Changes between Version 44 and Version 45 of u/bliu

Timestamp:

04/16/15 09:46:37 (10 years ago)

Author:

Baowei Liu

Comment:

—

u/bliu

@@ -1 @@
-= 1. AstroBEAR and Research =
-== Ablative RT Problem ==
-=== Implementation in the code ===
-* Important Equations and Parameters:[blog:bliu01092014] and [blog:bliu01142014]
-* Stencils for diffusion solver: [ThermalConduction]
-* Testing for the code: #309, #331, #345 [http://astrobear.pas.rochester.edu/trac/astrobear/blog/bliu01142014 blog] 
-* References: [http://www.pas.rochester.edu/~bliu/AblativeRT/Docs/reale_testing.pdf Thermal Conduction Test]
-* Transfer the initial data to coarse grid with AstroBEAR and so it can take advantage of AMR: [blog:bliu08282014]
+=  AstroBEAR and Research =
+ 1. [https://astrobear.pas.rochester.edu/trac/wiki/u/bliu/AblativeRT AblativeRT Ablative RT Problem]
+ 2. [https://astrobear.pas.rochester.edu/trac/wiki/u/bliu/PlanetaryWind Planetary Wind Problem]
+ [[BR]]
 
-=== 2D Case ===
-* Growth rate
-|| 200 Extended Zones ||[[Image(http://www.pas.rochester.edu/~bliu/AblativeRT/growthRate/GrowthLogVx_perid200.png,width=100)]];[[Image(http://www.pas.rochester.edu/~bliu/AblativeRT/growthRate/InstantGrowthRate_200Ext.png,width=100)]]; [[Image(http://www.pas.rochester.edu/~bliu/AblativeRT/growthRate/growthRate_2D_rui.png,width=100)]]; [http://www.pas.rochester.edu/~bliu/AblativeRT/bubble/rho_periodic_060414.gif movie] ||
-|| 5 Extended Zones ||[http://www.pas.rochester.edu/~bliu/AblativeRT/bubble/rho_periBC_5Ext_061014.gif movie] ||
-
-=== 3D Case ===
-*  Initial Profile from LLE
- || Original Doc || [http://www.pas.rochester.edu/~bliu/AblativeRT/3Dcase/initialProfile/3Dsetup.txt parameters ]; gravity=0.4*acceleration0 ||
-|| Original Data for thick Target || [http://www.pas.rochester.edu/~bliu/AblativeRT/3Dcase/initialProfile/crho-0000000.hdf density]; [http://www.pas.rochester.edu/~bliu/AblativeRT/3Dcase/initialProfile/cprs-0000000.hdf pressure]; [http://www.pas.rochester.edu/~bliu/AblativeRT/3Dcase/initialProfile/ctpr-0000000.hdf temperature]; [http://www.pas.rochester.edu/~bliu/AblativeRT/3Dcase/initialProfile/cvl1-0000000.hdf Vx];  [http://www.pas.rochester.edu/~bliu/AblativeRT/3Dcase/initialProfile/cvl2-0000000.hdf Vy];[http://www.pas.rochester.edu/~bliu/AblativeRT/3Dcase/initialProfile/cvl3-0000000.hdf Vz] ||
-|| Original Data for thin Target || [http://www.pas.rochester.edu/~bliu/AblativeRT/3Dcase/initialProfile_thin/crho-0000000.hdf density]; [http://www.pas.rochester.edu/~bliu/AblativeRT/3Dcase/initialProfile_thin/cprs-0000000.hdf pressure]; [http://www.pas.rochester.edu/~bliu/AblativeRT/3Dcase/initialProfile_thin/cvl3-0000000.hdf Vz] ||
-|| Thick Target Data files in text (normalized using parameters above, initial profile along z direction) ||   [http://www.pas.rochester.edu/~bliu/AblativeRT/3Dcase/initialProfile/Rho3D.data density]; [http://www.pas.rochester.edu/~bliu/AblativeRT/3Dcase/initialProfile/P3D.data  pressure]; [http://www.pas.rochester.edu/~bliu/AblativeRT/3Dcase/initialProfile/T3D.data  temperature]; [http://www.pas.rochester.edu/~bliu/AblativeRT/3Dcase/initialProfile/Vx3D.data  Vx];  [http://www.pas.rochester.edu/~bliu/AblativeRT/3Dcase/initialProfile/Vy3D.data  Vy];[http://www.pas.rochester.edu/~bliu/AblativeRT/3Dcase/initialProfile/Vz3D.data  Vz] ||
-|| Thin Target Data files in text (normalized using parameters above, initial profile along z direction) ||   [http://www.pas.rochester.edu/~bliu/AblativeRT/3Dcase/initialProfile_thin/Rho3D.data density]; [http://www.pas.rochester.edu/~bliu/AblativeRT/3Dcase/initialProfile_thin/P3D.data  pressure]; [http://www.pas.rochester.edu/~bliu/AblativeRT/3Dcase/initialProfile_thin/Vz3D.data  Vz] ||
