From ea13148633a6e6ce05dfcdbd1aabd693678b2be4 Mon Sep 17 00:00:00 2001
From: KEHANG <kehanghan@gmail.com>
Date: Fri, 10 Feb 2017 16:19:18 -0500
Subject: [PATCH] make atol and rtol modifiable for users

---
 pychemkin/chemkin.py | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/pychemkin/chemkin.py b/pychemkin/chemkin.py
index ddc26ba..9bd768b 100644
--- a/pychemkin/chemkin.py
+++ b/pychemkin/chemkin.py
@@ -321,7 +321,8 @@ def writeInputHomogeneousBatch(self,problemType, reactants, temperature, pressur
     def writeInputPlugFlow(self,problemType, reactants, 
                            startingAxialPosition, endingAxialPosition, diameter, momentum=True, massflowrate = None, sccmflowrate = None, 
                            temperature  = None, pressure  = None,  
-                           temperatureProfile = None, pressureProfile = None, sensitivity=[], rop=[]):
+                           temperatureProfile = None, pressureProfile = None, sensitivity=[], rop=[],
+                           atol=1e-9, rtol=1e-6):
     
         """
         Write input file for typical plug flow
@@ -427,14 +428,14 @@ def writeInputPlugFlow(self,problemType, reactants,
 ACHG 0.0   ! Maximum Absolute Change in Site Fractions
 ADAP   ! Save Additional Adaptive Points
 ATLS 1.0E-6   ! Sensitivity Absolute Tolerance
-ATOL 1.0E-9   ! Absolute Tolerance
+ATOL {0}  ! Absolute Tolerance
 MAXIT 4   ! Maximum Number of Iterations
 NNEG   ! Force Non-negative Solution
 PSV 1.0E-8   ! Scaling Factor for Relaxing Surface Equations (cm/sec)
 RCHG 1.0E-6   ! Maximum Relative Change in Site Fractions
 RTLS 0.0001   ! Sensitivity Relative Tolerance
-RTOL 1.0E-6   ! Relative Tolerance
-TSTP 1.0   ! Initial Integration Step (cm""")          
+RTOL {1}   ! Relative Tolerance
+TSTP 1.0   ! Initial Integration Step (cm""".format(atol, rtol))          
 
         input_stream+=("""
 !