Merge branch 'le3_gk' of github.com:gafusion/gacode into le3_gk

Makefile

@@ -6,6 +6,7 @@ all:
 	cd vgen ; make
 	cd tglf ; make
 	cd cgyro ; make
+	cd xgyro ; make
 	cd gyro ; make
 	cd tgyro ; make
 	cd profiles_gen ; make
@@ -21,6 +22,7 @@ clean:
 	cd vgen ; make clean
 	cd tglf ; make clean
 	cd cgyro ; make clean
+	cd xgyro ; make clean
 	cd gyro ; make clean
 	cd tgyro ; make clean
 	cd profiles_gen ; make clean
@@ -42,6 +44,7 @@ distclean:
 	cd neo ; make clean
 	cd tglf ; make clean
 	cd cgyro ; make clean
+	cd xgyro ; make clean
 	cd gyro ; make clean
 	cd tgyro ; make clean
 	cd profiles_gen ; make clean

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()
 
@@ -105,6 +105,8 @@ d['MACH'] = sim.mach
 d['GAMMA_E'] = sim.gamma_e
 d['GAMMA_P'] = sim.gamma_p
 d['BETAE_UNIT'] = sim.betae_unit
+d['NU_EE'] = sim.nu[ielec]
+d['Z_EFF'] = sim.z_eff
 
 d['ZMAG'] = sim.zmag
 d['DZMAG'] = sim.dzmag
@@ -129,7 +131,7 @@ 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')
 #==================================================================
@@ -138,7 +140,7 @@ 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:
@@ -164,6 +166,9 @@ print('cgyro_json: wrote out.cgyro.localdump')
 
 nmax = nmax+1
 
+if nmax < 3:
+    nmax = 3
+
 # Reference dimensions in CGYRO units
 lref=sim.rmaj
 vthref = np.sqrt(2.0)
@@ -227,7 +232,7 @@ 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_check_memory.F90

@@ -40,6 +40,12 @@ subroutine cgyro_check_memory(datafile)
      else
         call cgyro_alloc_add_3d(io,5,nc,nt_loc,8,'gcoef')
      endif
+     if ((collision_model /= 5) .AND. (collision_field_model == 1)) then
+       call cgyro_alloc_add_3d(io,n_field,nt_loc,nc,16,'field_v')
+       call cgyro_alloc_add_3d(io,n_field,nt_loc,nc_loc,16,'field_loc_v')
+       call cgyro_alloc_add_4d(io,n_field,nv,nt_loc,nc_loc,8,'dvjvec_v')
+     endif
+     call cgyro_alloc_add_4d(io,n_field,nc,nv_loc,nt_loc,8,'dvjvec_c')
 
      if (nonlinear_flag == 1) then
         write(io,*)

cgyro/src/cgyro_cleanup.F90

@@ -104,6 +104,14 @@ subroutine cgyro_cleanup
      ccl_del_device(gcoef)     
      deallocate(gcoef)
   endif
+  if(allocated(field_v))  then
+     ccl_del_device(field_v)     
+     deallocate(field_v)
+  endif
+  if(allocated(field_loc_v))  then
+     ccl_del_device(field_loc_v)     
+     deallocate(field_loc_v)
+  endif
   if(allocated(field))  then
      ccl_del_device(field)     
      deallocate(field)

cgyro/src/cgyro_field.F90

@@ -28,7 +28,7 @@ subroutine cgyro_field_v_notae_s(start_t)
 
   call timer_lib_in('field')
 
-  field_loc(:,:,start_t:nt2) = (0.0,0.0)
+  field_loc_v(:,:,:) = (0.0,0.0)
 
   ! Poisson and Ampere RHS integrals of H
 
@@ -37,13 +37,13 @@ subroutine cgyro_field_v_notae_s(start_t)
   call parallel_lib_nj_loc(nj_loc)
 
 !$omp parallel do collapse(2) private(ic_loc,iv,ic,k,j)
-  do itor=start_t,nt2
-   do ic=nc1,nc2
+  do ic=nc1,nc2
+   do itor=start_t,nt2
      ic_loc = ic-nc1+1
      do k=1,nproc
       do j=1,nj_loc
         iv = j+(k-1)*nj_loc
-        field_loc(:,ic,itor) = field_loc(:,ic,itor)+dvjvec_v(:,ic_loc,itor,iv)*fsendf(j,itor,ic_loc,k)
+        field_loc_v(:,itor,ic) = field_loc_v(:,itor,ic)+dvjvec_v(:,iv,itor,ic_loc)*fsendf(j,itor,ic_loc,k)
       enddo
      enddo
    enddo
@@ -53,8 +53,7 @@ subroutine cgyro_field_v_notae_s(start_t)
 
   call timer_lib_in('field_com')
 
