Fixed some typos that were preventing libraries from being linked pro…

…perly

.gitignore

@@ -26,6 +26,7 @@ dump*
 !python/swiftest/tests/test_suite.py
 !version.txt
 
+
 #Documentation
 !docs/*
 !docs/*/*

cmake/Modules/SetFortranFlags.cmake

@@ -123,9 +123,9 @@ IF (NOT BUILD_SHARED_LIBS)
                 IF (USE_OPENMP)
                         SET_COMPILE_FLAG(CMAKE_Fortran_LINK_FLAGS "${CMAKE_Fortran_LINK_FLAGS}"
                                 Fortran "-qopenmp-link=static"  # Intel
-                )
+                        )
                 ENDIF (USE_OPENMP)
-       ELSEIF (COMPIELR_OPTIONS STREQUAL "GNU") 
+       ELSEIF (COMPILER_OPTIONS STREQUAL "GNU") 
                 # Set GNU static libraries
                 SET_COMPILE_FLAG(CMAKE_Fortran_LINK_FLAGS "${CMAKE_Fortran_LINK_FLAGS}"
                         Fortran  "-static-libgfortran" 

python/.gitignore

@@ -0,0 +1 @@
+!setup.py.in

python/setup.py

@@ -19,14 +19,13 @@
 include_dirs = "/Users/daminton/git/swiftest/apple_install/usr/local/include;/Users/daminton/git/swiftest/apple_install/usr/local/include"
 include_dirs = include_dirs.split()
 include_dirs.append(root_dir)
-link_flags = "-lswiftest  /Users/daminton/git/swiftest/apple_install/usr/local/lib/libnetcdff.a /Users/daminton/git/swiftest/apple_install/usr/local/lib/libnetcdf.a -L/Users/daminton/git/swiftest/apple_install/usr/local/lib -lhdf5_hl -lhdf5 -lm -lz -lbz2 -lxml2 -lcurl"
+link_flags = " -static-libgfortran -static-libgcc -static-libstdc++"
 link_flags = link_flags.split()
 
 pybindings_extension = [Extension('swiftest.bindings',
                          [os.path.join(root_dir,'pybindings.pyx')],
-                         extra_compile_args=['-fPIC', '-O3','-fopenmp'],
+                         extra_compile_args=['-fPIC', '-O3'],
                          extra_link_args=link_flags,
-                         libraries=['gfortran','omp'],
                          include_dirs=include_dirs,
                          )]
 

python/setup.py.in

@@ -0,0 +1,38 @@
+"""
+ 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. 
+"""
+
+from setuptools import setup, find_packages, Extension
+from Cython.Build import cythonize
+import os
+
+# Build the pybindings extension that allows us to run the Fortran driver as a Python module. 
+root_dir = 'pybindings'
+include_dirs = "${SWIFTEST_INCLUDE_DIR}"
+include_dirs = include_dirs.split()
+include_dirs.append(root_dir)
+link_flags = "${CMAKE_Fortran_LINK_FLAGS}"
+link_flags = link_flags.split()
+
+pybindings_extension = [Extension('swiftest.bindings',
+                         [os.path.join(root_dir,'pybindings.pyx')],
+                         extra_compile_args=['-fPIC', '-O3'],
+                         extra_link_args=link_flags,
+                         include_dirs=include_dirs,
+                         )]
+
+setup(name='swiftest',
+      version='${CMAKE_PROJECT_VERSION}',
+      author='David A. Minton',
+      author_email='daminton@purdue.edu',
+      url='https://github.itap.purdue.edu/MintonGroup/swiftest',
+      ext_modules = cythonize(pybindings_extension),
+      packages=find_packages())

src/CMakeLists.txt

@@ -131,7 +131,7 @@ IF(USE_COARRAY)
     SET_PROPERTY(TARGET ${SWIFTEST_LIBRARY} ${SWIFTEST_DRIVER} APPEND_STRING PROPERTY LINK_FLAGS  "${Coarray_Fortran_FLAGS} ")
 ENDIF(USE_COARRAY)
 
-STRING(REPLACE ";" " " SWIFTEST_LINK_FLAGS "${CMAKE_LINK_LIBRARY_FLAG}${SWIFTEST_LIBRARY} ${NETCDF_FORTRAN_LIBRARIES} ${NETCDF_LIBRARIES} $ENV{LIBS}")
+STRING(REPLACE ";" " " SWIFTEST_LINK_FLAGS "${CMAKE_Fortran_LINK_FLAGS} ${CMAKE_LINK_LIBRARY_FLAG}${SWIFTEST_LIBRARY} ${NETCDF_FORTRAN_LIBRARIES} ${NETCDF_LIBRARIES} $ENV{LIBS}")
 SET(SWIFTEST_LINK_FLAGS "${SWIFTEST_LINK_FLAGS}" CACHE STRING "Link flags to pass to setup.py")
 
