merge with master restart capabilities

.github/workflows/build_test_serial.yml

@@ -16,14 +16,15 @@ jobs:
       - name: 'Install Dependencies for Serial Version'
         run: |
           sudo apt-get update
-          sudo apt-get -y install gfortran
+          sudo apt-get -y install gfortran parallel
       - name: 'Configure Serial Version'
         run: ./configure --serial --enablef --prefix $PWD/install gnu
       - name: 'Build and Install Serial Version Using 2 Jobs'
         run: make -j2 all install
       - name: 'Setup Environment Variables for Running Tests'
         run: |
           echo "QUICK_HOME=$PWD/install" >> "$GITHUB_ENV"
+          echo "PARALLEL_TEST_COUNT=2" >> "$GITHUB_ENV"
       - name: 'Run Tests for Serial Version (Make)'
         run: make fulltest
       - name: 'Archive Test Results for Serial Version'
@@ -45,7 +46,7 @@ jobs:
       - name: 'Install Dependencies for Serial Version (CMake)'
         run: |
           sudo apt-get update
-          sudo apt-get -y install gfortran cmake
+          sudo apt-get -y install gfortran cmake parallel
       - name: 'Configure Serial Version (CMake)'
         run: |
           mkdir build
@@ -59,6 +60,7 @@ jobs:
       - name: 'Setup Environment Variables for Running Tests'
         run: |
           echo "QUICK_HOME=$PWD/install" >> "$GITHUB_ENV"
+          echo "PARALLEL_TEST_COUNT=2" >> "$GITHUB_ENV"
       - name: 'Run Tests for Serial Version'
         run: |
           cd install

configure

@@ -19,7 +19,7 @@
 #  !---------------------------------------------------------------------!
 #  ! Set version                                                         !
 #  !---------------------------------------------------------------------!
-QUICK_VERSION='QUICK-22.03'
+QUICK_VERSION='QUICK-24.03'
 QUICK_HOME=`pwd`
 cdate=`date +'%m/%d/%Y'`
 ctime=`date +'%r'`

src/modules/quick_files_module.f90

@@ -148,6 +148,28 @@ subroutine set_quick_files(api,ierr)
 
     end subroutine
 
+    subroutine read_data_file(line)
+      use quick_exception_module
+      use quick_input_parser_module  
+
+      implicit none
+
+      character line*(*)
+
+      call read(line,'$DATA',datafilename)
+
+    end subroutine
+
+    subroutine print_data_file(io)
+        implicit none
+
+        ! pass-in Parameter
+        integer io
+
+        write (io,'("| DATA FILE  =    ",a)') trim(dataFileName)
+
+    end subroutine
+
     subroutine read_basis_file(keywd,ierr)
 
         use quick_exception_module
@@ -292,7 +314,6 @@ subroutine print_quick_io_file(io,ierr)
 
         write (io,'("| INPUT FILE :    ",a)') trim(inFileName)
         write (io,'("| OUTPUT FILE:    ",a)') trim(outFileName)
-        write (io,'("| DATA FILE  :    ",a)') trim(dataFileName)
         write (io,'("| BASIS SET PATH: ",a)') trim(basisdir)
 
         return

src/modules/quick_method_module.f90

@@ -44,8 +44,8 @@ module quick_method_module
         logical :: debug =  .false.    ! debug mode
         logical :: nodirect = .false.  ! conventional scf
         logical :: readDMX =  .false.  ! flag to read density matrix
-        logical :: readPMat = .false.  ! flag to read density matrix
-        logical :: writePMat = .false. ! flag to write density matrix
+        logical :: readden = .false.  ! flag to read density matrix
+        logical :: writeden = .false. ! flag to write density matrix
         logical :: readSAD = .true.    ! flag to read SAD guess
         logical :: writeSAD = .false.  ! flag to write SAD guess
         logical :: diisSCF =  .false.  ! DIIS SCF
@@ -247,8 +247,8 @@ subroutine broadcast_quick_method(self, ierr)
             call MPI_BCAST(self%calcDensLap,1,mpi_logical,0,MPI_COMM_WORLD,mpierror)
             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%readPMat,1,mpi_logical,0,MPI_COMM_WORLD,mpierror)
-            call MPI_BCAST(self%writePMat,1,mpi_logical,0,MPI_COMM_WORLD,mpierror)
+            call MPI_BCAST(self%readden,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%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 +424,8 @@ 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%readPMat) write(io,'(" READ DENSITY MATRIX From DATAFILE")')
-            if (self%writePMat) write(io,'(" WRITE DENSITY MATRIX TO FILE")')
+            if (self%readden) write(io,'(" READ DENSITY MATRIX From DATAFILE")')
+            if (self%writeden) write(io,'(" WRITE DENSITY MATRIX TO FILE")')
             if (self%readSAD)   write(io,'(" READ SAD GUESS FROM FILE")')
             if (self%writeSAD)   write(io,'(" WRITE SAD GUESS TO FILE")')
 
