Replace ADPRES with KOMODO in docs

imronuke · Jul 15, 2020 · 68afeec · 68afeec
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diff --git a/docs/_config.yml b/docs/_config.yml
@@ -1,3 +1 @@
 theme: jekyll-theme-cayman
-logo: https://raw.githubusercontent.com/imronuke/ADPRES/master/docs/images/adpres1.png
-google_analytics: UA-163207535-1
diff --git a/docs/adf.md b/docs/adf.md
@@ -6,7 +6,7 @@ filename: adf
 
 # %ADF Card
 
-ADF card can be incorporated into ADPRES input, if any, to make the solution more accurate.
+ADF card can be incorporated into KOMODO input, if any, to make the solution more accurate.
 
 | %ADF | Variable | Description | Remarks or examples |
 | --- | --- | --- | --- |

diff --git a/docs/card-desc.md b/docs/card-desc.md
@@ -6,7 +6,7 @@ filename: card-desc
 
 # General Rules
 
-Some general rules for ADPRES inputs:
+Some general rules for KOMODO inputs:
 1.  Input deck is in free-format form with maximum 200 columns
 2.	Comments are marked by `!`. Example:
 ```
@@ -15,7 +15,7 @@ Some general rules for ADPRES inputs:
 0.68866  0.04850  0.06099  0.06099  0.0  0.0  0.00000  !Group 2
 ```
 
-3.	ADPRES input is modular, where it is broken into several cards. Cards’ keywords shall be uppercase and marked by `%`. Example:
+3.	KOMODO input is modular, where it is broken into several cards. Cards’ keywords shall be uppercase and marked by `%`. Example:
 ```
 %MODE
 FORWARD
@@ -34,31 +34,51 @@ FORWARD
 10.0 8*20.0  !is equivalent to  10.0 20.0 20.0 20.0 20.0 20.0 20.0 20.0 20.0
 ```
 
+5. If you have identical cards for several main inputs, it is a good idea to place those cards in separated card files. In the main inputs, you just need to put location of the card files. For example, all cases in NEACRP benchmark have identical cross section data; hence we may place `%XSEC` card in a separated named `neacrp_xsec`
+```
+! XSEC CARD FILE
+2  11    ! Number of groups and number of materials
+!  sigtr        siga        nu*sigf     kappa*sigf  chi sigs_g1 sigs_g2
+5.32058E-02  3.73279E-04  0.00000E+00  0.00000E+00  1.0  0.0  2.64554E-02
+3.86406E-01  1.77215E-02  0.00000E+00  0.00000E+00  0.0  0.0  0.00000E+00  !COMP 1
+...
+...
+2.21878E-01  9.71937E-03  6.11444E-03  7.60778E-14  1.0  0.0  1.66175E-02
+7.64704E-01  8.85488E-02  1.12635E-01  1.47876E-12  0.0  0.0  0.00000E+00  !COMP 11
+```
+
+In the main input we may refer to the `neacrp_xsec` file by telling KOMODO the location of `neacrp_xsec`
+```
+! XSEC CARD
+%XSEC
+FILE /home/imronuke/KOMODO/smpl/static/NEACRP/neacrp_xsec
+```
+
 
 # Card Description
 
-ADPRES has several input cards. Card is a keyword marked with `%`. Each card can be placed arbitrarily in the input deck. Two cards are mandatory for any problems, while the rest are optional and conditional depend on the nature problem being solved. The description of input for each card is explained in this subsection. Following table lists all cards used in ADPRES. You can click each cards to get their description
+KOMODO has several input cards. Card is a keyword marked with `%`. Each card can be placed arbitrarily in the input deck. Two cards are mandatory for any problems, while the rest are optional and conditional depend on the nature problem being solved. The description of input for each card is explained in this subsection. Following table lists all cards used in KOMODO. You can click each cards to get their description
 
