Merge branch 'garysbranch' of github.com:/gafusion/gacode into garysb…

…ranch

.gitignore

@@ -39,6 +39,7 @@ glf23/src/glf23
 gyro/src/gyro
 cgyro/src/cgyro
 cgyro/mpi_tests/*
+qlgyro/src/qlgyro
 neo/src/neo
 neo/tools/pneo/src/pneo
 neo/tools/pneo/src/pneo_rbf

cgyro/Makefile

@@ -12,6 +12,7 @@ export EXTRA_LIBS = \
 all:
 	gacode_getversion > .VERSION
 	cd ${GACODE_ROOT}/shared/math ; make
+	cd ${GACODE_ROOT}/shared/landau ; make
 	cd ${GACODE_ROOT}/f2py ; make
 	cd src  && make
 
@@ -27,6 +28,7 @@ clean:
 
 deepclean:
 	cd ${GACODE_ROOT}/shared/math ; make clean
+	cd ${GACODE_ROOT}/shared/landau ; make clean
 	cd ${GACODE_ROOT}/f2py ; make clean
 	cd ${GACODE_ROOT}/modules ; rm -f cgyro*.mod
 	cd src && make clean

cgyro/bin/README_omp.txt

@@ -1,22 +1,18 @@
 Running CGYRO with high nomp
 ============================
 
-CGYRO allocates some of its data on the stack,
-and the amount is proportional with the 
-number of omp threads you use.
-(omp==openMP)
+CGYRO allocates some of its data on the stack, and the amount is 
+proportional to the number of omp (OpenMP) threads you use. The 
+default stack limit of 8M is only sufficient for up to about 4 omp 
+threads. Thus, when using CGYRO with openMP, it is recommended 
+that you put the following line into your .bashrc 
 
-The default stack limit of 8M is only sufficient
-for up to about 4 omp threads.
+ulimit -s 32768 
 
-Thus, when using CGYRO with openMP, 
-it is recommended that you put the following line 
-into your .bashrc
-ulimit -s 32768
-(must be set on all the nodes running CGYRO)
+(This must be set on all the nodes running CGYRO). Moreover, for 
+platforms that do not use the system stack limit for OpenMP 
+threads, also set
 
-Moreover, for platform that do not use the 
-system stack limit for OpenMP threads, also set
 export OMP_STACKSIZE=32M
 
 This should be sufficient for at least 128 omp threads.

cgyro/bin/cgyro

@@ -53,6 +53,9 @@ then
   echo "         -rs <case>"
   echo "         Run specified regression case."
   echo
+  echo "         -rt"
+  echo "         Enable restart regression testing."
+  echo
   echo "         -reset"
   echo "         Reset regression data."
   echo
@@ -104,6 +107,7 @@ MPINUMA=0
 TEST_FLAG=0
 GENERATE_FLAG=0
 REGRESS_FLAG=0
+REGRESS_RESTART=0
 MTEST_FLAG=0
 CLEAN=0
 COMPRESS_FLAG=0
@@ -142,6 +146,8 @@ while [ $# -gt 0 ] ; do
 
   -rs) REGRESS_FLAG=1 ; shift ; SCASE=$1 ;;
 
+  -rt) REGRESS_RESTART=1 ;;
+
   -reset) RESET=1 ;;
 
   -m) MTEST_FLAG=1 ;;
@@ -219,7 +225,12 @@ then
       exit 1
    fi
    # NOMP=1 RESET=0
-   gacode_reg_do $NPROC $NOMP $RESET cgyro 1e-6 $SCASE
+   if [ $REGRESS_RESTART -eq 0 ]
+   then
+      gacode_reg_do $NPROC $NOMP $RESET cgyro 1e-6 $SCASE
+   else
+      gacode_reg_do_restart $NPROC $NOMP $RESET cgyro 1e-6 $SCASE
+   fi
    exit 0
 fi
 #============================================================
@@ -325,7 +336,7 @@ then
    version_tag=`gacode_getversion`
    if [ -f out.cgyro.tag ]
    then
-      simtime=`tail -1 out.cgyro.tag`
+      simtime=`head -n2 out.cgyro.tag | tail -n1`
       simtime=`echo $simtime`
    else
       simtime=0.0

cgyro/bin/cgyro_converge

@@ -0,0 +1,116 @@
+#!/usr/bin/env python
+
+import numpy as np
+import os
+import matplotlib as mpl
+import matplotlib.pyplot as plt
+
+from pygacode.cgyro import data
+from pygacode.gacodefuncs import *
+
+
+# --- to visualize results for one case plot=True------
+plot=True
+
+if plot:
+    directory='./'
+    write_output=False
+else:
+    directory= "/global/cfs/cdirs/cgyrodb/"
+    write_output=True
+    fout = "./cases_results_20%.txt"
+    fo = open(fout, "w")
+
+
+for path, folders, files in os.walk(directory):
+    # Open file#
+    for filename in files:
+      if 'out.cgyro.info' in filename:
+        if write_output:          
+           fo.write(f"#-----{path}-----#")
+        # read minimal data for setup (look in current directory)
+        sim = data.cgyrodata(f'{path}/',fast=True,silent=True)
+
+        # copy time vector and number of species
+        t = sim.t
+        ns = sim.n_species
+        linestyles=['-','--',':','-.']
+        # read bin.cgyro.ky_flux
+        sim.getflux()
+
+
+        # Simulation length (max time)
+        tmax = t[-1]
+
+
+
+
+        # size and number of time windows
+        #dt = 50.0
+        #nwin = int(tmax/dt)
+        nwin=8
+        dt=tmax/nwin
+        t0 = tmax-nwin*dt
+
+
+        if plot:
+         #add plot for visualization
+         fig = plt.figure(figsize=(12,6))
+
+         plt.xlabel('time [$c_s$/a]')
+         plt.ylabel('Flux')
+         colors = mpl.cm.rainbow(np.linspace(0, 1, nwin))
+
+
+        convergance = True
+
+        # select field=0 (phi), moment=1 (Q), species (0), and sum over kx
+        for species_index in range(ns):
+          field=0 ; moment=1 ; 
+          species=species_index
+          y = np.sum(sim.ky_flux[species,moment,field,:,:],axis=0)
+
+          if plot:
+           plt.plot(t,y, label=f"Q_{species_index}", linestyle=linestyles[species_index], color=colors[species_index])
+
+          average_array=[]
+
+         # averaging over all windows (note that time_average function is fast/optimized)
+          for i in range(nwin):
+            w=str(tmax-(i+1)*dt)+','+str(tmax-i*dt)
+
+            imin,imax=time_index(t,w)               
+
+            ave = time_average(y[:],t,imin,imax)
+            average_array.append(ave)
+            if plot:
+              plt.hlines(y=ave, xmin=t[imin], xmax=t[imax], color=colors[i], lw=3, linestyle=linestyles[species_index])
+
+
+
+
+
+
+
+        # define the convergence by std between last free averaged regions as a pesentage to the total
+
+          if np.std(average_array[:3]/np.mean(average_array[:3])) > 0.2:
+            convergance = False
+
+        if convergance:
+            if write_output:
+              fo.write("TRUE \n")
+            else:
+               plt.title('Converged')
+        else:
+            if write_output:
+              fo.write("FALSE \n")
+            else:
+              plt.title("Didn't converge")
+
+        if plot:
+          plt.legend()
+          plt.show()
+
+
+