STORM 1.0

.gitignore

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+# Compiled source #
+###################
+*.com
+*.class
+*.dll
+*.exe
+*.o
+*.so
+
+# Packages #
+############
+# it's better to unpack these files and commit the raw source
+# git has its own built in compression methods
+*.7z
+*.dmg
+*.gz
+*.iso
+*.jar
+*.rar
+*.tar
+*.zip
+
+# Logs and databases #
+######################
+*.log
+*.sql
+*.sqlite
+
+# OS generated files #
+######################
+.DS_Store
+.DS_Store?
+._*
+.Spotlight-V100
+.Trashes
+ehthumbs.db
+Thumbs.db
+.nfs*
+
+# BOUT files #
+*dmp*
+*restart*
+*log*
+*.dat
+*.png
+*.mat
+*~
+*pyc
+*.pkl
+*.nc
+BOUT.settings
+
+# videos and images #
+*.png
+*.mp4
+*.gif
+*.jpeg
+*.bmp
+*.pdf
+
+*filaments
+data_*
+*.txt
+storm2d/storm2d

README.md

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+STORM
+-----
+
+STORM plasma simulation model, built using BOUT++ framework.
+
+Table of Contents
+-----------------
+
+* [Options](/doc/options.md)
+
+License
+-------
+
+If you use STORM, please cite the relevant papers (see
+[References](#references)) in any publication. We also request that you contact
+us (email:fulvio.[email protected]) if you want to use or modify STORM.
+
+Full text of the license is in the file COPYING.
+
+  Copyright L. Easy, F. Militello, T. Nicholas, J. Omotani, F. Riva, N.
+  Walkden, UKAEA, 2017, 2018
+  email: [email protected]
+
+  This file is part of the STORM module of BOUT++.
+
+  STORM is free software: you can redistribute it and/or modify
+  it under the terms of the GNU General Public License as published by
+  the Free Software Foundation, either version 3 of the License, or
+  (at your option) any later version.
+
+  STORM is distributed in the hope that it will be useful,
+  but WITHOUT ANY WARRANTY; without even the implied warranty of
+  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+  GNU General Public License for more details.
+
+  You should have received a copy of the GNU General Public License
+  along with STORM.  If not, see <https://www.gnu.org/licenses/>.
+
+References
+----------
+
+[1] L. Easy, F. Militello, J. Omotani, B. Dudson, E. Havlíčková, P. Tamain, V.
+Naulin, and A. H. Nielsen, Physics of Plasmas 21, 122515 (2014),
+https://doi.org/10.1063/1.4904207
+
+[2] L. Easy, F. Militello, J. Omotani, N.R. Walkden, and B. Dudson, Physics of
+Plasmas 23, 012512 (2016), https://doi.org/10.1063/1.4940330
+
+[3] N.R. Walkden, L. Easy, F. Militello and J.T. Omotani, Plasma Physics and
+Controlled Fusion 58, 115010 (2016),
+https://doi.org/10.1088/0741-3335/58/11/115010
+
+[4] F. Militello, B. Dudson, L. Easy, A. Kirk and P. Naylor, Plasma Physics and
+Controlled Fusion 59, 125013 (2017), https://doi.org/10.1088/1361-6587/aa9252

storm2d/data/BOUT.inp

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+timestep              = 25                  # Timestep length of outputted data
+nout                  = 20                  # Number of outputted timesteps
+
+MZ                    = 256                 # Number of Z points
+zmin                  = 0
+zmax                  = mesh:Lz/2./pi       # input z is fracs of 2pi
+myg                   = 0                   # No need for Y communications
+
+[mesh]
+Ly                    = 5500.0
+Lx                    = 150.0
+Lz                    = 100.0
+
+nx                    = 388                 # including 4 guard cells
+ny                    = 1                   # excluding guard cells
+dx                    = Lx/(nx-4)
+
+[storm]
+B_0                   = 0.5                 # Tesla
+T_e0                  = 20                  # eV
+T_i0                  = 20                  # eV
+m_i                   = 2                   # Atomic Units
+q                     = 7                   # Dimensionless
+R_c                   = 1.5                 # m
+n_0                   = 0.5e19              # m^-3
+Z                     = 1                   # Dimensionless
+loglambda             = -1                  # Dimensionless
+
+bracket               = 2                   # 0 = std, 1 = simple, 2 = arakawa
+isothermal            = true                # switch for isothermal simulations
+SOL_closure           = sheath_diss         # choice of parallel closure to use
+
+[blob]
+A = 2
+delta_x = 10
+delta_z = 10
+x0 = 0.25
+z0 = 0.5
+
+[All]
+bndry_all = neumann
+
+[n]
+function = 1.0 + (blob:A)*exp(-(mesh:Lx*(x-blob:x0)/blob:delta_x)*(mesh:Lx*(x-blob:x0)/blob:delta_x))*exp(-(mesh:Lz*((z/(2*pi))-blob:z0)/blob:delta_z)*(mesh:Lz*((z/(2*pi))- blob:z0)/blob:delta_z))
+
+[T]
+function = 1.
+
+[vort]
+#function = 0.
+
+[sigma_n]     # Density sink
+#function = 1.119e-4
+
+[sigma_T]     # Temperature sink
+#function = 2.326e-3
+
+[sigma_vort]  # Vorticity sink
+#function = 1.119e-4
+
+[mesh:ddx]
+first                 = C2
+second                = C2
+upwind                = C2
+
+[mesh:ddz]
+first                 = C2
+second                = C2
+upwind                = C2
+
+[laplace] 
+global_flags          = 0
+inner_boundary_flags  = 0
+outer_boundary_flags  = 0
+
+[solver]
+type=pvode
+mxstep = 100000000       # max steps before result is deemed not to converge
+#atol =   1e-12          # Absolute tolerance
+#rtol =   1e-5           # Relative tolerance
+

