Merge branch 'master' into dmd

cgyro/bin/cgyro_json

@@ -25,14 +25,14 @@ def opts():
         description="CGYRO localdump utility",
         epilog=textwrap.dedent(mytext))
 
-    parser.add_argument('-dir',
+    parser.add_argument('-e',
                         help="working directory (default: cwd)",
                         type=str,
                         default='.')
 
     args=parser.parse_args()
 
-    return args.dir
+    return args.e
 
 mydir = opts()
 
@@ -130,7 +130,7 @@ d['DLNNDR'] = sim.dlnndr[:].tolist()
 d['DLNTDR'] = sim.dlntdr[:].tolist()
 
 # JSON output
-with open('json.cgyro.localdump','w') as f:
+with open(mydir+'json.cgyro.localdump','w') as f:
    json.dump(d,f,indent=2,sort_keys=True)
    print('cgyro_json: wrote json.cgyro.localdump')
 #==================================================================
@@ -139,7 +139,7 @@ with open('json.cgyro.localdump','w') as f:
 # standard localdump output
 #
 nmax = 0
-with open('out.cgyro.localdump','w') as f:
+with open(mydir+'out.cgyro.localdump','w') as f:
    for key in d:
       x = d[key]
       if 'SHAPE' in key:
@@ -231,7 +231,7 @@ d['ds_dr_minor_norm'][1] = sim.s_delta*lref/sim.rmin/np.cos(np.arcsin(sim.delta)
 d['ds_dr_minor_norm'][2] = -sim.s_zeta*lref/sim.rmin 
 #-----------------------------------------------------------------------
 
-with open('json.cgyro.imas','w') as f:
+with open(mydir+'json.cgyro.imas','w') as f:
    json.dump(d,f,indent=2,sort_keys=True)
    print('cgyro_json: wrote json.cgyro.imas')
 #==================================================================

cgyro/bin/cgyrodb

@@ -13,6 +13,8 @@ from cgyro.data import cgyrodata
 
 pd.set_option('display.max_rows', None)
 
+ignore = 'eslshared'
+
 # Command line option parser
 def opts():
 
@@ -27,20 +29,32 @@ def opts():
         description="CGYRO database utility",
         epilog=textwrap.dedent(mytext))
 
-    parser.add_argument('-mode',
-                        help='Mode switch (data,update)',
-                        type=str,
-                        default='data')
+    parser.add_argument('-ref',
+                        help='Refresh directories',
+                        action='store_true')
+    parser.add_argument('-json',
+                        help='Generate IMAS and localdump files',
+                        action='store_true')
+    parser.add_argument('-db',
+                        help='Load the DB and print',
+                        action='store_true')
+    parser.add_argument('-flux',
+                        help='Add flux to DB',
+                        action='store_true')
 
     args=parser.parse_args()
 
-    return args.mode
+    return args.ref,args.json,args.db,args.flux
 
-mode = opts()
+ref,json,db,doflux = opts()
 
 meta = {}
 
-def gendict(sim,mode):
+if (not ref) and (not json) and (not db):
+    print('Type "cgyrodb -h" for help')
+    sys.exit()
+
+def gendict(sim,doflux):
 
    mydict = {}
 
@@ -60,9 +74,9 @@ def gendict(sim,mode):
       mydict['a/Ln1'] = 0.0
       mydict['a/Lt1'] = 0.0
 
-   if mode == 'flux':
+   if doflux:
       sim.getflux()
-      y = np.sum(sim.ky_flux,axis=(2,3))   
+      y = np.sum(sim.ky_flux,axis=(2,3))
       for ispec in range(sim.n_species):
          g = average(y[ispec,0,:],sim.t,0.5,0.0)
          q = average(y[ispec,1,:],sim.t,0.5,0.0)
@@ -73,25 +87,31 @@ def gendict(sim,mode):
 
    return mydict
 
-ignore = 'eslshared'
-
 # First locate all directories
 y = []
 for root,xd,xf in os.walk('./'):
    if xd == []:
       if ignore not in root:
           y.append(root)
 
-if mode == 'update':
+if ref:
    # Run through directories and update
    for mdir in y:
-      print('Updating '+mdir)
-      os.system('cgyro -t '+mdir)
-else:
+      print('Refreshing '+mdir)
+      os.system('cd '+mdir+' ; python $GACODE_ROOT/cgyro/bin/cgyro_parse.py')
+      os.system('cd '+mdir+' ; $GACODE_ROOT/cgyro/src/cgyro ')
+
+if json:
+   # Run through directories and update
+   for mdir in y:
+      print('Dumping '+mdir)
+      os.system('cgyro_json -e '+mdir)
+
+if db:
    # Create master dictionary "meta"
    for mdir in tqdm(y):
       sim = cgyrodata(mdir+'/',silent=True)
-      meta[mdir]=gendict(sim,mode)
+      meta[mdir]=gendict(sim,doflux)
 
    df = pd.DataFrame(meta)
    dfpart = df.T[['n_n','n_radial','n_theta','q','s','kappa','a/Ln0','a/Lt0','a/Ln1','a/Lt1','nuee']]

cgyro/src/cgyro_init_arrays.F90

@@ -13,8 +13,7 @@ subroutine cgyro_init_arrays
   integer :: ir,it,is,ie,ix
   integer :: itm,itl,itor,mytor,itf
   integer :: it_loc
-  integer :: jr,jt,id
-  integer :: i_field
+  integer :: jt
   integer :: l,ll
   integer :: iltheta_min
   complex :: carg