Recent changes to CAEBAT

CAEBAT modified by Dasha

Dasha — Wed, 25 Jun 2014 18:31:22 -0000

--- v38
+++ v39
@@ -255,6 +255,7 @@
 ### DUALFOIL

 Parameter  | Default Value
+------------- | -------------
 _CLASS_ | CHARTRAN
 _SUB_CLASS_ | 
 _NAME_ | DualFoil

CAEBAT modified by Dasha

Dasha — Wed, 25 Jun 2014 18:30:51 -0000

--- v37
+++ v38
@@ -168,7 +168,7 @@

   * _NODE_DETECTION_ = manual 
   * Description: This determines whether the user chooses the finer options in the manual allocation description section, or simply chooses a preset node detection option. 
-  * Allowed Values: checkjob | qstat | pbs_env | slurm_env [Default Value = manual]   
+  * Allowed Values: checkjob | qstat | pbs_env | slurm_env Default Value = manual   

 **Manual allocation description**

@@ -191,7 +191,7 @@
   * Description: This must adhere to the platform's capabilities, and describes the number of processes per node. 
   * Allowed Values: 
     * EXCLUSIVE: Allows only one task per node. 
-    * SHARED: Allows multiple tasks to share a node. [Default Value]
+    * SHARED: Allows multiple tasks to share a node. (Default Value)

 **In thermal_chartran_cell_twoway.conf:**

CAEBAT modified by Dasha

Dasha — Wed, 25 Jun 2014 18:29:49 -0000

--- v36
+++ v37
@@ -59,43 +59,43 @@

 To create the OASFramework : 

-1. Create a directory CAEBAT and cd to that directory 
-
-2. Check out the source code from the repository using the following command: 
-~~~~
+*Create a directory CAEBAT and cd to that directory 
+
+*Check out the source code from the repository using the following command:
+
     svn checkout http://svn.code.sf.net/p/ipsframework/code/trunk OASFramework
-~~~~
-3. To build the library, use the following terminal commands: 
-~~~~    
+
+*To build the library, use the following terminal commands:
+    
     cd OASFramework 
     mkdir build
     cd build
     ccmake ..
-~~~~
+
 * Press c to configure the build, then e to exit 
 * Edit the key _CMAKE_INSTALL_PREFIX_ to enter the bin installation directory /PATH/TO/OASFramework/install
 * Press c to reconfigure the build 
 * Enter g to generate and exit from ccmake
-~~~~    
+    
     make 
     make install
-~~~~
+
 ## VIBE

-1. Pre-install HDF5 and _32bit_ CGNS 
+*Pre-install HDF5 and _32bit_ CGNS 

 For CGNS: in ccmake enable Fortran, HDF5 and tests. Also enable the tools if you wish to query the output. 

 If you want to perform optimization or parameter sweep, you also need to install DAKOTA (Design Analysis Kit for Optimization and Terascale Applications). 

-2. Untar the VIBE compressed file into the CAEBAT directory. 
-~~~~    
+*Untar the VIBE compressed file into the CAEBAT directory.
+
     tar xzvf VIBE.tar.gz
     cd VIBE/trunk/components/config/
     ln -sf makeconfig.gnu makeconfig.local
     cd ../
     make
-~~~~
+
 * Configure the installation location to /usr/bin/install and remember not to end with a "/" 
 * make install (this will install everything in the bin directory under components) 

@@ -132,36 +132,33 @@
 * Change _SIM_ROOT_ = /RunExample/Results

 Next, do sourcing to use the cgns library, by using the following commands: 
-~~~~    
-     vi ~/.bash_profile 
-~~~~
+    
+    vi ~/.bash_profile 
+
 Create a new Library by typing the following below your current library: 
-~~~~   
+  
     LD_LIBRARY_PATH=/opt/cgns-3.1.3-i686_gcc-4.4.6/lib:$LD_LIBRARY_PATH
-~~~~
+
 Then you must restart the bash profile for this change to take effect by: 
-~~~~    
+   
     . ~/.bash_profile
-~~~~
+
 Check that this library assignment worked by using: 
-~~~~   
+  
     echo $LD_LIBRARY_PATH
-~~~~
-Every time the terminal is closed, the 
-~~~~    
-    . ~/.bash_profile
-~~~~
-must be run to reassign this library. Now, to actually run the example use the following command while in /RunExample 
-~~~~   
+
+Every time the terminal is closed, the . ~/.bash_profile must be run to reassign this library. Now, to actually run the example use the following command while in /RunExample:
+ 
     /CAEBAT/OASFramework/install/bin/ips.py --simulation=thermal_chartran_cell_twoway.conf --log=temp.log --platform=workstation.conf -a
-~~~~
+
 In order to run it again, the /RunExample/Results/work directory must be emptied each time between runs.

 # Input Parameters

 This is a list of all the values that the user may like to change. 

-**In workstation.conf:
+In workstation.conf:
+
 * _HOST_ = allu1, which is an arbitrary user set description of the host. 
 * _MPIRUN_ = eval, which is the only allowed value. 

@@ -215,9 +212,9 @@
 _NAMES_ | INIT DRIVER CHARTRAN THERMAL | DRIVER and INIT are required values in the port section.
 _IMPLEMENTATION_ | CHARTRAN_THERMAL_DRIVER | This tells how the simulation initialized, and will generate the first state if needed.

-For THERMAL, IMPLEMENTATION = AMPERES. 
-
-For CHARTRAN, IMPLEMENTATION = DUALFOIL. 
+For THERMAL, _IMPLEMENTATION_ = AMPERES. 
+
+For CHARTRAN, _IMPLEMENTATION_ = DUALFOIL. 

 These IMPLEMENTATIONs and DRIVERs are described below.

CAEBAT modified by Dasha

Dasha — Wed, 25 Jun 2014 18:19:31 -0000

--- v35
+++ v36
@@ -1,5 +1,7 @@
 This page describes the structure and usage of CAEBAT, building instructions, how to run an example, and how it is related to NiCE.

