exception handling and allocation improved

Author: Trebonius91

ML-FF/mlff_select.f90

@@ -136,6 +136,8 @@ program mlff_select
 logical::eval_stat(10)  ! the progress for evaluation loops
 logical::no_adf  ! if no angular distribution functions shall be calculated
 logical,allocatable::atom_used(:)  ! boolean mask for blocking of treated atoms
+integer::alloc_stat  ! if allocation of array was successful
+character(len=100)::alloc_err  ! the error message for failed allocation
 !   for time measurement
 character(8)  :: date
 character(10) :: time
@@ -1036,9 +1038,20 @@ program mlff_select
 allocate(el_nums_confs(nelems_glob,conf_num))
 allocate(el_nums_tmp(nelems_glob))
 !     The geometries (cartesian coordinates)
-allocate(xyz(3,natoms_max,conf_num))
+allocate(xyz(3,natoms_max,conf_num),stat=alloc_stat,errmsg=alloc_err)
+if (alloc_stat .ne. 0) then
+   write(*,*) "Allocation of xyz array failed:",trim(alloc_err)
+   write(*,*) "Please read in a smaller ML_AB or increase memory!"
+   stop
+end if
 !     The geometries (direct coordinates
-allocate(xyz_dir(3,natoms_max,conf_num))
+allocate(xyz_dir(3,natoms_max,conf_num),stat=alloc_stat,errmsg=alloc_err)
+if (alloc_stat .ne. 0) then
+   write(*,*) "Allocation of xyz_dir array failed:",trim(alloc_err)
+   write(*,*) "Please read in a smaller ML_AB or increase memory!"
+   stop
+end if
+
 !     The unit cell shapes
 allocate(cells(3,3,conf_num))
 !     The CTIFOR values
@@ -1048,7 +1061,13 @@ program mlff_select
 !     The reference energies
 allocate(energies(conf_num))
 !     The reference gradients
-allocate(grads(3,natoms_max,conf_num))
+allocate(grads(3,natoms_max,conf_num),stat=alloc_stat,errmsg=alloc_err)
+if (alloc_stat .ne. 0) then
+   write(*,*) "Allocation of grads array failed:",trim(alloc_err)
+   write(*,*) "Please read in a smaller ML_AB or increase memory!"
+   stop
+end if
+
 !     The reference stress tensors
 allocate(stress(6,conf_num))
 
@@ -1057,7 +1076,13 @@ program mlff_select
 !
 !     Again open the ML_AB file 
 !
-   open(unit=56,file=mlab_list(l),status="old")
+   open(unit=56,file=mlab_list(l),status="old",iostat=readstat)
+   if (readstat .ne. 0) then
+      write(*,*) 
+      write(*,*) "The file ",trim(mlab_list(l))," is not there!"
+      write(*,*) 
+      stop
+   end if
 
    write(*,*) "Read body of the file ",trim(mlab_list(l))," ..."
    write(34,*) "Read body of the file ",trim(mlab_list(l))," ..."
@@ -1302,17 +1327,43 @@ program mlff_select
 allocate(gradnorm_all(natoms_sum))
 !     The number of atoms in the surrounding (sorted by core charges)
 allocate(num_around(nelems,natoms_sum))
+allocate(num_around(nelems,natoms_sum),stat=alloc_stat,errmsg=alloc_err)
+if (alloc_stat .ne. 0) then
+   write(*,*) "Allocation of num_around array failed:",trim(alloc_err)
+   write(*,*) "Please read in a smaller ML_AB or increase memory!"
+   stop
+end if
 !     The coordinates of atoms in the surrounding (for xyz printout)
-allocate(environ(3,max_environ,natoms_sum))
+allocate(environ(3,max_environ,natoms_sum),stat=alloc_stat,errmsg=alloc_err)
+if (alloc_stat .ne. 0) then
+   write(*,*) "Allocation of environ array failed:",trim(alloc_err)
+   write(*,*) "Please read in a smaller ML_AB or increase memory!"
+   stop
+end if
 !     The core charges/elements of atoms in surrounding
-allocate(ind_env(max_environ,natoms_sum))
+allocate(ind_env(max_environ,natoms_sum),stat=alloc_stat,errmsg=alloc_err)
+if (alloc_stat .ne. 0) then
+   write(*,*) "Allocation of ind_env array failed:",trim(alloc_err)
+   write(*,*) "Please read in a smaller ML_AB or increase memory!"
+   stop
+end if
 !     The list of distances to atoms within surrounding (local)
 allocate(dist_list(max_environ))
 !     The radial distribution functions around all atoms
-allocate(rdf_all(ngrid,natoms_sum))
+allocate(rdf_all(ngrid,natoms_sum),stat=alloc_stat,errmsg=alloc_err)
+if (alloc_stat .ne. 0) then
+   write(*,*) "Allocation of rdf_all array failed:",trim(alloc_err)
+   write(*,*) "Please read in a smaller ML_AB or increase memory!"
+   stop
+end if
 !     The angular distribution functions around all atoms
 if (.not. no_adf) then        
-   allocate(adf_all(ngrid,natoms_sum))
+   allocate(adf_all(ngrid,natoms_sum),stat=alloc_stat,errmsg=alloc_err)
+   if (alloc_stat .ne. 0) then
+      write(*,*) "Allocation of adf_all array failed:",trim(alloc_err)
+      write(*,*) "Please read in a smaller ML_AB or increase memory!"
+      stop
+   end if
 end if
 !     The local list of angles in the environment
 allocate(angles(max_environ*max_environ))