-||Thick Target: Initial Profile along center line ||[[Image(http://www.pas.rochester.edu/~bliu/AblativeRT/3Dcase/initialProfile/init_Profile.png, width=100)]] ||
-|| Thick Target Results from AstroBEAR (fixed grid || [[Image(http://www.pas.rochester.edu/~bliu/AblativeRT/3Dcase/2ndCut/ThickSec0499.png,width=100)]]; [http://www.pas.rochester.edu/~bliu/AblativeRT/3Dcase/2ndCut/thick3Drho.gif movie1]; [http://www.pas.rochester.edu/~bliu/AblativeRT/3Dcase/2ndCut/thickSections.gif movie2];
-||Thin Target: Initial Profile along center line ||[[Image(http://www.pas.rochester.edu/~bliu/AblativeRT/3Dcase/ThinTarget/initialProfile_thin/init_Profile_thinTarget.png, width=100)]] ||
-|| Thin Target Results from AstroBEAR (fixed grid) || [[Image(http://www.pas.rochester.edu/~bliu/AblativeRT/3Dcase/2ndCut/ThinSec0340.png, width=100)]]; [http://www.pas.rochester.edu/~bliu/AblativeRT/3Dcase/2ndCut/thinSections.gif movie]; ||
-|| Thin Target Results from AstroBEAR (Coarse grid and AMR) || [[Image(http://www.pas.rochester.edu/~bliu/AblativeRT/3Dcase/CoarseGrid/test/CoarseGrid_1AMR_test_dt.png,width=100)]]; [http://www.pas.rochester.edu/~bliu/AblativeRT/3Dcase/CoarseGrid/ThinSec_Coarse1AMR.gif 1 level AMR]; [http://www.pas.rochester.edu/~bliu/AblativeRT/3Dcase/CoarseGrid/ThinSec3AMR.gif 3 levels AMR];[http://www.pas.rochester.edu/~bliu/AblativeRT/3Dcase/CoarseGrid/ABRT_mesh_3AMR.gif 3 levels AMR with mesh] ||
-[[BR]]
-== Atmosphere of Extrasolar Giant Planet ==
-=== Documents ===
-[http://www.pas.rochester.edu/~bliu/OutflowWind/StoneProga2009.pdf Stone&Proga2009]
-
-= 2. Teaching, Presentation, Posters and Other Useful Documents=
-|| 2015 CIRC Winter Boot Camp -- Bash || [http://www.pas.rochester.edu/~bliu/Teaching/bashScript_2015.pptx.pdf lecture slides]; [http://www.pas.rochester.edu/~bliu/Teaching/day1.tar.gz hands on examples 1 ]; [http://www.pas.rochester.edu/~bliu/Teaching/day2.tar.gz hands on examples 2 ]; [http://www.pas.rochester.edu/~bliu/Teaching/day3.tar.gz hands on examples 3 ]; [http://www.pas.rochester.edu/~bliu/Teaching/day4.tar.gz hands on examples 4 ]; [http://www.pas.rochester.edu/~bliu/Teaching/BashEvaluationSheets_2015.pdf Evaluation sheet from Students] || 2.9.2015-2.18.2015 ||
-|| Configure File for AstroBEAR || [http://www.pas.rochester.edu/~bliu/Documents/configure.pdf Working Notes] || The Notes for using AutoTools to generate configure files for AstroBEAR codes. 2014.10 ||
-|| 2014 CIRC Summer School -- Cuda || [http://www.pas.rochester.edu/~bliu/Teaching/Cuda2014.pdf CUDA] || CIRC Summer School 2014.8 ||
-|| 2014 BH2 System Test || [http://www.pas.rochester.edu/~bliu/Teaching/BH2.pdf Scaling Test of AstroBEAR on BlueHive2 and Stampede]; [http://www.pas.rochester.edu/~bliu/Teaching/BH2.tex tex file ] || CIRC All-Staff 2014.5 || 
-|| 2013 Presentation || [http://www.pas.rochester.edu/~bliu/Teaching/astrobear.pdf Introduction to AstroBEAR2.0] || CIRC All-Staff 2013.8 || 
-|| 2013&2014 Poster || [http://www.pas.rochester.edu/~bliu/Posters/poster_circ.pdf AstroBEAR2.0 and its Performance on BlueGene/Q] || Annual CIRC Poster Session 2013 & 2014.5  || 
-|| 2012 Poster || [http://www.pas.rochester.edu/~bliu/Posters/CIRC_BenchMark_Poster_2012.pdf Comparision of Benchmarks Across CIRC Supercomputing Architectures] || Annual CIRC Poster Session 2012.5  || 
+= Teaching and Presentations =
+ 1. [https://astrobear.pas.rochester.edu/trac/wiki/u/bliu/Teaching Useful Documents]
 [[BR]]
 