 
 | **No.** | **Cards** | **Description** | **Remark** |
 | --- | --- | --- | --- |
-| 1. | [`%MODE`](https://imronuke.github.io/ADPRES/mode) | Calculation mode | Mandatory |
-| 2. | [`%GEOM`](https://imronuke.github.io/ADPRES/geom) | Geometry of the problem | Mandatory |
-| 3. | [`%XSEC`](https://imronuke.github.io/ADPRES/xsec) | Cross Sections | Conditional |
-| 4. | [`%CASE`](https://imronuke.github.io/ADPRES/case) | Problem case | Optional |
-| 5. | [`%ESRC`](https://imronuke.github.io/ADPRES/esrc) | Extra source | Conditional |
-| 7. | [`%ITER`](https://imronuke.github.io/ADPRES/iter) | Iteration Control | Optional |
-| 8. | [`%PRNT`](https://imronuke.github.io/ADPRES/prnt) | Output print control | Optional |
-| 9. | [`%ADF`](https://imronuke.github.io/ADPRES/adf) | Assembly Discontinuity Factor | Optional |
-| 10. | [`%CROD`](https://imronuke.github.io/ADPRES/crod) | Control rods | Conditional |
-| 11. | [`%EJCT`](https://imronuke.github.io/ADPRES/ejct) | Control rods ejection and/or insertion | Conditional |
-| 12. | [`%FTEM`](https://imronuke.github.io/ADPRES/ftem) | Fuel temperature input card | Conditional |
-| 13. | [`%MTEM`](https://imronuke.github.io/ADPRES/mtem) | Moderator/Coolant temperature input card | Conditional |
-| 14. | [`%CDEN`](https://imronuke.github.io/ADPRES/cden) | Coolant density input card | Conditional |
-| 15. | [`%BCON`](https://imronuke.github.io/ADPRES/bcon) | Boron concentration input card | Conditional |
-| 16. | [`%CBCS`](https://imronuke.github.io/ADPRES/cbcs) | Critical boron concentration input card | Conditional |
-| 17. | [`%THER`](https://imronuke.github.io/ADPRES/ther) | TH input card | Conditional |
-| 18. | [`%XTAB`](https://imronuke.github.io/ADPRES/xtab) | XSEC library for branch calculations | Conditional |
-| 19. | [`%KERN`](https://imronuke.github.io/ADPRES/kern) | Nodal kernel options | Optional |
-| 20. | [`%EXTR`](https://imronuke.github.io/ADPRES/extr) | Exponential flux transformation option card for transient problem | Optional |
-| 21. | [`%THET`](https://imronuke.github.io/ADPRES/thet) | Used to set theta value for transient problem | Optional |
+| 1. | [`%MODE`](https://imronuke.github.io/KOMODO/mode) | Calculation mode | Mandatory |
+| 2. | [`%GEOM`](https://imronuke.github.io/KOMODO/geom) | Geometry of the problem | Mandatory |
+| 3. | [`%XSEC`](https://imronuke.github.io/KOMODO/xsec) | Cross Sections | Conditional |
+| 4. | [`%CASE`](https://imronuke.github.io/KOMODO/case) | Problem case | Optional |
+| 5. | [`%ESRC`](https://imronuke.github.io/KOMODO/esrc) | Extra source | Conditional |
+| 7. | [`%ITER`](https://imronuke.github.io/KOMODO/iter) | Iteration Control | Optional |
+| 8. | [`%PRNT`](https://imronuke.github.io/KOMODO/prnt) | Output print control | Optional |
+| 9. | [`%ADF`](https://imronuke.github.io/KOMODO/adf) | Assembly Discontinuity Factor | Optional |
+| 10. | [`%CROD`](https://imronuke.github.io/KOMODO/crod) | Control rods | Conditional |
+| 11. | [`%EJCT`](https://imronuke.github.io/KOMODO/ejct) | Control rods ejection and/or insertion | Conditional |
+| 12. | [`%FTEM`](https://imronuke.github.io/KOMODO/ftem) | Fuel temperature input card | Conditional |
+| 13. | [`%MTEM`](https://imronuke.github.io/KOMODO/mtem) | Moderator/Coolant temperature input card | Conditional |
+| 14. | [`%CDEN`](https://imronuke.github.io/KOMODO/cden) | Coolant density input card | Conditional |
+| 15. | [`%BCON`](https://imronuke.github.io/KOMODO/bcon) | Boron concentration input card | Conditional |
+| 16. | [`%CBCS`](https://imronuke.github.io/KOMODO/cbcs) | Critical boron concentration input card | Conditional |
+| 17. | [`%THER`](https://imronuke.github.io/KOMODO/ther) | TH input card | Conditional |
+| 18. | [`%XTAB`](https://imronuke.github.io/KOMODO/xtab) | XSEC library for branch calculations | Conditional |
+| 19. | [`%KERN`](https://imronuke.github.io/KOMODO/kern) | Nodal kernel options | Optional |
+| 20. | [`%EXTR`](https://imronuke.github.io/KOMODO/extr) | Exponential flux transformation option card for transient problem | Optional |
+| 21. | [`%THET`](https://imronuke.github.io/KOMODO/thet) | Used to set theta value for transient problem | Optional |
diff --git a/docs/install.md b/docs/install.md
@@ -5,7 +5,7 @@ filename: install
 ---
 