+**Table of Contents**
+
 [TOC]

 # Introduction to CAEBAT
@@ -28,18 +30,18 @@

 We plan to integrate CAEBAT into NiCE as a plugin so we have a tool for simulating battery codes. NiCE will simply use its current tools to run CAEBAT, behind the scenes. These are a compiled effort based on the meeting of 3/21/2013. We will design CAEBAT into three different pieces: 

-  * Model 
-  * Launcher 
-  * Analysis (tentative) 
+* Model 
+* Launcher 
+* Analysis (tentative) 

 ### Model

 There are multiple pieces to this particular module and will probably be the most complex. The CAEBAT program will require 3 types of input files in varying degrees of format and complexity:   

-A.) The workstation.config. This will probably be pre-generated under the hood by NiCE or another script and not be visible in the model builder.   
-B.) The Chartran.config file. This is a configuration setup file for the simulation. This will be pre-generated with NiCE's XML format for creating the model, and the input model will be generated in the listed format (a combination of key/value pairs with bracketing). Part of the k/v pair parsing is in NiCE, but will need to investigate K/V parsing for tables and MasterDetailsPairs.   
-C.) The "model" BatML.file. The schema will be provided by the CAEBAT Folks where we will investigate a way to generically handle the schema file in order to produce the GUI layout in the model, and then transform the values inputted into the schema enforced xml file. 
+* The workstation.config. This will probably be pre-generated under the hood by NiCE or another script and not be visible in the model builder.   
+* The Chartran.config file. This is a configuration setup file for the simulation. This will be pre-generated with NiCE's XML format for creating the model, and the input model will be generated in the listed format (a combination of key/value pairs with bracketing). Part of the k/v pair parsing is in NiCE, but will need to investigate K/V parsing for tables and MasterDetailsPairs.   
+* The "model" BatML.file. The schema will be provided by the CAEBAT Folks where we will investigate a way to generically handle the schema file in order to produce the GUI layout in the model, and then transform the values inputted into the schema enforced xml file. 

 ### Launcher

@@ -60,24 +62,24 @@
 1. Create a directory CAEBAT and cd to that directory 

 2. Check out the source code from the repository using the following command: 
-    
+~~~~
     svn checkout http://svn.code.sf.net/p/ipsframework/code/trunk OASFramework
-
+~~~~
 3. To build the library, use the following terminal commands: 
-    
+~~~~    
     cd OASFramework 
     mkdir build
     cd build
     ccmake ..
-
-  * Press c to configure the build, then e to exit 
-  * Edit the key _CMAKE_INSTALL_PREFIX_ to enter the bin installation directory /PATH/TO/OASFramework/install
-  * Press c to reconfigure the build 
-  * Enter g to generate and exit from ccmake
-    
+~~~~
+* Press c to configure the build, then e to exit 
+* Edit the key _CMAKE_INSTALL_PREFIX_ to enter the bin installation directory /PATH/TO/OASFramework/install
+* Press c to reconfigure the build 
+* Enter g to generate and exit from ccmake
+~~~~    
     make 
     make install
-
+~~~~
 ## VIBE

 1. Pre-install HDF5 and _32bit_ CGNS 
@@ -87,15 +89,15 @@
 If you want to perform optimization or parameter sweep, you also need to install DAKOTA (Design Analysis Kit for Optimization and Terascale Applications). 

 2. Untar the VIBE compressed file into the CAEBAT directory. 
-    
+~~~~    
     tar xzvf VIBE.tar.gz
     cd VIBE/trunk/components/config/
     ln -sf makeconfig.gnu makeconfig.local
     cd ../
     make
-
-  * Configure the installation location to /usr/bin/install and remember not to end with a "/" 
-  * make install (this will install everything in the bin directory under components) 
+~~~~
+* Configure the installation location to /usr/bin/install and remember not to end with a "/" 
+* make install (this will install everything in the bin directory under components) 

 ## DATA

@@ -105,9 +107,9 @@

 In order to run this, make a new directory in CAEBAT called RunExample. When going through these steps remember not to have "/" on the end, and that "Library" must be spelled correctly. Create the following directories in RunExample: 

-  * Data
-  * Results
-  * Physics
+* Data
+* Results
+* Physics

 Move the following configuration files into RunExample: 

@@ -119,72 +121,57 @@
 *li-ion-ebar.in
 *dualfoil5.in

-Configure the 
-    
-    workstation.conf
-
-  * Change _PHYS_BIN_ROOT_ = /RunExample/Physics
-  * Change _DATA_ROOT_ = /RunExample/Data
-
-Next, Configure the 
-    
-    thermal_chartran_cell_twoway.conf
-
-: 
-
-  * Change _CAEBAT_ROOT_ = /CAEBAT/VIBE/trunk/components
-  * Change _SIM_ROOT_ = /RunExample/Results
+Configure the workstation.conf
+
+* Change _PHYS_BIN_ROOT_ = /RunExample/Physics
+* Change _DATA_ROOT_ = /RunExample/Data
+
+Next, Configure the thermal_chartran_cell_twoway.conf
+
+* Change _CAEBAT_ROOT_ = /CAEBAT/VIBE/trunk/components
+* Change _SIM_ROOT_ = /RunExample/Results

 Next, do sourcing to use the cgns library, by using the following commands: 
-    
+~~~~    
      vi ~/.bash_profile 
-
+~~~~
 Create a new Library by typing the following below your current library: 
-    
+~~~~   
     LD_LIBRARY_PATH=/opt/cgns-3.1.3-i686_gcc-4.4.6/lib:$LD_LIBRARY_PATH
-
+~~~~
 Then you must restart the bash profile for this change to take effect by: 
-    
+~~~~    
     . ~/.bash_profile
-
+~~~~
 Check that this library assignment worked by using: 
-    
+~~~~   
     echo $LD_LIBRARY_PATH
-
+~~~~
 Every time the terminal is closed, the 
-    
+~~~~    
     . ~/.bash_profile
-
+~~~~
 must be run to reassign this library. Now, to actually run the example use the following command while in /RunExample 
-    
+~~~~   
     /CAEBAT/OASFramework/install/bin/ips.py --simulation=thermal_chartran_cell_twoway.conf --log=temp.log --platform=workstation.conf -a
-
-In order to run it again, the /RunExample/Results/work directory must be emptied each time between runs. 
+~~~~
+In order to run it again, the /RunExample/Results/work directory must be emptied each time between runs.

 # Input Parameters

 This is a list of all the values that the user may like to change. 

