merging after restart from coordinates

src/getMol.f90

@@ -21,6 +21,8 @@ subroutine getMol(ierr)
 
    implicit none
 
+   integer :: fail
+
    logical :: present
    integer :: i,j,k,itemp
    integer, intent(inout) :: ierr
@@ -33,11 +35,24 @@ subroutine getMol(ierr)
 
       ! read xyz coordinates from the .in file 
       if(.not. isTemplate) then
-       call quick_open(infile,inFileName,'O','F','W',.true.,ierr)
-       CHECK_ERROR(ierr)
-        ! read molecule coordinates
-        call read2(quick_molspec,inFile,ierr)
-        close(inFile)
+        if(quick_method%read_coord)then
+
+          open(unit=iDataFile,file=dataFileName,status='OLD',form='UNFORMATTED')
+          call rchk_darray(iDataFile, "xyz", 3, natom, 1, xyz, fail)
+          call rchk_iarray(iDataFile, "iattype", natom, 1, 1, quick_molspec%iattype, fail)
+          close(iDataFile)
+
+          quick_molspec%xyz => xyz
+
+        else
+
+          call quick_open(infile,inFileName,'O','F','W',.true.,ierr)
+          CHECK_ERROR(ierr)
+          ! read molecule coordinates
+          call read2(quick_molspec,inFile,ierr)
+          close(inFile)
+
+        endif
       endif
 
       quick_molspec%nbasis   => nbasis

src/main.f90

@@ -64,6 +64,9 @@ program quick
 
     implicit none
 
+
+    integer :: fail
+
 #if defined CUDA || defined HIP
     integer :: gpu_device_id = -1
 #endif
@@ -295,6 +298,16 @@ program quick
         else
             SAFE_CALL(lopt(ierr))         ! Cartesian
         endif
+
+        if(master) then
+          if(quick_method%writexyz)then
+            call quick_open(iDataFile, dataFileName, 'R', 'U', 'A',.true.,ierr)
+            call wchk_int(iDataFile, "natom", natom, fail)
+            call wchk_iarray(iDataFile, "iattype", natom, 1, 1, quick_molspec%iattype, fail)
+            call wchk_darray(iDataFile, "xyz", 3, natom, 1, quick_molspec%xyz, fail)
+            close(iDataFile)
+          endif 
+        endif
     endif
 
     if (.not.quick_method%opt .and. quick_method%grad) then

src/modules/quick_api_module.f90

@@ -62,8 +62,8 @@ module quick_api_module
     double precision, allocatable, dimension(:,:) :: ptchg_crd
 
     ! job card for quick job, essentially the first line of regular quick input file
-    ! default length is 256 characters
-    character(len=256) :: keywd
+    ! default length is 300 characters
+    character(len=300) :: keywd
 
     ! Is the job card provided by passing a string? default is false
     logical :: hasKeywd = .false.

src/modules/quick_files_module.f90

@@ -204,11 +204,13 @@ subroutine read_basis_file(keywd,ierr)
 
             i = index(keywd,'BASIS=',.false.)
 
-            j = scan(keywd(i:lenkwd),' ',.false.)
+!            j = scan(keywd(i:lenkwd),' ',.false.)
+            j = scan(keywd(i+6:),' ',.false.)
 
             basis_sets=trim(basisdir) // "/basis_link"
 
-            basisSetName = keywd(i+6:i+j-2)
+!            basisSetName = keywd(i+6:i+j-2)
+            basisSetName = keywd(i+6:i+5+j)
             search_keywd= "#" // trim(basisSetName)
             ! Check if the basis_link file exists
 

