erosional baselevel, periodicity, masks, stratigraphy

.github/PULL_REQUEST_TEMPLATE.md

@@ -4,14 +4,14 @@ Pull Request Checklist. Please read and check each box with an X. Delete any par
 
 ### Before your first pull request:
 
-* [ ] I have read the guidelines in our [CONTRIBUTING.md](../blob/master/CONTRIBUTING.md) document.
+* [ ] I have read the guidelines in our [CONTRIBUTING.md](../blob/main/CONTRIBUTING.md) document.
 
 ### For all pull requests:
 
-* [ ] I have followed the [instructions for indenting my code](../blob/master/CONTRIBUTING.md#making-aspect-better).
+* [ ] I have followed the [instructions for indenting my code](../blob/main/CONTRIBUTING.md#making-aspect-better).
 
 ### For new features/models or changes of existing features:
 
 * [ ] I have tested my new feature locally to ensure it is correct.
-* [ ] I have [created a testcase](http://www.math.clemson.edu/~heister/manual.pdf#sec%3Awriting_tests) for the new feature/benchmark in the [tests/](../blob/master/tests/) directory.
-* [ ] I have added a changelog entry in the [doc/modules/changes](../blob/master/doc/modules/changes) directory that will inform other users of my change.
+* [ ] I have [created a testcase](http://www.math.clemson.edu/~heister/manual.pdf#sec%3Awriting_tests) for the new feature/benchmark in the [tests/](../blob/main/tests/) directory.
+* [ ] I have added a changelog entry in the [doc/modules/changes](../blob/main/doc/modules/changes) directory that will inform other users of my change.

.github/workflows/linux.yml

@@ -17,7 +17,7 @@ jobs:
     - name: setup
       run: |
         sudo apt-get install -y software-properties-common
-        sudo add-apt-repository ppa:ginggs/deal.ii-9.3.0-backports
+        sudo add-apt-repository ppa:ginggs/deal.ii-9.3.2-backports
         sudo apt-get update
         sudo apt-get install -yq --no-install-recommends libdeal.ii-dev
     - name: compile
@@ -38,7 +38,7 @@ jobs:
     - name: setup
       run: |
         sudo apt-get install -y software-properties-common
-        sudo add-apt-repository ppa:ginggs/deal.ii-9.3.0-backports
+        sudo add-apt-repository ppa:ginggs/deal.ii-9.3.2-backports
         sudo apt-get update
         sudo apt-get install -yq --no-install-recommends texlive-plain-generic texlive-base texlive-latex-recommended texlive-latex-base texlive-fonts-recommended texlive-bibtex-extra lmodern texlive-latex-extra texlive-science graphviz python3-pip python-setuptools libdeal.ii-dev doxygen
         doxygen --version
@@ -94,13 +94,15 @@ jobs:
         -D ASPECT_UNITY_BUILD=ON \
         ..
         ninja
+        cat detailed.log
+        ./aspect -v
         ./aspect --test
 
   tests:
     #linux build including tests
     name: tests
     runs-on: [ubuntu-latest]
-    container: geodynamics/aspect-tester:focal-dealii-9.3-v1
+    container: geodynamics/aspect-tester:focal-dealii-9.3-v2
 
     steps:
     - uses: actions/checkout@v2

.gitignore

@@ -13,6 +13,7 @@
 /CTestTestfile.cmake
 /Makefile
 /aspect
+/benchmarks/**/*.prm.out
 /benchmarks/**/CMakeCache.txt
 /benchmarks/**/CMakeFiles/
 /benchmarks/**/Makefile

CMakeLists.txt

@@ -77,7 +77,7 @@ LIST(APPEND CMAKE_MODULE_PATH
   )
 
 FIND_PACKAGE(deal.II 9.3.0 QUIET
-  HINTS ${deal.II_DIR} ${DEAL_II_DIR} ../ ../../ $ENV{DEAL_II_DIR}
+  HINTS ${deal.II_DIR} ${DEAL_II_DIR} $ENV{DEAL_II_DIR}
   )
 IF(NOT ${deal.II_FOUND})
   MESSAGE(FATAL_ERROR "\n*** Could not find a suitably recent version of deal.II. ***\n"
@@ -287,11 +287,13 @@ IF(EXISTS ${CMAKE_SOURCE_DIR}/unit_tests/CMakeLists.txt)
   ADD_DEPENDENCIES(test run_unit_tests)
 ENDIF()
 
