Merge branch 'master' into debug

CMakeLists.txt

@@ -1,3 +1,12 @@
+# Copyright 2022 - David Minton, Carlisle Wishard, Jennifer Pouplin, Jake Elliott, & Dana Singh
+# This file is part of Swiftest.
+# Swiftest 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.
+# Swiftest 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 Swiftest. 
+# If not, see: https://www.gnu.org/licenses. 
+
 # CMake project file for FOO
 
 ##################################################

cmake/Modules/FindNETCDF.cmake

@@ -1,3 +1,12 @@
+# Copyright 2022 - David Minton, Carlisle Wishard, Jennifer Pouplin, Jake Elliott, & Dana Singh
+# This file is part of Swiftest.
+# Swiftest 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.
+# Swiftest 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 Swiftest. 
+# If not, see: https://www.gnu.org/licenses. 
+
 # - Finds the NetCDF libraries 
 find_path(NETCDF_INCLUDE_DIR NAMES netcdf.mod HINTS ENV NETCDF_FORTRAN_HOME)
 find_library(NETCDF_LIBRARY NAMES netcdf HINTS ENV NETCDF_FORTRAN_HOME)

cmake/Modules/FindOpenMP_Fortran.cmake

@@ -1,3 +1,12 @@
+# Copyright 2022 - David Minton, Carlisle Wishard, Jennifer Pouplin, Jake Elliott, & Dana Singh
+# This file is part of Swiftest.
+# Swiftest 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.
+# Swiftest 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 Swiftest. 
+# If not, see: https://www.gnu.org/licenses. 
+
 # - Finds OpenMP support
 # This module can be used to detect OpenMP support in a compiler.
 # If the compiler supports OpenMP, the flags required to compile with
@@ -13,18 +22,6 @@
 #   OMP_NUM_PROCS - the max number of processors available to OpenMP
 
 #=============================================================================
-# Copyright 2009 Kitware, Inc.
-# Copyright 2008-2009 André Rigland Brodtkorb <Andre.Brodtkorb@ifi.uio.no>
-#
-# Distributed under the OSI-approved BSD License (the "License");
-# see accompanying file Copyright.txt for details.
-#
-# This software is distributed WITHOUT ANY WARRANTY; without even the
-# implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-# See the License for more information.
-#=============================================================================
-# (To distribute this file outside of CMake, substitute the full
-#  License text for the above reference.)
 
 INCLUDE (${CMAKE_ROOT}/Modules/FindPackageHandleStandardArgs.cmake)
 

cmake/Modules/SetCompileFlag.cmake

@@ -1,3 +1,12 @@
+# Copyright 2022 - David Minton, Carlisle Wishard, Jennifer Pouplin, Jake Elliott, & Dana Singh
+# This file is part of Swiftest.
+# Swiftest 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.
+# Swiftest 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 Swiftest. 
+# If not, see: https://www.gnu.org/licenses. 
+
 #############################################################################
 # Given a list of flags, this function will try each, one at a time,
 # and choose the first flag that works.  If no flags work, then nothing

cmake/Modules/SetFortranFlags.cmake

@@ -1,3 +1,12 @@
+# Copyright 2022 - David Minton, Carlisle Wishard, Jennifer Pouplin, Jake Elliott, & Dana Singh
+# This file is part of Swiftest.
+# Swiftest 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.
+# Swiftest 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 Swiftest. 
+# If not, see: https://www.gnu.org/licenses. 
+
 ######################################################
 # Determine and set the Fortran compiler flags we want 
 ######################################################

cmake/Modules/SetParallelizationLibrary.cmake

@@ -1,3 +1,12 @@
+# Copyright 2022 - David Minton, Carlisle Wishard, Jennifer Pouplin, Jake Elliott, & Dana Singh
+# This file is part of Swiftest.
+# Swiftest 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.
+# Swiftest 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 Swiftest. 
+# If not, see: https://www.gnu.org/licenses. 
+
 # Turns on either OpenMP or MPI
 # If both are requested, the other is disabled
 # When one is turned on, the other is turned off