 GET_TARGET_PROPERTY(SWIFTEST_INCLUDE_DIR ${SWIFTEST_DRIVER} INCLUDE_DIRECTORIES)

src/globals/.gitignore

@@ -0,0 +1 @@
+!globals_module.f90.in

src/globals/globals_module.f90.in

@@ -0,0 +1,133 @@
+!! 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. 
+
+module globals
+   !! author: David A. Minton
+   !! graph: false
+   !!
+   !! Basic parameters, definitions, and global type definitions used throughout the Swiftest project
+   !! Adapted from David E. Kaufmann's Swifter routine: globals.f90 and module_swifter.f90
+   use, intrinsic :: iso_fortran_env  ! Use the intrinsic kind definitions
+   implicit none
+   public
+
+   integer, parameter :: I8B = int64 !! Symbolic name for kind types of 8-byte integers
+   integer, parameter :: I4B = int32 !! Symbolic name for kind types of 4-byte integers
+   integer, parameter :: I2B = int16 !! Symbolic name for kind types of 2-byte integers
+   integer, parameter :: I1B = int8  !! Symbolic name for kind types of 1-byte integers
+
+   integer, parameter :: SP = real32  !! Symbolic name for kind types of single-precision reals
+   integer, parameter :: DP = real64  !! Symbolic name for kind types of double-precision reals
+   integer, parameter :: QP = real128 !! Symbolic name for kind types of quad-precision reals
+
+   real(DP), parameter :: PIBY2  = 1.570796326794896619231321691639751442099_DP !! Definition of /(\pi / 2\)
+   real(DP), parameter :: PI     = 3.141592653589793238462643383279502884197_DP !! Definition of /(\pi\)
+   real(DP), parameter :: PI3BY2 = 4.712388980384689857693965074919254326296_DP !! Definition of /(3 \pi / 2\)
+   real(DP), parameter :: TWOPI  = 6.283185307179586476925286766559005768394_DP !! Definition of 2 \pi
+   real(DP), parameter :: THIRD  = 0.333333333333333333333333333333333333333_DP !! Definition of 1 / 3
+   real(DP), parameter :: SIXTH  = 0.166666666666666666666666666666666666667_DP !! Definition of 1 / 3
+   real(DP), parameter :: DEG2RAD = PI / 180.0_DP !! Definition of conversion factor from degrees to radians
+   real(DP), parameter :: RAD2DEG = 180.0_DP / PI !! Definition of conversion factor from degrees to radians
+   real(DP), parameter :: GC        = 6.6743E-11_DP   !! Universal gravitational constant in SI units
+   real(DP), parameter :: einsteinC = 299792458.0_DP  !! Speed of light in SI units
+
+   integer(I4B), parameter :: LOWERCASE_BEGIN  = iachar('a') !! ASCII character set parameter for lower to upper conversion - start 
+                                                             !! of lowercase
+   integer(I4B), parameter :: LOWERCASE_END    = iachar('z') !! ASCII character set parameter for lower to upper conversion - end of 
+                                                             !! lowercase
+   integer(I4B), parameter :: UPPERCASE_OFFSET = iachar('A') - iachar('a') !! ASCII character set parameter for lower to upper 
+                                                                           !! conversion - offset between upper and lower
+
+   character(*), parameter :: VERSION = "${CMAKE_PROJECT_VERSION}" !! Swiftest version
+
+   !> Symbolic name for integrator types
+   character(*), parameter :: UNKNOWN_INTEGRATOR = "UKNOWN INTEGRATOR"
+   character(*), parameter :: INT_BS                 = "Bulirsch-Stoer"
+   character(*), parameter :: INT_HELIO              = "Democratic Heliocentric"
+   character(*), parameter :: INT_RA15               = "Radau 15th order"
+   character(*), parameter :: INT_TU4                = "T+U 4th order"
+   character(*), parameter :: INT_WHM                = "Wisdom-Holman Method"
+   character(*), parameter :: INT_RMVS               = "Regularized Mixed Variable Symplectic"
+   character(*), parameter :: INT_SYMBA              = "SyMBA"
+   character(*), parameter :: INT_RINGMOONS          = "SyMBA-RINGMOONS"
+
+   integer(I4B), parameter :: STRMAX = 512 !! Maximum size of character strings
+   integer(I4B), parameter :: NAMELEN = 32 !! Maximum size of name strings
+
+   character(*), parameter :: CB_TYPE_NAME = "Central Body"
+   character(*), parameter :: PL_TYPE_NAME = "Massive Body"
+   character(*), parameter :: TP_TYPE_NAME = "Test Particle"
