Merge pull request #424 from gafusion/ssd/add_kinetic_pressure

Add kinetic pressure

Author: torrinba

omas/machine_mappings/d3d.json

@@ -71,16 +71,16 @@
  "charge_exchange.channel.:.ion.:": {
   "PYTHON": "charge_exchange_data(ods, {pulse}, {analysis_type!r})"
  },
- "charge_exchange.channel.:.ion.:.n_i_over_n_e.data": {
+ "charge_exchange.channel.:.ion.:.n_i.data": {
   "PYTHON": "charge_exchange_data(ods, {pulse}, {analysis_type!r})"
  },
- "charge_exchange.channel.:.ion.:.n_i_over_n_e.time": {
+ "charge_exchange.channel.:.ion.:.n_i.time": {
   "PYTHON": "charge_exchange_data(ods, {pulse}, {analysis_type!r})"
  },
-  "charge_exchange.channel.:.ion.:.n_i.data": {
+ "charge_exchange.channel.:.ion.:.n_i_over_n_e.data": {
   "PYTHON": "charge_exchange_data(ods, {pulse}, {analysis_type!r})"
  },
- "charge_exchange.channel.:.ion.:.n_i.time": {
+ "charge_exchange.channel.:.ion.:.n_i_over_n_e.time": {
   "PYTHON": "charge_exchange_data(ods, {pulse}, {analysis_type!r})"
  },
  "charge_exchange.channel.:.ion.:.t_i.data": {
@@ -188,6 +188,9 @@
  "core_profiles.profiles_1d.:.electrons.density_thermal_error_upper": {
   "PYTHON": "core_profiles_profile_1d(ods, {pulse}, {PROFILES_tree!r}, {PROFILES_run_id!r}, {core_profiles_strict_grid!r})"
  },
+ "core_profiles.profiles_1d.:.electrons.pressure": {
+  "PYTHON": "core_profiles_profile_1d(ods, {pulse}, {PROFILES_tree!r}, {PROFILES_run_id!r}, {core_profiles_strict_grid!r})"
+ },
  "core_profiles.profiles_1d.:.electrons.temperature": {
   "PYTHON": "core_profiles_profile_1d(ods, {pulse}, {PROFILES_tree!r}, {PROFILES_run_id!r}, {core_profiles_strict_grid!r})"
  },
@@ -296,14 +299,23 @@
   "COCOSIO": 11,
   "PYTHON": "core_profiles_profile_1d(ods, {pulse}, {PROFILES_tree!r}, {PROFILES_run_id!r}, {core_profiles_strict_grid!r})"
  },
+ "core_profiles.profiles_1d.:.pressure_ion_non_thermal": {
+  "PYTHON": "core_profiles_profile_1d(ods, {pulse}, {PROFILES_tree!r}, {PROFILES_run_id!r}, {core_profiles_strict_grid!r})"
+ },
+ "core_profiles.profiles_1d.:.pressure_ion_total": {
+  "PYTHON": "core_profiles_profile_1d(ods, {pulse}, {PROFILES_tree!r}, {PROFILES_run_id!r}, {core_profiles_strict_grid!r})"
+ },
  "core_profiles.profiles_1d.:.pressure_perpendicular": {
   "PYTHON": "core_profiles_profile_1d(ods, {pulse}, {PROFILES_tree!r}, {PROFILES_run_id!r}, {core_profiles_strict_grid!r})"
  },
+ "core_profiles.profiles_1d.:.pressure_total": {
+  "PYTHON": "core_profiles_profile_1d(ods, {pulse}, {PROFILES_tree!r}, {PROFILES_run_id!r}, {core_profiles_strict_grid!r})"
+ },
  "core_profiles.profiles_1d.:.time": {
   "PYTHON": "core_profiles_profile_1d(ods, {pulse}, {PROFILES_tree!r}, {PROFILES_run_id!r}, {core_profiles_strict_grid!r})"
  },
  "core_profiles.time": {
-  "PYTHON": "core_profiles_global_quantities_data(ods, {pulse}, {PROFILES_tree!r}, {PROFILES_run_id!r})"
+  "PYTHON": "core_profiles_profile_1d(ods, {pulse}, {PROFILES_tree!r}, {PROFILES_run_id!r}, {core_profiles_strict_grid!r})"
  },
  "ec_launchers.beam.:": {
   "PYTHON": "ec_launcher_active_hardware(ods, {pulse})"
@@ -968,4 +980,4 @@
  "wall.time": {
   "PYTHON": "wall(ods, {pulse}, {EFIT_tree!r}, {EFIT_run_id!r})"
  }
-}
+}

