Coordinates can now be read from data file

If the coordinates are being read from data file,
the input file does not need to have coordinates.
The facility to read external charges is not yet
implemented.

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

@@ -41,6 +41,9 @@ program quick
 
     implicit none
 
+
+    integer :: fail
+
 #if defined CUDA || defined HIP
     integer :: gpu_device_id = -1
 #endif
@@ -262,6 +265,16 @@ 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

@@ -184,11 +184,13 @@ 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
@@ -83,7 +85,7 @@ module quick_method_module
         integer :: iSG = 1             ! =0. SG0, =1. SG1(DEFAULT)
 
         ! Initial guess part
-        logical :: SAD = .true.        ! SAD initial guess(defualt
+        logical :: SAD = .true.        ! SAD initial guess(default)
         logical :: MFCC = .false.      ! MFCC
 
         ! this part is about ECP
@@ -236,7 +238,9 @@ 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%PDB,1,mpi_logical,0,MPI_COMM_WORLD,mpierror)
             call MPI_BCAST(self%SAD,1,mpi_logical,0,MPI_COMM_WORLD,mpierror)
@@ -410,8 +414,10 @@ 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")')
 
@@ -633,7 +639,11 @@ 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,'FORCE').ne.0)      self%grad=.true.
 
@@ -655,6 +665,9 @@ 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
@@ -844,7 +857,9 @@ 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%PDB = .false.         ! PDB input
             self%SAD = .true.          ! SAD initial guess

src/modules/quick_molspec_module.f90

@@ -287,21 +287,27 @@ 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
     integer :: ierror
     integer :: iAtomType
     integer :: nextatom
     double precision :: temp,rdnml
-    character(len=200) :: keywd
+    character(len=300) :: keywd
+    character(len=300) :: tempstring
     logical :: is_extcharge = .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
@@ -310,12 +316,19 @@ 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')
@@ -330,50 +343,75 @@ subroutine read_quick_molspec(self,input,isTemplate, hasKeywd, apiKeywd,ierr)
 
   if( .not. isTemplate) then
 
-    call findBlock(input,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
 
-    ! first is to read atom and atom kind
-    iAtomType = 1
-    natom = 0
-    nextatom = 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
+      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
+
+      self%iAtomType = iAtomType
+
+    ! Reading from input file
+    else
+      call findBlock(input,1)
 
-       do k=0,92
+      ! first is to read atom and atom kind
+      iAtomType = 1
+      natom = 0
+      nextatom = 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
+            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
+        enddo
+      enddo
+      111     continue
 
-    ! read external charge part
-    if (is_extcharge)  then
-       rewind(input)
-       call findBlock(input,2)
-       do
+      ! 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
+        enddo
+      endif
 
-    112     continue
+      112     continue
 
-    iAtomType=iAtomType-1
-    self%iAtomType = iAtomType
-    self%nextatom = nextatom
+      iAtomType=iAtomType-1
+      self%iAtomType = iAtomType
+      self%nextatom = nextatom
+    endif
   endif
 
   end subroutine read_quick_molspec
@@ -394,7 +432,7 @@ 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)
@@ -451,7 +489,7 @@ 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)
 
 

src/modules/quick_scf_module.f90

@@ -183,7 +183,7 @@ subroutine electdiis(jscf,ierr)
 
      implicit none
 
-     logical :: fail
+     integer :: fail
 
      ! variable inputed to return
      integer :: jscf                ! scf iteration

src/modules/quick_uscf_module.f90

@@ -148,7 +148,7 @@ subroutine uelectdiis(jscf,ierr)
 
      implicit none
 
-     logical :: fail
+     integer :: fail
 
      ! variable inputed to return
      integer :: jscf                ! scf interation