+   character(*), parameter :: PL_TINY_TYPE_NAME = "Semi-Interacting Massive Body"
+
+   ! OpenMP Parameters
+   integer(I4B)            :: nthreads = 1 !! Number of OpenMP threads
+   integer(I4B), parameter :: NTHERSHOLD = 1000 !! Threshold value for OpenMP loop parallelization
+
+   integer(I4B), parameter :: SUCCESS =  0 !! Symbolic name for function return/flag code for success
+   integer(I4B), parameter :: FAILURE = -1 !! Symbolic name for function return/flag code for failure
+   integer(I4B), parameter :: USAGE = -2 !! Symbolic name for function return/flag code for printing the usage message
+   integer(I4B), parameter :: HELP  = -3 !! Symbolic name for function return/flag code for printing the usage message
+
+   integer(I4B), parameter :: ELLIPSE   = -1 !! Symbolic names for orbit types - ellipse
+   integer(I4B), parameter :: PARABOLA  =  0 !! Symbolic names for orbit types - parabola
+   integer(I4B), parameter :: HYPERBOLA =  1 !! Symbolic names for orbit types - hyperbola
+
+   !> Symbolic names for body/particle status codes:
+   integer(I4B), parameter :: ACTIVE              =  0
+   integer(I4B), parameter :: INACTIVE            =  1
+   integer(I4B), parameter :: DISCARDED_RMAX      = -1
+   integer(I4B), parameter :: DISCARDED_RMIN      = -2
+   integer(I4B), parameter :: DISCARDED_RMAXU     = -3
+   integer(I4B), parameter :: DISCARDED_PERI      = -4
+   integer(I4B), parameter :: DISCARDED_PLR       = -5
+   integer(I4B), parameter :: DISCARDED_PLQ       = -6
+   integer(I4B), parameter :: DISCARDED_DRIFTERR  = -7
+   integer(I4B), parameter :: MERGED              = -8
+   integer(I4B), parameter :: DISRUPTED           = -9
+   integer(I4B), parameter :: SUPERCATASTROPHIC   = -10
+   integer(I4B), parameter :: GRAZE_AND_MERGE     = -11
+   integer(I4B), parameter :: HIT_AND_RUN_DISRUPT = -12
+   integer(I4B), parameter :: HIT_AND_RUN_PURE    = -13
+   integer(I4B), parameter :: COLLIDED            = -14
+   integer(I4B), parameter :: NEW_PARTICLE        = -15
+   integer(I4B), parameter :: OLD_PARTICLE        = -16
+
+   !> String labels for body/particle addition/subtraction in discard file
+   character(*), parameter :: ADD = '+1'
+   character(*), parameter :: SUB = '-1'
+
+   !> Standard file names
+   integer(I4B), parameter :: NDUMPFILES = 2
+   character(*), parameter :: PARAM_RESTART_FILE = "param.restart.in"
+#ifdef COARRAY
+   character(STRMAX)       :: SWIFTEST_LOG_FILE                  !! Name of file to use to log output when using "COMPACT" or 
+                                                                 !! "PROGRESS" display style (each co-image gets its own log file)
+#else
+   character(*), parameter :: SWIFTEST_LOG_FILE = "swiftest.log" !! Name of file to use to log output when using "COMPACT" or 
+                                                                 !! "PROGRESS" display style
+#endif
+   integer(I4B), parameter :: SWIFTEST_LOG_OUT = 33 !! File unit for log file when using "COMPACT" display style 
+
+   !> Default file names that can be changed by the user in the parameters file
+   character(*), parameter :: CB_INFILE        = 'cb.in'
+   character(*), parameter :: PL_INFILE        = 'pl.in'
+   character(*), parameter :: TP_INFILE        = 'tp.in'
+   character(*), parameter :: NC_INFILE        = 'init_cond.nc'
+   character(*), parameter :: BIN_OUTFILE      = 'data.nc'
+   integer(I4B), parameter :: BINUNIT          = 20 !! File unit number for the binary output file
+   integer(I4B), parameter :: PARTICLEUNIT     = 44 !! File unit number for the binary particle info output file
+   integer(I4B), parameter :: LUN              = 42 !! File unit number for files that are opened and closed within a single 
+                                                    !! subroutine call, and therefore should not collide
+
+   !> Miscellaneous constants:
+   integer(I4B), parameter :: NDIM   = 3                  !! Number of dimensions in our reality
+   integer(I4B), parameter :: NDIM2  = 2 * NDIM           !! 2x the number of dimensions
+   real(DP),     parameter :: VSMALL = sqrt(TINY(1._DP)) !! Very small number used to prevent floating underflow
+
+end module globals