cmake/Modules/SetUpNetCDF.cmake

@@ -1,3 +1,12 @@
+# Copyright 2022 - David Minton, Carlisle Wishard, Jennifer Pouplin, Jake Elliott, & Dana Singh
+# This file is part of Swiftest.
+# Swiftest 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.
+# Swiftest 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 Swiftest. 
+# If not, see: https://www.gnu.org/licenses. 
+
 # Find NetCDF if not already found
 IF(NOT NETCDF_FOUND)
     ENABLE_LANGUAGE(C) # Some libraries need a C compiler to find 

distclean.cmake

@@ -1,3 +1,12 @@
+# Copyright 2022 - David Minton, Carlisle Wishard, Jennifer Pouplin, Jake Elliott, & Dana Singh
+# This file is part of Swiftest.
+# Swiftest 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.
+# Swiftest 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 Swiftest. 
+# If not, see: https://www.gnu.org/licenses. 
+
 # This CMake script will delete build directories and files to bring the
 # package back to it's distribution state
 

python/swiftest/swiftest/init_cond.py

@@ -400,7 +400,7 @@ def vec2xr(param, idvals, namevals, v1, v2, v3, v4, v5, v6, GMpl=None, Rpl=None,
     frame_str = info_vec_str.T
     if param['IN_TYPE'] == 'NETCDF_FLOAT':
         ftype=np.float32
-    elif param['IN_TYPE'] == 'NETCDF_DOUBLE':
+    elif param['IN_TYPE'] == 'NETCDF_DOUBLE' or param['IN_TYPE'] == 'ASCII':
         ftype=np.float64
     da_float = xr.DataArray(frame_float, dims=infodims, coords={'id': idvals, 'vec': infolab_float}).astype(ftype)
     da_int = xr.DataArray(frame_int, dims=infodims, coords={'id': idvals, 'vec': infolab_int})

python/swiftest/swiftest/io.py

@@ -999,7 +999,9 @@ def swiftest_xr2infile(ds, param, in_type="NETCDF_DOUBLE", infile_name=None,fram
     -------
     A set of input files for a new Swiftest run
     """
-    frame = select_active_from_frame(ds, param, framenum)
+    param_tmp = param.copy()
+    param_tmp['OUT_FORM'] = param['IN_FORM']
+    frame = select_active_from_frame(ds, param_tmp, framenum)
 
     if in_type == "NETCDF_DOUBLE" or in_type == "NETCDF_FLOAT":
         # Convert strings back to byte form and save the NetCDF file
@@ -1051,128 +1053,39 @@ def swiftest_xr2infile(ds, param, in_type="NETCDF_DOUBLE", infile_name=None,fram
         for i in pl.id:
             pli = pl.sel(id=i)
             if param['RHILL_PRESENT'] == 'YES':
-               print(pli['name'].values, pli['Gmass'].values, pli['rhill'].values, file=plfile)
+               print(pli['name'].values[0], pli['Gmass'].values[0], pli['rhill'].values[0], file=plfile)
             else:
-               print(pli['name'].values, pli['Gmass'].values, file=plfile)
+               print(pli['name'].values[0], pli['Gmass'].values[0], file=plfile)
             if param['CHK_CLOSE'] == 'YES':
-               print(pli['radius'].values, file=plfile)
+               print(pli['radius'].values[0], file=plfile)
             if param['IN_FORM'] == 'XV':
-                print(pli['xhx'].values, pli['xhy'].values, pli['xhz'].values, file=plfile)
-                print(pli['vhx'].values, pli['vhy'].values, pli['vhz'].values, file=plfile)
+                print(pli['xhx'].values[0], pli['xhy'].values[0], pli['xhz'].values[0], file=plfile)
+                print(pli['vhx'].values[0], pli['vhy'].values[0], pli['vhz'].values[0], file=plfile)
             elif param['IN_FORM'] == 'EL':
-                print(pli['a'].values, pli['e'].values, pli['inc'].values, file=plfile)
-                print(pli['capom'].values, pli['omega'].values, pli['capm'].values, file=plfile)
+                print(pli['a'].values[0], pli['e'].values[0], pli['inc'].values[0], file=plfile)
+                print(pli['capom'].values[0], pli['omega'].values[0], pli['capm'].values[0], file=plfile)
             else:
                 print(f"{param['IN_FORM']} is not a valid input format type.")
             if param['ROTATION'] == 'YES':
-                print(pli['Ip1'].values, pli['Ip2'].values, pli['Ip3'].values, file=plfile)
-                print(pli['rotx'].values, pli['roty'].values, pli['rotz'].values, file=plfile)
+                print(pli['Ip1'].values[0], pli['Ip2'].values[0], pli['Ip3'].values[0], file=plfile)
+                print(pli['rotx'].values[0], pli['roty'].values[0], pli['rotz'].values[0], file=plfile)
         plfile.close()
 
