From 3854d511ccaca74f5c70fb76c57cb4e86fe7a35e Mon Sep 17 00:00:00 2001
From: Jeff Candy <candy@fusion.gat.com>
Date: Thu, 17 Oct 2024 20:44:18 -0700
Subject: [PATCH] Conversion seems to be working

---
 cgyro/bin/cgyro_json            | 11 ++++++++---
 cgyro/src/cgyro_globalshear.F90 | 10 +++++-----
 2 files changed, 13 insertions(+), 8 deletions(-)

diff --git a/cgyro/bin/cgyro_json b/cgyro/bin/cgyro_json
index 3ee904e33..5f4f97815 100755
--- a/cgyro/bin/cgyro_json
+++ b/cgyro/bin/cgyro_json
@@ -37,8 +37,8 @@ with open('input.cgyro.gen','r') as file:
       u = line.split()
       key = u[1]
       value = u[0]
-      if key in default.keys():
-         if str(value) != str(default[key]):
+      if key in default.keys() and 'SHAPE' not in key:
+         if str(value) != str(default[key]): 
             d[key] = value
 
 # Code-specific parameters
@@ -71,6 +71,8 @@ d['S_ZETA'] = sim.s_zeta
 
 d['SHAPE_SIN'] = sim.shape_sin[:].tolist()
 d['SHAPE_COS'] = sim.shape_cos[:].tolist()
+d['SHAPE_S_SIN'] = sim.shape_s_sin[:].tolist()
+d['SHAPE_S_COS'] = sim.shape_s_cos[:].tolist()
 
 d['Z'] = sim.z[:].tolist()
 d['MASS'] = sim.mass[:].tolist()
@@ -92,15 +94,18 @@ with open('out.cgyro.localdump','w') as f:
    for key in d:
       x = d[key]
       if 'SHAPE' in key:
+         # shape parameter
          for i in range(len(x)):
             if not x[i] == 0.0:
-               f.write(key+'_'+str(i)+'='+str(x[i])+'\n')
+               f.write(key+str(i)+'='+str(x[i])+'\n')
                if i > nmax:
                   nmax = i
       elif isinstance(x,list):
+         # species parameter
          for i in range(len(x)):
             f.write(key+'_'+str(i+1)+'='+str(x[i])+'\n')
       else:
+         # standard scalar parameter
          f.write(key+'='+str(x)+'\n')
          
 #==================================================================
diff --git a/cgyro/src/cgyro_globalshear.F90 b/cgyro/src/cgyro_globalshear.F90
index f443d2c6d..632d0317e 100644
--- a/cgyro/src/cgyro_globalshear.F90
+++ b/cgyro/src/cgyro_globalshear.F90
@@ -22,14 +22,14 @@ subroutine cgyro_globalshear(ij)
   
 #if defined(OMPGPU)
 !$omp target teams distribute parallel do simd collapse(4) &
-!$omp&         private(ivc,ir,l,iccj,j,ll,rl,llnt,h1,h2)
+!$omp private(ivc,ir,l,iccj,j,ll,rl,llnt,h1,h2)
 #elif defined(_OPENACC)
 !$acc parallel loop collapse(4) gang vector &
-!$acc&         private(ivc,ir,l,iccj,j,ll,rl,llnt,h1,h2) &
-!$acc&         present(rhs(:,:,:,ij),omega_ss,omega_sbeta,field,cap_h_c,h_x,c_wave)
+!$acc private(ivc,ir,l,iccj,j,ll,rl,llnt,h1,h2) &
+!$acc present(rhs(:,:,:,ij),omega_ss,omega_sbeta,field,cap_h_c,h_x,c_wave)
 #else
-!$omp parallel do collapse(3) private(ivc,ir,l,iccj,j,ll,rl,llnt,h1,h2)
-!$omp&         firstprivate(shear_method)
+!$omp parallel do collapse(3) private(ivc,ir,l,iccj,j,ll,rl,llnt,h1,h2) &
+!$omp firstprivate(shear_method)
 #endif
   do itor=nt1,nt2
      do ivc=1,nv_loc