remove _env suffixes in crystalmod environment routines

src/arithmetic@proc.F90

@@ -1335,10 +1335,10 @@ function structvareval(svar,fder,errmsg,x0,syl,periodic) result(q)
              errmsg = 'atom ID in rho0nuc structural variable out of range'
              return
           end if
-          call syl%c%nearest_atom_env(x0,icrd_cart,nid0,dist,lvec=lvec,id0=nid)
+          call syl%c%nearest_atom(x0,icrd_cart,nid0,dist,lvec=lvec,id0=nid)
           if (nid /= nid0) return ! fixme: the atom was too far
        else
-          call syl%c%nearest_atom_env(x0,icrd_cart,nid,dist,lvec=lvec)
+          call syl%c%nearest_atom(x0,icrd_cart,nid,dist,lvec=lvec)
        end if
 
        if (nid == 0) then

src/bader@proc.f90

@@ -163,7 +163,7 @@ module subroutine bader_integrate(s,bas,iref)
                    ! check if it is an atom (use ratom)
                    isassigned = .false.
                    if (bas%atexist) then
-                      nid = s%c%identify_atom_env(dv,icrd_crys,distmax=bas%ratom)
+                      nid = s%c%identify_atom(dv,icrd_crys,distmax=bas%ratom)
                       if (nid > 0) then
                          path_volnum = nid
                          isassigned = .true.

src/crystalmod.f90

@@ -128,15 +128,13 @@ module crystalmod
      ! core charges
      integer :: zpsp(maxzat0)
 
-     !! Initialization level: isenv !!
      ! atomic environment of the cell
      integer :: nblock(3) ! number of environemt blocks
      integer,allocatable :: iblock0(:,:,:) ! starting atomic index for each block
      real*8 :: blockrmax ! radius of the largest sphere contained in a block
      real*8 :: blockomega ! volume of a block
      real*8 :: blockcv(3) ! cross products of the block lattice vectors
 
-     !! Initialization level: isast !!
      ! asterisms
      type(neighstar), allocatable :: nstar(:) !< Neighbor stars
      integer :: nmol = 0 !< Number of molecules in the unit cell
@@ -180,9 +178,9 @@ module crystalmod
      ! atomic environments and distance calculations
      procedure :: build_env
      procedure :: list_near_atoms
-     procedure :: nearest_atom_env
-     procedure :: identify_atom_env
-     procedure :: promolecular_env
+     procedure :: nearest_atom
+     procedure :: identify_atom
+     procedure :: promolecular_atom
      procedure :: find_asterisms_covalent
      procedure :: list_near_lattice_points
      procedure :: nearest_lattice_point
@@ -359,33 +357,11 @@ module function are_lclose(c,x0,x1,eps,dd)
        real*8, intent(out), optional :: dd
        logical :: are_lclose
      end function are_lclose
-     module subroutine nearest_atom(c,xp,icrd,nid,dist,distmax,lvec,cidx0,idx0,is0,nozero)
-       class(crystal), intent(in) :: c
-       real*8, intent(in) :: xp(3)
-       integer, intent(in) :: icrd
-       integer, intent(out) :: nid
-       real*8, intent(out) :: dist
-       real*8, intent(in), optional :: distmax
-       integer, intent(out), optional :: lvec(3)
-       integer, intent(in), optional :: cidx0
-       integer, intent(in), optional :: idx0
-       integer, intent(in), optional :: is0
-       logical, intent(in), optional :: nozero
-     end subroutine nearest_atom
      module subroutine nearest_atom_grid(c,n,idg)
        class(crystal), intent(inout) :: c
        integer, intent(in) :: n(3)
        integer, allocatable, intent(inout) :: idg(:,:,:)
      end subroutine nearest_atom_grid
-     module function identify_atom(c,x0,icrd,lvec,dist,distmax)
-       class(crystal), intent(in) :: c
-       real*8, intent(in) :: x0(3)
-       integer, intent(in) :: icrd
-       integer, intent(out), optional :: lvec(3)
-       real*8, intent(out), optional :: dist
-       real*8, intent(in), optional :: distmax
-       integer :: identify_atom
-     end function identify_atom
      module function identify_spc(c,str) result(res)
        use crystalseedmod, only: crystalseed
        class(crystal), intent(inout) :: c
@@ -417,7 +393,7 @@ module subroutine list_near_atoms(c,xp,icrd,sorted,nat,eid,dist,lvec,ishell0,up2
        integer, intent(in), optional :: ispc0
        logical, intent(in), optional :: nozero
      end subroutine list_near_atoms
-     module subroutine nearest_atom_env(c,xp,icrd,nid,dist,distmax,lvec,nid0,id0,iz0,ispc0,nozero)
+     module subroutine nearest_atom(c,xp,icrd,nid,dist,distmax,lvec,nid0,id0,iz0,ispc0,nozero)
        class(crystal), intent(inout) :: c
        real*8, intent(in) :: xp(3)
        integer, intent(in) :: icrd
@@ -430,17 +406,17 @@ module subroutine nearest_atom_env(c,xp,icrd,nid,dist,distmax,lvec,nid0,id0,iz0,
        integer, intent(in), optional :: iz0
        integer, intent(in), optional :: ispc0
        logical, intent(in), optional :: nozero
-     end subroutine nearest_atom_env
-     module function identify_atom_env(c,x0,icrd,lvec,dist,distmax)
+     end subroutine nearest_atom
+     module function identify_atom(c,x0,icrd,lvec,dist,distmax)
        class(crystal), intent(inout) :: c
        real*8, intent(in) :: x0(3)
        integer, intent(in) :: icrd
        integer, intent(out), optional :: lvec(3)
        real*8, intent(out), optional :: dist
        real*8, intent(in), optional :: distmax
-       integer :: identify_atom_env
-     end function identify_atom_env
-     module subroutine promolecular_env(c,x0,icrd,f,fp,fpp,nder,zpsp,fr)
+       integer :: identify_atom
+     end function identify_atom
+     module subroutine promolecular_atom(c,x0,icrd,f,fp,fpp,nder,zpsp,fr)
        use fragmentmod, only: fragment
        class(crystal), intent(inout) :: c
        real*8, intent(in) :: x0(3)
@@ -451,7 +427,7 @@ module subroutine promolecular_env(c,x0,icrd,f,fp,fpp,nder,zpsp,fr)
        integer, intent(in) :: nder
        integer, intent(in), optional :: zpsp(:)
        type(fragment), intent(in), optional :: fr
-     end subroutine promolecular_env
+     end subroutine promolecular_atom
      module subroutine find_asterisms_covalent(c)
        class(crystal), intent(inout) :: c
      end subroutine find_asterisms_covalent

