Removed coarray for now

cmake/Modules/FindOpenMP_Fortran.cmake

@@ -27,11 +27,11 @@ INCLUDE (${CMAKE_ROOT}/Modules/FindPackageHandleStandardArgs.cmake)
 
 SET (OpenMP_Fortran_FLAG_CANDIDATES
      #Intel
-     "-qopenmp -coarray" 
+     "-qopenmp" 
      #Intel windows
-     "/Qopenmp /Qcoarray" 
+     "/Qopenmp" 
      #Gnu
-     "-fopenmp -fcoarray=lib"
+     "-fopenmp"
      #Portland Group
      "-mp"
      #Empty, if compiler automatically accepts openmp

examples/Basic_Simulation/run_from_file.ipynb

@@ -0,0 +1,119 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "aa57e957-f141-4373-9a62-a91845203aa3",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "env: OMP_NUM_THREADS=8\n"
+     ]
+    }
+   ],
+   "source": [
+    "import swiftest\n",
+    "import xarray as xr\n",
+    "import numpy as np\n",
+    "import os\n",
+    "%env OMP_NUM_THREADS=8"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "a9c020aa-0a87-4fa9-9b11-62213edb370c",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Reading Swiftest file /home/daminton/git_debug/swiftest/examples/Basic_Simulation/simdata/param.in\n",
+      "\n",
+      "Creating Dataset from NetCDF file\n",
+      "Successfully converted 1 output frames.\n"
+     ]
+    }
+   ],
+   "source": [
+    "sim = swiftest.Simulation(read_param=True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "id": "209523b6-d7a8-46f0-8687-54f199015c2d",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Writing parameter inputs to file /home/daminton/git_debug/swiftest/examples/Basic_Simulation/simdata/param.in\n",
+      "Running a Swiftest symba run from tstart=0.0 y to tstop=1000.0 y\n"
+     ]
+    },
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "ca7e9529651b46209bc86174955f7a01",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "Time:   0.0 / 1000.0 y :   0%|          , npl: 14 ntp: 10 nplm: 13"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/home/daminton/git_debug/swiftest/python/swiftest/swiftest/simulation_class.py:465: UserWarning: Error executing main swiftest_driver program\n",
+      "  self._run_swiftest_driver()\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\n",
+      "Creating Dataset from NetCDF file\n",
+      "Successfully converted 19 output frames.\n",
+      "Swiftest simulation data stored as xarray DataSet .data\n"
+     ]
+    }
+   ],
+   "source": [
+    "sim.run()"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python (My debug_env Kernel)",
+   "language": "python",
+   "name": "debug_env"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.8.5"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

python/swiftest/swiftest/simulation_class.py

@@ -383,11 +383,12 @@ def _type_scrub(output_data):
         process_output = False
         noutput = int((self.param['TSTOP'] - self.param['T0']) / self.param['DT'])
         iloop = int((self.param['TSTART'] - self.param['T0']) / self.param['DT'])
-        post_message = f"Time: {self.param['TSTART']} / {self.param['TSTOP']} {self.TU_name} "
-        post_message += f"npl: {self.data['npl'].values[0]} ntp: {self.data['ntp'].values[0]}"
+        if self.param['TSTOP'] < 1e4:
+           pre_message = f"Time: {self.param['TSTART']:>5} / {self.param['TSTOP']:>5} {self.TU_name} "
+        post_message = f"npl: {self.data['npl'].values[0]} ntp: {self.data['ntp'].values[0]}"
         if "nplm" in self.data:
             post_message += f" nplm: {self.data['nplm'].values[0]}"
-        pbar = tqdm(total=noutput, postfix=post_message, bar_format='{l_bar}{bar}{postfix}')
+        pbar = tqdm(total=noutput, desc=pre_message, postfix=post_message, bar_format='{l_bar}{bar}{postfix}')
         try:
             with subprocess.Popen(shlex.split(cmd),
                                   stdout=subprocess.PIPE,
@@ -402,13 +403,15 @@ def _type_scrub(output_data):
                     if process_output:
                         kvstream=line.replace('\n','').strip().split(';') # Removes the newline character,
                         output_data = _type_scrub({kv.split()[0]: kv.split()[1] for kv in kvstream[:-1]})
-                        post_message = f"Time: {output_data['T']} / {self.param['TSTOP']} {self.TU_name}"
-                        post_message += f" npl: {output_data['NPL']} ntp: {output_data['NTP']}"
+                        if self.param['TSTOP'] < 1e4:
+                           pre_message = f"Time: {output_data['T']:>5} / {self.param['TSTOP']:>5} {self.TU_name}"
+                        post_message = f" npl: {output_data['NPL']} ntp: {output_data['NTP']}"
                         if "NPLM" in output_data:
                             post_message += f" nplm: {output_data['NPLM']}"
                         interval = output_data['ILOOP'] - iloop
                         if interval > 0:
                            pbar.update(interval)
+                           pbar.set_description_str(pre_message)
                            pbar.set_postfix_str(post_message)
                         iloop = output_data['ILOOP']