-**In 
-    
-    workstation.conf
-
-:**
-
-  * _HOST_ = allu1, which is an arbitrary user set description of the host. 
-  * _MPIRUN_ = eval, which is the only allowed value. 
+**In workstation.conf:
+* _HOST_ = allu1, which is an arbitrary user set description of the host. 
+* _MPIRUN_ = eval, which is the only allowed value. 

-        mpirun
-
-is a shell script used to launch a job with MPI.   
-
+mpirun is a shell script used to launch a job with MPI.   

 **Resource detection method**

   * _NODE_DETECTION_ = manual 
   * Description: This determines whether the user chooses the finer options in the manual allocation description section, or simply chooses a preset node detection option. 
   * Allowed Values: checkjob | qstat | pbs_env | slurm_env [Default Value = manual]   
-

 **Manual allocation description**

@@ -194,7 +181,6 @@
   * Description: This only applies when _NODE_DETECTION_ = manual, and allows the user to choose how they want to process on their nodes. 
   * Allowed Values: These are shown with their default values, and can have all integer values up to the platform's capabilities.   

-
 **Node topology description**

   * _CORES_PER_NODE_ = 2 
@@ -202,85 +188,36 @@
   * Description: A node is a group of sockets, which are groups of cores that are single processing units capable of performing computations. 
   * Allowed Values: These are shown with their default values, and can have all integer values up to the platform's capabilities.   

-
 **Framework for setting for node allocation**

-  * _NODE_ALLOCATION_MODE_
+_NODE_ALLOCATION_MODE_
   * Description: This must adhere to the platform's capabilities, and describes the number of processes per node. 
   * Allowed Values: 
     * EXCLUSIVE: Allows only one task per node. 
-    * SHARED: Allows multiple tasks to share a node. [Default Value]   
-
-
+    * SHARED: Allows multiple tasks to share a node. [Default Value]

 **In thermal_chartran_cell_twoway.conf:**

 These will be shown with their default values, and allowed values are arbitrary strings unless otherwise stated. 

-Parameter  Default Value  Explanation 
-
-_RUN_ID_
-case1 
-Indentifier for this simulation run 
-    
-    CoupledCellElectroChemThermalTransport
-
-_SIM_NAME_
-${RUN_ID} 
-Name of current simulation, the default value automatically finds the name. 
-
-_PLASMA_STATE_WORK_DIR_
-    
-    $SIM_ROOT/work/battery_state
-
-Where to put state files as the simulation evolves, allowed values will be any existing directory. 
-
-_RUN_COMMENT_
-Coupled CAEBAT Module simulation 
-A run comment picked up by the portal. 
-
-_TAG_
-ElectroChemThermal 
-A tag that enables related runs to be retrieved together. 
-
-_USER_
-ul2 
-An optional parameter, if missing the unix username is used. 
-
-_NUM_ZONES, NUM_CHARTRAN_ZONES_
-15, 15 
-These are the number of zones for ---? 
-
-_SIMULATION_MODE_
-NORMAL 
-The Simulation mode setting, with the allowed values of ---? 
-
-_LOG_LEVEL_
-WARNING 
-This changes what will appear in the log, with the allowed values of ERROR or WARNING. 
-
-_LOG_FILE_
-    
-    $SIM_ROOT/${SIM_NAME}.log
-
-This determines the name and location of the created log file, and the allowed values are any path to an existing directory followed by ".log". 
-
-_NAMES_
-INIT DRIVER CHARTRAN THERMAL 
-DRIVER and INIT are required values in the port section. 
-
-_IMPLEMENTATION_
-CHARTRAN_THERMAL_DRIVER 
-This tells how the simulation initialized, and will generate the first state if needed. 
-
+Parameter | Default Value | Explanation
+------------- | ------------- | -------------
+_RUN_ID_ | CoupledCellElectroChemThermalTransport | Identifier for this simulation run
+_SIM_NAME_ |  ${RUN_ID} | Name of current simulation, the default value automatically finds the name.
+_PLASMA_STATE_WORK_DIR_ | $SIM_ROOT/work/battery_state | Where to put state files as the simulation evolves, allowed values will be any existing directory. 
+_RUN_COMMENT_ | Coupled CAEBAT Module simulation | A run comment picked up by the portal.
+_TAG_ | ElectroChemThermal | A tag that enables related runs to be retrieved together. 
+_USER_ | ul2 | An optional parameter, if missing the unix username is used.
+_NUM_ZONES, NUM_CHARTRAN_ZONES_ | 15, 15 | These are the number of zones for ---?
+_SIMULATION_MODE_ | NORMAL | The Simulation mode setting, with the allowed values of ---?
+_LOG_LEVEL_ | WARNING | This changes what will appear in the log, with the allowed values of ERROR or WARNING.
+_LOG_FILE_ | $SIM_ROOT/${SIM_NAME}.log | This determines the name and location of the created log file, and the allowed values are any path to an existing directory followed by ".log".
+_NAMES_ | INIT DRIVER CHARTRAN THERMAL | DRIVER and INIT are required values in the port section.
+_IMPLEMENTATION_ | CHARTRAN_THERMAL_DRIVER | This tells how the simulation initialized, and will generate the first state if needed.

-For THERMAL, 
-
-IMPLEMENTATION = AMPERES. 
-
-For CHARTRAN, 
-
-IMPLEMENTATION = DUALFOIL. 
+For THERMAL, IMPLEMENTATION = AMPERES. 
+
+For CHARTRAN, IMPLEMENTATION = DUALFOIL. 

 These IMPLEMENTATIONs and DRIVERs are described below. 

@@ -288,11 +225,10 @@

 Component specification, with entries similar for all components. NAME entry must match the name of the python class that implements the component. This section is where the user can fine tune the simulation to their liking. The user can determine which scripts to execute, the input and output files, and the classes to run for these main three types of simulations.   

