Merge pull request #134 from openmopac/jjps-1022-updates

October updates from Jimmy Stewart & pre-patch cleanup

.github/workflows/CI.yaml

@@ -34,7 +34,7 @@ jobs:
           lscpu | grep "CPU(s):                  " | awk '{print $2}' > num_cores
           echo "NUM_CORES=$(cat num_cores)" >> $GITHUB_ENV
 
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: actions/setup-python@v4
         with:
@@ -84,7 +84,7 @@ jobs:
           lscpu | grep "CPU(s):                  " | awk '{print $2}' > num_cores
           echo "NUM_CORES=$(cat num_cores)" >> $GITHUB_ENV
 
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: actions/setup-python@v4
         with:
@@ -97,7 +97,7 @@ jobs:
 
       - name: Cache Intel dependencies
         id: cache-intel
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: /opt/intel
           key: cache-${{ env.IFORT_LINUX_URL }}-${{ env.MKL_LINUX_URL }}
@@ -111,7 +111,7 @@ jobs:
           sudo sh mkl_download.sh -a --silent --eula accept
 
       - name: Clone glibc compatibility library
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           repository: wheybags/glibc_version_header
           path: glibc
@@ -149,23 +149,24 @@ jobs:
           name: linux-test-output
           path: build/tests
 
-      - name: Local installation test
-        run: |
-          cd build
-          sudo make install
-
       - name: Package MOPAC with CPack
         run: |
           source /opt/intel/oneapi/setvars.sh
           cd build
           cpack -G IFW
           ls -l
 
+      - name: Local installation test & minimal packaging
+        run: |
+          cd build
+          sudo make install
+          sudo cpack -G TGZ
+
       - name: Save executable as an artifact
         uses: actions/upload-artifact@v2
         with:
           name: linux-dist
-          path: build/mopac-*-linux.run
+          path: build/mopac-*-linux.*
 
   mac-build:
     runs-on: macos-latest
@@ -177,7 +178,7 @@ jobs:
           system_profiler SPHardwareDataType | grep "Total Number of Cores" | awk '{print $5}' > num_cores
           echo "NUM_CORES=$(cat num_cores)" >> $GITHUB_ENV
 
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: actions/setup-python@v4
         with:
@@ -195,7 +196,7 @@ jobs:
 
       - name: Cache Intel Fortran compiler
         id: cache-intel
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: /opt/intel
           key: cache-${{ env.IFORT_MAC_URL }}-${{ env.MKL_MAC_URL }}
@@ -281,7 +282,7 @@ jobs:
           WMIC CPU Get NumberOfLogicalProcessors | head -2 | tail -1 > num_cores
           echo "NUM_CORES=$(cat num_cores)" >> $GITHUB_ENV
 
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: actions/setup-python@v4
         with:
@@ -294,7 +295,7 @@ jobs:
 
       - name: Cache Intel Fortran compiler
         id: cache-intel
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: C:\Program Files (x86)\Intel
           key: cache-${{ env.IFORT_WINDOWS_URL }}-${{ env.MKL_WINDOWS_URL }}

CITATION.cff

@@ -2,9 +2,9 @@ cff-version: 1.2.0
 message: "If you use this software for a scientific publication, please cite it as below."
 title: MOPAC
 type: software
-version: 22.0.4
+version: 22.0.5
 doi: 10.5281/zenodo.6511958
-date-released: 2022-07-08
+date-released: 2022-11-07
 authors:
   - family-names: Stewart
     given-names: "James J. P."

CMakeLists.txt

@@ -274,6 +274,7 @@ elseif(WIN32)
 elseif(UNIX)
   set(CPACK_SYSTEM_NAME "linux")
 endif()
+set(CPACK_PROJECT_CONFIG_FILE "${CMAKE_SOURCE_DIR}/cmake/CPackOptions.cmake")
 
 # Package the Intel OpenMP library for the QT installer (hard-coded for each OS)
 if(CMAKE_Fortran_COMPILER_ID STREQUAL "Intel")
@@ -291,7 +292,7 @@ if(CMAKE_Fortran_COMPILER_ID STREQUAL "Intel")
     # resolve symbolic links
     get_filename_component(INTEL_OMP_LIB_PATH ${INTEL_OMP_LIB} REALPATH)
     message(STATUS "OMP packaging: ${INTEL_OMP_LIB} -> ${INTEL_OMP_LIB_PATH}")
-    install(FILES ${INTEL_OMP_LIB_PATH} DESTINATION ${CMAKE_INSTALL_LIBDIR} COMPONENT qtifw EXCLUDE_FROM_ALL)
+    install(FILES ${INTEL_OMP_LIB_PATH} DESTINATION ${CMAKE_INSTALL_LIBDIR} COMPONENT redist EXCLUDE_FROM_ALL)
   endif()
 endif()
 
