refactor: examples renaming to get rid of bad use of capital letters

yoctoyotta1024 · Sep 11, 2024 · d720d22 · d720d22
1 parent 41e47fb
commit d720d22
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diff --git a/examples/adiabaticparcel/as2017.py b/examples/adiabaticparcel/as2017.py
@@ -16,7 +16,7 @@
 https://opensource.org/licenses/BSD-3-Clause
 -----
 File Description:
-Script generate input files, runs CLEO adia0D executable to create data and
+Script generate input files, runs CLEO adia0d executable to create data and
 then creates plots for adiabatic parcel example similar to Figure 5 of "On
 the CCN (de)activation nonlinearities" S. Arabas and S. Shima 2017 to show
 example of adaibatic parcel expansion and contraction.
@@ -173,7 +173,7 @@ def displacement(time, w_avg, thalf):
 
         ### run model
         os.chdir(path2build)
-        executable = path2build + "/examples/adiabaticparcel/src/adia0D"
+        executable = path2build + "/examples/adiabaticparcel/src/adia0d"
         print("Executable: " + executable)
         print("Config file: " + configfile)
         os.system(executable + " " + configfile)

diff --git a/examples/adiabaticparcel/as2017.sh b/examples/adiabaticparcel/as2017.sh
@@ -19,9 +19,9 @@
 ### ---------------------------------------------------- ###
 buildtype="openmp"
 path2CLEO=${HOME}/CLEO/
-path2build=${HOME}/CLEO/build_adia0D/
+path2build=${HOME}/CLEO/build_adia0d/
 enableyac=false
-executables="adia0D"
+executables="adia0d"
 
 pythonscript=${path2CLEO}/examples/adiabaticparcel/as2017.py
 configfile=${path2CLEO}/examples/adiabaticparcel/src/config/as2017_config.yaml

diff --git a/examples/adiabaticparcel/cuspbifurc.py b/examples/adiabaticparcel/cuspbifurc.py
@@ -15,7 +15,7 @@
 Copyright (c) 2023 MPI-M, Clara Bayley
 -----
 File Description:
-Script generate input files, runs CLEO adia0D executable to
+Script generate input files, runs CLEO adia0d executable to
 create data and then creates plots for adiabatic parcel example
 similar to Figure 5 of "On the CCN (de)activation nonlinearities"
 S. Arabas and S. Shima 2017 to show example of cusp birfucation for
@@ -134,7 +134,7 @@ def displacement(time, w_avg, thalf):
 os.chdir(path2build)
 os.system("pwd")
 os.system("rm -rf " + dataset)  # delete any existing dataset
-executable = path2build + "/examples/adiabaticparcel/src/adia0D"
+executable = path2build + "/examples/adiabaticparcel/src/adia0d"
 print("Executable: " + executable)
 print("Config file: " + configfile)
 os.system(executable + " " + configfile)

diff --git a/examples/adiabaticparcel/cuspbifurc.sh b/examples/adiabaticparcel/cuspbifurc.sh
@@ -19,9 +19,9 @@
 ### ---------------------------------------------------- ###
 buildtype="serial"
 path2CLEO=${HOME}/CLEO/
-path2build=${HOME}/CLEO/build_adia0D/
+path2build=${HOME}/CLEO/build_adia0d/
 enableyac=false
-executables="adia0D"
+executables="adia0d"
 
 pythonscript=${path2CLEO}/examples/adiabaticparcel/cuspbifurc.py
 configfile=${path2CLEO}/examples/adiabaticparcel/src/config/cuspbifurc_config.yaml

diff --git a/examples/adiabaticparcel/src/CMakeLists.txt b/examples/adiabaticparcel/src/CMakeLists.txt
@@ -12,18 +12,18 @@ message("PROJECT_SOURCE_DIR: ${PROJECT_SOURCE_DIR}")
 set(CLEOLIBS gridboxes initialise observers runcleo superdrops zarr)
 
 # create primary executable for CVODE-CLEO coupled model adiabatic parcel setup
-add_executable(adia0D EXCLUDE_FROM_ALL "main_adia0D.cpp")
+add_executable(adia0d EXCLUDE_FROM_ALL "main_adia0d.cpp")
 
 # Add directories and link libraries to target
-target_link_libraries(adia0D PRIVATE coupldyn_cvode cartesiandomain "${CLEOLIBS}")
-target_link_libraries(adia0D PUBLIC Kokkos::kokkos)
-target_include_directories(adia0D PRIVATE "${CLEO_SOURCE_DIR}/libs") # CLEO libs directory
+target_link_libraries(adia0d PRIVATE coupldyn_cvode cartesiandomain "${CLEOLIBS}")
+target_link_libraries(adia0d PUBLIC Kokkos::kokkos)
+target_include_directories(adia0d PRIVATE "${CLEO_SOURCE_DIR}/libs") # CLEO libs directory
 
