From c910b8f8b61d18eabf0c3fd1fa89c41e5d971773 Mon Sep 17 00:00:00 2001
From: Jeff Candy <candy@jaamweb.com>
Date: Thu, 12 Sep 2024 19:44:37 -0700
Subject: [PATCH] Command-line time-averaging function

---
 cgyro/bin/cgyro_converge    | 34 ++++++++++++++++++++++++++++++++++
 f2py/pygacode/cgyro/data.py |  4 ++--
 2 files changed, 36 insertions(+), 2 deletions(-)
 create mode 100755 cgyro/bin/cgyro_converge

diff --git a/cgyro/bin/cgyro_converge b/cgyro/bin/cgyro_converge
new file mode 100755
index 000000000..3d547a423
--- /dev/null
+++ b/cgyro/bin/cgyro_converge
@@ -0,0 +1,34 @@
+#!/usr/bin/env python
+
+import numpy as np
+
+from pygacode.cgyro import data
+from pygacode.gacodefuncs import *
+
+# read minimal data for setup
+sim = data.cgyrodata('./',fast=True,silent=True)
+
+t = sim.t
+ns = sim.n_species
+
+# read bin.cgyro.ky_flux
+sim.getflux()
+
+# select field=0,moment=1, and sum over kx
+field=0 ; moment=1
+y = np.sum(sim.ky_flux[:,moment,field,:,:],axis=1)
+
+# averaging (note that time_average function is fast/optimized)
+w='0.5'
+imin,imax=time_index(t,w)
+for ispec in range(ns):
+   ave = time_average(y[ispec,:],t,imin,imax)
+   print(ave)
+
+w='0.75'
+imin,imax=time_index(t,w)
+for ispec in range(ns):
+   ave = time_average(y[ispec,:],t,imin,imax)
+   print(ave)
+
+   
diff --git a/f2py/pygacode/cgyro/data.py b/f2py/pygacode/cgyro/data.py
index 05ad1d423..721a38b79 100644
--- a/f2py/pygacode/cgyro/data.py
+++ b/f2py/pygacode/cgyro/data.py
@@ -13,13 +13,13 @@
 class cgyrodata:
 
    # constructor reads in basic (not all) simulation data
-   def __init__(self,sim_directory,silent=False):
+   def __init__(self,sim_directory,silent=False,fast=False):
 
       self.silent = silent
       self.dir = sim_directory
       hastime = self.gettime()
       self.getgrid()
-      if hastime:
+      if hastime and not fast:
          self.getdata()
       
    # standard routine to read binary or ASCII data