-
 **CHARTRAN_THERMAL_DRIVER**

 Parameter  | Default Value | Explanation
-------------- | -------------
+------------- | ------------- | -------------
 _CLASS_  | DRIVERS | This is a class from the initialized list in the PORTS section.
 _SUB_CLASS_  | CHARTRAN_THERMAL | This is an implementation for the above CLASS?
 _NAME_  | Driver | The name of the python class implementing the component.
@@ -305,66 +241,33 @@

 ### AMPERES

-_CLASS_ = THERMAL 
-
-_SUB_CLASS_ = 
-
-_NAME_ = Amperes 
-
-_NPROC_ = 1 
-
-_ELECTRICAL_ = 0 
-
-_BIN_PATH_ = 
+Parameter  | Default Value
+------------- | -------------
+_CLASS_ | THERMAL
+_SUB_CLASS_ |
+_NAME_ | Amperes
+_NPROC_ | 1
+_ELECTRICAL_ | 0
+_BIN_PATH_ | $CAEBAT_ROOT/bin
+_INPUT_DIR_ | $DATA_ROOT/amperes_thermal
+_INPUT_FILES_ | Battery-zones1.e
+_OUTPUT_FILES_ | $CURRENT_STATE
+_SCRIPT_ | $BIN_PATH/amperes_thermal.py
+ 
+
+### DUALFOIL
+
+Parameter  | Default Value
+_CLASS_ | CHARTRAN
+_SUB_CLASS_ | 
+_NAME_ | DualFoil
+_NPROC_ | 1
+_BIN_PATH_ | $CAEBAT_ROOT/bin
+_INPUT_DIR_ | $DATA_ROOT/dualfoil
+_INPUT_FILES_ | dualfoil5.in, li-ion-ebar.in
+_OUTPUT_FILES_ | df_caebat.out
+_SCRIPT_ | $BIN_PATH/dualfoil_chartran.py 

-    $CAEBAT_ROOT/bin
-
-_INPUT_DIR_ = 
-    
-    $DATA_ROOT/amperes_thermal
-
-_INPUT_FILES_ = 
-    
-    Battery-zones1.e
-
-_OUTPUT_FILES_ = 
-    
-    $CURRENT_STATE
-
-_SCRIPT_ = 
-    
-    $BIN_PATH/amperes_thermal.py
-
-### DUALFOIL
-
-_CLASS_ = CHARTRAN 
-
-_SUB_CLASS_ = 
-
-_NAME_ = DualFoil 
-
-_NPROC_ = 1 
-
-_BIN_PATH_ = 
-    
-    $CAEBAT_ROOT/bin
-
-_INPUT_DIR_ = 
-    
-    $DATA_ROOT/dualfoil
-
-_INPUT_FILES_ = 
-    
-    dualfoil5.in, li-ion-ebar.in
-
-_OUTPUT_FILES_ = 
-    
-    df_caebat.out
-
-_SCRIPT_ = 
-    
-    $BIN_PATH/dualfoil_chartran.py
-
 ## Time loop specification

 The two MODEs: 
@@ -372,10 +275,10 @@
 * REGULAR: The framework uses the variables _START_, _FINISH_, and _NSTEP_. 
 * EXPLICIT: The framework uses the variable _VALUES_ (a space separated list of time values). 

-Below are shown the default values: 
-
-* _MODE_ = REGULAR 
-* _START_ = 0.0 
-* _FINISH_ = 30. 
-* _NSTEP_ = 1 
-* _VALUES_ = 3.4 3.5 3.6 3.7 
+Shown below are the default values: 
+
+_MODE_ = REGULAR 
+_START_ = 0.0 
+_FINISH_ = 30. 
+_NSTEP_ = 1 
+_VALUES_ = 3.4 3.5 3.6 3.7

CAEBAT modified by Dasha

Dasha — Tue, 24 Jun 2014 09:19:57 -0000

--- v34
+++ v35
@@ -69,7 +69,6 @@
     mkdir build
     cd build
     ccmake ..
-

   * Press c to configure the build, then e to exit 
   * Edit the key _CMAKE_INSTALL_PREFIX_ to enter the bin installation directory /PATH/TO/OASFramework/install
@@ -285,9 +284,6 @@

 These IMPLEMENTATIONs and DRIVERs are described below. 

-  
-
-
 ## Individual configuration sections

 Component specification, with entries similar for all components. NAME entry must match the name of the python class that implements the component. This section is where the user can fine tune the simulation to their liking. The user can determine which scripts to execute, the input and output files, and the classes to run for these main three types of simulations.   
@@ -295,125 +291,91 @@

 **CHARTRAN_THERMAL_DRIVER**

-Parameter  Default Value  Explanation 
-
-_CLASS_
-DRIVERS 
-This is a class from the initialized list in the PORTS section. 
-
-_SUB_CLASS_
-CHARTRAN_THERMAL 
-This is an implementation for the above CLASS? 
-
-_NAME_
-Driver 
-The name of the python class implementing the component. 
-
-_NPROC_
-1 
-This is the number of processes that can run at once? 
-
-_BIN_PATH_
+Parameter  | Default Value | Explanation
+------------- | -------------
+_CLASS_  | DRIVERS | This is a class from the initialized list in the PORTS section.
+_SUB_CLASS_  | CHARTRAN_THERMAL | This is an implementation for the above CLASS?
+_NAME_  | Driver | The name of the python class implementing the component.
+_NPROC_  | 1 |  This is the number of processes that can run at once? 
+_BIN_PATH_ | $CAEBAT_ROOT/bin | This provides the location of the bin directory. 
+_INPUT_DIR_ | $DATA_ROOT/ | This provides the location of the input files. 
+_INPUT_FILES_ | | This provides each required input file by giving their names. 
+_OUTPUT_FILES_ | $CURRENT_STATE | This writes the output files to a certain file...? 
+_SCRIPT_ | $BIN_PATH/thermal_chartran_driver_n.py | This tells which script to execute. 
+
+### AMPERES
+
+_CLASS_ = THERMAL 
+
+_SUB_CLASS_ = 
+
+_NAME_ = Amperes 
+
+_NPROC_ = 1 
+
+_ELECTRICAL_ = 0 
+
+_BIN_PATH_ = 

