3.0.2 maintenance (#393)

.github/workflows/build.yml

@@ -29,7 +29,7 @@ jobs:
         build: [cmake]
         build-type: [debug]
         compiler: [gnu]
-        version: [11,12]
+        version: [11,12,14]
 
         include:
         - os: ubuntu-latest
@@ -48,11 +48,17 @@ jobs:
           build: cmake
           build-type: debugoptimized
           compiler: gnu
+          version: 14
+
+        - os: ubuntu-latest
+          build: cmake
+          build-type: static
+          compiler: gnu
           version: 12
 
         - os: ubuntu-latest
           build: meson
-          build-type: debugoptimized
+          build-type: static
           compiler: intel
           version: 2023.1.0
 
@@ -155,12 +161,6 @@ jobs:
         --prefix=$PWD/_dist
         --libdir=lib
         --warnlevel=0
-#        ${{ env.MESON_ARGS }}
-#      env:
-#        COVERAGE: ${{ matrix.build-type == 'coverage' }}
-#        MESON_ARGS: >-
-#          ${{ matrix.compiler == 'intel' && '-Dfortran_link_args=-qopenmp -Dapi=false' || '' }}
-#          ${{ contains(matrix.os, 'macos') && '-Dlapack=openblas' || '' }}
 
     - name: Configure build (CMake, debug)
       if: ${{ matrix.build == 'cmake'  && matrix.build-type == 'debug' }}
@@ -179,6 +179,16 @@ jobs:
         -DCMAKE_BUILD_TYPE=RelWithDebInfo
         -DCMAKE_INSTALL_PREFIX=$PWD/_dist
         -DCMAKE_INSTALL_LIBDIR=lib
+
+    - name: Configure build (CMake, static)
+      if: ${{ matrix.build == 'cmake' && matrix.build-type == 'static' }}
+      run: >-
+        cmake -B${{ env.BUILD_DIR }}
+        -GNinja
+        -DCMAKE_BUILD_TYPE=RelWithDebInfo
+        -DCMAKE_INSTALL_PREFIX=$PWD/_dist
+        -DCMAKE_INSTALL_LIBDIR=lib
+        -DWITH_TESTS=OFF
         -DSTATICBUILD=ON
 
     - name: Build project
@@ -198,7 +208,7 @@ jobs:
         echo "CREST_PREFIX=$PWD/_dist" >> $GITHUB_ENV
 
     - name: Create package
-      if: ${{ matrix.build-type == 'debugoptimized' }}
+      if: ${{ matrix.build-type == 'static' }}
       run: |
         mkdir crest
         cp COPYING crest/LICENSE
@@ -211,7 +221,7 @@ jobs:
         OUTPUT: crest-${{ matrix.compiler }}-${{ matrix.version }}-${{ matrix.os }}.tar
 
     - name: Upload package
-      if: ${{ matrix.build-type == 'debugoptimized' }}
+      if: ${{ matrix.build-type == 'static' }}
       uses: actions/upload-artifact@v4
       with:
         name: ${{ env.CREST_OUTPUT }}

.gitmodules

@@ -21,3 +21,6 @@
 	path = subprojects/tblite
 	url = https://github.com/pprcht/tblite.git
     branch = xtb_solvation
+[submodule "subprojects/pvol"]
+	path = subprojects/pvol
+	url = https://github.com/neudecker-group/libpvol.git

CMakeLists.txt

@@ -102,10 +102,10 @@ if(NOT TARGET "gfn0::gfn0" AND WITH_GFN0)
    add_compile_definitions(WITH_GFN0)
 endif()
 
-# XHCFF
-if(NOT TARGET "xhcff::xhcff" AND WITH_XHCFF)
-   find_package("xhcff" REQUIRED)
-   add_compile_definitions(WITH_XHCFF)
+# libpvol
+if(NOT TARGET "pvol::pvol" AND WITH_LIBPVOL)
+   find_package("libpvol" REQUIRED)
+   add_compile_definitions(WITH_LIBPVOL)
 endif()
 