src/crystalmod@complex.f90

@@ -175,7 +175,7 @@ module function ewald_pot(c,x)
     end if
 
     ! is this a nuclear position? -> get charge
-    idnuc = c%identify_atom_env(x,icrd_crys)
+    idnuc = c%identify_atom(x,icrd_crys)
     if (idnuc > 0) then
        qnuc = c%spc(c%atcel(idnuc)%is)%qat
     else
@@ -268,7 +268,7 @@ module subroutine promolecular_grid(c,f,n,zpsp,fr)
        do j = 1, n(2)
           do i = 1, n(1)
              x = (i-1) * xdelta(:,1) + (j-1) * xdelta(:,2) + (k-1) * xdelta(:,3)
-             call c%promolecular_env(x,icrd_crys,rho,rdum1,rdum2,0,zpsp,fr)
+             call c%promolecular_atom(x,icrd_crys,rho,rdum1,rdum2,0,zpsp,fr)
 
              !$omp critical(write)
              f%f(i,j,k) = rho

src/crystalmod@edit.f90

@@ -618,7 +618,7 @@ module subroutine wholemols(c,ti)
                 if (ldone(c%atcel(k)%idx)) cycle
 
                 x0 = matmul(c%rotm(1:3,1:3,i),c%atcel(k)%x) + c%rotm(:,4,i) + c%cen(:,j)
-                id = c%identify_atom_env(x0,icrd_crys)
+                id = c%identify_atom(x0,icrd_crys)
 
                 if (id == 0) &
                    call ferror('wholemols','error identifying rotated atom',faterr)
@@ -649,7 +649,7 @@ module subroutine wholemols(c,ti)
           if (.not.sgroup(j,ig)) cycle
           do k = 1, c%ncv
              x0 = matmul(c%rotm(1:3,1:3,j),c%atcel(i)%x) + c%rotm(:,4,j) + c%cen(:,k)
-             id = c%identify_atom_env(x0,icrd_crys)
+             id = c%identify_atom(x0,icrd_crys)
              if (id == 0) &
                 call ferror('wholemols','error identifying rotated atom',faterr)
              isuse(id) = .true.

