Check if snapshot directory exists and add a digit to the output #321

examples/CoolingBox/energy_plot.py

@@ -34,7 +34,7 @@ import sys
 stats_filename = "./energy.txt"
 
 # First snapshot
-snap_filename = "coolingBox_000.hdf5"
+snap_filename = "coolingBox_0000.hdf5"
 
 # Some constants in cgs units
 k_b = 1.38E-16 #boltzmann
@@ -104,7 +104,7 @@ print "Cooling time:", cooling_time_cgs, "[s]"
 u_snapshots_cgs = zeros(25)
 t_snapshots_cgs = zeros(25)
 for i in range(25):
-    snap = h5.File("coolingBox_%0.3d.hdf5"%i,'r')
+    snap = h5.File("coolingBox_%0.4d.hdf5"%i,'r')
     u_snapshots_cgs[i] = sum(snap["/PartType0/InternalEnergy"][:] * snap["/PartType0/Masses"][:])  / total_mass[0] * unit_length**2 / (unit_time)**2
     t_snapshots_cgs[i] = snap["/Header"].attrs["Time"] * unit_time
 

examples/CoolingHalo/density_profile.py

@@ -20,7 +20,7 @@ H_0_cgs = 100. * h * KM_PER_SEC_IN_CGS / (1.0e6 * PARSEC_IN_CGS)
 
 #read some header/parameter information from the first snapshot
 
-filename = "Hydrostatic_000.hdf5"
+filename = "Hydrostatic_0000.hdf5"
 f = h5.File(filename,'r')
 params = f["Parameters"]
 unit_mass_cgs = float(params.attrs["InternalUnitSystem:UnitMass_in_cgs"])
@@ -39,7 +39,7 @@ M_vir_cgs = r_vir_cgs * v_c_cgs**2 / CONST_G_CGS
 
 for i in range(n_snaps):
 
-    filename = "Hydrostatic_%03d.hdf5" %i
+    filename = "Hydrostatic_%04d.hdf5" %i
     f = h5.File(filename,'r')
     coords_dset = f["PartType0/Coordinates"]
     coords = np.array(coords_dset)

examples/CoolingHalo/internal_energy_profile.py

@@ -38,7 +38,7 @@ H_0_cgs = 100. * h * KM_PER_SEC_IN_CGS / (1.0e6 * PARSEC_IN_CGS)
 
 #read some header/parameter information from the first snapshot
 
-filename = "Hydrostatic_000.hdf5"
+filename = "Hydrostatic_0000.hdf5"
 f = h5.File(filename,'r')
 params = f["Parameters"]
 unit_mass_cgs = float(params.attrs["InternalUnitSystem:UnitMass_in_cgs"])
@@ -57,7 +57,7 @@ M_vir_cgs = r_vir_cgs * v_c_cgs**2 / CONST_G_CGS
 
 for i in range(n_snaps):
 
-    filename = "Hydrostatic_%03d.hdf5" %i
+    filename = "Hydrostatic_%04d.hdf5" %i
     f = h5.File(filename,'r')
     coords_dset = f["PartType0/Coordinates"]
     coords = np.array(coords_dset)

examples/CoolingHalo/test_energy_conservation.py

@@ -17,7 +17,7 @@ H_0_cgs = 100. * h * KM_PER_SEC_IN_CGS / (1.0e6 * PARSEC_IN_CGS)
 
 #read some header/parameter information from the first snapshot
 
-filename = "CoolingHalo_000.hdf5"
+filename = "CoolingHalo_0000.hdf5"
 f = h5.File(filename,'r')
 params = f["Parameters"]
 unit_mass_cgs = float(params.attrs["InternalUnitSystem:UnitMass_in_cgs"])
@@ -41,7 +41,7 @@ time_array_cgs = []
 
 for i in range(n_snaps):
 
-    filename = "CoolingHalo_%03d.hdf5" %i
+    filename = "CoolingHalo_%04d.hdf5" %i
     f = h5.File(filename,'r')
     coords_dset = f["PartType0/Coordinates"]
     coords = np.array(coords_dset)

examples/CoolingHalo/velocity_profile.py

@@ -39,7 +39,7 @@ H_0_cgs = 100. * h * KM_PER_SEC_IN_CGS / (1.0e6 * PARSEC_IN_CGS)
 