 # lwONIOM
@@ -150,7 +150,7 @@ if(WITH_OBJECT AND NOT STATICBUILD)
       $<$<BOOL:${WITH_TBLITE}>:tblite::tblite>
       $<$<BOOL:${WITH_GFN0}>:gfn0::gfn0>
       $<$<BOOL:${WITH_GFNFF}>:gfnff::gfnff>
-      $<$<BOOL:${WITH_XHCFF}>:xhcff::xhcff>
+      $<$<BOOL:${WITH_LIBPVOL}>:pvol::pvol>
       $<$<BOOL:${WITH_TOMLF}>:toml-f::toml-f>
       $<$<BOOL:${WITH_LWONIOM}>:lwoniom::lwoniom>
       $<$<BOOL:${WITH_OpenMP}>:OpenMP::OpenMP_Fortran>
@@ -201,7 +201,7 @@ target_link_libraries(
    $<$<BOOL:${WITH_TBLITE}>:tblite::tblite>
    $<$<BOOL:${WITH_GFN0}>:gfn0::gfn0>
    $<$<BOOL:${WITH_GFNFF}>:gfnff::gfnff>
-   $<$<BOOL:${WITH_XHCFF}>:xhcff::xhcff>
+   $<$<BOOL:${WITH_LIBPVOL}>:pvol::pvol>
    $<$<BOOL:${WITH_TOMLF}>:toml-f::toml-f>
    $<$<BOOL:${WITH_LWONIOM}>:lwoniom::lwoniom>
    $<$<BOOL:${STATICBUILD}>:-static>
@@ -246,7 +246,7 @@ if (WITH_OBJECT AND NOT STATICBUILD)
       $<$<BOOL:${WITH_TBLITE}>:tblite::tblite>
       $<$<BOOL:${WITH_GFN0}>:gfn0::gfn0>
       $<$<BOOL:${WITH_GFNFF}>:gfnff::gfnff>
-      $<$<BOOL:${WITH_XHCFF}>:xhcff::xhcff>
+      $<$<BOOL:${WITH_LIBPVOL}>:pvol::pvol>
       $<$<BOOL:${WITH_TOMLF}>:toml-f::toml-f>
       $<$<BOOL:${WITH_LWONIOM}>:lwoniom::lwoniom>
    )

assets/template/metadata.f90

@@ -9,5 +9,5 @@
 character(len=*),parameter :: gfn0var = "@gfn0var@"
 character(len=*),parameter :: gfnffvar = "@gfnffvar@"
 character(len=*),parameter :: tblitevar = "@tblitevar@"
-character(len=*),parameter :: xhcffvar = "@xhcffvar@"
+character(len=*),parameter :: libpvolvar = "@libpvolvar@"
 character(len=*),parameter :: lwoniomvar = "@lwoniomvar@"

config/CMakeLists.txt

@@ -34,11 +34,12 @@ option(WITH_TBLITE  "Enable support for tblite"   TRUE)
 option(WITH_TOMLF   "Enable support for toml-f"   TRUE)
 option(WITH_GFN0    "Enable support for GFN0-xTB" TRUE)
 option(WITH_GFNFF   "Enable support for GFN-FF"   TRUE)
-option(WITH_XHCFF   "Enable support for XHCFF"    FALSE)
+option(WITH_LIBPVOL "Enable support for LIBPVOL"  FALSE)
 option(WITH_LWONIOM "Enable support for lwONIOM"  TRUE)
 option(WITH_TESTS   "Enable unit tests"           TRUE)
 
-option(STATICBUILD  "Attempt to link everything statically" FALSE) # doesn't work yet
+option(STATICBUILD  "Attempt to link everything statically" FALSE) 
+set(PYTHON_BINDINGS OFF CACHE BOOL "Disable python bindings for submodules that have them" FORCE)
 
 #########################################################################################
 #########################################################################################
@@ -100,7 +101,7 @@ set(tomlfvar "${WITH_TOMLF}")
 set(gfn0var "${WITH_GFN0}")
 set(gfnffvar "${WITH_GFNFF}")
 set(tblitevar "${WITH_TBLITE}")
-set(xhcffvar "${WITH_XHCFF}")
+set(libpvolvar "${WITH_LIBPVOL}")
 set(lwoniomvar "${WITH_LWONIOM}")
 
 configure_file(

config/meson.build

@@ -239,15 +239,15 @@ if get_option('WITH_GFNFF')
 endif
 
 
-# XHCFF
-if get_option('WITH_XHCFF')
- add_project_arguments('-DWITH_XHCFF', language: 'fortran')
- xhcff_dep = dependency(
-   'xhcff',
-   fallback: ['xhcff', 'xhcfflib_dep'],
+# LIBPVOL
+if get_option('WITH_LIBPVOL')
+ add_project_arguments('-DWITH_LIBPVOL', language: 'fortran')
+ libpvol_dep = dependency(
+   'libpvol',
+   fallback: ['libpvol', 'libpvollib_dep'],
    default_options: ['default_library=static'],
  )
- exe_deps += xhcff_dep
+ exe_deps += libpvol_dep
 endif
 