storm2d/data/viewdata.py

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+#!/usr/bin/env python3
+
+from boututils.showdata import showdata
+from boutdata import collect
+from numpy import *
+from matplotlib import pyplot as plt
+import sys
+import os
+
+# T = collect('T', tind = [5500,6000], yguards = False)
+phi = collect('phi', yguards = False)
+n = collect('n',  yguards = False)
+vort = collect('vort', yguards = False)
+
+x = slice(2,-2)
+y = 0
+z = slice(None)
+t = slice(None)
+
+n =       n[t,x,y,z]
+phi =   phi[t,x,y,z]
+# T =       T[t,x,y,z]
+vort = vort[t,x,y,z]
+
+showdata([[n], [phi], [vort]], titles = ['n', 'phi', 'vort'])

storm2d/filament_scan

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+#!/usr/bin/env python
+
+# Copyright L. Easy, F. Militello, T. Nicholas, J. Omotani, F. Riva, N.
+# Walkden, UKAEA, 2017, 2018
+# email: [email protected]
+#
+# This file is part of the STORM module of BOUT++.
+#
+# STORM is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# STORM is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with STORM.  If not, see <https://www.gnu.org/licenses/>.
+
+from boututils.run_wrapper import shell, launch, getmpirun
+from boutdata import collect
+from boutdata.data import BoutOptionsFile
+import numpy as np
+import os
+import shutil
+
+delta_perp_list = [10,12,14,16,18,20,25,30,35,40,45,50,55,60]
+sheath_dissipation = True
+short_run = True  
+nproc = 8
+
+MPIRUN = getmpirun()
+
+for delta_perp in delta_perp_list:
+  print "running delta_perp =", delta_perp
+  path = "d" + str(delta_perp)
+  if (sheath_dissipation):
+    path = path + "_SD"
+  else:
+    path = path + "_VA"
+
+  if(short_run):
+    path = path + "_s"
+  if not os.path.exists(path):
+    os.makedirs(path)
+
+  shutil.copy("data/BOUT.inp", path)
+
+  # Determine timestep to use
+  options = BoutOptionsFile(path+"/BOUT.inp")
+  storm_options = options["storm"]
+  Te = storm_options.evaluate_scalar("T_e0")
+  e = 1.602176565e-19
+  m_i = storm_options.evaluate_scalar("m_i")*1.66053892e-27
+  B0 = storm_options.evaluate_scalar("B_0")
+  Omega_i = e*B0/m_i
+  c_s = (Te*e/m_i)**0.5
+  rho_s = c_s/Omega_i
+  R_c = storm_options.evaluate_scalar("R_c")
+  g = 2*(rho_s)/R_c
+  interchange_time = (float(delta_perp)/g)**0.5
+
+  timestep = 100 
+
+  if(short_run):
+    timestep = interchange_time/3
+
+  # Need to scale dx, Zmax by delta_perp
+  Lx = 15.0*delta_perp
+  Lz = 10.0*delta_perp
+
+  arguments = "-d " + path + " timestep=" + str(timestep) + " mesh:Lx=" + str(Lx) + " mesh:Lz=" + str(Lz) + " blob:delta_x=" + str(delta_perp) + " blob:delta_z=" + str(delta_perp)
+
+  # Command to run
+  cmd = "./storm2d " + arguments
+  # Launch using MPI
+  s, out = launch(cmd, runcmd=MPIRUN, nproc=nproc, pipe=True)
+
+  # Save output to log file
+  f = open(path+"/output.log", "w")
+  f.write(out)
+  f.close()

storm2d/make.config.example

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+# make.config sets user-defined values, for example the path to the BOUT++ directory
+BOUT_TOP       =../../BOUT-dev

storm2d/makefile

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+# Copyright L. Easy, F. Militello, T. Nicholas, J. Omotani, F. Riva, N.
+# Walkden, UKAEA, 2017, 2018
+# email: [email protected]
+#
+# This file is part of the STORM module of BOUT++.
+#
+# STORM is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# STORM is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with STORM.  If not, see <https://www.gnu.org/licenses/>.
+
+# Set user-specified values
+ifneq ("$(wildcard make.config)","")
+  include make.config
+else
+  $(error "The 'make.config' file does not exist. You must create it for STORM to compile. See the example in 'make.config.example'")
+endif
+
+SOURCEC		= storm2d.cxx 
+
+include $(BOUT_TOP)/make.config

storm2d/savematlab2d

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+#!/usr/bin/env python
+
+# Copyright L. Easy, F. Militello, T. Nicholas, J. Omotani, F. Riva, N.
+# Walkden, UKAEA, 2017, 2018
+# email: [email protected]
+#
+# This file is part of the STORM module of BOUT++.
+#
+# STORM is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# STORM is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with STORM.  If not, see <https://www.gnu.org/licenses/>.
+
+#from boututils import shell, launch, getmpirun
+from boutdata import collect
+from scipy import io as sio
+import numpy as np
+import os
+import shutil
+
+os.chdir('data')
+
+    #Read in Data
+t = collect('t_array')
+n    = collect('n',    yguards = True)
+T    = collect('T',    yguards = True)
+phi  = collect('phi',  yguards = True)
+vort = collect('vort', yguards = True)
+
+sio.savemat("matlab_output.mat", mdict={'t':t, 'n':n, 'T':T, 'phi':phi, 'vort':vort})
+
+os.chdir('../')