omas/machine_mappings/d3d.py

@@ -1964,6 +1964,13 @@ def add_extra_profile_structures():
     extra_structures["core_profiles"][f"core_profiles.profiles_1d[:].ion[:].velocity.toroidal_fit.psi_norm"] = velo_struct
     extra_structures["core_profiles"][f"core_profiles.profiles_1d[:].ion[:].velocity.toroidal_fit.measured"] = velo_struct
     extra_structures["core_profiles"][f"core_profiles.profiles_1d[:].ion[:].velocity.toroidal_fit.measured_error_upper"] = velo_struct
+    # electrons.pressure and pressure_ion_total are standard IMAS nodes; these two are not
+    pressure_struct = {"coordinates": sh + "[:].grid.rho_tor_norm"}
+    pressure_struct["documentation"] = "Pressure profile added for DIII-D OMFIT_PROFS"
+    pressure_struct["data_type"] = "FLT_1D"
+    pressure_struct["units"] = "Pa"
+    for quant in ["pressure_ion_non_thermal", "pressure_total"]:
+        extra_structures["core_profiles"][f"core_profiles.profiles_1d[:].{quant}"] = pressure_struct
     add_extra_structures(extra_structures)
 
 
@@ -2006,10 +2013,16 @@ def core_profiles_profile_1d(ods, pulse, PROFILES_tree="OMFIT_PROFS", PROFILES_r
         query["ion[1].velocity.toroidal_fit.psi_norm"]= "PS_V_TOR_C"
         query["e_field.radial"] = "ER_C"
         query["grid.rho_tor_norm"] = "rho"
+        query["electrons.pressure"] = "P_E"
+        query["pressure_ion_non_thermal"] = "P_FAST_D"
         #query["j_total"] = "J_TOT"
         #query["pressur_perpendicular"] = "P_TOT"
-        
+
         normal_entries = set(query.keys()) - set(uncertain_entries)
+        # Raw ion pressures fetched here but written manually below: pressure_ion_total
+        # and pressure_total are sums and pressure_total is a non-standard structure.
+        query["_pressure_deuterium"] = "P_D"
+        query["_pressure_carbon"] = "P_C"
         omfit_profiles_node = '\\TOP.'
         for entry in query:
             query[entry] = omfit_profiles_node + query[entry]
@@ -2086,6 +2099,15 @@ def core_profiles_profile_1d(ods, pulse, PROFILES_tree="OMFIT_PROFS", PROFILES_r
                     print("================ DATA =================")
                     print(data[entry][i_time])
                     print(e)
+        # pressure_ion_total = P_D + P_C; pressure_total sums the IMAS pressure fields
+        pressure_inputs = ["electrons.pressure", "pressure_ion_non_thermal",
+                           "_pressure_deuterium", "_pressure_carbon"]
+        if not any(isinstance(data[entry], Exception) for entry in pressure_inputs):
+            p_ion_total = data["_pressure_deuterium"] + data["_pressure_carbon"]
+            p_total = data["electrons.pressure"] + data["pressure_ion_non_thermal"] + p_ion_total
+            for i_time, time in enumerate(data["time"]):
+                ods[f"{sh}[{i_time}].pressure_ion_total"] = p_ion_total[i_time][mask[i_time]]
+                ods[f"{sh}[{i_time}].pressure_total"] = p_total[i_time][mask[i_time]]
         for i_time, time in enumerate(data["time"]):
             ods[f"{sh}[{i_time}].ion[0].element[0].z_n"] = 1
             ods[f"{sh}[{i_time}].ion[0].element[0].a"] = 2.0141