-IF(EXISTS ${CMAKE_SOURCE_DIR}/tests/CMakeLists.txt
-  AND ${ASPECT_NEED_TEST_CONFIGURE})
-
+IF(EXISTS ${CMAKE_SOURCE_DIR}/tests/CMakeLists.txt)
   # Hook up the tests:
   FILE(APPEND ${CMAKE_BINARY_DIR}/CTestTestfile.cmake "SUBDIRS(tests)\n")
+ENDIF()
+
+IF(EXISTS ${CMAKE_SOURCE_DIR}/tests/CMakeLists.txt
+  AND ${ASPECT_NEED_TEST_CONFIGURE})
 
   FILE(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/tests)
 
@@ -477,16 +479,45 @@ IF(NOT ASPECT_ADDITIONAL_CXX_FLAGS STREQUAL "")
   MESSAGE(STATUS "  DEAL_II_CXX_FLAGS_RELEASE: ${DEAL_II_CXX_FLAGS_RELEASE}")
 ENDIF()
 
+# Check if a fastscape library is available, if so link it with aspect.
+# If the library is not found, then remove fastscape .cc and .h from list
+# so aspect can still compile.
+# TODO: likely need to switch ENV and normal positions so it checks ENV second.
+FIND_LIBRARY(FASTSCAPE NAMES fastscapelib_fortran PATHS $ENV{FASTSCAPE_DIR} ${FASTSCAPE_DIR} PATH_SUFFIXES lib NO_DEFAULT_PATH)
+IF(FASTSCAPE)
+  MESSAGE(STATUS "FastScape found at ${FASTSCAPE}")
+ELSE()
+  FIND_FILE(FASTSCAPE_SRC fastscape.cc HINTS "${CMAKE_SOURCE_DIR}/source/mesh_deformation")
+  LIST(REMOVE_ITEM TARGET_SRC ${FASTSCAPE_SRC})
+  MESSAGE(STATUS "FastScape library not found")
+ENDIF()
+
 ADD_EXECUTABLE(${TARGET} ${TARGET_SRC})
 DEAL_II_SETUP_TARGET(${TARGET})
 
+# Library needs to be linked after executable is added, but if fastscape isn't found
+# then the .cc files need to be removed before.
+# TODO: find a way to do this where they don't have to be separated.
+IF(FASTSCAPE)
+  TARGET_LINK_LIBRARIES(${TARGET} ${FASTSCAPE})
+ENDIF()
+
 # deal.II does not define NDEBUG, but the world builder relies on it to disable
 # its asserts in release mode. Set it manually for anything but debug mode.
 # Note: If deal.II decides in the future to define this, this can be removed.
 IF (NOT CMAKE_BUILD_TYPE MATCHES Debug)
     ADD_DEFINITIONS("-DNDEBUG")
 ENDIF()
 
+# find zlib if it is installed in a non-standard location
+SET(ZLIB_DIR "" CACHE PATH "An optional hint to a ZLIB installation")
+IF("${ZLIB_DIR}" STREQUAL "")
+  SET(ZLIB_DIR "$ENV{ZLIB_DIR}" CACHE PATH "An optional hint to a ZLIB installation" FORCE)
+ENDIF()
+FIND_PACKAGE(ZLIB)
+INCLUDE_DIRECTORIES(${ZLIB_INCLUDE_DIR})
+TARGET_LINK_LIBRARIES(${TARGET} ${ZLIB_LIBRARY})
+
 FIND_PACKAGE(PerpleX QUIET
   HINTS ./contrib/perplex/install/ ../ ../../ ${PERPLEX_DIR} $ENV{PERPLEX_DIR})
 IF(${PerpleX_FOUND})

Folder_output.f90

@@ -0,0 +1,17 @@
+subroutine Folder_output (k, istep, foldername)
+
+
+    use FastScapeContext
+    implicit none
+
+    integer, intent(in) :: k, istep
+    character(len=k), intent(in) :: foldername
+
+
+    ffoldername = foldername
+    kk = k
+    iistep = istep
+
+
+    return
+  end subroutine Folder_output