 
@@ -292,7 +292,7 @@ config = configuration_data({
   'gfn0var': get_option('WITH_GFN0'),
   'gfnffvar': get_option('WITH_GFNFF'), 
   'tblitevar': get_option('WITH_TBLITE'),
-  'xhcffvar': get_option('WITH_XHCFF'),
+  'libpvolvar': get_option('WITH_LIBPVOL'),
   'lwoniomvar': get_option('WITH_LWONIOM'),
 })
 

config/modules/Findxhcff.cmake → config/modules/Findlibpvol.cmake

@@ -14,9 +14,9 @@
 # You should have received a copy of the GNU Lesser General Public License
 # along with crest.  If not, see <https://www.gnu.org/licenses/>.
 
-set(_lib "xhcff")
-set(_pkg "XHCFF")
-set(_url "https://github.com/zellerf/xhcff-lib")
+set(_lib "pvol")
+set(_pkg "PVOL")
+set(_url "https://github.com/neudecker-group/libpvol.git")
 
 if(NOT DEFINED "${_pkg}_FIND_METHOD")
   set("${_pkg}_FIND_METHOD" "subproject" "cmake" "fetch" "pkgconf" )
@@ -27,10 +27,10 @@ include("${CMAKE_CURRENT_LIST_DIR}/crest-utils.cmake")
 crest_find_package("${_lib}" "${${_pkg}_FIND_METHOD}" "${_url}")
 
 set(found FALSE)
-if(TARGET "xhcff::xhcff")
+if(TARGET "pvol::pvol")
   set (found TRUE)
 endif()
-message(STATUS "Found xhcff: ${found}")
+message(STATUS "Found libpvol: ${found}")
 
 unset(_lib)
 unset(_pkg)

meson_options.txt

@@ -60,10 +60,10 @@ option(
   description: 'build with toml-f integration',
 )
 option(
-  'WITH_XHCFF',
+  'WITH_LIBPVOL',
   type: 'boolean',
   value: false,
-  description: 'build with XHCFF integration',
+  description: 'build with libpvol integration',
 )
 
 option(

src/algos/crossing.f90

@@ -33,7 +33,7 @@ subroutine crest_crossing(env,maxgen,fname,maxpairs)
   implicit none
   !> INPUT
   type(systemdata),intent(inout) :: env
-  integer,intent(in)             :: maxgen
+  integer,intent(inout)          :: maxgen
   character(len=*),intent(in),optional   :: fname
   real(wp),intent(in),optional :: maxpairs
   !> LOCAL
@@ -69,6 +69,7 @@ subroutine crest_crossing(env,maxgen,fname,maxpairs)
   call rdensemble(ensnam,nat,nall,at,xyz,eread)
   if (nall .lt. 2) then
     write (stdout,*) 'Not enough structures to perform GC!'
+    maxgen=0
     return
   end if
 

src/algos/search_conformers.f90

@@ -615,6 +615,7 @@ subroutine crest_newcross3(env)
     call touch(trim(tmppath)) 
     call crest_crossing(env,imax,trim(refnam),env%gcmaxparent)
     if (imax .lt. 1) then
+      call remove(trim(tmppath))
       return
       exit
     end if

src/calculator/CMakeLists.txt

@@ -31,7 +31,7 @@ list(APPEND srcs
   "${dir}/api_helpers.F90"
   "${dir}/api_engrad.f90"
   "${dir}/gradreader.f90"
-  "${dir}/xhcff.F90"
+  "${dir}/libpvol.F90"
   "${dir}/subprocess_types.f90"
   "${dir}/xtb_sc.f90"
   "${dir}/orca_sc.f90"

src/calculator/api_engrad.f90

@@ -33,7 +33,7 @@ module api_engrad
   use tblite_api
   use gfn0_api
   use gfnff_api
-  use xhcff_api
+  use libpvol_api
   use lj
   implicit none
 !>--- private module variables and parameters
@@ -42,7 +42,7 @@ module api_engrad
   public :: tblite_engrad
   public :: gfn0_engrad,gfn0occ_engrad
   public :: gfnff_engrad
-  public :: xhcff_engrad
+  public :: libpvol_engrad
   public :: lj_engrad !> RE-EXPORT
 