 # set specific C++ compiler options for target (optional)
-#target_compile_options(adia0D PRIVATE)
+#target_compile_options(adia0d PRIVATE)
 
 # set compiler properties for target(s)
-set_target_properties(adia0D PROPERTIES
+set_target_properties(adia0d PROPERTIES
   CMAKE_CXX_STANDARD_REQUIRED ON
   CMAKE_CXX_EXTENSIONS ON
   CXX_STANDARD 20)
diff --git a/examples/adiabaticparcel/src/config/as2017_config.yaml b/examples/adiabaticparcel/src/config/as2017_config.yaml
@@ -46,9 +46,9 @@ initsupers:
 
 ### Output Parameters ###
 outputdata:
-  setup_filename: /home/m/m300950/CLEO/build_adia0D//bin/as2017_setup.txt   # .txt filename to copy configuration to
-  stats_filename: /home/m/m300950/CLEO/build_adia0D//bin/as2017_stats.txt   # .txt file to output runtime statistics to
-  zarrbasedir: /home/m/m300950/CLEO/build_adia0D//bin/as2017_sol8.zarr      # zarr store base directory
+  setup_filename: /home/m/m300950/CLEO/build_adia0d//bin/as2017_setup.txt   # .txt filename to copy configuration to
+  stats_filename: /home/m/m300950/CLEO/build_adia0d//bin/as2017_stats.txt   # .txt file to output runtime statistics to
+  zarrbasedir: /home/m/m300950/CLEO/build_adia0d//bin/as2017_sol8.zarr      # zarr store base directory
   maxchunk: 2500000                                                         # maximum no. of elements in chunks of zarr store array
 
 ### Microphysics Parameters ###

diff --git a/examples/adiabaticparcel/src/main_adia0D.cpp → examples/adiabaticparcel/src/main_adia0d.cpp b/examples/adiabaticparcel/src/main_adia0D.cpp → examples/adiabaticparcel/src/main_adia0d.cpp
@@ -3,21 +3,21 @@
  *
  *
  * ----- CLEO -----
- * File: main_adia0D.cpp
+ * File: main_adia0d.cpp
  * Project: src
  * Created Date: Monday 29th January 2024
  * Author: Clara Bayley (CB)
  * Additional Contributors:
  * -----
- * Last Modified: Tuesday 18th June 2024
+ * Last Modified: Wednesday 11th September 2024
  * Modified By: CB
  * -----
  * License: BSD 3-Clause "New" or "Revised" License
  * https://opensource.org/licenses/BSD-3-Clause
  * -----
  * runs the CLEO super-droplet model (SDM) for adiabatic parcel model example.
  * After make/compiling, execute for example via:
- * ./src/adia0D ../src/config/config.yaml
+ * ./src/adia0d ../src/config/config.yaml
  */
 
 #include <Kokkos_Core.hpp>

diff --git a/examples/boxmodelcollisions/breakup.sh b/examples/boxmodelcollisions/breakup.sh
@@ -20,7 +20,7 @@
 ### ---------------------------------------------------- ###
 buildtype="cuda"
 path2CLEO=${HOME}/CLEO/
-path2build=${HOME}/CLEO/build_colls0D/
+path2build=${HOME}/CLEO/build_colls0d/
 enableyac=false
 executables="longcolls lowlistcolls szakallurbichcolls testikstraubcolls"
 

diff --git a/examples/boxmodelcollisions/breakup_config.yaml b/examples/boxmodelcollisions/breakup_config.yaml
@@ -46,9 +46,9 @@ initsupers:
 
 ### Output Parameters ###
 outputdata:
-  setup_filename: /home/m/m300950/CLEO/build_colls0D/bin/testikstraub_setup.txt  # .txt filename to copy configuration to
-  stats_filename: /home/m/m300950/CLEO/build_colls0D/bin/testikstraub_stats.txt  # .txt file to output runtime statistics to
-  zarrbasedir: /home/m/m300950/CLEO/build_colls0D/bin/testikstraub_sol.zarr  # zarr store base directory
+  setup_filename: /home/m/m300950/CLEO/build_colls0d/bin/testikstraub_setup.txt  # .txt filename to copy configuration to
+  stats_filename: /home/m/m300950/CLEO/build_colls0d/bin/testikstraub_stats.txt  # .txt file to output runtime statistics to
+  zarrbasedir: /home/m/m300950/CLEO/build_colls0d/bin/testikstraub_sol.zarr  # zarr store base directory
   maxchunk: 2500000                                           # maximum no. of elements in chunks of zarr store array
 