src/crystalmod@env.f90

@@ -513,7 +513,7 @@ end subroutine list_near_atoms
   !> - nozero = disregard zero-distance atoms.
   !>
   !> This routine is thread-safe.
-  module subroutine nearest_atom_env(c,xp,icrd,nid,dist,distmax,lvec,nid0,id0,iz0,ispc0,nozero)
+  module subroutine nearest_atom(c,xp,icrd,nid,dist,distmax,lvec,nid0,id0,iz0,ispc0,nozero)
     class(crystal), intent(inout) :: c
     real*8, intent(in) :: xp(3)
     integer, intent(in) :: icrd
@@ -553,44 +553,44 @@ module subroutine nearest_atom_env(c,xp,icrd,nid,dist,distmax,lvec,nid0,id0,iz0,
     dist = dist_(1)
     if (present(lvec)) lvec = lvec_(:,1)
 
-  end subroutine nearest_atom_env
+  end subroutine nearest_atom
 
   !> Given point x0 (with icrd input coordinates), if x0 corresponds
   !> to an atomic position (to within distmax or atomeps if distmax is
   !> not given), return the complete-list ID of the atom. Otherwise,
   !> return 0. Optionally, return the lattice vector translation
   !> (lvec) and the distance (dist) to the closest atom. This routine
   !> is thread-safe.
-  module function identify_atom_env(c,x0,icrd,lvec,dist,distmax)
+  module function identify_atom(c,x0,icrd,lvec,dist,distmax)
     use global, only: atomeps
     class(crystal), intent(inout) :: c
     real*8, intent(in) :: x0(3)
     integer, intent(in) :: icrd
     integer, intent(out), optional :: lvec(3)
     real*8, intent(out), optional :: dist
     real*8, intent(in), optional :: distmax
-    integer :: identify_atom_env
+    integer :: identify_atom
 
     real*8 :: distmax_, dist0
     integer :: lvec0(3)
 
-    identify_atom_env = 0
+    identify_atom = 0
     distmax_ = atomeps
     if (present(distmax)) distmax_ = distmax
 
-    call c%nearest_atom_env(x0,icrd,identify_atom_env,dist0,distmax=distmax_,lvec=lvec0)
+    call c%nearest_atom(x0,icrd,identify_atom,dist0,distmax=distmax_,lvec=lvec0)
     if (present(lvec)) lvec = lvec0
     if (present(dist)) dist = dist0
 
-  end function identify_atom_env
+  end function identify_atom
 
   !> Calculate the core (if zpsp is present) or promolecular densities
   !> at a point x0 (coord format given by icrd) using atomic radial
   !> grids up to a number of derivatives nder (max: 2). Returns the
   !> density (f), gradient (fp, nder >= 1), and Hessian (fpp, nder >=
   !> 2). If a fragment (fr) is given, then only the atoms in it
   !> contribute. This routine is thread-safe.
-  module subroutine promolecular_env(c,x0,icrd,f,fp,fpp,nder,zpsp,fr)
+  module subroutine promolecular_atom(c,x0,icrd,f,fp,fpp,nder,zpsp,fr)
     use grid1mod, only: cgrid, agrid, grid1
     use global, only: cutrad
     use fragmentmod, only: fragment
@@ -721,7 +721,7 @@ module subroutine promolecular_env(c,x0,icrd,f,fp,fpp,nder,zpsp,fr)
 
     if (allocated(isinfr)) deallocate(isinfr)
 
-  end subroutine promolecular_env
+  end subroutine promolecular_atom
 
   !> Find the covalent bond connectivity and return the bonds in the
   !> c%nstar array.

src/crystalmod@mols.f90

@@ -41,7 +41,7 @@ module function identify_fragment(c,nat,x0) result(fr)
 
     n = 0
     do i = 1, nat
-       id = c%identify_atom_env(x0(:,i),icrd_cart)
+       id = c%identify_atom(x0(:,i),icrd_cart)
        if (id > 0) then
           n = n + 1
           fr%at(n)%r = x0(:,i)
@@ -90,7 +90,7 @@ module function identify_fragment_from_xyz(c,file,errmsg,ti) result(fr)
     do i = 1, nat
        read(lu,*,err=999,end=999) word, x0
        x0 = x0 / bohrtoa - c%molx0
-       id = c%identify_atom_env(x0,icrd_cart)
+       id = c%identify_atom(x0,icrd_cart)
        if (id == 0) then
           fr%nat = 0
           deallocate(fr%at)