     $CAEBAT_ROOT/bin

-This provides the location of the bin directory. 
-
-_INPUT_DIR_
-    
-    $DATA_ROOT/
-
-This provides the location of the input files. 
-
-_INPUT_FILES_
-This provides each required input file by giving their names. 
-
-_OUTPUT_FILES_
-$CURRENT_STATE 
-This writes the output files to a certain file...? 
-
-_SCRIPT_
-    
-    $BIN_PATH/thermal_chartran_driver_n.py
-
-This tells which script to execute. 
-
-### AMPERES
-
-_CLASS_ = THERMAL 
+_INPUT_DIR_ = 
+    
+    $DATA_ROOT/amperes_thermal
+
+_INPUT_FILES_ = 
+    
+    Battery-zones1.e
+
+_OUTPUT_FILES_ = 
+    
+    $CURRENT_STATE
+
+_SCRIPT_ = 
+    
+    $BIN_PATH/amperes_thermal.py
+
+### DUALFOIL
+
+_CLASS_ = CHARTRAN 

 _SUB_CLASS_ = 

-_NAME_ = Amperes 
+_NAME_ = DualFoil 

 _NPROC_ = 1 

-_ELECTRICAL_ = 0 
-
 _BIN_PATH_ = 

     $CAEBAT_ROOT/bin

 _INPUT_DIR_ = 

-    $DATA_ROOT/amperes_thermal
+    $DATA_ROOT/dualfoil

 _INPUT_FILES_ = 

-    Battery-zones1.e
+    dualfoil5.in, li-ion-ebar.in

 _OUTPUT_FILES_ = 

-    $CURRENT_STATE
+    df_caebat.out

 _SCRIPT_ = 

-    $BIN_PATH/amperes_thermal.py
-
-  
-
-
-### DUALFOIL
-
-_CLASS_ = CHARTRAN 
-
-_SUB_CLASS_ = 
-
-_NAME_ = DualFoil 
-
-_NPROC_ = 1 
-
-_BIN_PATH_ = 
-    
-    $CAEBAT_ROOT/bin
-
-_INPUT_DIR_ = 
-    
-    $DATA_ROOT/dualfoil
-
-_INPUT_FILES_ = 
-    
-    dualfoil5.in, li-ion-ebar.in
-
-_OUTPUT_FILES_ = 
-    
-    df_caebat.out
-
-_SCRIPT_ = 
-    
     $BIN_PATH/dualfoil_chartran.py

 ## Time loop specification

 The two MODEs: 

-  * REGULAR: The framework uses the variables _START_, _FINISH_, and _NSTEP_. 
-  * EXPLICIT: The framework uses the variable _VALUES_ (a space separated list of time values). 
+* REGULAR: The framework uses the variables _START_, _FINISH_, and _NSTEP_. 
+* EXPLICIT: The framework uses the variable _VALUES_ (a space separated list of time values). 

 Below are shown the default values: 

-  * _MODE_ = REGULAR 
-  * _START_ = 0.0 
-  * _FINISH_ = 30. 
-  * _NSTEP_ = 1 
-  * _VALUES_ = 3.4 3.5 3.6 3.7 
+* _MODE_ = REGULAR 
+* _START_ = 0.0 
+* _FINISH_ = 30. 
+* _NSTEP_ = 1 
+* _VALUES_ = 3.4 3.5 3.6 3.7

CAEBAT modified by Dasha

Dasha — Tue, 24 Jun 2014 09:13:37 -0000

--- v33
+++ v34
@@ -18,11 +18,7 @@

 ## Other

-The data for CAEBAT is in a 
-    
-    tar.gz
-
-file available upon request. 
+The data for CAEBAT is in a tar.gz file available upon request. 

 The Battery Markup Language (Battery ML) provides standardized format for the definition of all the necessary information. 

@@ -41,25 +37,9 @@
 There are multiple pieces to this particular module and will probably be the most complex. The CAEBAT program will require 3 types of input files in varying degrees of format and complexity:   

-A.) The 
-    
-    workstation.config
-
-. This will probably be pre-generated under the hood by NiCE or another script and not be visible in the model builder.   
-B.) The 
-    
-    Chartran.config
-
-file. This is a configuration setup file for the simulation. This will be pre-generated with NiCE's XML format for creating the model, and the input model will be generated in the listed format (a combination of key/value pairs with bracketing). Part of the k/v pair parsing is in NiCE, but will need to investigate K/V parsing for tables and 
-    
-    MasterDetailsPairs
-
-.   
-C.) The "model" 
-    
-    BatML.file
-
-. The schema will be provided by the CAEBAT Folks where we will investigate a way to generically handle the schema file in order to produce the GUI layout in the model, and then transform the values inputted into the schema enforced xml file. 
+A.) The workstation.config. This will probably be pre-generated under the hood by NiCE or another script and not be visible in the model builder.   
+B.) The Chartran.config file. This is a configuration setup file for the simulation. This will be pre-generated with NiCE's XML format for creating the model, and the input model will be generated in the listed format (a combination of key/value pairs with bracketing). Part of the k/v pair parsing is in NiCE, but will need to investigate K/V parsing for tables and MasterDetailsPairs.   
+C.) The "model" BatML.file. The schema will be provided by the CAEBAT Folks where we will investigate a way to generically handle the schema file in order to produce the GUI layout in the model, and then transform the values inputted into the schema enforced xml file. 

 ### Launcher

@@ -77,21 +57,13 @@

 To create the OASFramework : 

-1\. Create a directory 
-    
-    CAEBAT
-
-and 
-    
-    cd
-
-to that directory 
-
-2\. Check out the source code from the repository using the following command: 
+1. Create a directory CAEBAT and cd to that directory 
+
+2. Check out the source code from the repository using the following command: 

     svn checkout http://svn.code.sf.net/p/ipsframework/code/trunk OASFramework

-3\. To build the library, use the following terminal commands: 
+3. To build the library, use the following terminal commands: 

     cd OASFramework 
     mkdir build
@@ -99,153 +71,72 @@
     ccmake ..

-  * Press 
-        
-        c
-
-to configure the build, then 
-        
-        e
-
-to exit 
-  * Edit the key _CMAKE_INSTALL_PREFIX_ to enter the bin installation directory 
-        
-        /PATH/TO/OASFramework/install
-
-  * Press 
-        
-        c
-
-to reconfigure the build 
-  * Enter 
-        
-        g
-
-to generate and exit from 
-        
-        ccmake
+  * Press c to configure the build, then e to exit 
+  * Edit the key _CMAKE_INSTALL_PREFIX_ to enter the bin installation directory /PATH/TO/OASFramework/install
+  * Press c to reconfigure the build 
+  * Enter g to generate and exit from ccmake

     make 
     make install
-    

 ## VIBE

-1\. Pre-install HDF5 and _32bit_ CGNS 
+1. Pre-install HDF5 and _32bit_ CGNS 

 For CGNS: in ccmake enable Fortran, HDF5 and tests. Also enable the tools if you wish to query the output. 