 #read some header/parameter information from the first snapshot
 
-filename = "CoolingHalo_000.hdf5"
+filename = "CoolingHalo_0000.hdf5"
 f = h5.File(filename,'r')
 params = f["Parameters"]
 unit_mass_cgs = float(params.attrs["InternalUnitSystem:UnitMass_in_cgs"])
@@ -58,7 +58,7 @@ M_vir_cgs = r_vir_cgs * v_c_cgs**2 / CONST_G_CGS
 
 for i in range(n_snaps):
 
-    filename = "CoolingHalo_%03d.hdf5" %i
+    filename = "CoolingHalo_%04d.hdf5" %i
     f = h5.File(filename,'r')
     coords_dset = f["PartType0/Coordinates"]
     coords = np.array(coords_dset)

examples/CoolingHaloWithSpin/density_profile.py

@@ -21,7 +21,7 @@ H_0_cgs = 100. * h * KM_PER_SEC_IN_CGS / (1.0e6 * PARSEC_IN_CGS)
 
 #read some header/parameter information from the first snapshot
 
-filename = "CoolingHalo_000.hdf5"
+filename = "CoolingHalo_0000.hdf5"
 f = h5.File(filename,'r')
 params = f["Parameters"]
 unit_mass_cgs = float(params.attrs["InternalUnitSystem:UnitMass_in_cgs"])
@@ -42,7 +42,7 @@ M_vir_cgs = r_vir_cgs * v_c_cgs**2 / CONST_G_CGS
 
 for i in range(n_snaps):
 
-    filename = "CoolingHalo_%03d.hdf5" %i
+    filename = "CoolingHalo_%04d.hdf5" %i
     f = h5.File(filename,'r')
     coords_dset = f["PartType0/Coordinates"]
     coords = np.array(coords_dset)

examples/CoolingHaloWithSpin/internal_energy_profile.py

@@ -39,7 +39,7 @@ H_0_cgs = 100. * h * KM_PER_SEC_IN_CGS / (1.0e6 * PARSEC_IN_CGS)
 
 #read some header/parameter information from the first snapshot
 
-filename = "CoolingHalo_000.hdf5"
+filename = "CoolingHalo_0000.hdf5"
 f = h5.File(filename,'r')
 params = f["Parameters"]
 unit_mass_cgs = float(params.attrs["InternalUnitSystem:UnitMass_in_cgs"])
@@ -60,7 +60,7 @@ M_vir_cgs = r_vir_cgs * v_c_cgs**2 / CONST_G_CGS
 
 for i in range(n_snaps):
 
-    filename = "CoolingHalo_%03d.hdf5" %i
+    filename = "CoolingHalo_%04d.hdf5" %i
     f = h5.File(filename,'r')
     coords_dset = f["PartType0/Coordinates"]
     coords = np.array(coords_dset)

examples/CoolingHaloWithSpin/test_energy_conservation.py

@@ -20,7 +20,7 @@ H_0_cgs = 100. * h * KM_PER_SEC_IN_CGS / (1.0e6 * PARSEC_IN_CGS)
 
 #read some header/parameter information from the first snapshot
 
-filename = "CoolingHalo_000.hdf5"
+filename = "CoolingHalo_0000.hdf5"
 f = h5.File(filename,'r')
 params = f["Parameters"]
 unit_mass_cgs = float(params.attrs["InternalUnitSystem:UnitMass_in_cgs"])
@@ -44,7 +44,7 @@ time_array_cgs = []
 
 for i in range(n_snaps):
 
-    filename = "CoolingHalo_%03d.hdf5" %i
+    filename = "CoolingHalo_%04d.hdf5" %i
     f = h5.File(filename,'r')
     coords_dset = f["PartType0/Coordinates"]
     coords = np.array(coords_dset)

examples/CoolingHaloWithSpin/velocity_profile.py

@@ -39,7 +39,7 @@ H_0_cgs = 100. * h * KM_PER_SEC_IN_CGS / (1.0e6 * PARSEC_IN_CGS)
 
 #read some header/parameter information from the first snapshot
 
-filename = "CoolingHalo_000.hdf5"
+filename = "CoolingHalo_0000.hdf5"
 f = h5.File(filename,'r')
 params = f["Parameters"]
 unit_mass_cgs = float(params.attrs["InternalUnitSystem:UnitMass_in_cgs"])
@@ -58,7 +58,7 @@ M_vir_cgs = r_vir_cgs * v_c_cgs**2 / CONST_G_CGS
 
 for i in range(n_snaps):
 
