From 739bef38b51471206eca19c77f45e31b312d08b2 Mon Sep 17 00:00:00 2001
From: Schulik <mschulik@ic.ac.uk>
Date: Thu, 15 Oct 2020 15:52:16 +0100
Subject: [PATCH] Finished first working version

---
 aiolos.h            |  3 ++-
 helpers.cpp         |  2 +-
 init_and_bounds.cpp | 29 ++++++++++++++++++-----------
 3 files changed, 21 insertions(+), 13 deletions(-)

diff --git a/aiolos.h b/aiolos.h
index d9b1949..8fd7060 100644
--- a/aiolos.h
+++ b/aiolos.h
@@ -195,8 +195,9 @@ class hydro_run
     double rs_time;
     int    init_static_atmosphere;
     int    static_atmosphere_tempprofile;
+    
     double gamma_adiabat;           //ratio of specific heats
-    double ggminusone;
+    //double ggminusone;
     double mdot;
     double cv;
     double const_T;
diff --git a/helpers.cpp b/helpers.cpp
index 6783c72..7efd982 100644
--- a/helpers.cpp
+++ b/helpers.cpp
@@ -92,7 +92,7 @@ std::vector<double> np_zeros(int size) {
 //
 // Return a 1-D array of one, identical to the numpy function
 //
-std::vector<double> nnp_ones(int size) {
+std::vector<double> np_ones(int size) {
 
     return std::vector<double>(size, 1.0) ;
 }
diff --git a/init_and_bounds.cpp b/init_and_bounds.cpp
index 832895d..2673003 100644
--- a/init_and_bounds.cpp
+++ b/init_and_bounds.cpp
@@ -123,16 +123,6 @@ hydro_run::hydro_run(string filename, double debug_) {
         //finalplotnumber = 1
         solver = 0;
 
-        ////~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-        //
-        // Physical
-        //
-        ////~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-        gamma_adiabat   = read_parameter_from_file<double>(filename,"PARI_GAMMA", debug).value; //ratio of specific heats
-        ggminusone      = gamma_adiabat*(gamma_adiabat-1.);
-        const_T         = read_parameter_from_file<double>(filename,"PARI_CONST_TEMP",  debug).value;
-        T_increment     = read_parameter_from_file<double>(filename,"PARI_TEMP_INCR", debug).value;
         
         ////~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
         //
@@ -276,6 +266,23 @@ hydro_run::hydro_run(string filename, double debug_) {
         source          = init_AOS(num_cells+2);  //Parabolic Variables: gravitational potential
         source_pressure = init_AOS(num_cells+2);  //Parabolic Variables: gravitational potential
         flux            = init_AOS(num_cells+1);
+        
+        
+        ////~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+        //
+        // Physical
+        //
+        ////~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+        
+        //double const_gamma_adiabat = read_parameter_from_file<double>(filename,"PARI_GAMMA", debug).value; //ratio of specific heats
+        gamma_adiabat   = read_parameter_from_file<double>(filename,"PARI_GAMMA", debug).value;
+        //double const_cv = read_parameter_from_file<double>(filename,"PARI_CV", debug).value; //ratio of specific heats
+        cv   =  1; 
+        const_T         = read_parameter_from_file<double>(filename,"PARI_CONST_TEMP",  debug).value;
+        T_increment     = read_parameter_from_file<double>(filename,"PARI_TEMP_INCR", debug).value;
+        
+        
+        
         //left_ghost = AOS(0,0,0);
         //right_ghost= AOS(0,0,0);
         
@@ -411,7 +418,7 @@ hydro_run::hydro_run(string filename, double debug_) {
 void hydro_run::initialize_hydrostatic_atmosphere_nonuniform() {
     
     cout<<"ATTENTION: Initializing nonuniform hydrostatic atmosphere and overwriting prior initial values."<<endl;
-    cv      = 1.;
+    //cv      = 1.;
     
     long double temp_rhofinal;
     long double factor_inner, factor_outer;