3004 remove remnants of plasmod functionality

.gitignore

@@ -51,19 +51,7 @@ untracked.info
 com.msg
 Katy_test/*
 KatyTest/*
-PLASMOD/CHARTST/*
-PLASMOD/*.DAT
-PLASMOD/*.dat
-PLASMOD/fort.*
-PLASMOD/output_list.txt
-PLASMOD/KE*
 *~
-lib/PLASMOD/CHARTST/*
-lib/PLASMOD/*.DAT
-/lib/PLASMOD/*.dat
-/lib/PLASMOD/fort.*
-/lib/PLASMOD/output_list.txt
-/lib/PLASMOD/KE*
 /utilities/run_process.conf
 *.fdb_latexmk
 *.fls

documentation/proc-pages/fusion-devices/stellarator.md

@@ -154,7 +154,7 @@ Here $\bar{\iota}$ is the rotational transform, which is equivalent to the recip
 
 ### Gradient informed neoclassical transport checks
 
-As no 1D solver options are available for stellarators yet (the PLASMOD module can not be called yet for stellarator-PROCESS), PROCESS prints several neoclassics parameters as obtained from the 1/$\nu$ regime.
+As no 1D solver options are available for stellarators yet, PROCESS prints several neoclassics parameters as obtained from the 1/$\nu$ regime.
 The two most important parameters are `q_PROCESS` and `total_q_neo_e`.
 `q_PROCESS` is the heat flux that PROCESS obtaines from the 0D confinement time scalings.
 `total_q_neo_e` is the estimated total neoclassical flux as obtained from the 1/$\nu$ electron transport regime, multiplied by a factor of 4 (2 for the ion contribution and another factor of 2 for the radial electrical field influence).

documentation/proc-pages/physics-models/plasma.md

@@ -190,7 +190,6 @@ be described as 1/2-D.  The relevant profile index variables are
 
 If `ipedestal` = 1, 2 or 3 the density and temperature profiles include a pedestal.  
 If `ipedestal` = 1 the density and temperature profiles use the forms given below [^6].  
-If `ipedestal` = 2 or 3 the profiles are determined by the transport code PLASMOD.
 
 $$\begin{aligned}
 \mbox{density:} \qquad n(\rho) = \left\{ 

documentation/proc-pages/usage/running-process.md

@@ -59,7 +59,7 @@ ORIGINAL_IN_DAT = ref_IN.DAT
 * PROCESS= ../../../process.exe
 
 * ONE line comment to be put into README.txt
-COMMENT = ipedestal = 1, with other variables appropriate for running PLASMOD
+COMMENT = 
 
 * Max no. iterations
 NITER = 1000

process/caller.py

@@ -64,15 +64,6 @@ def call_models(self, xc):
 
         self.models.physics.physics()
 
-        # call build subroutines again if PLASMOD used, issue #650
-        if ft.physics_variables.ipedestal == 3:
-            # Radial build
-            self.models.build.radialb(output=False)
-
-            # TODO: is the vertical build needed again?
-            # Vertical build
-            self.models.build.vbuild(output=False)
-
         # startup model (not used)
         # call startup(ft.constants.nout,0)  !  commented-out for speed reasons
 

process/current_drive.py

@@ -256,21 +256,12 @@ def cudriv(self, output: bool):
                     0.999, current_drive_variables.forbitloss
                 )  # Should never be needed
 
-                if physics_variables.ipedestal != 3:  # When not using PLASMOD
-                    pnbitotfix = current_drive_variables.pinjfixmw / (
-                        1.0e0
-                        - current_drive_variables.forbitloss
-                        + current_drive_variables.forbitloss
-                        * current_drive_variables.nbshinef
-                    )
-                else:
-                    # Netural beam power calculated by PLASMOD
-                    pnbitotfix = current_drive_variables.pinjmw / (
-                        1.0e0
-                        - current_drive_variables.forbitloss
-                        + current_drive_variables.forbitloss
-                        * current_drive_variables.nbshinef
-                    )
+                pnbitotfix = current_drive_variables.pinjfixmw / (
+                    1.0e0
+                    - current_drive_variables.forbitloss
+                    + current_drive_variables.forbitloss
+                    * current_drive_variables.nbshinef
+                )
 
                 # Shinethrough power (atoms that are not ionised) [MW]:
                 nbshinemwfix = pnbitotfix * current_drive_variables.nbshinef
@@ -478,21 +469,12 @@ def cudriv(self, output: bool):
                     0.999, current_drive_variables.forbitloss
                 )  # Should never be needed
 