 If you want to perform optimization or parameter sweep, you also need to install DAKOTA (Design Analysis Kit for Optimization and Terascale Applications). 

-2\. Untar the VIBE compressed file into the CAEBAT directory. 
-    
+2. Untar the VIBE compressed file into the CAEBAT directory. 

     tar xzvf VIBE.tar.gz
     cd VIBE/trunk/components/config/
     ln -sf makeconfig.gnu makeconfig.local
     cd ../
     make
-    
-
-  * Configure the installation location to 
+
+  * Configure the installation location to /usr/bin/install and remember not to end with a "/" 
+  * make install (this will install everything in the bin directory under components) 
+
+## DATA
+
+1. Untar the DATA directory (tar xzvf CAEBAT-DATA.tar.gz) into the /CAEBAT directory. 
+
+# Running a Simulation with CAEBAT
+
+In order to run this, make a new directory in CAEBAT called RunExample. When going through these steps remember not to have "/" on the end, and that "Library" must be spelled correctly. Create the following directories in RunExample: 
+
+  * Data
+  * Results
+  * Physics
+
+Move the following configuration files into RunExample: 

-        /usr/bin/install
-
-and remember not to end with a "/" 
-  * make install
-
-(this will install everything in the bin directory under components) 
-
-  
-
-
-## DATA
-
-1\. Untar the DATA directory (
-    
-    tar xzvf CAEBAT-DATA.tar.gz
-
-) into the 
-    
-    /CAEBAT directory
-
-. 
-
-# Running a Simulation with CAEBAT
-
-In order to run this, make a new directory in CAEBAT called 
-    
-    RunExample
-
-. When going through these steps remember not to have "/" on the end, and that "Library" must be spelled correctly. Create the following directories in 
-    
-    RunExample
+*thermal_chartran_cell_twoway.conf
+*workstation.conf
+
+Move the following data files into RunExample/Data/dualfoil/
+
+*li-ion-ebar.in
+*dualfoil5.in
+
+Configure the 
+    
+    workstation.conf
+
+  * Change _PHYS_BIN_ROOT_ = /RunExample/Physics
+  * Change _DATA_ROOT_ = /RunExample/Data
+
+Next, Configure the 
+    
+    thermal_chartran_cell_twoway.conf

 : 

-  * Data
-
-  * Results
-
-  * Physics
-
-Move the following files into 
-    
-    RunExample
-
-: 
-
-  * Configuration files: 
-        
-        thermal_chartran_cell_twoway.conf
-
-and 
-        
-        workstation.conf
-
-Move the following files into 
-    
-    RunExample/Data/dualfoil/
-
-  * Data: 
-        
-        li-ion-ebar.in
-
-and 
-        
-        dualfoil5.in
-
-Configure the 
-    
-    workstation.conf
-
-  * Change _PHYS_BIN_ROOT_ = 
-        
-        /RunExample/Physics
-
-  * Change _DATA_ROOT_ = 
-        
-        /RunExample/Data
-
-Next, Configure the 
-    
-    thermal_chartran_cell_twoway.conf
-
-: 
-
-  * Change _CAEBAT_ROOT_ = 
-        
-        /CAEBAT/VIBE/trunk/components
-
-  * Change _SIM_ROOT_ = 
-        
-        /RunExample/Results
-
-Next, do sourcing to use the 
-    
-    cgns
-
-library, by using the following commands: 
+  * Change _CAEBAT_ROOT_ = /CAEBAT/VIBE/trunk/components
+  * Change _SIM_ROOT_ = /RunExample/Results
+
+Next, do sourcing to use the cgns library, by using the following commands: 

      vi ~/.bash_profile 

@@ -265,19 +156,11 @@

     . ~/.bash_profile

-must be run to reassign this library. Now, to actually run the example use the following command while in 
-    
-    /RunExample
-
-. 
+must be run to reassign this library. Now, to actually run the example use the following command while in /RunExample 

     /CAEBAT/OASFramework/install/bin/ips.py --simulation=thermal_chartran_cell_twoway.conf --log=temp.log --platform=workstation.conf -a

-In order to run it again, the 
-    
-    /RunExample/Results/work
-
-directory must be emptied each time between runs. 
+In order to run it again, the /RunExample/Results/work directory must be emptied each time between runs. 

 # Input Parameters

CAEBAT modified by Dasha

Dasha — Mon, 23 Jun 2014 16:42:20 -0000

--- v32
+++ v33
@@ -1,8 +1,5 @@
 This page describes the structure and usage of CAEBAT, building instructions, how to run an example, and how it is related to NiCE.

-  
-
-
 [TOC]

 # Introduction to CAEBAT
@@ -15,15 +12,9 @@

 The component adapters interact with the components by preparing the necessary inputs to run the components and by scheduling the component runs. The state adapters interact with the battery state file by updating all the necessary information about the battery state and the methods for coupling the components. The Battery state file is the core for passing data between components. 

-  
-
-
 ## VIBE

 VIBE expands to Virtual Integrated Battery Environment. The OAS framework, along with physics and support components and the adapters constitute the VIBE. The current components are electrochemistry, thermal, electrical, and cost model. 
-
-  
-

 ## Other

@@ -101,44 +92,42 @@
     svn checkout http://svn.code.sf.net/p/ipsframework/code/trunk OASFramework

 3\. To build the library, use the following terminal commands: 
-
-  * cd OASFramework
-
-  * mkdir build
-
-  * cd build
-
-  * ccmake .. 
-
-  *     * Press 
-            
-            c
+    
+    cd OASFramework 
+    mkdir build
+    cd build
+    ccmake ..
+    
+
+  * Press 
+        
+        c

 to configure the build, then 
-            
-            e
+        
+        e

 to exit 
-    * Edit the key _CMAKE_INSTALL_PREFIX_ to enter the bin installation directory 
-            
-            /PATH/TO/OASFramework/install
-
-    * Press 
-            
-            c
+  * Edit the key _CMAKE_INSTALL_PREFIX_ to enter the bin installation directory 
+        
+        /PATH/TO/OASFramework/install
+
+  * Press 
+        
+        c

 to reconfigure the build 
-    * Enter 
-            
-            g
+  * Enter 
+        
+        g

 to generate and exit from 
-            
-            ccmake
-
-  * make
-
-  * make install
+        
+        ccmake
+    
+    make 
+    make install
+    

 ## VIBE

@@ -146,30 +135,21 @@

 For CGNS: in ccmake enable Fortran, HDF5 and tests. Also enable the tools if you wish to query the output. 