 !=========================================================================================!
@@ -76,7 +76,7 @@ subroutine tblite_engrad(mol,calc,energy,grad,iostatus)
     call tblite_init(calc,loadnew)
 !>--- tblite printout handling
     call api_handle_output(calc,'tblite.out',mol,pr)
-    if (pr) then
+    if (pr .or. calc%prstdout) then
       !> tblite uses its context (ctx) type, rather than calc%prch
       calc%tblite%ctx%unit = calc%prch
       calc%tblite%ctx%verbosity = 1
@@ -105,7 +105,8 @@ subroutine tblite_engrad(mol,calc,energy,grad,iostatus)
     call tblite_singlepoint(mol,calc%chrg,calc%uhf,calc%tblite, &
     &                       energy,grad,iostatus)
     if (iostatus /= 0) return
-    call api_print_e_grd(pr,calc%prch,mol,energy,grad)
+    if(.not.calc%prstdout) &
+    & call api_print_e_grd(pr,calc%prch,mol,energy,grad)
 
 !>--- postprocessing, getting other data
     !$omp critical
@@ -160,7 +161,8 @@ subroutine gfn0_engrad(mol,calc,g0calc,energy,grad,iostatus)
     if (iostatus /= 0) return
     if (pr) then
       call gfn0_print(calc%prch,g0calc,res)
-      call api_print_e_grd(pr,calc%prch,mol,energy,grad)
+      if(.not.calc%prstdout) &
+      & call api_print_e_grd(pr,calc%prch,mol,energy,grad)
     end if
 
 !>--- postprocessing, getting other data
@@ -215,7 +217,8 @@ subroutine gfn0occ_engrad(mol,calc,g0calc,energy,grad,iostatus)
     if (iostatus /= 0) return
     if (pr) then
       call gfn0_print(calc%prch,g0calc,res)
-      call api_print_e_grd(pr,calc%prch,mol,energy,grad)
+      if(.not.calc%prstdout) &
+      & call api_print_e_grd(pr,calc%prch,mol,energy,grad)
     end if
 
 !>--- postprocessing, getting other data
@@ -267,7 +270,8 @@ subroutine gfnff_engrad(mol,calc,energy,grad,iostatus)
 !>--- printout
     if (pr) then
       call gfnff_printout(calc%prch,calc%ff_dat)
-      call api_print_e_grd(pr,calc%prch,mol,energy,grad)
+      if(.not.calc%prstdout) & 
+      & call api_print_e_grd(pr,calc%prch,mol,energy,grad)
     end if
 
 !>--- postprocessing, getting other data
@@ -280,7 +284,7 @@ end subroutine gfnff_engrad
 
 !========================================================================================!
 
-  subroutine xhcff_engrad(mol,calc,energy,grad,iostatus)
+  subroutine libpvol_engrad(mol,calc,energy,grad,iostatus)
 !***************************************************************
 !* Interface singlepoint call between CREST and XHC force field
 !***************************************************************
@@ -300,33 +304,34 @@ subroutine xhcff_engrad(mol,calc,energy,grad,iostatus)
     pr = .false.
 !>--- setup system call information
     !$omp critical
-    call xhcff_initcheck(calc,loadnew)
+    call libpvol_initcheck(calc,loadnew)
 !>--- printout handling
-    call api_handle_output(calc,'xhcff.out',mol,pr)
+    call api_handle_output(calc,'libpvol.out',mol,pr)
 !>--- populate parameters
     if (loadnew) then
-      !> call xhcff with verbosity turned off
-      call xhcff_setup(mol,calc%xhcff,calc%extpressure,calc%ngrid,calc%proberad, &
-      &                calc%vdwset,pr,calc%prch,iostatus)
+      !> call libpvol with verbosity turned off
+      call libpvol_setup(mol,calc%libpvol,calc%extpressure,calc%pvmodel, &
+      &        calc%ngrid,calc%proberad,calc%vdwset,calc%pvradscal,pr,calc%prch,iostatus)
     end if
     !$omp end critical
     if (iostatus /= 0) return
 
 !>--- do the engrad call
     call initsignal()
-    call xhcff_sp(mol,calc%xhcff,energy,grad,iostatus)
+    call libpvol_sp(mol,calc%libpvol,energy,grad,iostatus)
     if (iostatus /= 0) return
 
 !>--- printout
     if (pr) then
-      !> the xhcff_sp call includes the printout within xhcff-lib
-      call api_print_e_grd(pr,calc%prch,mol,energy,grad)
+      !> the libpvol_sp call includes the printout within libpvol-lib
+      if(.not.calc%prstdout) &
+      & call api_print_e_grd(pr,calc%prch,mol,energy,grad)
     end if
 
 !>--- postprocessing, getting other data
 
     return
-  end subroutine xhcff_engrad
+  end subroutine libpvol_engrad
 
 !========================================================================================!
 !========================================================================================!