Merge branch 'IO'

Makefile

@@ -45,9 +45,11 @@
 #******************************************************************************
 
 SWIFTEST_MODULES =   swiftest_globals.f90 \
+                     swiftest_operators.f90 \
 							lambda_function.f90\
+							walltime_classes.f90 \
                      swiftest_classes.f90 \
-                     swiftest_operators.f90 \
+                     fraggle_classes.f90 \
                      whm_classes.f90 \
                      rmvs_classes.f90 \
                      helio_classes.f90 \
@@ -57,13 +59,13 @@ SWIFTEST_MODULES =   swiftest_globals.f90 \
 
 include Makefile.Defines
 
-MODULES         = $(SWIFTEST_MODULES) $(USER_MODULES)
+MODULES         = $(SWIFTEST_MODULES) $(USER_MODULES) 
 
 .PHONY : all mod lib libdir drivers bin clean force 
 
 % : %.f90 force
-	$(FORTRAN) $(FFLAGS) -I$(SWIFTEST_HOME)/include $< -o $@ \
-	  -L$(SWIFTEST_HOME)/lib -lswiftest 
+	$(FORTRAN) $(FFLAGS) -I$(SWIFTEST_HOME)/include -I$(NETCDF_FORTRAN_HOME)/include  $< -o $@ \
+	  -L$(SWIFTEST_HOME)/lib -lswiftest -L$(NETCDF_FORTRAN_HOME)/lib -lnetcdf -lnetcdff
 	$(INSTALL_PROGRAM) $@ $(SWIFTEST_HOME)/bin
 	rm -f $@
 
@@ -75,7 +77,7 @@ all:
 
 mod:
 	cd $(SWIFTEST_HOME)/src/modules/; \
-	  $(FORTRAN) $(FFLAGS) -I$(SWIFTEST_HOME)/include -c $(MODULES); \
+	  $(FORTRAN) $(FFLAGS) -I$(SWIFTEST_HOME)/include -I$(NETCDF_FORTRAN_HOME)/include -c $(MODULES); \
 	  $(AR) rv $(SWIFTEST_HOME)/lib/libswiftest.a *.o; \
 	  $(INSTALL_DATA) *.mod *.smod $(SWIFTEST_HOME)/include; \
 	  rm -f *.o *.mod  *.smod
@@ -91,7 +93,7 @@ lib:
 	  ln -s $(SWIFTEST_HOME)/Makefile.Defines .; \
 	  ln -s $(SWIFTEST_HOME)/Makefile .; \
 	  make libdir
-	cd $(SWIFTEST_HOME)/src/fragmentation; \
+	cd $(SWIFTEST_HOME)/src/fraggle; \
 	  rm -f Makefile.Defines Makefile; \
 	  ln -s $(SWIFTEST_HOME)/Makefile.Defines .; \
 	  ln -s $(SWIFTEST_HOME)/Makefile .; \
@@ -111,6 +113,11 @@ lib:
 	  ln -s $(SWIFTEST_HOME)/Makefile.Defines .; \
 	  ln -s $(SWIFTEST_HOME)/Makefile .; \
 	  make libdir
+	cd $(SWIFTEST_HOME)/src/netcdf; \
+	  rm -f Makefile.Defines Makefile; \
+	  ln -s $(SWIFTEST_HOME)/Makefile.Defines .; \
+	  ln -s $(SWIFTEST_HOME)/Makefile .; \
+	  make libdir
 	cd $(SWIFTEST_HOME)/src/obl; \
 	  rm -f Makefile.Defines Makefile; \
 	  ln -s $(SWIFTEST_HOME)/Makefile.Defines .; \
@@ -168,7 +175,7 @@ lib:
 	  make libdir
 