-= 3. Scripts =
-Collects for useful shell, gnuplot and python scripts & codes
-|| Find all xml files in source and run saxon to transform and save the object files to output files with same directory structures || [http://www.pas.rochester.edu/~bliu/Scripts/xml_script/xml_script.sh XML transform script];[http://www.pas.rochester.edu/~bliu/Scripts/xml_script/xml_script_tests.tar.gz testing cases] || The java files folder and stylesheets folder are all located under the same folder as the script ||
-|| Get Max and Min of one column of all ASCII data files using gnuplot || [http://www.pas.rochester.edu/~bliu/Scripts/plot/testAscii.sh shell script];[http://www.pas.rochester.edu/~bliu/Scripts/plot/gnuTest.inc gnuplot script] || data files example Rho000.data and Vy000.data. All located under test/ ||
-|| Python function with multiple returns || [http://www.pas.rochester.edu/~bliu/Scripts/Python/multiReturns.py multiple return function] || test. one return is a list ||
-|| Python script to read csv file || [http://www.pas.rochester.edu/~bliu/Scripts/Python/csvRead.py read csv file]; [http://www.pas.rochester.edu/~bliu/Scripts/Python/snv.csv example csv file] || the example csv file comes from DDiMAP || 
-|| Python scripts to read, write and parse fasta files ||[http://www.pas.rochester.edu/~bliu/Scripts/Python/fastaParsing.py read];[http://www.pas.rochester.edu/~bliu/Scripts/Python/fastaWrite.py write]; [http://www.pas.rochester.edu/~bliu/Scripts/Python/fastaParsing2.py parse]; [http://www.pas.rochester.edu/~bliu/Scripts/Python/fasta2List.py fasta file to a List]; [http://www.pas.rochester.edu/~bliu/Scripts/Python/128_Public_DDiMAP.fa example fasta file] || biopython needed. The example fasta file comes from DDiMAP ||
-|| Python Script to rotate and save Window in VisIt || [http://www.pas.rochester.edu/~bliu/Scripts/Visit/savePlot.py Save to curve] || Save line plot to curve/text file ||
-|| Python Script to rotate and save Window in VisIt || [http://www.pas.rochester.edu/~bliu/Scripts/Visit/rotateSave.py Rotate&Save] || Tested with VisIt 2.6.2 ||
-|| Relink all executable files in all the subdirectories || [http://www.pas.rochester.edu/~bliu/Scripts/cleanLinks.sh Relink astrobear for all subfolders] || For Bruce, on alfalfa  ||
-|| Convert gif files to movie files on Mac || [http://www.pas.rochester.edu/~bliu/Scripts/convertMovieOnMac.sh Movie Convert] || Using ffmpeg; For Mac  ||
-|| Interpolate from fine grids to coarse grids with AstroBEAR || blog:bliu08282014 || Set Info%ErrFlag to be 1; Read in data and set as level 1 AMR grid instead of 0 ||
