Merge branch 'release/0.2.1'

Author: szaghi

.travis.yml

@@ -1,7 +1,4 @@
-language: python
-
-python:
-  - 2.7
+language: generic
 
 sudo: false
 
@@ -17,38 +14,58 @@ addons:
     sources:
       - ubuntu-toolchain-r-test
     packages:
-      - gfortran-4.9
+      - gfortran-6
       - binutils
       - python-pip
-      - graphviz      
+      - graphviz
 
 env:
   global:
-    - SCRIPT="FoBiS.py rule -ex makecoverage"
+    - MAKECOVERAGE="FoBiS.py rule -ex makecoverage"
+    - MAKEDOC="./scripts/makedoc.sh Fortran-FOSS-Programmers/FOODIE"
+    - CLEAN="FoBiS.py rule -ex clean"
+    - MAKETAR="FoBiS.py rule -ex maketar"
 
 before_install:
-  - git submodule update --init --recursive
+  - git submodule update --init
 
 install:
   - |
     if [[ ! -d "$HOME/.local/bin" ]]; then
       mkdir "$HOME/.local/bin"
     fi
   - export PATH="$HOME/.local/bin:$PATH"
-  - export FC=/usr/bin/gfortran-4.9
-  - ln -fs /usr/bin/gfortran-4.9 "$HOME/.local/bin/gfortran" && gfortran --version
-  - ls -l /usr/bin/gfortran-4.9
-  - ln -fs /usr/bin/gcov-4.9 "$HOME/.local/bin/gcov" && gcov --version
-  - pip install --upgrade pygooglechart
-  - pip install --upgrade graphviz
-  - pip install --upgrade FoBiS.py
-  - pip install --upgrade markdown-checklist 
-  - pip install --upgrade ford
+  - export FC=/usr/bin/gfortran-6
+  - ln -fs /usr/bin/gfortran-6 "$HOME/.local/bin/gfortran" && gfortran --version
+  - ls -l /usr/bin/gfortran-6
+  - ln -fs /usr/bin/gcov-6 "$HOME/.local/bin/gcov" && gcov --version
+  - pip install --user --upgrade pygooglechart
+  - pip install --user --upgrade graphviz
+  - pip install --user --upgrade FoBiS.py
+  - pip install --user --upgrade markdown-checklist 
+  - pip install --user --upgrade ford
 
 script:
-  - $SCRIPT
+  - $MAKECOVERAGE
 
 after_success:
-  - cd $TRAVIS_BUILD_DIR
-  - cd build/lib/obj/ ; bash <(curl -s https://codecov.io/bash) ; cd -
-  - ./makedoc.sh Fortran-FOSS-Programmers/FOODiE
+  - find . -name '*.gcno' -print
+  - bash <(curl -s https://codecov.io/bash)
+  - $MAKEDOC
+
+before_deploy:
+  - $CLEAN
+  - $MAKETAR
+  - mv FOODIE.tar.gz FOODIE-$TRAVIS_TAG.tar.gz
+
+deploy:
+  provider: releases
+  api_key:
+    secure: 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
+  file: 
+    - FOODIE-$TRAVIS_TAG.tar.gz
+    - ./scripts/install.sh
+  skip_cleanup: true
+  overwrite: true
+  on:
+    tags: true

README.md

@@ -76,8 +76,12 @@ FOODIE is aimed to be a KISS-pure-Fortran library for integrating Ordinary Diffe
             + [x] unfiltered leapfrog, 2nd order accurate, mostly unstable, see [4];
             + [x] Robert-Asselin filtered leapfrog, 1st order accurate, see [4, 5, 6];
             + [x] Robert-Asselin-Williams filtered leapfrog, 3rd order accurate, see [5, 6];
+        + [x] [Linear Multistep Methods SSP](http://fortran-foss-programmers.github.io/FOODIE/module/foodie_integrator_lmm_ssp.html) schemes see [16]:
+            + [x] 3 steps, 2nd order accurate;
+            + [x] 4 steps, 3rd order accurate;
+            + [x] 5 steps, 3rd order accurate;
         + [ ] Runge-Kutta schemes:
-            + [ ] [low-storage](http://fortran-foss-programmers.github.io/FOODIE/module/foodie_integrator_low_storage_runge_kutta.html) schemes, see [1, 2, 3]:
+            + [ ] [low-storage](http://fortran-foss-programmers.github.io/FOODIE/module/foodie_integrator_runge_kutta_low_storage.html) schemes, see [1, 2, 3]:
                 + [x] 1 stage, namely the forward explicit Euler scheme, 1st order accurate;
                 + [ ] 2 stages;
                 + [ ] 3 stages;
@@ -88,13 +92,13 @@ FOODIE is aimed to be a KISS-pure-Fortran library for integrating Ordinary Diffe
                 + [x] 12 stages, 4th order accurate, 2N registers, see [10];
                 + [x] 13 stages, 4th order accurate, 2N registers, see [10];
                 + [x] 14 stages, 4th order accurate, 2N registers, see [10];
-            + [ ] [TVD/SSP](http://fortran-foss-programmers.github.io/FOODIE/module/foodie_integrator_tvd_runge_kutta.html) schemes, see [1]:
+            + [ ] [TVD/SSP](http://fortran-foss-programmers.github.io/FOODIE/module/foodie_integrator_kutta_tvd_runge.html) schemes, see [1]:
                 + [x] 1 stage, namely the forward explicit Euler scheme, 1st order accurate;
                 + [x] 2 stages, 2nd order accurate;
                 + [x] 3 stages, 3rd order accurate;
                 + [ ] 4 stages;
                 + [x] 5 stages, 4th order accurate;
-            + [ ] [embedded (adaptive)](http://fortran-foss-programmers.github.io/FOODIE/module/foodie_integrator_emd_runge_kutta.html) schemes:
+            + [ ] [embedded (adaptive)](http://fortran-foss-programmers.github.io/FOODIE/module/foodie_integrator_runge_kutta_embeddedd.html) schemes:
                 + [x] Heun-Euler, 2 stages, 2nd order accurate;
                 + [ ] Runge-Kutta-Fehlberg, 5 stages, 4th order accurate;
                 + [x] Runge-Kutta-Cash-Karp, 6 stages, 5th order accurate, see [13];
@@ -165,6 +169,8 @@ Any feature request is welcome.
 