 libdir:
-	$(FORTRAN) $(FFLAGS) -I$(SWIFTEST_HOME)/include -c *.f90; \
+	$(FORTRAN) $(FFLAGS) -I$(SWIFTEST_HOME)/include -I$(NETCDF_FORTRAN_HOME)/include -c *.f90; \
 	$(AR) rv $(SWIFTEST_HOME)/lib/libswiftest.a *.o *.smod; \
 	$(INSTALL_DATA) *.smod $(SWIFTEST_HOME)/include; \
 	rm -f *.o *.smod
@@ -188,12 +195,13 @@ clean:
 	cd $(SWIFTEST_HOME)/src/modules;  rm -f Makefile.Defines Makefile *.gc*
 	cd $(SWIFTEST_HOME)/src/discard; rm -f Makefile.Defines Makefile *.gc*
 	cd $(SWIFTEST_HOME)/src/drift;   rm -f Makefile.Defines Makefile *.gc*
-	cd $(SWIFTEST_HOME)/src/fragmentation;   rm -f Makefile.Defines Makefile *.gc*
+	cd $(SWIFTEST_HOME)/src/fraggle;   rm -f Makefile.Defines Makefile *.gc*
 	cd $(SWIFTEST_HOME)/src/gr;          rm -f Makefile.Defines Makefile *.gc*
 	cd $(SWIFTEST_HOME)/src/helio;    rm -f Makefile.Defines Makefile *.gc*
 	cd $(SWIFTEST_HOME)/src/io;      rm -f Makefile.Defines Makefile *.gc*
 	cd $(SWIFTEST_HOME)/src/kick;   rm -f Makefile.Defines Makefile *.gc*
 	cd $(SWIFTEST_HOME)/src/main;    rm -f Makefile.Defines Makefile *.gc*
+	cd $(SWIFTEST_HOME)/src/netcdf;    rm -f Makefile.Defines Makefile *.gc*
 	cd $(SWIFTEST_HOME)/src/obl;     rm -f Makefile.Defines Makefile *.gc*
 	cd $(SWIFTEST_HOME)/src/operators;      rm -f Makefile.Defines Makefile *.gc*
 	cd $(SWIFTEST_HOME)/src/orbel;   rm -f Makefile.Defines Makefile *.gc*

Makefile.Defines

@@ -51,18 +51,18 @@ ADVIXE_FLAGS = -g -O2 -qopt-report=5 -vec -vecabi=cmdtarget -simd -shared-intel
 VTUNE_FLAGS = -g -O2 -vec -simd -shared-intel -qopenmp -debug inline-debug-info -parallel-source-info=2 -parallel -DTBB_DEBUG -DTBB_USE_THREADING_TOOLS -qopenmp -fp-model no-except -mp1 -xhost -traceback 
 #Be sure to set the environment variable KMP_FORKJOIN_FRAMES=1 for OpenMP debuging in vtune
 
-IDEBUG = -O0 -nogen-interfaces -no-pie -no-ftz -fpe-all=0 -g -traceback -mp1 -fp-model strict -fpe0 -debug all -align all -pad -ip -prec-div -prec-sqrt -assume protect-parens -CB -no-wrap-margin -init=snan,arrays 
+IDEBUG = -O0 -init=snan,arrays  -nogen-interfaces -no-pie -no-ftz -fpe-all=0 -g -traceback -mp1 -fp-model strict -fpe0 -debug all -align all -pad -ip -prec-div -prec-sqrt -assume protect-parens -CB -no-wrap-margin
 STRICTREAL = -fp-model strict -fp-model no-except -prec-div -prec-sqrt -assume protect-parens 
 SIMDVEC = -simd -xhost -align all -assume contiguous_assumed_shape -vecabi=cmdtarget -prec-div -prec-sqrt -assume protect-parens
 PAR = -qopenmp #-parallel  #Something goes wrong in SyMBA at the moment with auto-paralellization enabled
 HEAPARR = -heap-arrays 1048576 
 OPTREPORT = -qopt-report=5 
-IPRODUCTION = -init=snan,arrays -no-wrap-margin -O3 $(STRICTREAL) $(PAR) $(SIMDVEC) $(HEAPARR) 
+IPRODUCTION = -init=snan,arrays  -no-wrap-margin -O3 $(STRICTREAL) $(PAR) $(SIMDVEC) $(HEAPARR) 
 