 # Building from source codes
-To build ADPRES from the source codes you just need a Fortran compiler, that's it. We design ADPRES to be very portable, so we expect it can be installed using any Fortran compiler on any machine.
+To build KOMODO from the source codes you just need a Fortran compiler, that's it. We design KOMODO to be very portable, so we expect it can be installed using any Fortran compiler on any machine.
 
 ## Building in Ubuntu or other GNU-Linux based OS
 In Ubuntu, other GNU-Linux based OS or CYGWIN you can use either gfotran or Intel fortran to build the source codes. You can install gfortran in Ubuntu OS by using this command in your computer's terminal
@@ -14,16 +14,16 @@ In Ubuntu, other GNU-Linux based OS or CYGWIN you can use either gfotran or Inte
 sudo apt install gfortran
 ```
 
-Then you can download the [ADPRES zip files](https://github.com/imronuke/ADPRES/archive/master.zip) then extract that zip file, or you can clone them (note: you need to download git first if you don't have it)
+Then you can download the [KOMODO zip files](https://github.com/imronuke/KOMODO/archive/master.zip) then extract that zip file, or you can clone them (note: you need to download git first if you don't have it)
 
 ```
-git clone https://github.com/imronuke/ADPRES.git
+git clone https://github.com/imronuke/KOMODO.git
 ```
 
-In a machine where the gfortran is already installed, go to the ADPRES folder which you had been extracted or cloned
+In a machine where the gfortran is already installed, go to the KOMODO folder which you had been extracted or cloned
 
 ```
-cd ADPRES-master
+cd KOMODO-master
 ```
 
 and build the source codes by using command:
@@ -32,7 +32,7 @@ and build the source codes by using command:
 sudo ./install.sh
 ```
 
-If this way didn't work, try to install bash into your computer. Alternatively, you can build ADPRES manually
+If this way didn't work, try to install bash into your computer. Alternatively, you can build KOMODO manually
 
 ```
 gfortran -O4 -c src/mod_data.f90
@@ -43,29 +43,29 @@ gfortran -O4 -c src/mod_cmfd.f90
 gfortran -O4 -c src/mod_th.f90
 gfortran -O4 -c src/mod_trans.f90
 gfortran -O4 -c src/mod_control.f90
-gfortran -O4 -c src/ADPRES.f90
-gfortran *.o -o adpres
-sudo cp adpres /usr/bin
+gfortran -O4 -c src/komodo.f90
+gfortran *.o -o komodo
+sudo cp KOMODO /usr/bin
 ```
 
 (NOTE: you need to have admin privilege to run these commands)
 
-These command will create an executable file named `adpres` and copied the executable file to `/usr/bin`. Now, you can run a test using several examples of inputs file in folder [smpl](https://github.com/imronuke/ADPRES/tree/master/smpl) to see if you had built ADPRES properly. You can run ADPRES using command
+These command will create an executable file named `komodo` and copied the executable file to `/usr/bin`. Now, you can run a test using several examples of inputs file in folder [smpl](https://github.com/imronuke/KOMODO/tree/master/smpl) to see if you had built KOMODO properly. You can run KOMODO using command
 
 ```
-adpres [INPUT_FILE_PATH_NAME]
+komodo [INPUT_FILE_PATH_NAME]
 ```
 