Jenkinsfile.cig

@@ -32,7 +32,7 @@ pipeline {
     stage ("Check Permissions") {
       when {
         allOf {
-          not {branch 'master'}
+          changeRequest()
           not {changeRequest authorEmail: "rene.gassmoeller@mailbox.org"}
           not {changeRequest authorEmail: "timo.heister@gmail.com"}
           not {changeRequest authorEmail: "bangerth@colostate.edu"}

Named_VTK.f90

@@ -0,0 +1,122 @@
+subroutine Fastscape_Named_VTK (f, vex, istep, foldername, k)
+
+    ! subroutine to create a simple VTK file for plotting inside of aspect folder.
+    ! To use, add this file into the fastscape src directory, and then add
+    ! the line ${FASTSCAPELIB_SRC_DIR}/Named_VTK.f90 to the appropriate place
+    ! in cmakelists.txt
+
+    use FastScapeContext
+    implicit none
+
+    integer, intent(in) :: k, istep !,atime
+    double precision, intent(in) :: vex
+    double precision, intent(in), dimension(*) :: f
+    character(len=k), intent(in) :: foldername
+    character*7 cstep
+
+    integer nheader,nfooter,npart1,npart2, ftime
+    character header*1024,footer*1024,part1*1024,part2*1024,nxc*6,nyc*6,nnc*12
+    integer i,j
+    character*10 fwtime
+    double precision dx,dy
+
+
+    dx = xl/(nx - 1)
+    dy = yl/(ny - 1)
+
+    ! Finding the fastscape time incremented by dt. dt may be a double
+    ! that is converted to an integer, but we don't care about then
+    ! exact time that much.
+    ! ftime = (atime + step*dt)
+
+    !Writing the fastscape time to a string, up to 1 billion years. (add another zero if needed eventually)
+   ! write (fwtime,'(i10)') ftime
+   ! if (ftime.lt.10) fwtime(1:9)='000000000'
+   ! if (ftime.lt.100) fwtime(1:8)='00000000'
+   ! if (ftime.lt.1000) fwtime(1:7)='0000000'
+   ! if (ftime.lt.10000) fwtime(1:6)='000000'
+   ! if (ftime.lt.100000) fwtime(1:5)='00000'
+   ! if (ftime.lt.1000000) fwtime(1:4)='0000'
+   ! if (ftime.lt.10000000) fwtime(1:3)='000'
+   ! if (ftime.lt.100000000) fwtime(1:2)='00'
+   ! if (ftime.lt.1000000000) fwtime(1:1)='0'
+
+    write (cstep,'(i7)') istep
+    if (istep.lt.10) cstep(1:6)='000000'
+    if (istep.lt.100) cstep(1:5)='00000'
+    if (istep.lt.1000) cstep(1:4)='0000'
+    if (istep.lt.10000) cstep(1:3)='000'
+    if (istep.lt.100000) cstep(1:2)='00'
+    if (istep.lt.1000000) cstep(1:1)='0'
+
+
+
+!Use the output folder of aspect and create a vtk folder inside of it.
+!#ifdef ON_WINDOWS
+!    call system ('if not exist "'//trim(foldername)//'/VTK" mkdir '//trim(foldername)//'/VTK')
+!#else
+call system ('mkdir -p '//trim(foldername)//'/VTK')
+!call system ('pwd')
+!#endif
+
+    write (nxc,'(i6)') nx
+    write (nyc,'(i6)') ny
+    write (nnc,'(i12)') nn
+
+    header(1:1024)=''
+    header='# vtk DataFile Version 3.0'//char(10)//'FastScape'//char(10) &
+    //'BINARY'//char(10)//'DATASET STRUCTURED_GRID'//char(10) &
+    //'DIMENSIONS '//nxc//' '//nyc//' 1'//char(10)//'POINTS' &
+    //nnc//' float'//char(10)
+    nheader=len_trim(header)
+    footer(1:1024)=''
