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Merge branch 'master' of https://github.com/SlaybaughLab/Coeus
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@jamesbevins
jamesbevins committed Aug 1, 2017
2 parents 761f48b + 5b90165 commit cda1e3c
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11 changes: 9 additions & 2 deletions Code/.bash_profile
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Expand Up @@ -18,8 +18,16 @@ module load mpi4py
# Aliases

alias groupdir="cd /global/home/groups/co_nuclear"

alias stat='squeue | grep youdongz'

alias nuc='squeue -q nuclear_normal'

alias scratch="cd /global/scratch/youdongz/"

# wwall -j jobid


# User specific environment and startup programs
PATH=$PATH:$HOME/bin:/global/home/groups/co_nuclear/bin:/global/home/groups/co_nuclear/ADVANTG/bin
DATAPATH=/global/scratch/co_nuclear/MCNP/MCNP_DATA/
Expand All @@ -28,7 +36,6 @@ export PATH
export DATAPATH

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/global/home/groups/co_nuclear/pyne/lib
export PYTHONPATH=$PYTHONPATH:/global/home/groups/co_nuclear/python-pkgs

PYTHONPATH=$PYTHONPATH:/global/home/groups/co_nuclear/python-pkgs/pp-1.6.5
PYTHONPATH=$PYTHONPATH:/global/home/groups/co_nuclear/python-pkgs/pyDOE-0.3.8-py2.7.egg
export PYTHONPATH=$PYTHONPATH:/global/home/groups/co_nuclear/pyne/lib/python2.7/site-packages
148 changes: 53 additions & 95 deletions Code/ADVANTG_Utilities.py
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Expand Up @@ -24,74 +24,50 @@

#---------------------------------------------------------------------------------------#
class ADVANTG_Settings:
"""
Creates a object representing the settings for running the ADVANTG deterministic radiation trasport code calculations.
Attributes
==========
lib : string
The multi-group library used
[Default: "dplus"]
method : string
The solution method for ADVANTG (CADIS or DX)
[Default: "cadis"]
ouputs : string
The output files to be produced
[Default: "mcnp"]
tnum : int
The tally number for calculating the adjoint flux
[Default: 24]
pt_src : string
Whether or not the source should be treated as a point source in deterministic transport
[Default: False]
mix_tol : string
The material mix tolerance fraction. Controls the precision of mixed cells.
[Default: 0.01]
pn_order : integer
The scattering order
[Default: 1]
eta_x : float
The spacing of the mesh intervals in the x (radial) axis in cm in the ETA.
[Default: 0.5 cm]
eta_y : float
The spacing of the mesh intervals in the y (radial) axis in cm in the ETA.
[Default: 0.5 cm]
eta_z : float
The spacing of the mesh intervals in the z (axial) axis in cm in the ETA.
[Default: 0.5 cm]
foil_x : float
The spacing of the mesh intervals in the x (radial) axis in cm near the foil.
[Default: 0.25 cm]
foil_y : float
The spacing of the mesh intervals in the y (radial) axis in cm near the foil.
[Default: 0.25 cm]
foil_z : float
The spacing of the mesh intervals in the z (axial) axis in cm near the foil.
[Default: 0.05 cm]
ext_spacing : float
The spacing of the mesh intervals in x,y, and z axis in cm outside the ETA.
[Default: 1 cm]
Returns
=======
None
"""