@@ -307,6 +308,9 @@ else()
   set(CPACK_IFW_TARGET_DIRECTORY "/opt/mopac")
 endif()
 install(FILES "${CMAKE_SOURCE_DIR}/.github/mopac.ico" DESTINATION "." COMPONENT qtifw EXCLUDE_FROM_ALL)
+install(FILES "${CMAKE_SOURCE_DIR}/CITATION.cff"
+              "${CMAKE_SOURCE_DIR}/COPYING"
+              "${CMAKE_SOURCE_DIR}/COPYING.lesser" DESTINATION "." COMPONENT redist EXCLUDE_FROM_ALL)
 
 # Install the executables and library
 install(TARGETS mopac RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} COMPONENT main)
@@ -322,7 +326,7 @@ else()
   install(TARGETS mopac-core LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} COMPONENT main)
 endif()
 
-# Add packaging
+# Add IFW packaging
 include(CPack)
 include(CPackIFW)
 cpack_ifw_configure_component(main DISPLAY_NAME "main program" SORTING_PRIORITY 2 FORCED_INSTALLATION
@@ -332,3 +336,4 @@ cpack_ifw_configure_component(main DISPLAY_NAME "main program" SORTING_PRIORITY
   USER_INTERFACES "${CMAKE_SOURCE_DIR}/.github/pathcheckboxform.ui" "${CMAKE_SOURCE_DIR}/.github/filecheckboxform.ui" "${CMAKE_SOURCE_DIR}/.github/iconcheckboxform.ui")
 cpack_ifw_configure_component(extra DISPLAY_NAME "extra utilities" SORTING_PRIORITY 1 DEFAULT FALSE)
 cpack_ifw_configure_component(qtifw VIRTUAL FORCED_INSTALLATION)
+cpack_ifw_configure_component(redist VIRTUAL FORCED_INSTALLATION)

cmake/CPackOptions.cmake

@@ -0,0 +1,6 @@
+set(CPACK_ARCHIVE_COMPONENT_INSTALL ON)
+
+if("${CPACK_GENERATOR}" MATCHES "TGZ")
+   set(CPACK_COMPONENTS_ALL_IN_ONE_PACKAGE ON)
+   set(CPACK_COMPONENTS_ALL main extra redist)
+endif()

src/corrections/gdisp.F90

@@ -20,8 +20,8 @@ subroutine gdisp(r0ab, rs6, alp6, c6ab, s6, s8, mxc, r2r4, rcov, rs8, alp8, dxyz
 ! based on material provided by Stefan Grimme, University of Muenster, Germany
 ! v3.1 of the DFTD3 library
 !
-  use common_arrays_C, only: nat, Vab
-  use molkst_C, only : numat
+  use common_arrays_C, only: nat, cell_ijk, Vab
+  use molkst_C, only : numat, l123, l1u, l2u, l3u
   implicit none
   double precision, parameter :: k1 = 16.d0
   integer, parameter :: max_elem = 94, maxc = 5 ! maximum coordination number references per element
@@ -36,7 +36,7 @@ subroutine gdisp(r0ab, rs6, alp6, c6ab, s6, s8, mxc, r2r4, rcov, rs8, alp8, dxyz
 !
 !  Local variables
 !
-  integer :: i, j, linij
+  integer :: i, j, linij, iii, jjj, i_cell, j_cell, kkkk
   double precision :: R0, r2, damp6, damp8, c6, tmp1, tmp2, r, dc6_rest, rij(3), dc6iji, dc6ijj, r6, r7, t6, t8, &
   rcovij, expterm, dcn,x1, r42, r8, r9
   double precision, allocatable :: drij(:), dc6i(:)
@@ -107,8 +107,13 @@ subroutine gdisp(r0ab, rs6, alp6, c6ab, s6, s8, mxc, r2r4, rcov, rs8, alp8, dxyz
         dcn = 0.d0
       end if
       x1 = drij(linij) + dcn*(dc6i(i) + dc6i(j))
-      dxyz_temp(:,i) = dxyz_temp(:,i) + x1*rij/r
-      dxyz_temp(:,j) = dxyz_temp(:,j) - x1*rij/r
+      iii = l123*(i - 1)
+      jjj = l123*(j - 1)
+      kkkk = (l3u - cell_ijk(3)) + (2*l3u + 1)*(l2u - cell_ijk(2) + (2*l2u + 1)*(l1u - cell_ijk(1))) + 1
+      i_cell = iii + kkkk 
+      j_cell = jjj + kkkk       
+      dxyz_temp(:,i_cell) = dxyz_temp(:,i_cell) + x1*rij/r
+      dxyz_temp(:,j_cell) = dxyz_temp(:,j_cell) - x1*rij/r
     end do
   end do
   return