 [15] *A tenth-order Runge-Kutta method with error estimate*, Feagin, T., Proceedings of the IAENG Conf. on Scientific Computing. 2007.
 
+[16] *Strong Stability Preserving Runge-Kutta and Multistep Time Discretizations*, S. Gottlieb, D. Ketcheson, C.W. Shu, 2011, 978-981-4289-26-9, doi:10.1142/7498, World Scientific Publishing Co. Pte. Ltd.
+
 Go to [Top](#top)
 
 ## Status [![Status](https://img.shields.io/badge/status-beta-orange.svg)]()

codecov.yml

@@ -0,0 +1,4 @@
+coverage:
+  ignore:
+    - src/third_party/
+    - doc

doc/README-FOODIE.md

@@ -1,11 +1,20 @@
+---
 project: FOODIE
-project_dir: ./src/
-output_dir: ./doc/html/publish/
+src_dir: ../src/lib
+src_dir: ../src/tests
+src_dir: ../src/third_party/PENF/src/lib
+src_dir: ../src/third_party/FACE/src/lib
+src_dir: ../src/third_party/FLAP/src/lib
+src_dir: ../src/third_party/WenOOF/src/lib
+
+output_dir: html/publish/
 project_github: https://github.com/Fortran-FOSS-Programmers/FOODIE
+project_download: https://github.com/Fortran-FOSS-Programmers/FOODIE/releases/latest
 summary: Fortran Object oriented Ordinary Differential Equations integration library
 author: Fortran-FOSS-Programmers Group
 github: http://fortran-foss-programmers.github.io/
 website: http://fortran-foss-programmers.github.io/
+email: stefano.zaghi@gmail.com
 md_extensions: markdown.extensions.toc(anchorlink=True)
                markdown.extensions.smarty(smart_quotes=False)
                markdown.extensions.extra
@@ -17,6 +26,10 @@ display: public
 source: true
 warn: true
 graph: true
+sort: alpha
+print_creation_date: true
+creation_date: %Y-%m-%d %H:%M %z
 extra_mods: iso_fortran_env:https://gcc.gnu.org/onlinedocs/gfortran/ISO_005fFORTRAN_005fENV.html
 
-{!README-FOODIE.md!}
+{!../README.md!}
+---

doc/README-IR_Precision.md

@@ -10,6 +10,7 @@ emd_rk=0
 euler=0
 lf=0
 lf_raw=0
+lmm_ssp=0
 ls_rk=0
 tvd_rk=0
 
@@ -19,25 +20,23 @@ function print_usage {
   echo "script automotion for FOODIE's errors analysis"
   echo "Usage: `basename $0` #solver"
   echo "Valid solver switches are:"
-  echo "  -ab     # => adams-bashforth"
-  echo "  -abm    # => adams-bashforth-moulton"
-  echo "  -am     # => adams-moulton"
-  echo "  -bdf    # => backward differentiation formula"
-  echo "  -emd-rk # => embeded RK"
-  echo "  -euler  # => euler"
-  echo "  -lf     # => leapfrog"
-  echo "  -lf-raw # => leapfrog raw filtered"
-  echo "  -ls-rk  # => low storage RK"
-  echo "  -tvd-rk # => TVD RK"
-  echo "  -all    # => all solvers!"
+  echo "  -ab      # => adams-bashforth"
+  echo "  -abm     # => adams-bashforth-moulton"
+  echo "  -am      # => adams-moulton"
+  echo "  -bdf     # => backward differentiation formula"
+  echo "  -emd-rk  # => embeded RK"
+  echo "  -euler   # => euler"
+  echo "  -lf      # => leapfrog"
+  echo "  -lf-raw  # => leapfrog raw filtered"
+  echo "  -lmm-ssp # => linear multistep methods SSP"
+  echo "  -ls-rk   # => low storage RK"
+  echo "  -tvd-rk  # => TVD RK"
+  echo "  -all     # => all solvers!"
 }
 