         # TP file
         tpfile = open(param['TP_IN'], 'w')
         print(tp.id.count().values, file=tpfile)
         for i in tp.id:
             tpi = tp.sel(id=i)
-            print(tpi['name'].values, file=tpfile)
+            print(tpi['name'].values[0], file=tpfile)
             if param['IN_FORM'] == 'XV':
-                print(tpi['xhx'].values, tpi['xhy'].values, tpi['xhz'].values, file=tpfile)
-                print(tpi['vhx'].values, tpi['vhy'].values, tpi['vhz'].values, file=tpfile)
+                print(tpi['xhx'].values[0], tpi['xhy'].values[0], tpi['xhz'].values[0], file=tpfile)
+                print(tpi['vhx'].values[0], tpi['vhy'].values[0], tpi['vhz'].values[0], file=tpfile)
             elif param['IN_FORM'] == 'EL':
-                print(tpi['a'].values, tpi['e'].values, tpi['inc'].values, file=tpfile)
-                print(tpi['capom'].values, tpi['omega'].values, tpi['capm'].values, file=tpfile)
+                print(tpi['a'].values[0], tpi['e'].values[0], tpi['inc'].values[0], file=tpfile)
+                print(tpi['capom'].values[0], tpi['omega'].values[0], tpi['capm'].values[0], file=tpfile)
             else:
                 print(f"{param['IN_FORM']} is not a valid input format type.")
         tpfile.close()
-    elif in_type == 'REAL8':
-        # Now make Swiftest files
-        cbfile = FortranFile(param['CB_IN'], 'w')
-        cbfile.write_record(cbid)
-        cbfile.write_record(np.double(GMSun))
-        cbfile.write_record(np.double(RSun))
-        cbfile.write_record(np.double(J2))
-        cbfile.write_record(np.double(J4))
-        if param['ROTATION'] == 'YES':
-            cbfile.write_record(np.double(Ip1cb))
-            cbfile.write_record(np.double(Ip2cb))
-            cbfile.write_record(np.double(Ip3cb))
-            cbfile.write_record(np.double(rotxcb))
-            cbfile.write_record(np.double(rotycb))
-            cbfile.write_record(np.double(rotzcb))
-
-        cbfile.close()
-
-        plfile = FortranFile(param['PL_IN'], 'w')
-        npl = pl.id.count().values
-        plid = pl.id.values
-        if param['IN_FORM'] == 'XV':
-            v1 = pl['xhx'].values
-            v2 = pl['xhy'].values
-            v3 = pl['xhz'].values
-            v4 = pl['vhx'].values
-            v5 = pl['vhy'].values
-            v6 = pl['vhz'].values
-        elif param['IN_FORM'] == 'EL':
-            v1 = pl['a'].values
-            v2 = pl['e'].values
-            v3 = pl['inc'].values
-            v4 = pl['capom'].values
-            v5 = pl['omega'].values
-            v6 = pl['capm'].values
-        else:
-            print(f"{param['IN_FORM']} is not a valid input format type.")
-        Gmass = pl['Gmass'].values
-        if param['CHK_CLOSE'] == 'YES':
-           radius = pl['radius'].values  
-
-        plfile.write_record(npl)
-        plfile.write_record(plid)
-        plfile.write_record(v1)
-        plfile.write_record(v2)
-        plfile.write_record(v3)
-        plfile.write_record(v4)
-        plfile.write_record(v5)
-        plfile.write_record(v6)
-        plfile.write_record(Gmass)
-        if param['RHILL_PRESENT'] == 'YES':
-            plfile.write_record(pl['rhill'].values)
-        if param['CHK_CLOSE'] == 'YES':
-           plfile.write_record(radius)
-        if param['ROTATION'] == 'YES':
-            plfile.write_record(pl['Ip1'].values)
-            plfile.write_record(pl['Ip2'].values)
-            plfile.write_record(pl['Ip3'].values)
-            plfile.write_record(pl['rotx'].values)
-            plfile.write_record(pl['roty'].values)
-            plfile.write_record(pl['rotz'].values)
-        plfile.close()
-        tpfile = FortranFile(param['TP_IN'], 'w')
-        ntp = tp.id.count().values
-        tpid = tp.id.values
-        if param['IN_FORM'] == 'XV':
-            v1 = tp['xhx'].values
-            v2 = tp['xhy'].values
-            v3 = tp['xhz'].values
-            v4 = tp['vhx'].values
-            v5 = tp['vhy'].values
-            v6 = tp['vhz'].values
-        elif param['IN_FORM'] == 'EL':
-            v1 = tp['a'].values
-            v2 = tp['e'].values
-            v3 = tp['inc'].values
-            v4 = tp['capom'].values
-            v5 = tp['omega'].values
-            v6 = tp['capm'].values
-        else:
-            print(f"{param['IN_FORM']} is not a valid input format type.")
-        tpfile.write_record(ntp)
-        tpfile.write_record(tpid)
-        tpfile.write_record(v1)
-        tpfile.write_record(v2)
-        tpfile.write_record(v3)
-        tpfile.write_record(v4)
-        tpfile.write_record(v5)
-        tpfile.write_record(v6)
     else:
         print(f"{in_type} is an unknown file type")
 