 #gfortran flags
 GDEBUG = -g -Og -fbacktrace -fbounds-check -ffree-line-length-none
 GPAR = -fopenmp #-ftree-parallelize-loops=4
-GMEM = -fsanitize=undefined -fsanitize=address -fsanitize=leak 
+GMEM =  -fsanitize-address-use-after-scope -fstack-check  -fsanitize=bounds-strict -fsanitize=undefined -fsanitize=signed-integer-overflow -fsanitize=object-size -fstack-protector-all
 GWARNINGS = -Wall -Warray-bounds  -Wimplicit-interface -Wextra -Warray-temporaries
 GPRODUCTION = -O3 -ffree-line-length-none $(GPAR)
 
@@ -73,7 +73,7 @@ FORTRAN = ifort
 
 #FORTRAN = gfortran
 #FFLAGS =  $(GDEBUG) $(GMEM) $(GPAR)
-#FFLAGS =  $(GPRODUCTION)
+#FFLAGS =  $(GPRODUCTION) -g -fbacktrace #-fcheck=all #-Wall 
 AR     = ar
 
 # DO NOT include in CFLAGS the "-c" option to compile object only

examples/helio_gr_test/cb.swiftest.in

@@ -1,4 +1,4 @@
-0
+Sun
 39.476926408897626
 0.004650467260962157
 4.7535806948127355e-12

examples/helio_gr_test/init_cond.py

@@ -5,8 +5,7 @@
 sim.param['PL_IN'] = "pl.swiftest.in"
 sim.param['TP_IN'] = "tp.swiftest.in"
 sim.param['CB_IN'] = "cb.swiftest.in"
-sim.param['BIN_OUT'] = "bin.swiftest.dat"
-sim.param['ENC_OUT'] = "enc.swiftest.dat"
+sim.param['BIN_OUT'] = "bin.swiftest.nc"
 
 sim.param['MU2KG'] = swiftest.MSun
 sim.param['TU2S'] = swiftest.YR2S
@@ -22,9 +21,11 @@
 sim.param['CHK_RMIN'] = swiftest.RSun / swiftest.AU2M
 sim.param['CHK_RMAX'] = 1000.0
 sim.param['CHK_EJECT'] = 1000.0
-sim.param['OUT_FORM'] = "EL"
 sim.param['OUT_STAT'] = "UNKNOWN"
-sim.param['RHILL_PRESENT'] = "NO"
+sim.param['IN_FORM'] = "EL"
+sim.param['OUT_FORM'] = "XVEL"
+sim.param['OUT_TYPE'] = "NETCDF_DOUBLE"
+sim.param['RHILL_PRESENT'] = "YES"
 sim.param['GR'] = 'YES'
 
 bodyid = {

examples/helio_gr_test/param.swifter.in

@@ -4,24 +4,24 @@ TSTOP            1000.0
 DT               0.0006844626967830253
 ISTEP_OUT        1461
 ISTEP_DUMP       1461
-OUT_FORM         EL
-OUT_TYPE         REAL8
+OUT_FORM         XVEL
+OUT_TYPE         NETCDF_DOUBLE
 OUT_STAT         UNKNOWN
 IN_TYPE          ASCII
 PL_IN            pl.swifter.in
 TP_IN            tp.swifter.in
 BIN_OUT          bin.swifter.dat
-ENC_OUT          enc.swifter.dat
 CHK_QMIN         0.004650467260962157
 CHK_RMIN         0.004650467260962157
 CHK_RMAX         1000.0
 CHK_EJECT        1000.0
 CHK_QMIN_COORD   HELIO
 CHK_QMIN_RANGE   0.004650467260962157 1000.0
+ENC_OUT          enc.swifter.dat
 EXTRA_FORCE      NO
 BIG_DISCARD      NO
 CHK_CLOSE        YES
-RHILL_PRESENT    NO
+RHILL_PRESENT    YES
 C                63241.07708426628
 J2               4.7535806948127355e-12
 J4               -2.2473967953572827e-18