src/crystalmod@proc.f90

@@ -548,7 +548,7 @@ module subroutine struct_new(c,seed,crashfail,noenv,ti)
        ! Write the half nearest-neighbor distance
        do i = 1, c%nneq
           if (.not.c%ismolecule .or. c%ncel > 1) then
-             call c%nearest_atom_env(c%at(i)%r,icrd_cart,iat,dist,nozero=.true.)
+             call c%nearest_atom(c%at(i)%r,icrd_cart,iat,dist,nozero=.true.)
              c%at(i)%rnn2 = 0.5d0 * dist
           else
              c%at(i)%rnn2 = 0d0
@@ -816,7 +816,7 @@ module subroutine nearest_atom_grid(c,n,idg)
        do j = 1, n(2)
           do i = 1, n(1)
              x = (i-1) * xdelta(:,1) + (j-1) * xdelta(:,2) + (k-1) * xdelta(:,3)
-             call c%nearest_atom_env(x,icrd_crys,nid,dist)
+             call c%nearest_atom(x,icrd_crys,nid,dist)
              !$omp critical(write)
              idg(i,j,k) = nid
              !$omp end critical(write)

src/elk_private@proc.f90

@@ -134,7 +134,7 @@ module subroutine rho2(f,vpl,nder,frho,gfrho,hfrho)
     frho = 0d0
     gfrho = 0d0
     hfrho = 0d0
-    call c%nearest_atom_env(vpl,icrd_crys,nid,dist,lvec=lvec)
+    call c%nearest_atom(vpl,icrd_crys,nid,dist,lvec=lvec)
 
     ! inside a muffin tin
     inmt = (nid > 0)

src/fieldmod@proc.f90

@@ -876,11 +876,11 @@ recursive module subroutine grd(f,v,nder,res,fder,periodic)
        ! all work done in Cartesians in a finite environment.
 
     case(type_promol)
-       call f%c%promolecular_env(wcr,icrd_cart,res%f,res%gf,res%hf,nder)
+       call f%c%promolecular_atom(wcr,icrd_cart,res%f,res%gf,res%hf,nder)
        ! not needed because grd_atomic uses struct.
 
     case(type_promol_frag)
-       call f%c%promolecular_env(wcr,icrd_cart,res%f,res%gf,res%hf,nder,fr=f%fr)
+       call f%c%promolecular_atom(wcr,icrd_cart,res%f,res%gf,res%hf,nder,fr=f%fr)
        ! not needed because grd_atomic uses struct.
 
     case(type_ghost)
@@ -903,7 +903,7 @@ recursive module subroutine grd(f,v,nder,res,fder,periodic)
 
     ! augment with the core if applicable
     if (f%usecore .and. any(f%zpsp /= -1)) then
-       call f%c%promolecular_env(wc,icrd_cart,rho,grad,h,nder,zpsp=f%zpsp)
+       call f%c%promolecular_atom(wc,icrd_cart,rho,grad,h,nder,zpsp=f%zpsp)
        res%f = res%f + rho
        res%gf  = res%gf + grad
        res%hf = res%hf + h
@@ -914,7 +914,7 @@ recursive module subroutine grd(f,v,nder,res,fder,periodic)
 
     ! If it's on a nucleus, nullify the gradient (may not be zero in
     ! grid fields, for instance)
-    nid = f%c%identify_atom_env(wc,icrd_cart,distmax=1d-5)
+    nid = f%c%identify_atom(wc,icrd_cart,distmax=1d-5)
     res%isnuc = (nid > 0)
 
     ! gradient
@@ -1002,9 +1002,9 @@ recursive module function grd0(f,v,periodic)
     case(type_dftb)
        call f%dftb%rho2(wcr,f%exact,0,rho,grad,h,gkin)
     case(type_promol)
-       call f%c%promolecular_env(wcr,icrd_cart,rho,grad,h,0)
+       call f%c%promolecular_atom(wcr,icrd_cart,rho,grad,h,0)
     case(type_promol_frag)
-       call f%c%promolecular_env(wcr,icrd_cart,rho,grad,h,0,fr=f%fr)
+       call f%c%promolecular_atom(wcr,icrd_cart,rho,grad,h,0,fr=f%fr)
     case(type_ghost)
        rho = eval(f%expr,errmsg,wc,f%sptr,periodic)
        if (len_trim(errmsg) > 0) &
@@ -1014,7 +1014,7 @@ recursive module function grd0(f,v,periodic)
     end select
 
     if (f%usecore .and. any(f%zpsp /= -1)) then
-       call f%c%promolecular_env(wc,icrd_cart,rhoaux,grad,h,0,zpsp=f%zpsp)
+       call f%c%promolecular_atom(wc,icrd_cart,rhoaux,grad,h,0,zpsp=f%zpsp)
        rho = rho + rhoaux
     end if
     grd0 = rho
@@ -2050,7 +2050,7 @@ module subroutine addcp(f,x0,cpeps,nuceps,nucepsh,gfnormeps,itype)
     end if
 