-If you want to perform optimization or parameter sweep, you need to also install DAKOTA (Design Analysis Kit for Optimization and Terascale Applications). 
-
-2\. Untar the VIBE compressed file (
+If you want to perform optimization or parameter sweep, you also need to install DAKOTA (Design Analysis Kit for Optimization and Terascale Applications). 
+
+2\. Untar the VIBE compressed file into the CAEBAT directory. 
+    

     tar xzvf VIBE.tar.gz
-
-) into the CAEBAT directory. 
-
-  * cd VIBE/trunk/components/config/
-
-  * ln -sf makeconfig.gnu makeconfig.local
-
-  * cd ../
-
-(go back to 
-        
-        components
-
-directory) 
-  * make
-
-  *     * Configure the installation location to 
-            
-            /usr/bin/install
+    cd VIBE/trunk/components/config/
+    ln -sf makeconfig.gnu makeconfig.local
+    cd ../
+    make
+    
+
+  * Configure the installation location to 
+        
+        /usr/bin/install

 and remember not to end with a "/" 
   * make install

CAEBAT modified by Dasha

Dasha — Mon, 23 Jun 2014 16:42:20 -0000

--- v31
+++ v32
@@ -303,41 +303,50 @@

 This is a list of all the values that the user may like to change. 

-  * **In **
-        
-        workstation.conf
-
-: 
-
-_HOST_ = allu1, which is an arbitrary user set description of the host. 
-
-_MPIRUN_ = eval, which is the only allowed value. 
-    
-    mpirun
+**In 
+    
+    workstation.conf
+
+:**
+
+  * _HOST_ = allu1, which is an arbitrary user set description of the host. 
+  * _MPIRUN_ = eval, which is the only allowed value. 
+        
+        mpirun

 is a shell script used to launch a job with MPI.   

-  * **Resource detection method**
-
-_NODE_DETECTION_ = manual Description: This determines whether the user chooses the finer options in the manual allocation description section, or simply chooses a preset node detection option. Allowed Values: checkjob | qstat | pbs_env | slurm_env [Default Value = manual]   
-
-
-  * **Manual allocation description**
-
-_TOTAL_PROCS_ = 2, _NODES_ = 1, _PROCS_PER_NODE_ = 2 Description: This only applies when _NODE_DETECTION_ = manual, and allows the user to choose how they want to process on their nodes. Allowed Values: These are shown with their default values, and can have all integer values up to the platform's capabilities.   
-
-
-  * **Node topology description**
-
-_CORES_PER_NODE_ = 2 and _SOCKETS_PER_NODE_ = 1 Description: A node is a group of sockets, which are groups of cores that are single processing units capable of performing computations. Allowed Values: These are shown with their default values, and can have all integer values up to the platform's capabilities.   
-
-
-  * **Framework for setting for node allocation**
-
-_NODE_ALLOCATION_MODE_ Description: This must adhere to the platform's capabilities, and describes the number of processes per node. Allowed Values: 
-
-  *     * EXCLUSIVE: Allows only one task per node. 
+**Resource detection method**
+
+  * _NODE_DETECTION_ = manual 
+  * Description: This determines whether the user chooses the finer options in the manual allocation description section, or simply chooses a preset node detection option. 
+  * Allowed Values: checkjob | qstat | pbs_env | slurm_env [Default Value = manual]   
+
+
+**Manual allocation description**
+
+  * _TOTAL_PROCS_ = 2 
+  * _NODES_ = 1 
+  * _PROCS_PER_NODE_ = 2 
+  * Description: This only applies when _NODE_DETECTION_ = manual, and allows the user to choose how they want to process on their nodes. 
+  * Allowed Values: These are shown with their default values, and can have all integer values up to the platform's capabilities.   
+
+
+**Node topology description**
+
+  * _CORES_PER_NODE_ = 2 
+  * _SOCKETS_PER_NODE_ = 1 
+  * Description: A node is a group of sockets, which are groups of cores that are single processing units capable of performing computations. 
+  * Allowed Values: These are shown with their default values, and can have all integer values up to the platform's capabilities.   
+
+
+**Framework for setting for node allocation**
+
+  * _NODE_ALLOCATION_MODE_
+  * Description: This must adhere to the platform's capabilities, and describes the number of processes per node. 
+  * Allowed Values: 
+    * EXCLUSIVE: Allows only one task per node. 
     * SHARED: Allows multiple tasks to share a node. [Default Value]   

@@ -345,9 +354,6 @@
 **In thermal_chartran_cell_twoway.conf:**

 These will be shown with their default values, and allowed values are arbitrary strings unless otherwise stated. 
-
-  
-

 Parameter  Default Value  Explanation 

@@ -539,7 +545,7 @@
 The two MODEs: 

   * REGULAR: The framework uses the variables _START_, _FINISH_, and _NSTEP_. 
-  * EXPLICIT: The framework uses the variable VALUES (a space separated list of time values). 
+  * EXPLICIT: The framework uses the variable _VALUES_ (a space separated list of time values). 

 Below are shown the default values:

CAEBAT modified by Dasha

Dasha — Mon, 23 Jun 2014 16:42:19 -0000

--- v30
+++ v31
@@ -303,52 +303,43 @@

 This is a list of all the values that the user may like to change. 

-**In workstation.conf:**
+  * **In **
+        
+        workstation.conf
+
+: 

 _HOST_ = allu1, which is an arbitrary user set description of the host. 