 #parsing command line
 while [ $# -gt 0 ]; do
   case "$1" in
-    # "-g")
-      # shift; FileGRD=$1
-      # ;;
     "-ab")
       ab=1
       ;;
@@ -62,6 +61,9 @@ while [ $# -gt 0 ]; do
     "-lf-raw")
       lf_raw=1
       ;;
+    "-lmm-ssp")
+      lmm_ssp=1
+      ;;
     "-ls-rk")
       ls_rk=1
       ;;
@@ -144,6 +146,9 @@ fi
 if [ $lf_raw -eq 1 ] ; then
   ../tests/oscillation -r -tf 1e6 --solver leapfrog-raw --ss 2 -Dt 5000.d0 2500.d0 1250.d0 625.d0 320.d0 100.d0 --errors_analysis #> analysis-leapfrog.log
 fi
+if [ $lmm_ssp -eq 1 ] ; then
+  ../tests/oscillation -r -tf 1e6 --solver lmm-ssp --ss 3 5 -Dt 5000.d0 2500.d0 1250.d0 625.d0 320.d0 100.d0 50.d0 10.d0 --errors_analysis > analysis-lmm-ssp.log
+fi
 if [ $ls_rk -eq 1 ] ; then
   ../tests/oscillation -r -tf 1e6 --solver ls-runge-kutta --ss 1 -Dt 5000.d0 2500.d0 1250.d0 625.d0 320.d0 100.d0 --errors_analysis #> analysis-leapfrog.log
   ../tests/oscillation -r -tf 1e6 --solver ls-runge-kutta --ss 5 7 -Dt 5000.d0 2500.d0 1250.d0 625.d0 320.d0 100.d0 --errors_analysis #> analysis-leapfrog.log

doc/main_page.md

@@ -71,6 +71,7 @@ module foodie
 use foodie_integrator_backward_differentiation_formula, only : integrator_back_df
 use foodie_integrator_euler_explicit, only : integrator_euler_explicit
 use foodie_integrator_leapfrog, only : integrator_leapfrog
+use foodie_integrator_lmm_ssp, only : integrator_lmm_ssp
 use foodie_integrator_runge_kutta_emd, only : integrator_runge_kutta_emd
 use foodie_integrator_runge_kutta_low_storage, only : integrator_runge_kutta_ls
 use foodie_integrator_runge_kutta_tvd, only : integrator_runge_kutta_tvd
@@ -85,6 +86,7 @@ module foodie
 public :: integrator_back_df
 public :: integrator_euler_explicit
 public :: integrator_leapfrog
+public :: integrator_lmm_ssp
 public :: integrator_runge_kutta_emd
 public :: integrator_runge_kutta_ls
 public :: foodie_integrator
@@ -162,6 +164,18 @@ function foodie_integrator(scheme, steps, stages, tolerance, nu, alpha) result(i
     type is(integrator_leapfrog)
       call integrator%init(nu=nu, alpha=alpha)
     endselect
+  case('lmm_ssp')
+    allocate(integrator_lmm_ssp :: integrator)
+    if (present(steps)) then
+      select type(integrator)
+      type is(integrator_lmm_ssp)
+        call integrator%init(steps=steps)
+      endselect
+    else
+      call integrator%trigger_error(error=ERROR_MISSING_STEPS_NUMBER,                                  &
+                                    error_message='missing steps number for initializing integrator!', &
+                                    is_severe=.true.)
+    endif
   case('runge_kutta_emd')
     allocate(integrator_runge_kutta_emd :: integrator)
     if (present(stages)) then

papers/announcement/errors_analysis/errors_analysis.sh

@@ -36,9 +36,9 @@ module foodie_integrator_adams_bashforth
 private
 public :: integrator_adams_bashforth
 
-character(len=99), parameter :: supported_steps='1-16'       !< List of supported steps number. Valid format is `1-2,4,9-23...`.
-integer(I_P),      parameter :: min_ss=1                     !< Minimum number of steps supported.
-integer(I_P),      parameter :: max_ss=16                    !< Maximum number of steps supported.
+character(len=99), parameter :: supported_steps='1-16' !< List of supported steps number. Valid format is `1-2,4,9-23...`.
+integer(I_P),      parameter :: min_ss=1               !< Minimum number of steps supported.
+integer(I_P),      parameter :: max_ss=16              !< Maximum number of steps supported.
 
 type, extends(integrator_object) :: integrator_adams_bashforth
   !< FOODIE integrator: provide an explicit class of Adams-Bashforth multi-step schemes, from 1st to 16th order accurate.
@@ -93,7 +93,7 @@ pure subroutine integr_assign_integr(lhs, rhs)
   ! public methods
   elemental subroutine destroy(self)
   !< Destroy the integrator.
-  class(integrator_adams_bashforth), intent(INOUT) :: self !< Integrator.
+  class(integrator_adams_bashforth), intent(inout) :: self !< Integrator.
 
   call self%destroy_abstract
   self%steps = 0