@@ -526,24 +526,12 @@ subroutine read_quick_method(self,keywd,ierr)
             use quick_exception_module
             use quick_mpi_module
             use quick_files_module, only : write_molden
-            use quick_files_module, only : dataFileName
             implicit none
             character(len=300) :: keyWD
             character(len=300) :: tempstring
             integer :: itemp,i,j
             type (quick_method_type) self
             integer, intent(inout) :: ierr
-            logical :: found
-
-            tempstring = keyWD
-            call upcase(tempstring,300)
-            if (index(tempstring,'READPMAT').ne.0)then
-                self%readPMat=.true.
-                call read(tempstring, 'READPMAT', i, j, .false., found)
-                if(found)then
-                  dataFileName = keyWD(i:i+j-2)
-                endif
-            endif
 
             call upcase(keyWD,300)
             if (index(keyWD,'PDB').ne. 0)       self%PDB=.true.
@@ -668,8 +656,7 @@ 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%writePMat=.true.
+            if (index(keyWD,'WRITE').ne.0)      self%writeden=.true.
             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.
@@ -690,6 +677,9 @@ subroutine read_quick_method(self,keywd,ierr)
                 endif
             endif
 
+            !Read density matrix
+            if (index(keyWD,'READDEN').ne.0) self%readden=.true.
+
             if (self%DFT) then
                 if (index(keyWD,'SG0').ne.0) then
                     self%iSG=0
@@ -908,8 +898,8 @@ subroutine init_quick_method(self,ierr)
             self%hasF = .false.            ! If f orbitial is contained
             self%calcDens = .false.    ! calculate density
             self%calcDensLap = .false. ! calculate density lap
-            self%readPMat = .false.    ! Input density matrix
-            self%writePMat = .false.   ! Output density matrix
+            self%readden = .false.    ! Input density matrix
+            self%writeden = .false.   ! Output density matrix
             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_scf_module.f90

@@ -182,9 +182,9 @@ subroutine electdiis(jscf,ierr)
 #endif
 
      implicit none
-
-     logical fail
-
+ 
+     logical :: fail
+ 
      ! variable inputed to return
      integer :: jscf                ! scf iteration
      integer, intent(inout) :: ierr
@@ -269,17 +269,16 @@ subroutine electdiis(jscf,ierr)
      if (bMPI) call MPI_setup_hfoperator
      !-------------- END MPI / ALL NODE -----------
 #endif
-
-   if(quick_method%readPMat)then
-     nbasis = quick_molspec%nbasis
-     if(master)then
-       open(unit=iDataFile,file=dataFileName,status='OLD',form='UNFORMATTED')
-       call rchk_int(iDataFile, "nbasis", nbasis, fail)
-       call rchk_darray(iDataFile, "dense", nbasis, nbasis, 1, quick_qm_struct%dense, fail)
-       close(iDataFile)
-     endif
-   endif
-
+        if(quick_method%readden)then
+          nbasis = quick_molspec%nbasis
+          if(master)then
+            open(unit=iDataFile,file=dataFileName,status='OLD',form='UNFORMATTED')
+            call rchk_int(iDataFile, "nbasis", nbasis, fail)
+            call rchk_darray(iDataFile, "dense", nbasis, nbasis, 1, quick_qm_struct%dense, fail)
+            close(iDataFile)
+          endif
+        endif
+
 #ifdef MPIV
      if (bMPI) then
   !      call MPI_BCAST(quick_qm_struct%o,nbasis*nbasis,mpi_double_precision,0,MPI_COMM_WORLD,mpierror)
@@ -726,17 +725,15 @@ subroutine electdiis(jscf,ierr)
         !--------------- END MPI/ALL NODES -------------------------------------
 
         if (master) then
- 
-          if(quick_method%writepmat)then
+
+           if(quick_method%writeden)then 
              ! open data file then write calculated info to dat file
              call quick_open(iDataFile, dataFileName, 'R', 'U', 'A',.true.,ierr)
-!             rewind(iDataFile)
              call wchk_int(iDataFile, "nbasis", nbasis, fail)
              call wchk_darray(iDataFile, "dense",    nbasis, nbasis, 1, quick_qm_struct%dense,    fail)
-!             call wchk_darray(iDataFile, "denseSave",    nbasis, nbasis, 1, quick_qm_struct%denseSave,    fail)
              close(iDataFile)
-          endif
- 
+           endif 
+
 #ifdef USEDAT
            ! open data file then write calculated info to dat file
            SAFE_CALL(quick_open(iDataFile, dataFileName, 'R', 'U', 'R',.true.,ierr)