src/modules/quick_method_module.f90

@@ -45,7 +45,9 @@ module quick_method_module
         logical :: nodirect = .false.  ! conventional scf
         logical :: readDMX =  .false.  ! flag to read density matrix
         logical :: readden = .false.  ! flag to read density matrix
+        logical :: read_coord = .false.  ! flag to read coordinates
         logical :: writeden = .false. ! flag to write density matrix
+        logical :: writexyz = .false. ! flag to write coordinates
         logical :: readSAD = .true.    ! flag to read SAD guess
         logical :: writeSAD = .false.  ! flag to write SAD guess
         logical :: diisSCF =  .false.  ! DIIS SCF
@@ -248,7 +250,9 @@ subroutine broadcast_quick_method(self, ierr)
             call MPI_BCAST(self%gridspacing,1,mpi_double_precision,0,MPI_COMM_WORLD,mpierror)
             call MPI_BCAST(self%lapGridSpacing,1,mpi_double_precision,0,MPI_COMM_WORLD,mpierror)
             call MPI_BCAST(self%readden,1,mpi_logical,0,MPI_COMM_WORLD,mpierror)
+            call MPI_BCAST(self%read_coord,1,mpi_logical,0,MPI_COMM_WORLD,mpierror)
             call MPI_BCAST(self%writeden,1,mpi_logical,0,MPI_COMM_WORLD,mpierror)
+            call MPI_BCAST(self%writexyz,1,mpi_logical,0,MPI_COMM_WORLD,mpierror)
             call MPI_BCAST(self%extCharges,1,mpi_logical,0,MPI_COMM_WORLD,mpierror)
             call MPI_BCAST(self%ext_grid,1,mpi_logical,0,MPI_COMM_WORLD,mpierror)
             call MPI_BCAST(self%extgrid_angstrom,1,mpi_logical,0,MPI_COMM_WORLD,mpierror)
@@ -424,8 +428,10 @@ subroutine print_quick_method(self,io,ierr)
             if (self%printEnergy) write(io,'(" PRINT ENERGY EVERY CYCLE")')
 
             if (self%readDMX)   write(io,'(" READ DENSITY MATRIX FROM FILE")')
+            if (self%read_coord) write(io,'(" READ COORDINATES From DATAFILE")')
             if (self%readden) write(io,'(" READ DENSITY MATRIX From DATAFILE")')
-            if (self%writeden) write(io,'(" WRITE DENSITY MATRIX TO FILE")')
+            if (self%writeden) write(io,'(" WRITE DENSITY MATRIX TO DATA FILE")')
+            if (self%writexyz) write(io,'(" WRITE COORDINATES TO DATA FILE")')
             if (self%readSAD)   write(io,'(" READ SAD GUESS FROM FILE")')
             if (self%writeSAD)   write(io,'(" WRITE SAD GUESS TO FILE")')
 
@@ -656,7 +662,11 @@ subroutine read_quick_method(self,keywd,ierr)
             end if
             if (index(keyWD,'ZMAKE').ne.0)      self%zmat=.true.
             if (index(keyWD,'DIPOLE').ne.0)     self%dipole=.true.
-            if (index(keyWD,'WRITE').ne.0)      self%writeden=.true.
+            if (index(keyWD,'WRITE').ne.0)then
+                self%writeden=.true.
+                self%writexyz=.true.
+            end if
+
             if (index(keyWD,'EXTCHARGES').ne.0) self%EXTCHARGES=.true.
             if (index(keyWD,'EXTGRID').ne.0) self%ext_grid=.true.
             !if (index(keyWD,'EXTGRID_ANGSTROM').ne.0) self%extgrid_angstrom=.true.
@@ -680,6 +690,9 @@ subroutine read_quick_method(self,keywd,ierr)
             !Read density matrix
             if (index(keyWD,'READDEN').ne.0) self%readden=.true.
 
+            !Read coordinates
+            if (index(keyWD,'READ_COORD').ne.0) self%read_coord=.true.
+
             if (self%DFT) then
                 if (index(keyWD,'SG0').ne.0) then
                     self%iSG=0
@@ -899,7 +912,9 @@ subroutine init_quick_method(self,ierr)
             self%calcDens = .false.    ! calculate density
             self%calcDensLap = .false. ! calculate density lap
             self%readden = .false.    ! Input density matrix
-            self%writeden = .false.   ! Output density matrix
+            self%read_coord = .false.    ! Input coordinates
+            self%writeden = .false.   ! Write density matrix to data file
+            self%writexyz = .false.   ! Write coordinates to data file
             self%extCharges = .false.  ! external charge
             self%ext_grid = .false.    ! external grid points
             self%extgrid_angstrom = .false.   ! external grid points (same as above) output in angstrom