src/input/wrtkey.F90

@@ -35,7 +35,7 @@ subroutine wrtkey
 !
 !  Do not tidy up allkey earlier in the job, instead fill allkey here from keywrd,
 !  and do all the tidying up at this one point.  The old style of tidying up allkey
-!  as the job progressed was very error-prone and hadr to debug.
+!  as the job progressed was very error-prone and hard to debug.
 !
   allkey = trim(keywrd)
   j = 1
@@ -59,6 +59,9 @@ subroutine wrtkey
       do
         i = index(allkey, "(")
         if (i == 0) exit
+        if (i > 6) then
+          if (allkey(i-6:i) == "OUTPUT(") exit
+        end if
         j = index(allkey(i + 1:), ')') + i
         allkey(i:j) = " "
       end do
@@ -1462,17 +1465,15 @@ subroutine wrtcon (allkey)
    write (iw,'(" *  STEP1      - FIRST STEP-SIZE IN GRID =", f7.2)') &
    reada (keywrd, Index (keywrd, "STEP1")+6)
    if (index(keywrd, " POINT1") == 0) then
-     write (iw,'("*",/," *             - **** KEYWORD POINT1 MISSING ****",/,"*")')
-     call mopend("KEYWORD POINT1 MISSING")
+    call l_control("POINT1=11", len_trim("POINT1=11"), 1)
    end if
    i = 2
  end if
  if (myword(allkey, " STEP2"))  then
    write (iw,'(" *  STEP2      - SECOND STEP-SIZE IN GRID =", f7.2)') &
    reada (keywrd, Index (keywrd, "STEP2")+6)
    if (index(keywrd, " POINT2") == 0) then
-     write (iw,'("*",/," *             - **** KEYWORD POINT2 MISSING ****",/,"*")')
-     call mopend("KEYWORD POINT2 MISSING")
+    call l_control("POINT2=11", len_trim("POINT2=11"), 1)
    end if
  end if
  if (myword(allkey, " STEP="))  then

src/reactions/big_swap.F90

@@ -870,7 +870,7 @@ subroutine l_control(txt, nt, mode)
     end do
     store = " "
     if (mode == 1) then
-      i = index(keywrd, store(:mt + 2))
+      i = index(keywrd, store(:mt + 50))
       keywrd = keywrd(:i)//line(:mt)//trim(keywrd(i + mt + 1:))
     end if
     if (local_txt == " ") exit

src/reactions/grid.F90

@@ -21,8 +21,10 @@ subroutine grid
       use chanel_C, only : iw0, iw, iarc, ires, iump, archive_fn, ump_fn, &
       restart_fn
 !
-      use common_arrays_C, only : geo, xparam, geoa, &
+      use common_arrays_C, only : geo, xparam, geoa, labels, coord, &
       na, nb, nc, pa, pb, p
+!      
+      use elemts_C, only : elemnt
 !
       use molkst_C, only : nvar, keywrd, tleft, line, norbs, &
       natoms, moperr, uhf, numat, mpack, gui
@@ -359,6 +361,16 @@ subroutine grid
           write (iw, "(/'       FIRST VARIABLE   ',  'SECOND VARIABLE FUNCTION')")
           write (iw, "(' :',F16.5,F16.5,F16.6)") geo(lpara1, latom1)*c1, geo(lpara2, latom2)*c2, escf
           call geout (iw)
+          if (index(keywrd, " PRTXYZ") /= 0) then
+            write (iw, '(29X,''CARTESIAN COORDINATES '',/)')
+            call gmetry(geo, coord)
+            l = 0 
+            do i = 1, natoms 
+              if (labels(i) == 99 .or. labels(i) == 107) cycle
+              l = l + 1
+              write (iw, '(I4,3X,A2,3x, 3F16.9)') l, elemnt(labels(i)), (coord(k,l),k=1,3) 
+            end do
+          end if
           if (gui) then
             if (use_p) then
               ij = 0