python/swiftest/swiftest/simulation_class.py

@@ -33,6 +33,9 @@ def __init__(self, codename="Swiftest", param_file="param.in", readbin=True, ver
             'IN_FORM': "XV",
             'IN_TYPE': "NETCDF_DOUBLE",
             'NC_IN' : "init_cond.nc",
+            'CB_IN' : "cb.in",
+            'PL_IN' : "pl.in",
+            'TP_IN' : "tp.in",
             'ISTEP_OUT': "1",
             'ISTEP_DUMP': "1",
             'BIN_OUT': "bin.nc",
@@ -191,6 +194,12 @@ def write_param(self, param_file, param=None):
         # Check to see if the parameter type matches the output type. If not, we need to convert
         codename = param['! VERSION'].split()[0]
         if codename == "Swifter" or codename == "Swiftest":
+            if param['IN_TYPE'] == "ASCII":
+                param.pop("NC_IN", None)
+            else:
+                param.pop("CB_IN",None)
+                param.pop("PL_IN",None)
+                param.pop("TP_IN",None)
             io.write_labeled_param(param, param_file)
         elif codename == "Swift":
             io.write_swift_param(param, param_file)
@@ -335,7 +344,7 @@ def save(self, param_file, framenum=-1, codename="Swiftest"):
         """
 
         if codename == "Swiftest":
-            io.swiftest_xr2infile(ds=self.ds, param=self.param, framenum=framenum,infile_name=self.param['NC_IN'])
+            io.swiftest_xr2infile(ds=self.ds, param=self.param, in_type=self.param['IN_TYPE'], framenum=framenum,infile_name=self.param['NC_IN'])
             self.write_param(param_file)
         elif codename == "Swifter":
             if self.codename == "Swiftest":