 ### Microphysics Parameters ###

diff --git a/examples/boxmodelcollisions/shima2009.sh b/examples/boxmodelcollisions/shima2009.sh
@@ -20,7 +20,7 @@
 ### ---------------------------------------------------- ###
 buildtype="cuda"
 path2CLEO=${HOME}/CLEO/
-path2build=${HOME}/CLEO/build_colls0D/
+path2build=${HOME}/CLEO/build_colls0d/
 enableyac=false
 executables="golcolls longcolls"
 

diff --git a/examples/boxmodelcollisions/shima2009_config.yaml b/examples/boxmodelcollisions/shima2009_config.yaml
@@ -42,7 +42,7 @@ inputfiles:
 
 initsupers:
   type: frombinary                                              # type of initialisation of super-droplets
-  initsupers_filename: /home/m/m300950/CLEO/build_colls0D//share/shima2009_dimlessSDsinit_2.dat # binary filename for initialisation of SDs
+  initsupers_filename: /home/m/m300950/CLEO/build_colls0d//share/shima2009_dimlessSDsinit_2.dat # binary filename for initialisation of SDs
 
 ### Output Parameters ###
 outputdata:

diff --git a/examples/bubble3d/bubble3d.py b/examples/bubble3d/bubble3d.py
@@ -9,14 +9,14 @@
 Author: Clara Bayley (CB)
 Additional Contributors:
 -----
-Last Modified: Tuesday 9th July 2024
+Last Modified: Wednesday 11th September 2024
 Modified By: CB
 -----
 License: BSD 3-Clause "New" or "Revised" License
 https://opensource.org/licenses/BSD-3-Clause
 -----
 File Description:
-Script generates input files, then runs CLEO executable "bubble3D" to
+Script generates input files, then runs CLEO executable "bubble3d" to
 piggyback ICON bubble test case
 """
 
@@ -78,7 +78,7 @@ def run_exectuable(path2CLEO, path2build, configfile, dataset):
     os.chdir(path2build)
     os.system("pwd")
     os.system("rm -rf " + dataset)  # delete any existing dataset
-    executable = path2build + "/examples/yac/bubble3d/src/bubble3D"
+    executable = path2build + "/examples/yac/bubble3d/src/bubble3d"
     print("Executable: " + executable)
     print("Config file: " + configfile)
 

diff --git a/examples/bubble3d/bubble3d.sh b/examples/bubble3d/bubble3d.sh
@@ -23,7 +23,7 @@ buildtype="openmp"
 path2CLEO=${HOME}/CLEO/
 path2build=${HOME}/CLEO/build_bubble3d/
 enableyac=true
-executables="bubble3D"
+executables="bubble3d"
 
 pythonscript=${path2CLEO}/examples/bubble3d/bubble3d.py
 configfile=${path2CLEO}/examples/bubble3d/src/config/bubble3d_config.yaml

diff --git a/examples/bubble3d/run_bubble_tmp.sh b/examples/bubble3d/run_bubble_tmp.sh
@@ -41,7 +41,7 @@ then
   spack load [email protected]%gcc@=11.2.0
 
   ${path2CLEO}/scripts/bash/compile_cleo.sh \
-     /work/mh1126/m300950/cleoenv openmp ${path2build} bubble3D
+     /work/mh1126/m300950/cleoenv openmp ${path2build} bubble3d
 
 elif [ "${action}" == "inputfiles" ]
 then
@@ -79,7 +79,7 @@ then
   cleo_t_end=7200 # must match CLEO config file [seconds]
   cleo_num_vertical_levels=24 # must match CLEO gridfile
 
-  mpiexec -n 1 ${path2build}/examples/bubble3d/src/bubble3D \
+  mpiexec -n 1 ${path2build}/examples/bubble3d/src/bubble3d \
     ${path2CLEO}/examples/bubble3d/src/config/bubble3d_config.yaml \
     : -n 1 python \
     ${path2CLEO}/examples/bubble3d/yac_bubble_data_reader.py \

diff --git a/examples/bubble3d/src/CMakeLists.txt b/examples/bubble3d/src/CMakeLists.txt
@@ -12,18 +12,18 @@ message("PROJECT_SOURCE_DIR: ${PROJECT_SOURCE_DIR}")
 set(CLEOLIBS gridboxes initialise observers runcleo superdrops zarr)
 
 # create primary executable for CLEO in 2-D coupled to thermodynamics from file setup
-add_executable(bubble3D EXCLUDE_FROM_ALL "main_bubble3d.cpp")
+add_executable(bubble3d EXCLUDE_FROM_ALL "main_bubble3d.cpp")
 