-for example, you can run [`IAEA3Ds`](https://github.com/imronuke/ADPRES/blob/master/smpl/static/IAEA3Ds) input by
+for example, you can run [`IAEA3Ds`](https://github.com/imronuke/KOMODO/blob/master/smpl/static/IAEA3Ds) input by
 
 ```
-adpres smpl/static/IAEA3Ds
+komodo smpl/static/IAEA3Ds
 ```
 
-If you see `ADPRES EXIT NORMALLY` at the end of terminal output, then congratulations! you have successfully installed ADPRES. By the way, it should take about 0.2 seconds for ADPRES to solve IAEA3Ds problem if you build using gfortran in a typical today's computer. The way to build using Intel fortran is similar, just change `gfortran` with `ifort` in the commands above.
+If you see `KOMODO EXIT NORMALLY` at the end of terminal output, then congratulations! you have successfully installed KOMODO. By the way, it should take about 0.2 seconds for KOMODO to solve IAEA3Ds problem if you build using gfortran in a typical today's computer. The way to build using Intel fortran is similar, just change `gfortran` with `ifort` in the commands above.
 
 ## Building in Mac OS
-The way to install ADPRES on Mac OS is similar to installing ADPRES on Ubuntu. First you need to install gfortran to your computer. You can find the information on how to install gfortran for Mac OS from [here](https://gcc.gnu.org/wiki/GFortranBinariesMacOS). And instead of executing this command as you were supposed to do in Ubuntu
+The way to install KOMODO on Mac OS is similar to installing KOMODO on Ubuntu. First you need to install gfortran to your computer. You can find the information on how to install gfortran for Mac OS from [here](https://gcc.gnu.org/wiki/GFortranBinariesMacOS). And instead of executing this command as you were supposed to do in Ubuntu
 
 ```
 sudo ./install.sh
@@ -81,20 +81,20 @@ The rest of the steps are the same.
 
 
 ## Building in Windows
-There are at least two ways installing ADPRES on Windows.
+There are at least two ways installing KOMODO on Windows.
 
 ### Using Windows Subsystem for Linux (WSL) in Windows 10
-Using this way, you can go to Microsoft Store and install Ubuntu from there for free. Open the Ubuntu app and follow the same steps on installing ADPRES on Ubuntu OS.
+Using this way, you can go to Microsoft Store and install Ubuntu from there for free. Open the Ubuntu app and follow the same steps on installing KOMODO on Ubuntu OS.
 
 ### Using g95 Fortran Compiler
-You can also intsall ADPRES directly into Windows by using free fortran compiler g95 which can be obtained from [here](https://www.fortran.com/wp-content/uploads/2013/05/g95-Mingw_201210.exe). Then install g95 to your computer.
+You can also intsall KOMODO directly into Windows by using free fortran compiler g95 which can be obtained from [here](https://www.fortran.com/wp-content/uploads/2013/05/g95-Mingw_201210.exe). Then install g95 to your computer.
 
-Now you can download the [ADPRES zip files](https://github.com/imronuke/ADPRES/archive/master.zip) from Github then extract that zip file.
+Now you can download the [KOMODO zip files](https://github.com/imronuke/KOMODO/archive/master.zip) from Github then extract that zip file.
 
-After you installed g95 and extracted ADPRES zip file, open the command prompt. And from the command prompt, using `cd` command, go to the  ADPRES folder which you had been extracted
+After you installed g95 and extracted KOMODO zip file, open the command prompt. And from the command prompt, using `cd` command, go to the  KOMODO folder which you had been extracted
 
 ```
-cd ADPRES-master
+cd KOMODO-master
 ```
 
 and build the source codes using g95:
@@ -108,20 +108,20 @@ g95 -O4 -c src\mod_cmfd.f90
 g95 -O4 -c src\mod_th.f90
 g95 -O4 -c src\mod_trans.f90
 g95 -O4 -c src\mod_control.f90
-g95 -O4 -c src\ADPRES.f90
-g95 *.o -o adpres
+g95 -O4 -c src\komodo.f90
+g95 *.o -o komodo
 ```
 