src/modules/quick_uscf_module.f90

@@ -151,7 +151,9 @@ subroutine uelectdiis(jscf,ierr)
 #endif
 
      implicit none
-
+
+     logical :: fail
+
      ! variable inputed to return
      integer :: jscf                ! scf iteration
      integer, intent(inout) :: ierr
@@ -235,6 +237,17 @@ subroutine uelectdiis(jscf,ierr)
      !-------------- END MPI / ALL NODE -----------
 #endif
 
+        if(quick_method%readden)then
+          nbasis = quick_molspec%nbasis
+          if(master)then
+            open(unit=iDataFile,file=dataFileName,status='OLD',form='UNFORMATTED')
+            call rchk_int(iDataFile, "nbasis", nbasis, fail)
+            call rchk_darray(iDataFile, "dense", nbasis, nbasis, 1, quick_qm_struct%dense, fail)
+            call rchk_darray(iDataFile, "denseb", nbasis, nbasis, 1, quick_qm_struct%denseb, fail)
+            close(iDataFile)
+          endif
+        endif
+
 #ifdef MPIV
      if (bMPI) then
         call MPI_BCAST(quick_qm_struct%dense,nbasis*nbasis,mpi_double_precision,0,MPI_COMM_WORLD,mpierror)
@@ -826,6 +839,15 @@ subroutine uelectdiis(jscf,ierr)
 
         if (master) then
 
+           if(quick_method%writeden)then 
+             ! open data file then write calculated info to dat file
+             call quick_open(iDataFile, dataFileName, 'R', 'U', 'A',.true.,ierr)
+             call wchk_int(iDataFile, "nbasis", nbasis, fail)
+             call wchk_darray(iDataFile, "dense",    nbasis, nbasis, 1, quick_qm_struct%dense,    fail)
+             call wchk_darray(iDataFile, "denseb",    nbasis, nbasis, 1, quick_qm_struct%denseb,    fail)
+             close(iDataFile)
+           endif 
+
 #ifdef USEDAT
            ! open data file then write calculated info to dat file
            SAFE_CALL(quick_open(iDataFile, dataFileName, 'R', 'U', 'R',.true.,ierr)

src/read_job_and_atom.f90

@@ -49,24 +49,33 @@ subroutine read_job_and_atom(ierr)
         do while(.true.)
           read (inFile,'(A100)') tempstring
           if(trim(tempstring).eq.'') exit
-          keyWD=trim(keyWD)//' '//trim(tempstring)
+          if(tempstring(1:1).eq.'$')then
+            call upcase(tempstring(2:2),4)
+            if (tempstring(2:5).eq.'DATA')then
+              ! read data file
+              SAFE_CALL(read_data_file(tempstring))
+            endif
+          else
+            keyWD=trim(keyWD)//' '//trim(tempstring)
+          endif
         end do
       endif
 
+      call upcase(keyWD,300)
+      write(iOutFile,'("  KEYWORD=",a)') trim(keyWD)
+
       ! These interfaces,"read","check" and "print" are from quick_method_module
       SAFE_CALL(read(quick_method,keyWD,ierr))     ! read method from Keyword
 
-      write(iOutFile,'("  KEYWORD=",a)') trim(keyWD)
-!      call upcase(keyWD,300)
-
       call read(quick_qm_struct,keyWD)  ! read qm struct from Keyword
       call check(quick_method,iOutFile,ierr) ! check the correctness
       call print(quick_method,iOutFile,ierr) ! then print method
 
       ! read basis file
       SAFE_CALL(read_basis_file(keywd,ierr))
       call print_basis_file(iOutFile)
-      if (quick_method%ecp) call print_ecp_file(iOutFile)
+      call print_data_file(iOutFile) 
+     if (quick_method%ecp) call print_ecp_file(iOutFile)
 
       ! If PDB flag is on, then call readPDB to read PDB file and 
       ! rewrite input file so that there will be no difference between

src/subs/io.f90

@@ -381,7 +381,7 @@ subroutine wchk_darray(chk,key,x,y,z,dim,fail)
 !   do
 !      read(chk,end=100,err=200)
 !   enddo
-!
+
 !   100  rewind(chk)
    write(chk) '#'//kline(1:40)
    write(chk) 'RR'