+    footer='POINT_DATA'//nnc//char(10)
+    nfooter=len_trim(footer)
+    part1(1:1024)=''
+    part1='SCALARS '
+    npart1=len_trim(part1)+1
+    part2(1:1024)=''
+    part2=' float 1'//char(10)//'LOOKUP_TABLE default'//char(10)
+    npart2=len_trim(part2)
+
+    open(unit=77,file=(foldername//'/VTK/Topography'//cstep//'.vtk'),status='unknown', &
+    form='unformatted',access='direct', recl=nheader+3*4*nn+nfooter+(npart1+10+npart2+4*nn) &
+    +(npart1+5+npart2+4*nn)+(npart1+8+npart2+4*nn)+(npart1+12+npart2+4*nn)+(npart1+13+npart2+4*nn) &
+    +(npart1+13+npart2+4*nn)+(npart1+9+npart2+4*nn),convert='big_endian')
+    write (77,rec=1) &
+    header(1:nheader), &
+    ((sngl(dx*(i-1)),sngl(dy*(j-1)),sngl(h(i+(j-1)*nx)*abs(vex)),i=1,nx),j=1,ny), &
+    footer(1:nfooter), &
+    part1(1:npart1)//'topography'//part2(1:npart2),sngl(h(1:nn)), &
+    part1(1:npart1)//'HHHHH'//part2(1:npart2),sngl(f(1:nn)), &
+    part1(1:npart1)//'basement'//part2(1:npart2),sngl(b(1:nn)), &
+    part1(1:npart1)//'erosion_rate'//part2(1:npart2),sngl(erate(1:nn)), &
+    part1(1:npart1)//'total_erosion'//part2(1:npart2),sngl(etot(1:nn)), &
+    part1(1:npart1)//'drainage_area'//part2(1:npart2),sngl(a(1:nn)) , &
+    part1(1:npart1)//'catchment'//part2(1:npart2),sngl(catch(1:nn))
+    close(77)
+
+    if (vex.lt.0.d0) then
+      open(unit=77,file=(foldername//'/VTK/Basement'//cstep//'.vtk'),status='unknown',form='unformatted',access='direct', &
+      recl=nheader+3*4*nn+nfooter+(npart1+1+npart2+4*nn) &
+      +(npart1+5+npart2+4*nn),convert='big_endian')
+      write (77,rec=1) &
+      header(1:nheader), &
+      ((sngl(dx*(i-1)),sngl(dy*(j-1)),sngl(b(i+(j-1)*nx)*abs(vex)),i=1,nx),j=1,ny), &
+      footer(1:nfooter), &
+      part1(1:npart1)//'B'//part2(1:npart2),sngl(b(1:nn)), &
+      part1(1:npart1)//'HHHHH'//part2(1:npart2),sngl(f(1:nn))
+      close(77)
+      open(unit=77,file=(foldername//'/VTK/SeaLevel'//cstep//'.vtk'),status='unknown',form='unformatted',access='direct', &
+      recl=nheader+3*4*nn+nfooter+(npart1+2+npart2+4*nn),convert='big_endian')
+      write (77,rec=1) &
+      header(1:nheader), &
+      ((sngl(dx*(i-1)),sngl(dy*(j-1)),sngl(sealevel*abs(vex)),i=1,nx),j=1,ny), &
+      footer(1:nfooter), &
+      part1(1:npart1)//'SL'//part2(1:npart2),(sngl(sealevel),i=1,nn)
+      close(77)
+    endif
+
+
+    return
+  end subroutine Fastscape_Named_VTK

README.md

@@ -1,6 +1,6 @@
 ASPECT - Advanced Solver for Problems in Earth's ConvecTion
 ===========================================================
-[![License GPL2+:](https://img.shields.io/badge/License-GPL%202%2B-red)](https://github.com/geodynamics/aspect/blob/master/LICENSE)
+[![License GPL2+:](https://img.shields.io/badge/License-GPL%202%2B-red)](https://github.com/geodynamics/aspect/blob/main/LICENSE)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5131909.svg)](https://doi.org/10.5281/zenodo.5131909)
 [![pdf manual](https://img.shields.io/badge/get-PDF-green.svg)](https://doi.org/10.6084/m9.figshare.4865333)