 # Add directories and link libraries to target
-target_link_libraries(bubble3D PRIVATE coupldyn_yac cartesiandomain "${CLEOLIBS}")
-target_link_libraries(bubble3D PUBLIC Kokkos::kokkos)
-target_include_directories(bubble3D PRIVATE "${CLEO_SOURCE_DIR}/libs") # CLEO libs directory
+target_link_libraries(bubble3d PRIVATE coupldyn_yac cartesiandomain "${CLEOLIBS}")
+target_link_libraries(bubble3d PUBLIC Kokkos::kokkos)
+target_include_directories(bubble3d PRIVATE "${CLEO_SOURCE_DIR}/libs") # CLEO libs directory
 
 # set specific C++ compiler options for target (optional)
-#target_compile_options(bubble3D PRIVATE)
+#target_compile_options(bubble3d PRIVATE)
 
 # set compiler properties for target(s)
-set_target_properties(bubble3D PROPERTIES
+set_target_properties(bubble3d PROPERTIES
   CMAKE_CXX_STANDARD_REQUIRED ON
   CMAKE_CXX_EXTENSIONS ON
   CXX_STANDARD 20)
diff --git a/examples/bubble3d/src/config/bubble3d_config.yaml b/examples/bubble3d/src/config/bubble3d_config.yaml
@@ -15,7 +15,7 @@
 # Copyright (c) 2023 MPI-M, Clara Bayley
 # -----
 # File Description:
-# Configuration file for test of YAC with 3D time varying thermodyanamics example.
+# Configuration file for test of YAC with 3D time varying thermodynamics example.
 # Note: The inital superdroplets data read from file "initsupers_filename" can be made with
 # CLEO's pySD module (see Python script "create_initsuperdropsbinary_script.py" for usage).
 # Likewise the "grid_filename" can be made using pySD (see "create_gbxboundariesbinary_script.py"),

diff --git a/examples/bubble3d/src/main_bubble3d.cpp b/examples/bubble3d/src/main_bubble3d.cpp
@@ -9,7 +9,7 @@
  * Author: Clara Bayley (CB)
  * Additional Contributors:
  * -----
- * Last Modified: Friday 16th August 2024
+ * Last Modified: Wednesday 11th September 2024
  * Modified By: CB
  * -----
  * License: BSD 3-Clause "New" or "Revised" License
@@ -18,7 +18,7 @@
  * File Description:
  * runs the CLEO super-droplet model (SDM) for bubble3d example using YAC.
  * after make/compiling, execute for example via:
- * ./src/bubble3D ../src/config/config.yaml
+ * ./src/bubble3d ../src/config/config.yaml
  */
 
 #include <Kokkos_Core.hpp>

diff --git a/examples/constthermo2d/constthermo2d.py b/examples/constthermo2d/constthermo2d.py
@@ -9,14 +9,14 @@
 Author: Clara Bayley (CB)
 Additional Contributors:
 -----
-Last Modified: Tuesday 7th May 2024
+Last Modified: Wednesday 11th September 2024
 Modified By: CB
 -----
 License: BSD 3-Clause "New" or "Revised" License
 https://opensource.org/licenses/BSD-3-Clause
 -----
 File Description:
-Script generatees input files, runs CLEO executable "const2D" to create
+Script generatees input files, runs CLEO executable "const2d" to create
 data and then plots precipitation example given 2-D flow field and
 constant thermodynamics read from a file.
 """
@@ -187,7 +187,7 @@
 os.chdir(path2build)
 os.system("pwd")
 os.system("rm -rf " + dataset)  # delete any existing dataset
-executable = path2build + "/examples/constthermo2d/src/const2D"
+executable = path2build + "/examples/constthermo2d/src/const2d"
 print("Executable: " + executable)
 print("Config file: " + configfile)
 os.system(executable + " " + configfile)

diff --git a/examples/constthermo2d/constthermo2d.sh b/examples/constthermo2d/constthermo2d.sh
@@ -20,9 +20,9 @@
 ### ---------------------------------------------------- ###
 buildtype="cuda"
 path2CLEO=${HOME}/CLEO/
-path2build=${HOME}/CLEO/build_const2D/
+path2build=${HOME}/CLEO/build_const2d/
 enableyac=false
-executables="const2D"
+executables="const2d"
 
 pythonscript=${path2CLEO}/examples/constthermo2d/constthermo2d.py
 configfile=${path2CLEO}/examples/constthermo2d/src/config/const2d_config.yaml

diff --git a/examples/constthermo2d/src/CMakeLists.txt b/examples/constthermo2d/src/CMakeLists.txt
@@ -12,18 +12,18 @@ message("PROJECT_SOURCE_DIR: ${PROJECT_SOURCE_DIR}")
 set(CLEOLIBS gridboxes initialise observers runcleo superdrops zarr)
 