ML-FF/mlp_quality.f90 ML-FF/mlip_quality.f90ML-FF/mlp_quality.f90 renamed to ML-FF/mlip_quality.f90

@@ -1,5 +1,5 @@
 !
-!    mlp_quality: Evaluate the quality of a MLP with respect to the 
+!    mlip_quality: Evaluate the quality of a MLP with respect to the 
 !      reproduction of a given training or verification set.
 !      Currently, Behler neural networks, message-passing atomic cluster
 !      expansion (MACE) and VASP ML-FF production runs can be evaluated.
@@ -82,7 +82,7 @@ program mlp_quality
 !
 write(*,*)
 write(*,*) " *** utils4VASP -- utility scripts and programs for VASP ***"
-write(*,*) "PROGRAM mlp_quality: Evaluation of a MLP with respect to the "
+write(*,*) "PROGRAM mlip_quality: Evaluation of a MLP with respect to the "
 write(*,*) " reproduction of a given training or verification set."
 write(*,*) "The analysis can be done for Behler neural network potentials "
 write(*,*) " optimized with the aenet program (ANN) or for message-passing "

ML-FF/vasp2trainset.f90

@@ -46,7 +46,8 @@ program vasp2trainset
 character(len=2)::el_syms(10)
 character(len=150)::cdum
 real(kind=8)::factor,scale_dum
-integer::openstat
+integer::openstat,alloc_stat
+character(len=100)::alloc_err
 integer::traj_freq
 !
 !    only print the overview of utils4VASP scripts/programs and stop
@@ -555,11 +556,27 @@ program vasp2trainset
             read(27,*)
          end do
          if (allocated(xyz)) deallocate(xyz)
-         allocate(xyz(3,natoms))
+         allocate(xyz(3,natoms),stat=alloc_stat,errmsg=alloc_err)
+            if (alloc_stat .ne. 0) then
+            write(*,*) "Allocation of xyz array failed:",trim(alloc_err)
+            write(*,*) "Please read in a smaller ML_AB or increase memory!"
+            stop
+         end if
          if (allocated(grad)) deallocate(grad)
-         allocate(grad(3,natoms))
+         allocate(grad(3,natoms),stat=alloc_stat,errmsg=alloc_err)
+            if (alloc_stat .ne. 0) then
+            write(*,*) "Allocation of grad array failed:",trim(alloc_err)
+            write(*,*) "Please read in a smaller ML_AB or increase memory!"
+            stop
+         end if
          if (allocated(at_names)) deallocate(at_names)
-         allocate(at_names(natoms))
+         allocate(at_names(natoms),stat=alloc_stat,errmsg=alloc_err)
+            if (alloc_stat .ne. 0) then
+            write(*,*) "Allocation of at_names array failed:",trim(alloc_err)
+            write(*,*) "Please read in a smaller ML_AB or increase memory!"
+            stop
+         end if
+
 !
 !     Determine element symbols for all atoms
 !
@@ -740,7 +757,14 @@ program vasp2trainset
    write(*,*) "  Number of frames: ",nframes
    write(*,*) "  ... completed!"
    write(*,*) " Read XDATCAR content ..."
-   allocate(xdat_content(xdat_lines))
+   allocate(xdat_content(xdat_lines),stat=alloc_stat,errmsg=alloc_err)
+   if (alloc_stat .ne. 0) then
+      write(*,*) "Allocation of xdat_content array failed:",trim(alloc_err)
+      write(*,*) "Please read in a smaller XDATCAR or increase memory!"
+      stop
+   end if
+
+
    open(unit=56,file="XDATCAR",status="old")
    do i=1,xdat_lines
       read(56,'(a)') xdat_content(i)