## Creates a object representing the settings for running the ADVANTG deterministic radiation trasport code calculations.
def __init__(self, lib="dplus", method="cadis", outputs="mcnp silo", tnum=24, pt_src="True", mix_tol=0.01, pn_order=1, eta_x=0.5, eta_y=0.5, eta_z =0.5, foil_x=0.25, foil_y=0.25, foil_z=0.05, ext_spacing=1.0):
## string The multi-group library used
# [Default: "dplus"]
self.lib=lib
## string The solution method for ADVANTG (CADIS or DX)
# [Default: "cadis"]
self.method=method
## string The output files to be produced
# [Default: "mcnp"]
self.outputs=outputs
## int The tally number for calculating the adjoint flux
# [Default: 24]
self.tnum=tnum
## string Whether or not the source should be treated as a point source in deterministic transport
# [Default: False]
self.pt_src=pt_src
## string The material mix tolerance fraction. Controls the precision of mixed cells.
# [Default: 0.01]
self.mix_tol=mix_tol
## integer The scattering order
# [Default: 1]
self.pn_order=pn_order
## float The spacing of the mesh intervals in the x (radial) axis in cm in the ETA.
# [Default: 0.5 cm]
self.eta_x=eta_x
## float The spacing of the mesh intervals in the y (radial) axis in cm in the ETA.
# [Default: 0.5 cm]
self.eta_y=eta_y
## float The spacing of the mesh intervals in the z (axial) axis in cm in the ETA.
# [Default: 0.5 cm]
self.eta_z=eta_z
## float The spacing of the mesh intervals in the x (radial) axis in cm near the foil.
# [Default: 0.25 cm]
self.foil_x=foil_x
## float The spacing of the mesh intervals in the y (radial) axis in cm near the foil.
# [Default: 0.25 cm]
self.foil_y=foil_y
## float The spacing of the mesh intervals in the z (axial) axis in cm near the foil.
# [Default: 0.05 cm]
self.foil_z=foil_z
## float The spacing of the mesh intervals in x,y, and z axis in cm outside the ETA.
# [Default: 1 cm]
self.ext=ext_spacing


Expand Down Expand Up @@ -119,25 +95,24 @@ def __str__(self):
s = header
return s


## Parses a ADVANTG settings csv input file.
# The key word options are:
# Library
# Method
# Outputs
# Tally Number
# Point Source
# Material Mix Tolerance
# Scattering Order
# ETA X Spacing Interval
# ETA Y Spacing Interval
# ETA Z Spacing Interval
# Foil X Spacing Interval
# Foil Y Spacing Interval
# Foil Z Spacing Interval
# External Spacing Interval
def read_settings(self, filename):
"""Parses a ADVANTG settings csv input file.
The key word options are:
Library
Method
Outputs
Tally Number
Point Source
Material Mix Tolerance
Scattering Order
ETA X Spacing Interval
ETA Y Spacing Interval
ETA Z Spacing Interval
Foil X Spacing Interval
Foil Y Spacing Interval
Foil Z Spacing Interval
External Spacing Interval
"""

# Open file
try:
self.f = open(filename, 'r')
Expand Down Expand Up @@ -202,31 +177,14 @@ def read_settings(self, filename):
# Test that the file closed
assert self.f.closed==True, "File did not close properly."

#-------------------------------------------------------------------------------------------------------------#
## Print the generated MCNP input deck to file
# @param eta [ETA parameters object] An object that contains all of the constraints required to initialize the geometry
# @param geom [MCNP_Geometry object] The geometry for running the MCNP radiation trasport code. Contains the surfaces, cells, and material information
# @param S [ADVANTG_Settings object] An object representing the settings for running the ADVANTG radiation trasport code.
# @param num integer The current cuckoo number being generated
# @param cluster boolean (optional) An indicator to change the file to run on a cluster using Run_Transport function and slurm job submission
def Print_ADVANTG_Input(eta,geom,S,num,cluster=False):
"""
Print the generated MCNP input deck to file
Parameters
==========
eta : ETA parameters object
An object that contains all of the constraints required to initialize the geometry
geom : MCNP_Geometry object
The geometry for running the MCNP radiation trasport code. Contains the surfaces, cells, and material information
S : ADVANTG_Settings object
An object representing the settings for running the ADVANTG radiation trasport code.
num : integer
The current cuckoo number being generated
Optional
========
cluster : boolean
An indicator to change the file to run on a cluster using Run_Transport function and slurm job submission
Returns
=======
None
"""

path=os.path.abspath(os.path.join(os.path.abspath(os.getcwd()), os.pardir))

# Delete previous input file if present
Expand Down
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