examples/helio_gr_test/param.swiftest.in

@@ -4,15 +4,14 @@ TSTOP            1000.0
 DT               0.0006844626967830253
 ISTEP_OUT        1461
 ISTEP_DUMP       1461
-OUT_FORM         EL
-OUT_TYPE         REAL8
+OUT_FORM         XVEL
+OUT_TYPE         NETCDF_DOUBLE
 OUT_STAT         UNKNOWN
 IN_TYPE          ASCII
 PL_IN            pl.swiftest.in
 TP_IN            tp.swiftest.in
 CB_IN            cb.swiftest.in
-BIN_OUT          bin.swiftest.dat
-ENC_OUT          enc.swiftest.dat
+BIN_OUT          bin.swiftest.nc
 CHK_QMIN         0.004650467260962157
 CHK_RMIN         0.004650467260962157
 CHK_RMAX         1000.0
@@ -22,15 +21,15 @@ CHK_QMIN_RANGE   0.004650467260962157 1000.0
 MU2KG            1.988409870698051e+30
 TU2S             31557600.0
 DU2M             149597870700.0
+IN_FORM          EL
+ENC_OUT          enc.dat
 EXTRA_FORCE      NO
+DISCARD_OUT      discard.out
 BIG_DISCARD      NO
 CHK_CLOSE        YES
-RHILL_PRESENT    NO
+RHILL_PRESENT    YES
 FRAGMENTATION    NO
 ROTATION         NO
 TIDES            NO
 ENERGY           NO
 GR               YES
-YARKOVSKY        NO
-YORP             NO
-MTINY            0.0

examples/helio_gr_test/pl.swifter.in

@@ -1,36 +1,36 @@
 9
-0 39.476926408897625196
+0 39.476926408897626
 0.0 0.0 0.0
 0.0 0.0 0.0
-1 6.5537098095653139645e-06
+1 6.5537098095653139645e-06 0.001475131156288637831
 1.6306381826061645943e-05
--0.30949970210807342674 0.1619004125820537876 0.041620272188990829754
--6.8742992150644793847 -8.672423996611946485 -0.078109307586001638286
-2 9.663313399581537916e-05
+-0.0361820239646683528 -0.46276010580341980782 -0.034496398006472611675
+8.183688458560222766 -0.27616682338432374386 -0.7732476400340904169
+2 9.663313399581537916e-05 0.0067590747715647875607
 4.0453784346544178454e-05
--0.5567137338251560985 -0.46074173273652380134 0.02580196630219121906
-4.6580776303108450487 -5.726444072926637749 -0.3473859047161406309
-3 0.000120026935827952453094
+0.04707194870345993154 -0.7255425078625500346 -0.012673782840571969424
+7.3226765098927520106 0.45143529808423807744 -0.4163607714267330732
+3 0.000120026935827952453094 0.01004493295891520948
 4.25875607065040958e-05
-0.6978790186886838498 -0.73607603319120218366 3.261671020506711323e-05
-4.4579240279134950613 4.300011122687349501 -0.00022055769049333364448
-4 1.2739802010675941456e-05
+0.9784182446151709067 -0.2394545623617302943 7.8432240502479141865e-06
+1.3916805835822199726 6.0802455505175572043 -0.00029695052429473289775
+4 1.2739802010675941456e-05 0.007246527815634877893
 2.265740805092889601e-05
--1.617661473167097963 0.38314370807747849534 0.04771055403546069218
--0.98751874613118001086 -4.5371239937302254657 -0.07086074102213555221
-5 0.037692251088985676735
+-1.64827450584581503 -0.04818173529735803734 0.039422108862210397673
+0.3393812176064170994 -4.672429323734897043 -0.1062469093563351878
+5 0.037692251088985676735 0.3552712221482522291
 0.00046732617030490929307
-4.1527454588897487753 -2.8347492039446908763 -0.081136554176388195336
-1.5225069137843642898 2.4087104911325327961 -0.044067446366273183833
-6 0.011285899820091272997
+4.2888079225575648223 -2.6068082746690541818 -0.08512743586621877856
+1.4000629754656241179 2.4876377693334669565 -0.04165606656604725836
+6 0.011285899820091272997 0.4376655756331854547
 0.00038925687730393611812
-6.39471595410062843 -7.621162747287802297 -0.121992225877669294154
-1.4493167787574136286 1.3075474785896286071 -0.08039429377859412155
-7 0.0017236589478267730203
+6.528501376442308768 -7.4981197287393284157 -0.12945412016904539465
+1.4250071771025915456 1.33599992135721594 -0.07992159012428249671
+7 0.0017236589478267730203 0.46970222329693796102
 0.00016953449859497231466
-14.793135356927480828 13.074218343364380601 -0.14311846037737518955
--0.9605086875596024784 1.0118431725941020164 0.016148779866732710198
-8 0.0020336100526728302319
+14.703390521074780395 13.168120788311910019 -0.14161196287363458923
+-0.96768368440931795183 1.0056701102995595347 0.01621895610074016891
+8 0.0020336100526728302319 0.78148373992374883156
 0.000164587904124493665
-29.568629894896030663 -4.5543028991960081697 -0.58771107137394917874
-0.16867624969736024011 1.1427992197933557251 -0.027387722828706092838
+29.584136736556288838 -4.4478894754775319953 -0.5902566603324214123
+0.16448791459483679965 1.1435219564135608914 -0.027304639012640681262