-|| cherry pick the values for specific time steps || [http://www.pas.rochester.edu/~bliu/Scripts/gravity.cpp  transfer gravity]; || pick up gravity values around ts ||
-|| hdf5 data to txt ||[http://www.pas.rochester.edu/~bliu/Scripts/hdf5_2_asc.sh  HDF5 to ASCII]; [http://www.pas.rochester.edu/~bliu/Scripts/trans2txt.cpp ASCII to TXT]; || The hdf5 files need to be from single-core runs ||
-|| Read in chombo files with multi-processors and reWrite the same frame using single-core. Useful when transferring hdf5 files to txt files. || [http://www.pas.rochester.edu/~bliu/Scripts/scrambler.f90.save2singleProcessor scrambler.f90]; [http://www.pas.rochester.edu/~bliu/Scripts/subst.s subst for run-directory]; [http://www.pas.rochester.edu/~bliu/Scripts/transfer2_1c.sh  script]; || Replace the scrambler.f90 file with the new one. The frame number in script need to be updated. 8.19.2014 || 
-|| bash and gnuplot script: plot Multiple Data files to Multiple eps || [http://www.pas.rochester.edu/~bliu/Scripts/plot/plot.sh plot.sh] [http://www.pas.rochester.edu/~bliu/Scripts/plot/gnuplot.inc gnuplot template] || bash arithmetic expressions; use gnuplot to generate multiple figures; special symbols in gnuplot; use gnuplot variables in title; string parse in bash script; multiplots; multipanels; convert eps to png file...  ||
-|| Scripts to transfer the hdf4 file to text on BH2 || [http://www.pas.rochester.edu/~bliu/AblativeRT/3Dcase/initialProfile/hdf4_2_asc.sh hdf4_to_ascii];  [http://www.pas.rochester.edu/~bliu/AblativeRT/3Dcase/initialProfile/run.sh combine_pos_var]; [http://www.pas.rochester.edu/~bliu/AblativeRT/3Dcase/initialProfile/trans2txt.cpp combine_pos_var]; [http://www.pas.rochester.edu/~bliu/AblativeRT/3Dcase/initialProfile/tran2txt_v2.cpp combine_pos_var_v2] || hdf4 module needed ||
-|| Extended 2D data to 3D (Set Precisions!) || [http://www.pas.rochester.edu/~bliu/Scripts/2Dto3D_alongy.cpp SI along y];[http://www.pas.rochester.edu/~bliu/Scripts/2Dto3D.cpp SI along z]; [http://www.pas.rochester.edu/~bliu/Scripts/2Dto3D_cgs.cpp cgs along z];  || Generate 3D initial data to testing the Ablative RT 3D module code. The initial profile is along y/z direction. Everything along z is same. 2D data in 2Ddata/ and 3D data generated in 3Ddata/ ||
+= Programming =
+ 1. [https://astrobear.pas.rochester.edu/trac/wiki/u/bliu/Scripts Useful Scripts and Programs]
 
-
-[[CollapsibleStart(Tests)]]
-[[Tests(250px, nolink)]]
-[[CollapsibleEnd]]
-MyCurentTests