-                if physics_variables.ipedestal != 3:  # When not using PLASMOD
-                    current_drive_variables.pnbitot = power1 / (
-                        1.0e0
-                        - current_drive_variables.forbitloss
-                        + current_drive_variables.forbitloss
-                        * current_drive_variables.nbshinef
-                    )
-                else:
-                    # Neutral beam power calculated by PLASMOD
-                    current_drive_variables.pnbitot = current_drive_variables.pinjmw / (
-                        1.0e0
-                        - current_drive_variables.forbitloss
-                        + current_drive_variables.forbitloss
-                        * current_drive_variables.nbshinef
-                    )
+                current_drive_variables.pnbitot = power1 / (
+                    1.0e0
+                    - current_drive_variables.forbitloss
+                    + current_drive_variables.forbitloss
+                    * current_drive_variables.nbshinef
+                )
 
                 # Shinethrough power (atoms that are not ionised) [MW]:
                 current_drive_variables.nbshinemw = (

process/io/plot_proc.py

@@ -800,34 +800,6 @@ def plot_nprofile(prof, demo_ranges):
     # ---
 
 
-def plot_plasmod_nprofile(prof, demo_ranges):
-    """Function to plot plasmod density profile
-    Arguments:
-      prof --> axis object to add plot to
-    """
-
-    prof.set_xlabel("r/a")
-    prof.set_ylabel(r"$n_{e}\cdot 10^{19} \mathrm{m}^{-3}$")
-    prof.set_title("Density profile")
-    prof.plot(pmod_r, pmod_ne, label="plasmod $n_e$")
-    prof.plot(pmod_r, pmod_ni, label="plasmod $n_i$")
-    prof.plot(pmod_r, pmod_nt, label="plasmod $n_T$")
-    prof.plot(pmod_r, pmod_nd, label="plasmod $n_D$")
-    prof.legend()
-
-    # Ranges
-    # ---
-    # DEMO : Fixed ranges for comparison
-    prof.set_xlim([0, 1])
-    if demo_ranges:
-        prof.set_ylim([0, 20])
-
-    # Adapatative ranges
-    else:
-        prof.set_ylim([0, prof.get_ylim()[1]])
-    # ---
-
-
 def plot_tprofile(prof, demo_ranges):
     """Function to plot temperature profile
     Arguments:
@@ -869,32 +841,6 @@ def plot_tprofile(prof, demo_ranges):
     # ---
 
 
-def plot_plasmod_tprofile(prof, demo_ranges):
-    """Function to plot plasmod temperature profile
-    Arguments:
-      prof --> axis object to add plot to
-    """
-
-    prof.set_xlabel("r/a")
-    prof.set_ylabel("$T_{e}$ [keV]")
-    prof.set_title("Temperature profile")
-    prof.plot(pmod_r, pmod_te, label="plasmod $T_e$")
-    prof.plot(pmod_r, pmod_ti, label="plasmod $T_i$")
-    prof.legend()
-
-    # Ranges
-    # ---
-    prof.set_xlim([0, 1])
-    # DEMO : Fixed ranges for comparison
-    if demo_ranges:
-        prof.set_ylim([0, 50])
-
-    # Adapatative ranges
-    else:
-        prof.set_ylim([0, prof.get_ylim()[1]])
-    # ---
-
-
 def plot_qprofile(prof, demo_ranges):
     """Function to plot q profile, formula taken from Nevins bootstrap model.
 
@@ -927,31 +873,6 @@ def plot_qprofile(prof, demo_ranges):
     # ---
 
 
-def plot_plasmod_qprofile(prof, demo_ranges):
-    """Function to plot plasmod q profile
-    Arguments:
-      prof --> axis object to add plot to
-    """
-
-    prof.set_xlabel("r/a")
-    prof.set_ylabel("-")
-    prof.set_title("q profile")
-    prof.plot(pmod_r, pmod_q, label="plasmod $q(r/a)$")
-    prof.legend()
-
-    # Ranges
-    # ---
-    prof.set_xlim([0, 1])
-    # DEMO : Fixed ranges for comparison
-    if demo_ranges:
-        prof.set_ylim([0, 10])
-
-    # Adapatative ranges
-    else:
-        prof.set_ylim([0, prof.get_ylim()[1]])
-    # ---
-
-
 def read_imprad_data(skiprows, data_path):
     """Function to read all data needed for creation of radiation profile
 
@@ -2443,7 +2364,6 @@ def main_plot(
     fig2,
     m_file_data,
     scan,
-    plasmod=False,
     imp="../data/lz_non_corona_14_elements/",
     demo_ranges=False,
 ):
@@ -2454,7 +2374,6 @@ def main_plot(
       fig2 --> figure object to add plot to.
       m_file_data --> MFILE.DAT data to read
       scan --> scan to read from MFILE.DAT
-      plasmod --> plasmod data or not
       imp --> path to impurity data
     """
 
@@ -2488,26 +2407,16 @@ def main_plot(
 
     # Plot density profiles
     plot_4 = fig2.add_subplot(234)  # , aspect= 0.05)
-    if plasmod:
-        plot_plasmod_nprofile(plot_4, demo_ranges)
-    else:
-        plot_nprofile(plot_4, demo_ranges)
+    plot_nprofile(plot_4, demo_ranges)
 