     ! distance to atoms
-    nid = f%c%identify_atom_env(xc,icrd_crys,dist=dist,distmax=max(nuceps,nucepsh))
+    nid = f%c%identify_atom(xc,icrd_crys,dist=dist,distmax=max(nuceps,nucepsh))
     if (nid > 0) then
        if (dist < nuceps) goto 999
        if (f%c%spc(f%c%atcel(nid)%is)%z == 1 .and. dist < nucepsh) goto 999
@@ -2295,7 +2295,7 @@ module subroutine gradient(fid,xpoint,iup,nstep,ier,up2beta,plen,path,prune,path
        end if
 
        ! nearest nucleus
-       call fid%c%nearest_atom_env(xpoint,icrd_crys,idnuc,sphrad,lvec=lvec)
+       call fid%c%nearest_atom(xpoint,icrd_crys,idnuc,sphrad,lvec=lvec)
        xnuc = fid%c%x2c(fid%c%atcel(idnuc)%x + lvec)
        xnucr = fid%c%atcel(idnuc)%x + lvec
        idnuc = fid%c%atcel(idnuc)%idx

src/flux@proc.f90

@@ -961,7 +961,7 @@ subroutine flx_prepareprintpath(x,title,iup,dir,icp)
        call sy%f(sy%iref)%nearest_cp(flx_path(flx_n)%x,flx_cpcelid(2),dist)
        if (dist <= cpeps) goto 999
 
-       flx_cpcelid(2) = sy%c%identify_atom_env(flx_path(flx_n)%x,icrd_crys,dist=dist,distmax=max(nuceps,nucepsh))
+       flx_cpcelid(2) = sy%c%identify_atom(flx_path(flx_n)%x,icrd_crys,dist=dist,distmax=max(nuceps,nucepsh))
        if (flx_cpcelid(2) > 0) then
           if (dist < nuceps) goto 999
           if (sy%c%spc(sy%c%atcel(flx_cpcelid(2))%is)%z == 1 .and. dist < nucepsh) goto 999

src/grid3mod@proc.f90

@@ -3154,7 +3154,7 @@ subroutine crystalmod_promolecular(cptr,x0,icrd,f,fp,fpp,nder,zpsp,fr)
      type(crystal), pointer :: c
 
      call c_f_pointer(cptr,c)
-     call c%promolecular_env(x0,icrd,f,fp,fpp,nder,zpsp,fr)
+     call c%promolecular_atom(x0,icrd,f,fp,fpp,nder,zpsp,fr)
 
    end subroutine crystalmod_promolecular
 

src/integration@proc.f90

@@ -1035,7 +1035,7 @@ subroutine int_reorder_gridout(ff,bas)
     ! assign attractors to atoms
     if (bas%atexist) then
        do i = 1, nattr0
-          nid = ff%c%identify_atom_env(bas%xattr(:,i),icrd_crys,distmax=bas%ratom)
+          nid = ff%c%identify_atom(bas%xattr(:,i),icrd_crys,distmax=bas%ratom)
           if (nid > 0) then
              assigned(i) = nid
           else

src/nci@proc.f90

@@ -951,7 +951,7 @@ function read_fragment(lu) result(fr)
           ok = ok .and. eval_next(x(3),line,lp)
           if (.not.ok) call ferror('nciplot','bad atom in fragment',faterr)
           x = x / bohrtoa - sy%c%molx0
-          id = sy%c%identify_atom_env(x,icrd_cart)
+          id = sy%c%identify_atom(x,icrd_cart)
 
           if (id > 0) then
              fr%nat = fr%nat + 1

src/rhoplot@proc.f90

@@ -2524,8 +2524,8 @@ subroutine wrtpath(xpath,nptf,udat,rp0,r01,r02,cosalfa,sinalfa)
     logical :: wasblank
 
     ! identify the endpoints
-    nid1 = sy%c%identify_atom_env(xpath(1)%x,icrd_crys,dist=dist1,distmax=1.1d0*prunedist)
-    nid2 = sy%c%identify_atom_env(xpath(nptf)%x,icrd_crys,dist=dist2,distmax=1.1d0*prunedist)
+    nid1 = sy%c%identify_atom(xpath(1)%x,icrd_crys,dist=dist1,distmax=1.1d0*prunedist)
+    nid2 = sy%c%identify_atom(xpath(nptf)%x,icrd_crys,dist=dist2,distmax=1.1d0*prunedist)
     rgb = (/0,0,0/)
     if (nid1 > 0 .and. (dist1 < dist2 .or. nid2 == 0)) then
        iz = sy%c%spc(sy%c%atcel(nid1)%is)%z