src/modules/quick_molspec_module.f90

@@ -325,8 +325,13 @@ subroutine read_quick_molspec(self,input,isTemplate, hasKeywd, apiKeywd,ierr)
 
     use quick_constants_module
     use quick_exception_module
+    use quick_method_module, only: quick_method
+    use quick_files_module, only : iDataFile, dataFileName
 
     implicit none
+
+    integer :: fail
+
     type (quick_molspec_type) :: self
     integer, intent(inout) :: ierr
     integer :: input,rdinml,i,j,k
@@ -335,13 +340,14 @@ subroutine read_quick_molspec(self,input,isTemplate, hasKeywd, apiKeywd,ierr)
     integer :: nextatom
     integer :: nextpoint
     double precision :: temp,rdnml
-    character(len=200) :: keywd
+    character(len=300) :: keywd
+    character(len=300) :: tempstring
     logical :: is_extcharge = .false.
     logical :: is_extgrid = .false.
     logical :: is_blank
     logical, intent(in)   :: isTemplate
     logical, intent(in)   :: hasKeywd
-    character(len=200), intent(in) :: apikeywd
+    character(len=300), intent(in) :: apikeywd
 
     !---------------------
     ! PART I
@@ -350,12 +356,19 @@ subroutine read_quick_molspec(self,input,isTemplate, hasKeywd, apiKeywd,ierr)
 
     if( .not. hasKeywd ) then
       rewind(input)
-      read (input,'(A132)') keywd
+      keyWD(:)=''
+      do while(.true.)
+        read (input,'(A300)') tempstring
+        if(trim(tempstring).eq.'') exit
+        if(tempstring(1:1).ne.'$')then
+          keyWD=trim(keyWD)//' '//trim(tempstring)
+        endif
+      enddo
     else
       keywd = apikeywd
     endif
 
-    call upcase(keywd,200)
+    call upcase(keywd,300)
 
     ! Read Charge
     if (index(keywd,'CHARGE=') /= 0) self%molchg = rdinml(keywd,'CHARGE')
@@ -379,85 +392,89 @@ subroutine read_quick_molspec(self,input,isTemplate, hasKeywd, apiKeywd,ierr)
 