     # Plot temperature profiles
     plot_5 = fig2.add_subplot(235)  # , aspect= 1/35)
-    if plasmod:
-        plot_plasmod_tprofile(plot_5, demo_ranges)
-    else:
-        plot_tprofile(plot_5, demo_ranges)
+    plot_tprofile(plot_5, demo_ranges)
 
-    if plasmod:
-        plot_6 = fig2.add_subplot(236)  # , aspect=1/10)
-        plot_plasmod_qprofile(plot_6, demo_ranges)
-    else:
-        # plot_qprofile(plot_6)
-        plot_6 = fig2.add_subplot(236)  # , aspect=2)
-        if os.path.isdir(imp):
-            plot_radprofile(plot_6, m_file_data, scan, imp, demo_ranges)
+    # plot_qprofile(plot_6)
+    plot_6 = fig2.add_subplot(236)  # , aspect=2)
+    if os.path.isdir(imp):
+        plot_radprofile(plot_6, m_file_data, scan, imp, demo_ranges)
 
     # plot_7 =
     # plot_radprofile(plot_7)
@@ -2807,8 +2716,7 @@ def parse_args(args):
     # Setup command line arguments
     parser = argparse.ArgumentParser(
         description="Produces a two page summary of the PROCESS MFILE output, using the MFILE.  "
-        "For info contact michael.kovari@ukaea.uk or james.morris2@ukaea.uk.  "
-        "If using PLASMOD you must specify the profile file using -m."
+        "For info please see https://github.com/ukaea/PROCESS?tab=readme-ov-file#contacts "
     )
 
     parser.add_argument(
@@ -2818,14 +2726,6 @@ def parse_args(args):
         default="",
         help="specify input/output file path",
     )
-    parser.add_argument(
-        "-m",
-        metavar="PLASMODFILE",
-        type=str,
-        default="",
-        help="specify PLASMOD profile file",
-    )
-
     parser.add_argument("-s", "--show", help="show plot", action="store_true")
 
     parser.add_argument("-n", type=int, help="Which scan to plot?")
@@ -3005,32 +2905,6 @@ def main(args=None):
     # Alpha press(keV*10^10 m^-3) -- 14
     # Ion dens(10^19 m^-3) -- 15
     # Poloidal flux (Wb) -- 16
-    if args.m != "":
-        global pmod_r
-        global pmod_ne
-        global pmod_te
-        global pmod_ti
-        global pmod_nd
-        global pmod_nt
-        global pmod_q
-        global pmod_ni
-
-        plasmod_profiles = np.loadtxt(args.m).transpose()
-        pmod_r = plasmod_profiles[0]
-        pmod_ne = plasmod_profiles[1]
-        pmod_te = plasmod_profiles[2]
-        pmod_ti = plasmod_profiles[3]
-        pmod_nd = plasmod_profiles[4]
-        pmod_nt = plasmod_profiles[5]
-        pmod_q = plasmod_profiles[10]
-        pmod_ni = plasmod_profiles[15]
-        pmod_switch = True
-        print("plasmod!")
-    else:
-        if ipedestal == 2 or ipedestal == 3:
-            print("\n ERROR: Specify the PLASMOD profile file using -m \n")
-            exit()
-        pmod_switch = False
     # rad profile
     global ssync
     global bt
@@ -3104,9 +2978,7 @@ def main(args=None):
     page2 = plt.figure(figsize=(12, 9), dpi=80)
 
     # run main_plot
-    main_plot(
-        page1, page2, m_file, scan=scan, plasmod=pmod_switch, demo_ranges=demo_ranges
-    )
+    main_plot(page1, page2, m_file, scan=scan, demo_ranges=demo_ranges)
 
     # with bpdf.PdfPages(args.o) as pdf:
     with bpdf.PdfPages(args.f + "SUMMARY.pdf") as pdf:

process/io/run_process.conf

@@ -16,7 +16,7 @@ ORIGINAL_IN_DAT = PROCESS_DIR/RUN_DIR/STEP_IN.DAT
 * PROCESS= PROCESS_DIR/bin/process.exe
 
 * ONE line comment to be put into README.txt
-COMMENT = ipedestal = 1, with other variables appropriate for running PLASMOD
+COMMENT = 
 
 * Max no. iterations
 NITER = 50

process/output.py

@@ -48,10 +48,6 @@ def write(models, outfile):
     # Writing the output from physics.f90 into OUT.DAT + MFILE.DAT
     ft.physics_module.outplas(outfile)
 
-    # Writing
-    if ft.physics_variables.ipedestal == 2 or ft.physics_variables.ipedestal == 3:
-        ft.plasmod_module.outputplasmod(outfile)
-
     # TODO what is this? not in caller.f90
     ft.physics_module.igmarcal(outfile)
 

process/physics.py

@@ -182,7 +182,6 @@ def physics(self):
             physics_variables.vol,
         )
 
-        # Profile parameters are meaningless with ipedestal=3
         betat = (
             physics_variables.beta
             * physics_variables.btot**2