src/reactions/pathk.F90

@@ -202,6 +202,15 @@ subroutine pathk()
         end if
         call to_screen("To_file: Reaction path")
         call geout (iw)
+        if (index(keywrd, " PRTXYZ") /= 0) then
+          write (iw, '(29X,''CARTESIAN COORDINATES '',/)')
+          l = 0 
+          do i = 1, natoms
+            if (labels(i) == 99 .or. labels(i) == 107) cycle
+            l = l + 1
+            write (iw, '(I4,3X,A2,3x, 3F16.9)') l, elemnt(labels(i)), (coord(k,l),k=1,3)
+          end do
+        end if
         if (index(keywrd, " PDBOUT") /= 0) then
           imodel = imodel + 1
           write(line,'(F13.5)') escf

src/run_mopac.F90

@@ -1028,7 +1028,7 @@ subroutine run_mopac
       write (iw, '(3/,'' TOTAL JOB TIME: '',F16.2,'' SECONDS'')') tim
       write (iw, '(/,'' == MOPAC DONE =='')')
       call fdate (line)
-      write(0,'(//10x,a,/)')"MOPAC Job: """//trim(job_fn)//""" ended normally on "// &
+      write(*,'(//10x,a,/)')"MOPAC Job: """//trim(job_fn)//""" ended normally on "// &
       line(5:10)//", "//trim(line(21:))//", at"//line(11:16)//"."
 !
 !  Delete files that are definitely not wanted

tests/CMakeLists.txt

@@ -62,3 +62,5 @@ set_tests_properties(salt PROPERTIES DEPENDS ionize) # uses Neutral.mop
 add_mopac_test(salt2 "SALT_2.mop")
 add_mopac_test(residues "SITE_Individual_residues.mop")
 set_tests_properties(residues PROPERTIES DEPENDS ionize) # uses IONIZE.arc
+add_mopac_test(erratic-1 "erratic1.mop")
+add_mopac_test(erratic-2 "erratic2.mop")

tests/erratic1.mop

@@ -0,0 +1,34 @@
+EF PM7 PRECISE T=48H ENPART DISP
+Crashed at "Geometry optimization using EF" on a Linux machine
+
+C  -2.40330 1 -2.80250 1  0.06670 1
+C  -1.97490 1 -1.37110 1  0.25670 1
+O  -2.32280 1 -0.70200 1  1.25220 1
+O  -1.16670 1 -0.71900 1 -0.67070 1
+C  -0.75930 1  0.63730 1 -0.49020 1
+C  -1.36230 1  1.43290 1 -1.60520 1
+C  -1.10870 1  2.86320 1 -1.61960 1
+O  -0.48520 1  3.45080 1 -0.72520 1
+O  -1.59210 1  3.60080 1 -2.69170 1
+C   0.72090 1  0.77160 1 -0.47290 1
+N   1.39920 1  0.03370 1  0.56020 1
+C   1.62120 1 -1.32420 1  0.09310 1
+C   2.73740 1  0.62590 1  0.71830 1
+C   0.77940 1  0.05150 1  1.84150 1
+H  -2.79340 1 -2.88280 1 -0.95970 1
+H  -1.58970 1 -3.48610 1  0.29570 1
+H  -3.24050 1 -2.97730 1  0.78380 1
+H  -1.18460 1  0.98460 1  0.46390 1
+H  -1.13850 1  0.96550 1 -2.61500 1
+H  -2.48330 1  1.28380 1 -1.48680 1
+H   1.14260 1  0.42590 1 -1.45970 1
+H   1.00880 1  1.82810 1 -0.38450 1
+H   1.39810 1 -2.05510 1  0.87880 1
+H   1.01070 1 -1.53930 1 -0.82450 1
+H   2.67980 1 -1.49590 1 -0.23160 1
+H   3.42440 1 -0.14000 1  1.10820 1
+H   3.08560 1  1.07720 1 -0.24810 1
+H   2.62480 1  1.42070 1  1.47130 1
+H   0.10570 1  0.89260 1  2.03730 1
+H   0.30170 1 -0.95410 1  2.00550 1
+H   1.56480 1  0.10310 1  2.65230 1