 # create primary executable for CLEO in 2-D coupled to thermodynamics from file setup
-add_executable(const2D EXCLUDE_FROM_ALL "main_const2D.cpp")
+add_executable(const2d EXCLUDE_FROM_ALL "main_const2d.cpp")
 
 # Add directories and link libraries to target
-target_link_libraries(const2D PRIVATE coupldyn_fromfile cartesiandomain "${CLEOLIBS}")
-target_link_libraries(const2D PUBLIC Kokkos::kokkos)
-target_include_directories(const2D PRIVATE "${CLEO_SOURCE_DIR}/libs") # CLEO libs directory
+target_link_libraries(const2d PRIVATE coupldyn_fromfile cartesiandomain "${CLEOLIBS}")
+target_link_libraries(const2d PUBLIC Kokkos::kokkos)
+target_include_directories(const2d PRIVATE "${CLEO_SOURCE_DIR}/libs") # CLEO libs directory
 
 # set specific C++ compiler options for target (optional)
-#target_compile_options(const2D PRIVATE)
+#target_compile_options(const2d PRIVATE)
 
 # set compiler properties for target(s)
-set_target_properties(const2D PROPERTIES
+set_target_properties(const2d PROPERTIES
   CMAKE_CXX_STANDARD_REQUIRED ON
   CMAKE_CXX_EXTENSIONS ON
   CXX_STANDARD 20)
diff --git a/examples/constthermo2d/src/main_const2D.cpp → examples/constthermo2d/src/main_const2d.cpp b/examples/constthermo2d/src/main_const2D.cpp → examples/constthermo2d/src/main_const2d.cpp
@@ -3,13 +3,13 @@
  *
  *
  * ----- CLEO -----
- * File: main_const2D.cpp
+ * File: main_const2d.cpp
  * Project: src
  * Created Date: Monday 29th January 2024
  * Author: Clara Bayley (CB)
  * Additional Contributors:
  * -----
- * Last Modified: Tuesday 18th June 2024
+ * Last Modified: Wednesday 11th September 2024
  * Modified By: CB
  * -----
  * License: BSD 3-Clause "New" or "Revised" License
@@ -18,7 +18,7 @@
  * File Description:
  * runs the CLEO super-droplet model (SDM) for 2-D example with divergence free flow.
  * After make/compiling, execute for example via:
- * ./src/const2D ../src/config/config.yaml
+ * ./src/const2d ../src/config/config.yaml
  */
 
 #include <Kokkos_Core.hpp>

diff --git a/examples/divfreemotion/divfree2d.py b/examples/divfreemotion/divfree2d.py
@@ -9,16 +9,15 @@
 Author: Clara Bayley (CB)
 Additional Contributors:
 -----
-Last Modified: Tuesday 7th May 2024
+Last Modified: Wednesday 11th September 2024
 Modified By: CB
 -----
 License: BSD 3-Clause "New" or "Revised" License
 https://opensource.org/licenses/BSD-3-Clause
 -----
 File Description:
-Script generates input files, then runs CLEO executable "divfree2D" to create the
+Script generates input files, then runs CLEO executable "divfree2d" to create the
 data to then plot for divergence free motion of superdroplets in a 2-D divergence
-free wind field.
 """
 
 import os
@@ -83,7 +82,7 @@
 os.chdir(path2build)
 os.system("pwd")
 os.system("rm -rf " + dataset)  # delete any existing dataset
-executable = path2build + "/examples/divfreemotion/src/divfree2D"
+executable = path2build + "/examples/divfreemotion/src/divfree2d"
 print("Executable: " + executable)
 print("Config file: " + configfile)
 os.system(executable + " " + configfile)

diff --git a/examples/divfreemotion/divfree2d.sh b/examples/divfreemotion/divfree2d.sh
@@ -19,9 +19,9 @@
 ### ---------------------------------------------------- ###
 buildtype="cuda"
 path2CLEO=${HOME}/CLEO/
-path2build=${HOME}/CLEO/build_divfree2D/
+path2build=${HOME}/CLEO/build_divfree2d/
 enableyac=false
-executables="divfree2D"
+executables="divfree2d"
 
 pythonscript=${path2CLEO}/examples/divfreemotion/divfree2d.py
 configfile=${path2CLEO}/examples/divfreemotion/src/config/divfree2d_config.yaml