evaluation/analyze_md.f90

@@ -95,7 +95,8 @@ program analyze_md
 real(kind=8),allocatable::xlens_p(:),ylens_p(:),zlens_p(:) ! ... for call of subroutines
 character(len=2)::el_eval_list(20)  ! the elements to be set to COM (density mode)
 integer::el_eval_num  ! number of elements for the COM (density mode)
-integer::readstat,openstat
+integer::readstat,openstat,status,alloc_stat
+character(len=100)::alloc_err
 integer::counter,endl 
 real(kind=8)::scale_dum
 logical::npt_format
@@ -226,7 +227,12 @@ program analyze_md
    write(*,*)
    stop
 end if   
-call system("wc -l XDATCAR > xdat_length")
+status = system("wc -l XDATCAR > xdat_length")
+if (status .ne. 0) then
+   write(*,*) "The number of atoms/frames could not be determined! XDATCAR missing?"
+   stop
+end if
+
 open(unit=45,file="xdat_length",status="old")
 read(45,*) xdat_lines
 close(45)
@@ -349,7 +355,13 @@ program analyze_md
    open(unit=14,file="XDATCAR",status="old")
 end if        
 
-allocate(xyz(3,natoms,nframes))
+allocate(xyz(3,natoms,nframes),stat=alloc_stat,errmsg=alloc_err)
+if (alloc_stat .ne. 0) then
+   write(*,*) "Allocation of xyz array failed:",trim(alloc_err)
+   write(*,*) "Please read in a smaller trajectory or increase memory!"
+   stop
+end if
+
 !
 !    Read in the coordinates of the frames and correct for image flags
 !

evaluation/manage_neb.py

@@ -224,6 +224,10 @@ def COM(xyz,natoms,names,elements_dict,move):
       sys.exit(1)
 
 #   Open POSCAR file of first frame
+   if not os.path.isfile(poscar1):
+      print("\n No "+poscar1+" file could be found! \n")
+      sys.exit(1)
+
    poscar_in = open(poscar1,"r")
 
    cartesian=False
@@ -302,6 +306,10 @@ def COM(xyz,natoms,names,elements_dict,move):
             xyz1[i][j]=float(xyz_read[j]) 
 
 #   Open POSCAR file of last frame
+   if not os.path.isfile(poscar2):
+      print("\n No "+poscar2+" file could be found! \n")
+      sys.exit(1)
+
    poscar_in = open(poscar2,"r")
 
    cartesian=False

evaluation/modify_xdatcar.f90

@@ -23,7 +23,7 @@ program modify_xdatcar
 real(kind=8)::shift_vec(3),act_val,xyz_print(3)
 integer::multiply_vec(3),pick_ind,pos_new,multiply_prod
 integer::frame_first,frame_last,line_num
-integer::read_freq
+integer::read_freq,status
 logical::npt,print_npt
 logical::remove_mode
 character(len=40)::remove_com
@@ -37,7 +37,8 @@ program modify_xdatcar
 character(len=120)::a120,cdum,arg,adum
 character(len=220)::a220
 character(len=50)::atest
-
+integer::alloc_stat
+character(len=100)::alloc_err
 !
 !    only print the overview of utils4VASP scripts/programs and stop
 !
@@ -301,7 +302,11 @@ program modify_xdatcar
 !
 write(*,*)
 write(*,*) "Determine number of atoms and frames in XDATCAR..."
-call system("wc -l XDATCAR > xdat_length")
+status = system("wc -l XDATCAR > xdat_length")
+if (status .ne. 0) then
+   write(*,*) "The number of atoms/frames could not be determined! XDATCAR missing?"
+   stop
+end if
 open(unit=45,file="xdat_length",status="old")
 read(45,*) xdat_lines
 close(45)
@@ -396,7 +401,12 @@ program modify_xdatcar
 !
 !    Allocate global coordinate arrays
 !
-allocate(xyz(3,natoms,nframes))
+allocate(xyz(3,natoms,nframes),stat=alloc_stat,errmsg=alloc_err)
+if (alloc_stat .ne. 0) then
+   write(*,*) "Allocation of xyz array failed:",trim(alloc_err)
+   write(*,*) "Please read in a smaller trajectory or increase memory!"
+   stop
+end if
 if (npt) then
    allocate(a_vecs(3,nframes))
    allocate(b_vecs(3,nframes))

setup/analyze_poscar.py

@@ -134,6 +134,14 @@
 # Read in the POSCAR file
 poscar_name="POSCAR"
 