-These command will create an executable file named `adpres`. If you use Intel fortran compiler, just change `g95` with `ifort` in the commands above. Now, you can run a test using several examples of inputs file in folder [smpl](https://github.com/imronuke/ADPRES/tree/master/smpl) to see if you had built ADPRES properly. You can run ADPRES using command
+These command will create an executable file named `komodo`. If you use Intel fortran compiler, just change `g95` with `ifort` in the commands above. Now, you can run a test using several examples of inputs file in folder [smpl](https://github.com/imronuke/KOMODO/tree/master/smpl) to see if you had built KOMODO properly. You can run KOMODO using command
 
 ```
-adpres [INPUT_FILE_PATH_NAME]
+komodo [INPUT_FILE_PATH_NAME]
 ```
 
-for example, you can run [`IAEA3Ds`](https://github.com/imronuke/ADPRES/blob/master/smpl/static/IAEA3Ds) input by
+for example, you can run [`IAEA3Ds`](https://github.com/imronuke/KOMODO/blob/master/smpl/static/IAEA3Ds) input by
 
 ```
-adpres smpl\static\IAEA3Ds
+komodo smpl\static\IAEA3Ds
 ```
 
-If you see `ADPRES EXIT NORMALLY` at the end of terminal output, then congratulations! you have successfully installed ADPRES on Windows.
+If you see `KOMODO EXIT NORMALLY` at the end of terminal output, then congratulations! you have successfully installed KOMODO on Windows.
diff --git a/docs/iter.md b/docs/iter.md
@@ -6,7 +6,7 @@ filename: iter
 
 # %ITER Card
 
-This card can be used to control the iterations in ADPRES calculation
+This card can be used to control the iterations in KOMODO calculation
 
 | %ITER | Variable | Description | Remarks |
 | --- | --- | --- | --- |
@@ -15,9 +15,9 @@ This card can be used to control the iterations in ADPRES calculation
 |        | SERC  | Fission source error criteria (relative error) | Default = 1.e-5 |
 |        | FERC  | Flux error criteria (relative error) | Default = 1.e-5 |
 |        | NAC   | Outer iteration fission source extrapolation interval | Default = 5 |
-|        | NUPD  | Nodal update interval through outer iteration | Default = (NX+NY+NZ)/2.5. Effective only for ANM and PNM [nodal kernel](https://imronuke.github.io/ADPRES/kern) |
-|        | TH_NITER  | Maximum number of T-H iteration | Default = 30. Effective only if [`%THER`](https://imronuke.github.io/ADPRES/ther) present  |
-|        | NTH  | Maximum number of outer iteration per T-H iteration | Default = 20. Effective only if [`%THER`](https://imronuke.github.io/ADPRES/ther) present |
+|        | NUPD  | Nodal update interval through outer iteration | Default = (NX+NY+NZ)/2.5. Effective only for ANM and PNM [nodal kernel](https://imronuke.github.io/KOMODO/kern) |
+|        | TH_NITER  | Maximum number of T-H iteration | Default = 30. Effective only if [`%THER`](https://imronuke.github.io/KOMODO/ther) present  |
+|        | NTH  | Maximum number of outer iteration per T-H iteration | Default = 20. Effective only if [`%THER`](https://imronuke.github.io/KOMODO/ther) present |
 
 Note: TH iteration is non-linear iteration to determine TH parameters
 

diff --git a/docs/kern.md b/docs/kern.md
@@ -6,7 +6,7 @@ filename: kern
 
 # %KERN Card
 
-This card is used to choose other nodal kernel. By default, ADPRES uses Semi-Analytic Nodal Method.
+This card is used to choose other nodal kernel. By default, KOMODO uses Semi-Analytic Nodal Method.
 
 | `%KERN` | Variable | Description | Available options |
 | --- | --- | --- | --- |