-  call parallel_lib_sum_field(field_loc(:,:,start_t:nt2), &
-                              field(:,:,start_t:nt2))
+  call parallel_lib_collect_field(field_loc_v, field_v)
 
   call timer_lib_out('field_com')
 
@@ -63,8 +62,10 @@ subroutine cgyro_field_v_notae_s(start_t)
   ! Poisson LHS factors
 !$omp parallel do
   do itor=start_t,nt2
+    do ic=1,nc
      ! assuming  (.not.(itor == 0 .and. ae_flag == 1))
-     field(:,:,itor) = fcoef(:,:,itor)*field(:,:,itor)
+     field(:,ic,itor) = fcoef(:,ic,itor)*field_v(:,itor,ic)
+    enddo
   enddo
 
   call timer_lib_out('field')
@@ -117,37 +118,21 @@ subroutine cgyro_field_v_notae_s_gpu(start_t)
 
 #if (!defined(OMPGPU)) && defined(_OPENACC)
 !$acc data present(fsendf)
-!$acc data present(field,field_loc)
+!$acc data present(field,field_v,field_loc_v)
 #endif
 
   ! Poisson and Ampere RHS integrals of H
 
-#if defined(OMPGPU)
-!$omp target teams distribute parallel do simd collapse(3) &
-!$omp&   map(to:start_t)
-#elif defined(_OPENACC)
-!$acc parallel loop collapse(3) gang vector &
-!$acc&         independent copyin(start_t) &
-!$acc&         present(nt2,nc,n_field) default(none)
-#endif
-  do itor=start_t,nt2
-   do ic=1,nc
-       do i_f=1,n_field
-        field_loc(i_f,ic,itor) = (0.0,0.0)
-       enddo
-   enddo
-  enddo
-
 #if defined(OMPGPU)
 !$omp target teams distribute collapse(3) &
 !$omp&       private(ic_loc,field_loc_l) map(to:start_t,nproc,nj_loc)
 #elif defined(_OPENACC)
 !$acc parallel loop collapse(3) gang private(ic_loc,field_loc_l) &
-!$acc&         present(dvjvec_v,fsendf,field_loc) copyin(start_t,nproc,nj_loc) &
+!$acc&         present(dvjvec_v,fsendf) copyin(start_t,nproc,nj_loc) &
 !$acc&         present(nt2,nc1,nc2,n_field,nv) default(none)
 #endif
-  do itor=start_t,nt2
-   do ic=nc1,nc2
+  do ic=nc1,nc2
+   do itor=start_t,nt2
     do i_f=1,n_field
       ic_loc = ic-nc1+1
       field_loc_l = (0.0,0.0)
@@ -160,10 +145,10 @@ subroutine cgyro_field_v_notae_s_gpu(start_t)
       do k=1,nproc
        do j=1,nj_loc
         iv = j+(k-1)*nj_loc
-        field_loc_l = field_loc_l+dvjvec_v(i_f,ic_loc,itor,iv)*fsendf(j,itor,ic_loc,k)
+        field_loc_l = field_loc_l+dvjvec_v(i_f,iv,itor,ic_loc)*fsendf(j,itor,ic_loc,k)
       enddo
      enddo
-     field_loc(i_f,ic,itor) = field_loc_l
+     field_loc_v(i_f,itor,ic) = field_loc_l
     enddo
    enddo
   enddo
@@ -172,8 +157,7 @@ subroutine cgyro_field_v_notae_s_gpu(start_t)
 
   call timer_lib_in('field_com')
 
-  call parallel_lib_sum_field_gpu(field_loc(:,:,start_t:nt2), &
-                                  field(:,:,start_t:nt2))
+  call parallel_lib_collect_field_gpu(field_loc_v, field_v)
 
   call timer_lib_out('field_com')
 
@@ -191,7 +175,7 @@ subroutine cgyro_field_v_notae_s_gpu(start_t)
      ! assuming  (.not.(itor == 0 .and. ae_flag == 1))
      do ic=1,nc
        do i_f=1,n_field
-        field(i_f,ic,itor) = fcoef(i_f,ic,itor)*field(i_f,ic,itor)
+        field(i_f,ic,itor) = fcoef(i_f,ic,itor)*field_v(i_f,itor,ic)
        enddo
      enddo
   enddo