-_MPIRUN_ = eval, which is the only allowed value. "mpirun" is a shell script used to launch a job with mpi. 
-
-  
-
-
-    **Resource detection method**
-
-_NODE_DETECTION_ = manual 
-
-Description: This determines whether the user chooses the finer options in the manual allocation description section, or simply chooses a preset node detection option. 
-
-Allowed Values: checkjob | qstat | pbs_env | slurm_env [Default Value = manual] 
-
-  
-
-
-    **Manual allocation description**
-
-_TOTAL_PROCS_ = 2, _NODES_ = 1, _PROCS_PER_NODE_ = 2 
-
-Description: This only applies when _NODE_DETECTION_ = manual, and allows the user to choose how they want to process on their nodes. 
-
-Allowed Values: These are shown with their default values, and can have all integer values up to the platform's capabilities. 
-
-    **Node topology description**
-
-_CORES_PER_NODE_ = 2 and _SOCKETS_PER_NODE_ = 1 
-
-Description: A node is a group of sockets, which are groups of cores that are single processing units capable of performing computations. 
-
-Allowed Values: These are shown with their default values, and can have all integer values up to the platform's capabilities. 
-
-    **Framework for setting for node allocation**
-
-_NODE_ALLOCATION_MODE_
-
-Description: This must adhere to the platform's capabilities, and describes the number of processes per node. 
-
-Allowed Values: 
-
-  * EXCLUSIVE: Allows only one task per node. 
-  * SHARED: Allows multiple tasks to share a node. [Default Value] 
+_MPIRUN_ = eval, which is the only allowed value. 
+    
+    mpirun
+
+is a shell script used to launch a job with MPI.   
+
+
+  * **Resource detection method**
+
+_NODE_DETECTION_ = manual Description: This determines whether the user chooses the finer options in the manual allocation description section, or simply chooses a preset node detection option. Allowed Values: checkjob | qstat | pbs_env | slurm_env [Default Value = manual]   
+
+
+  * **Manual allocation description**
+
+_TOTAL_PROCS_ = 2, _NODES_ = 1, _PROCS_PER_NODE_ = 2 Description: This only applies when _NODE_DETECTION_ = manual, and allows the user to choose how they want to process on their nodes. Allowed Values: These are shown with their default values, and can have all integer values up to the platform's capabilities.   
+
+
+  * **Node topology description**
+
+_CORES_PER_NODE_ = 2 and _SOCKETS_PER_NODE_ = 1 Description: A node is a group of sockets, which are groups of cores that are single processing units capable of performing computations. Allowed Values: These are shown with their default values, and can have all integer values up to the platform's capabilities.   
+
+
+  * **Framework for setting for node allocation**
+
+_NODE_ALLOCATION_MODE_ Description: This must adhere to the platform's capabilities, and describes the number of processes per node. Allowed Values: 
+
+  *     * EXCLUSIVE: Allows only one task per node. 
+    * SHARED: Allows multiple tasks to share a node. [Default Value]   
+

 **In thermal_chartran_cell_twoway.conf:**

CAEBAT modified by Dasha

Dasha — Mon, 23 Jun 2014 16:42:19 -0000

--- v29
+++ v30
@@ -305,16 +305,16 @@

 **In workstation.conf:**

-HOST = allu1, which is an arbitrary user set description of the host. 
-
-MPIRUN = eval, which is the only allowed value. "mpirun" is a shell script used to launch a job with mpi. 
+_HOST_ = allu1, which is an arbitrary user set description of the host. 
+
+_MPIRUN_ = eval, which is the only allowed value. "mpirun" is a shell script used to launch a job with mpi. 

     **Resource detection method**

-NODE_DETECTION = manual 
+_NODE_DETECTION_ = manual 

 Description: This determines whether the user chooses the finer options in the manual allocation description section, or simply chooses a preset node detection option. 

@@ -325,29 +325,23 @@

     **Manual allocation description**

-TOTAL_PROCS = 2, NODES = 1, PROCS_PER_NODE = 2 
-
-Description: This only applies when NODE_DETECTION = manual, and allows the user to choose how they want to process on their nodes. 
+_TOTAL_PROCS_ = 2, _NODES_ = 1, _PROCS_PER_NODE_ = 2 
+
+Description: This only applies when _NODE_DETECTION_ = manual, and allows the user to choose how they want to process on their nodes. 

 Allowed Values: These are shown with their default values, and can have all integer values up to the platform's capabilities. 

-  
-
-
     **Node topology description**

-CORES_PER_NODE = 2 and SOCKETS_PER_NODE = 1 
+_CORES_PER_NODE_ = 2 and _SOCKETS_PER_NODE_ = 1 

 Description: A node is a group of sockets, which are groups of cores that are single processing units capable of performing computations. 

 Allowed Values: These are shown with their default values, and can have all integer values up to the platform's capabilities. 

-  
-
-
     **Framework for setting for node allocation**

-NODE_ALLOCATION_MODE 
+_NODE_ALLOCATION_MODE_

 Description: This must adhere to the platform's capabilities, and describes the number of processes per node. 

@@ -368,7 +362,9 @@

 _RUN_ID_
 case1 
-Indentifier for this simulation run CoupledCellElectroChemThermalTransport 
+Indentifier for this simulation run 
+    
+    CoupledCellElectroChemThermalTransport

 _SIM_NAME_
 ${RUN_ID} 
@@ -427,7 +423,6 @@

 IMPLEMENTATION = DUALFOIL. 

-  
 These IMPLEMENTATIONs and DRIVERs are described below. 

@@ -552,13 +547,13 @@

 The two MODEs: 

-  * REGULAR: The framework uses the variables START, FINISH, and NSTEP. 
+  * REGULAR: The framework uses the variables _START_, _FINISH_, and _NSTEP_. 
   * EXPLICIT: The framework uses the variable VALUES (a space separated list of time values). 

-Below is shown the default values: 
-
-  * MODE = REGULAR 
-  * START = 0.0 
-  * FINISH = 30. 
-  * NSTEP = 1 
-  * VALUES = 3.4 3.5 3.6 3.7 
+Below are shown the default values: 
+
+  * _MODE_ = REGULAR 
+  * _START_ = 0.0 
+  * _FINISH_ = 30. 
+  * _NSTEP_ = 1 
+  * _VALUES_ = 3.4 3.5 3.6 3.7