examples/helio_gr_test/pl.swiftest.in

@@ -1,33 +1,33 @@
 8
-1 6.5537098095653139645e-06
+Mercury 6.5537098095653139645e-06 0.001475131156288637831
 1.6306381826061645943e-05
--0.30949970210807342674 0.1619004125820537876 0.041620272188990829754
--6.8742992150644793847 -8.672423996611946485 -0.078109307586001638286
-2 9.663313399581537916e-05
+0.38709993253896590737 0.20562614632859010921 7.0036272314159866426
+48.303648911363737284 29.187750438580689405 192.22398026813181104
+Venus 9.663313399581537916e-05 0.0067590747715647875607
 4.0453784346544178454e-05
--0.5567137338251560985 -0.46074173273652380134 0.02580196630219121906
-4.6580776303108450487 -5.726444072926637749 -0.3473859047161406309
-3 0.000120026935827952453094
+0.7233249152313999675 0.006782779674600277614 3.3945084679511872139
+76.62172192899298295 55.11871576732421829 141.51944714681908977
+Earth 0.000120026935827952453094 0.01004493295891520948
 4.25875607065040958e-05
-0.6978790186886838498 -0.73607603319120218366 3.261671020506711323e-05
-4.4579240279134950613 4.300011122687349501 -0.00022055769049333364448
-4 1.2739802010675941456e-05
+1.0000207198983319667 0.01667731166077134064 0.0027576432734417160447
+175.55813761562768605 287.40166532678227895 245.00485341438161413
+Mars 1.2739802010675941456e-05 0.007246527815634877893
 2.265740805092889601e-05
--1.617661473167097963 0.38314370807747849534 0.04771055403546069218
--0.98751874613118001086 -4.5371239937302254657 -0.07086074102213555221
-5 0.037692251088985676735
+1.5236922769560579116 0.093361659829406723476 1.8479133359077690724
+49.490611477105659333 286.70751815915190264 210.36775515565921069
+Jupiter 0.037692251088985676735 0.3552712221482522291
 0.00046732617030490929307
-4.1527454588897487753 -2.8347492039446908763 -0.081136554176388195336
-1.5225069137843642898 2.4087104911325327961 -0.044067446366273183833
-6 0.011285899820091272997
+5.203523661489898977 0.04851833897394460665 1.3035686835324369337
+100.51671881401649955 273.38319313278452682 318.65986979714938343
+Saturn 0.011285899820091272997 0.4376655756331854547
 0.00038925687730393611812
-6.39471595410062843 -7.621162747287802297 -0.121992225877669294154
-1.4493167787574136286 1.3075474785896286071 -0.08039429377859412155
-7 0.0017236589478267730203
+9.581904852310625387 0.052236260603057811658 2.486258128114103183
+113.595257336893098454 335.64742317800698856 225.92836894588160135
+Uranus 0.0017236589478267730203 0.46970222329693796102
 0.00016953449859497231466
-14.793135356927480828 13.074218343364380601 -0.14311846037737518955
--0.9605086875596024784 1.0118431725941020164 0.016148779866732710198
-8 0.0020336100526728302319
+19.238019712529130345 0.0442880601027018303 0.770350326736000679
+74.09520891350530292 95.7524345508490029 236.07863258800219342
+Neptune 0.0020336100526728302319 0.78148373992374883156
 0.000164587904124493665
-29.568629894896030663 -4.5543028991960081697 -0.58771107137394917874
-0.16867624969736024011 1.1427992197933557251 -0.027387722828706092838
+30.291369954344219195 0.013531244039650480379 1.7689741418447819665
+131.74449502957048708 245.89296040993210113 334.5035290478779757