+# Check first if it is there!
+
+if os.path.isfile(poscar_name):
+   print("\n The POSCAR file could be located.\n")
+else:
+   print("\n No POSCAR file could be found! \n")
+   sys.exit(1)
+
 poscar_in = open(poscar_name,"r")
 
 # array for selective dynamics specifiers
@@ -380,7 +388,13 @@ def vector_angle(v1, v2):
    if os.path.isfile("POTCAR"):
       os.system("rm POTCAR")
    for el in elements:
-      os.system("cat "+pot_path+"potcar/PAW_PBE.52/"+el+"/POTCAR >> POTCAR")
+      path_current=pot_path+"potcar/PAW_PBE.52/"+el+"/POTCAR"
+      path_current = os.path.expanduser(path_current)
+      if os.path.isfile(path_current):
+         os.system("cat "+path_current+" >> POTCAR")
+      else:
+         print("\n No POTCAR template for "+el+" could be found! \n")
+         sys.exit(1)
 
    print(" The POTCAR file was written.")
 #

setup/build_adsorb.py

@@ -593,12 +593,24 @@ def ReadMolecule(self):
 #
       if self.type == "large": 
          if self.spec == "local1":
+            if not os.path.isfile("POSCAR_ads1"):
+               print("\n No POSCAR_ads1 file could be found! \n")
+               sys.exit(1)
             mol_in = open("POSCAR_ads1","r")
          elif self.spec == "local2":
+            if not os.path.isfile("POSCAR_ads2"):
+               print("\n No POSCAR_ads2 file could be found! \n")
+               sys.exit(1)
             mol_in = open("POSCAR_ads2","r")
          elif self.spec == "local3":
+            if not os.path.isfile("POSCAR_ads3"):
+               print("\n No POSCAR_ads3 file could be found! \n")
+               sys.exit(1)
             mol_in = open("POSCAR_ads3","r")
          elif self.spec == "local4":
+            if not os.path.isfile("POSCAR_ads3"):
+               print("\n No POSCAR_ads3 file could be found! \n")
+               sys.exit(1)
             mol_in = open("POSCAR_ads4","r")
          else:   
             mol_in = io.StringIO(adsorbate_dict[self.spec])
@@ -800,6 +812,12 @@ def Rot_Molecule(self,matrix):
 # First, read in the POSCAR file for the metal surface
 surface_name="POSCAR_surf"
 
+if os.path.isfile(surface_name):
+   print("\n The POSCAR_surf file could be located.\n")
+else:
+   print("\n No POSCAR_surf file could be found! \n")
+   sys.exit(1)
+
 surface_in = open(surface_name,"r")
 
 with surface_in as infile:
@@ -915,31 +933,24 @@ def Rot_Molecule(self,matrix):
 print(" ")
 
 nspecs=0
-#while True:
-#   try: 
-#      nspecs = int(input(" Number of ionic liquid molecules?  "))
-#      if nspecs <= 0 or nspecs > 8:
-#          raise ValueError
-#      break 
-#   except NameError:
-#      print(" ERROR! No valid number given! Please try again!")
-#   except ValueError:
-#      print(" ERROR! Only numbers between 1 and 8 are allowed!")
 
 # Read in the species and positions/rotations from file!
 
-# Second, read in the data file with the bromine positions
 list_name="adsorb_list.dat"
 
+
+if not os.path.isfile(list_name):
+   print("\n No adsorb_list.dat file could be found! \n")
+   sys.exit(1)
+
+
 list_in = open(list_name,"r")
 
+
 with list_in as infile:
    IL_lines = list_in.readlines()
 
 nspecs = len(IL_lines)
-#if len(IL_lines) != nspecs:
-#   print("Error! The file IL_list.dat must contain as many lines as the")
-#   print("  number of desired IL molecules.")
 
 #
 #    Now read in all surface molecules as class instances!