
+    buffer = lines.pop(0).split()
+    self.inp.opposite = map(float,buffer)
+
+    buffer = lines.pop(0).split()
+    self.inp.step_size = self.step_size
+
+      
 
 def edit(x,inp):
   d = { "geometry": GeometryEditor,
+        "grid_parameters": GridEditor,
       }
   d[x](inp,x.replace("_"," ")).edit()
 
@@ -139,6 +204,28 @@ def edit_temp_file(input_file,write_file,read_file,saved_file=None):
 
   os.remove(filename)
 
+
+def build_script(inp):
+  grid = "${EPLF_PATH}/bin/to_cube %s"%(inp.name)
+  run_script = "run_"+inp.name
+  file = open(run_script,'w')
+  buffer = """
+  #!/bin/bash
+source ${HOME}/.eplfrc
+$RUNCOMMAND
+$RUNGRID
+""".lstrip()
+  command = "${EPLF_PATH}/bin/eplf %s"%(inp.name)
+  if inp.has_mpi:
+    command = "${MPIRUN} -np %d "%(inp.nproc)+command
+    grid = "${MPIRUN} -np 1 "+command
+  buffer = buffer.replace("$RUNCOMMAND",command)
+  buffer = buffer.replace("$RUNGRID",grid)
+  print >>file, buffer
+  file.close()
+  os.chmod(run_script,0744)
+
+
 def main():
   if len(sys.argv) not in [2,3]:
     print "Syntax : %s <EZFIO_File> [input_file]"%(sys.argv[0])
@@ -149,5 +236,6 @@ def main():
   else:
     saved_file = None
   edit_temp_file(inp,write_main_file,read_main_file,saved_file)
+  build_script(inp)
 
 main()

scripts/input_wrapper.py

@@ -6,10 +6,10 @@ import os
 geom_data = """
 nucl_charge nucl_coord
 """.split()
-ro_data = """det_num nucl_num mo_num ao_num 
+ro_data = """det_num nucl_num mo_num ao_num has_mpi
 """.split()
 rw_data = """
-point_num step_size origin opposite
+point_num step_size origin opposite nproc
 compute_elf compute_eplf compute_density
 compute_elf_grad compute_eplf_grad compute_density_grad
 compute_elf_lapl compute_eplf_lapl compute_density_lapl
@@ -60,9 +60,18 @@ class InputFile(object):
       raise InputFileExn("This directory is not a EZFIO file.")
     os.chdir(wd)
     ezfio.set_filename(name)
-    self.name = name
+    l = len(name)
+    while name[l-1] == '/':
+      l -= 1
+    self.name = name[:l]
       
   # Read-only values
+  def get_has_mpi(self):
+    if os.getenv("EPLF_HAS_MPI","1") == "1":
+      return True
+    else:
+      return False
+
   def get_det_num(self):
     if ezfio.has_determinants_det_num():
       return ezfio.get_determinants_det_num()
@@ -168,10 +177,9 @@ class InputFile(object):
     if len(value) != 3:
       raise InputFileExn("Wrong type")
     for i in value:
-      if not isinstance(i,list):
+      if not isinstance(i,float):
         raise InputFileExn("Wrong type")
-    for i in value:
+    for j in value:
-     for j in i:
       try:
         float(j)
       except:
@@ -191,16 +199,28 @@ class InputFile(object):
     if len(value) != 3:
       raise InputFileExn("Wrong type")
     for i in value:
-      if not isinstance(i,list):
+      if not isinstance(i,float):
         raise InputFileExn("Wrong type")
-    for i in value:
+    for j in value:
-     for j in i:
       try:
         float(j)
       except:
         raise InputFileExn("Wrong type")
     ezfio.set_grid_opposite(value)
 
+  def get_nproc(self):
+    if ezfio.has_compute_nproc():
+      return ezfio.get_compute_nproc()
+    else:
+      return 1
+
+  def set_nproc(self,value):
+    if not isinstance(value,int):
+      raise InputFileExn("Wrong type")
+    if value < 1:
+      raise InputFileExn("Wrong type")
+    ezfio.set_compute_nproc(value)
+
   def get_compute_elf(self):
     if ezfio.has_compute_elf():
       return ezfio.get_compute_elf()