examples/rmvs_swifter_comparison/1pl_1tp_encounter/init_cond.py

@@ -55,15 +55,15 @@
 p_tp = np.array([atp, 0.0, 0.0], dtype=np.double)
 v_tp = np.array([0.0, vtp, 0.0], dtype=np.double)
 
-Rhill = np.double(apl * 0.0100447248332378922085)
+rhill = np.double(apl * 0.0100447248332378922085)
 
 #Make Swifter files
 plfile = open(swifter_pl, 'w')
 print(npl+1, f'! Planet input file generated using init_cond.py',file=plfile)
 print(1,GMSun,file=plfile)
 print('0.0 0.0 0.0',file=plfile)
 print('0.0 0.0 0.0',file=plfile)
-print(plid,"{:.23g}".format(Gmass),Rhill, file=plfile)
+print(plid,"{:.23g}".format(Gmass),rhill, file=plfile)
 print(radius, file=plfile)
 print(*p_pl, file=plfile)
 print(*v_pl, file=plfile)
@@ -126,7 +126,7 @@
 plfile.write_record(v_pl[1])
 plfile.write_record(v_pl[2])
 plfile.write_record(Gmass)
-plfile.write_record(Rhill)
+plfile.write_record(rhill)
 plfile.write_record(radius)
 plfile.close()
 tpfile = FortranFile(swiftest_tp, 'w')

examples/rmvs_swifter_comparison/8pl_16tp_encounters/init_cond.py

@@ -84,16 +84,16 @@
 
 for i in pl.id:
     pli = pl.sel(id=i)
-    rstart = 2 * np.double(pli['Radius'])  # Start the test particles at a multiple of the planet radius away
-    vstart = 1.5 * np.sqrt(2 * np.double(pli['GMass'])  / rstart)  # Start the test particle velocities at a multiple of the escape speed
+    rstart = 2 * np.double(pli['radius'])  # Start the test particles at a multiple of the planet radius away
+    vstart = 1.5 * np.sqrt(2 * np.double(pli['Gmass'])  / rstart)  # Start the test particle velocities at a multiple of the escape speed
     xvstart = np.array([rstart / np.sqrt(2.0), rstart / np.sqrt(2.0), 0.0, vstart, 0.0, 0.0])
     # The positions and velocities of each pair of test particles will be in reference to a planet
-    plvec = np.array([np.double(pli['px']),
-                      np.double(pli['py']),
-                      np.double(pli['pz']),
-                      np.double(pli['vx']),
-                      np.double(pli['vy']),
-                      np.double(pli['vz'])])
+    plvec = np.array([np.double(pli['xhx']),
+                      np.double(pli['xhy']),
+                      np.double(pli['xhz']),
+                      np.double(pli['vhx']),
+                      np.double(pli['vhy']),
+                      np.double(pli['vhz'])])
     tpxv1 = plvec + xvstart
     tpxv2 = plvec - xvstart
     p1.append(tpxv1[0])