   if( .not. isTemplate) then
 
-    call findBlock(input,1)
-
-    ! first is to read atom and atom kind
-    iAtomType = 1
-    natom = 0
-    nextatom = 0
-    nextpoint = 0
-    do
-       read(input,'(A80)',end=111,err=111) keywd
-       i=1;j=80
-       call upcase(keywd,80)
-       call rdword(keywd,i,j)
-       if (is_blank(keywd,1,80)) exit
-
-       do k=0,92
-          if (keywd(i:j) == symbol(k)) then
-             natom=natom+1
-             ! check if atom type has been shown before
-             if (.not.(any(self%atom_type_sym(1:iatomtype).eq.symbol(k)))) then
-                !write(*,*) "Assigning value to atom_type_sym:", k, symbol(k)
-                self%atom_type_sym(iAtomType)=symbol(k)
-                iAtomType=iAtomType+1
-             endif
-          endif
-       enddo
-    enddo
-
-    111     continue
-
-!    ! read external charge part
-!    if (is_extcharge)  then
-!       rewind(input)
-!       call findBlock(input,2)
-!       do
-!          read(input,'(A80)',end=112,err=112) keywd
-!          if (is_blank(keywd,1,80)) exit
-!          nextatom=nextatom+1
-!       enddo
-!    endif
-
-! read external charge part
-    if (is_extcharge) then
-      rewind(input)
-      call findBlock(input,2)
-      do
-         read(input,'(A80)',end=112,err=112) keywd
-         if (is_blank(keywd,1,80)) exit
-         nextatom = nextatom + 1
+    ! If reading from data file
+    if(quick_method%read_coord)then
+
+      open(unit=iDataFile,file=dataFileName,status='OLD',form='UNFORMATTED')
+      call rchk_int(iDataFile, "natom", natom, fail)
+      if (.not. allocated(self%iattype)) allocate(self%iattype(natom))
+      call rchk_iarray(iDataFile, "iattype", natom, 1, 1, self%iattype, fail)
+      close(iDataFile)
+
+      ! Reading external charges from data file is not yet implemented
+      nextatom = 0
+      self%nextatom = nextatom
+
+      iAtomType = 0
+
+      do i = 1, natom
+        if (.not.(any(self%atom_type_sym(1:iAtomType).eq.symbol(self%iattype(i))))) then
+          iAtomType=iAtomType+1
+          self%atom_type_sym(iAtomType) = symbol(self%iattype(i))
+        endif
       enddo
-   endif
-
-   ! read external grid part
-   if (is_extgrid) then
-      rewind(input)
-      call findBlock(input,2)
+
+      self%iAtomType = iAtomType
+
+    ! Reading from input file
+    else
+      call findBlock(input,1)
+
+      ! first is to read atom and atom kind
+      iAtomType = 1
+      natom = 0
+      nextatom = 0
+      nextpoint = 0
       do
-         read(input,'(A80)',end=112,err=112) keywd
-         if (is_blank(keywd,1,80)) exit
-         nextpoint = nextpoint + 1
+        read(input,'(A80)',end=111,err=111) keywd
+        i=1;j=80
+        call upcase(keywd,80)
+        call rdword(keywd,i,j)
+        if (is_blank(keywd,1,80)) exit
+        do k=0,92
+          if (keywd(i:j) == symbol(k)) then
+            natom=natom+1
+            ! check if atom type has been shown before
+            if (.not.(any(self%atom_type_sym(1:iatomtype).eq.symbol(k)))) then
+              !write(*,*) "Assigning value to atom_type_sym:", k, symbol(k)
+              self%atom_type_sym(iAtomType)=symbol(k)
+              iAtomType=iAtomType+1
+            endif
+          endif
+        enddo
       enddo
-   endif
+      111     continue
 
-!    112     continue
+      ! read external charge part
+      if (is_extcharge)  then
+        rewind(input)
+        call findBlock(input,2)
+        do
+          read(input,'(A80)',end=112,err=112) keywd
+          if (is_blank(keywd,1,80)) exit
+          nextatom=nextatom+1
+        enddo
+      endif
 
-!    iAtomType=iAtomType-1
-!    self%iAtomType = iAtomType
-!    self%nextatom = nextatom
-!  endif
-   112     continue
+      ! read external grid part
+      if (is_extgrid) then
+         rewind(input)
+         call findBlock(input,2)
+         do
+            read(input,'(A80)',end=112,err=112) keywd
+            if (is_blank(keywd,1,80)) exit
+            nextpoint = nextpoint + 1
+         enddo
+      endif
 
-   iAtomType = iAtomType - 1
-   self%iAtomType = iAtomType
-   self%nextatom = nextatom
+      112     continue
 
-   ! Check if the external grid part was processed
-   if (is_extgrid) then
+      iAtomType=iAtomType-1
+      self%iAtomType = iAtomType
+      self%nextatom = nextatom
       self%nextpoint = nextpoint
-   endif
- endif
+    endif
+  endif
 
   end subroutine read_quick_molspec
 
@@ -477,7 +494,7 @@ subroutine read_quick_molspec_2(self,input,ierr)
       integer i,j,k,istart,ifinal
       integer ierror
       double precision temp
-      character(len=200) keywd
+      character(len=300) keywd
 
 
       rewind(input)
@@ -537,7 +554,7 @@ subroutine read_quick_molespec_extcharges(self,input,ierr)
         integer i,j,k,istart,ifinal
         integer nextatom,ierror
         double precision temp
-        character(len=200) keywd
+        character(len=300) keywd
 
         rewind(input)
         call findBlock(input,2)

src/modules/quick_sad_guess_module.f90

@@ -83,6 +83,7 @@ subroutine getmolsad(ierr)
      quick_method%ZMAT=.false.
      quick_method%divcon=.false.
      quick_method%nodirect=.false.
+
      call allocate_mol_sad(quick_molspec%iatomtype)