-    filename = "CoolingHalo_%03d.hdf5" %i
+    filename = "CoolingHalo_%04d.hdf5" %i
     f = h5.File(filename,'r')
     coords_dset = f["PartType0/Coordinates"]
     coords = np.array(coords_dset)

examples/ExternalPointMass/energy_plot.py

@@ -34,7 +34,7 @@ import sys
 stats_filename = "./energy.txt"
 
 # First snapshot
-snap_filename = "pointMass_000.hdf5"
+snap_filename = "pointMass_0000.hdf5"
 f = h5.File(snap_filename,'r')
 
 # Read the units parameters from the snapshot
@@ -71,7 +71,7 @@ Lz_snap = np.zeros(402)
 
 # Read all the particles from the snapshots
 for i in range(402):
-    snap_filename = "pointMass_%0.3d.hdf5"%i
+    snap_filename = "pointMass_%0.4d.hdf5"%i
     f = h5.File(snap_filename,'r')
 
     pos_x = f["PartType1/Coordinates"][:,0]

examples/Gradients/run.sh

@@ -2,12 +2,12 @@
 
 python makeICs.py stretched
 ../swift -s -t 2 gradientsStretched.yml
-python plot.py gradients_stretched_001.hdf5 stretched
+python plot.py gradients_stretched_0001.hdf5 stretched
 
 python makeICs.py cartesian
 ../swift -s -t 2 gradientsCartesian.yml
-python plot.py gradients_cartesian_001.hdf5 cartesian
+python plot.py gradients_cartesian_0001.hdf5 cartesian
 
 python makeICs.py random
 ../swift -s -t 2 gradientsRandom.yml
-python plot.py gradients_random_001.hdf5 random
+python plot.py gradients_random_0001.hdf5 random

examples/GreshoVortex_2D/plotSolution.py

@@ -83,7 +83,7 @@ solution_s = solution_P / solution_rho**gas_gamma
 solution_u = solution_P /((gas_gamma - 1.)*solution_rho)
 
 # Read the simulation data
-sim = h5py.File("gresho_%03d.hdf5"%snap, "r")
+sim = h5py.File("gresho_%04d.hdf5"%snap, "r")
 boxSize = sim["/Header"].attrs["BoxSize"][0]
 time = sim["/Header"].attrs["Time"][0]
 scheme = sim["/HydroScheme"].attrs["Scheme"]

examples/HydrostaticHalo/density_profile.py

@@ -42,7 +42,7 @@ H_0_cgs = 100. * h * KM_PER_SEC_IN_CGS / (1.0e6 * PARSEC_IN_CGS)
 
 #read some header/parameter information from the first snapshot
 
-filename = "Hydrostatic_000.hdf5"
+filename = "Hydrostatic_0000.hdf5"
 f = h5.File(filename,'r')
 params = f["Parameters"]
 unit_mass_cgs = float(params.attrs["InternalUnitSystem:UnitMass_in_cgs"])
@@ -63,7 +63,7 @@ M_vir_cgs = r_vir_cgs * v_c_cgs**2 / CONST_G_CGS
 
 for i in range(n_snaps):
 
-    filename = "Hydrostatic_%03d.hdf5" %i
+    filename = "Hydrostatic_%04d.hdf5" %i
     f = h5.File(filename,'r')
     coords_dset = f["PartType0/Coordinates"]
     coords = np.array(coords_dset)

examples/HydrostaticHalo/internal_energy_profile.py

@@ -60,7 +60,7 @@ H_0_cgs = 100. * h * KM_PER_SEC_IN_CGS / (1.0e6 * PARSEC_IN_CGS)
 
 #read some header/parameter information from the first snapshot
 
-filename = "Hydrostatic_000.hdf5"
+filename = "Hydrostatic_0000.hdf5"
 f = h5.File(filename,'r')
 params = f["Parameters"]
 unit_mass_cgs = float(params.attrs["InternalUnitSystem:UnitMass_in_cgs"])
@@ -79,7 +79,7 @@ M_vir_cgs = r_vir_cgs * v_c_cgs**2 / CONST_G_CGS
 
 for i in range(n_snaps):
 
-    filename = "Hydrostatic_%03d.hdf5" %i
+    filename = "Hydrostatic_%04d.hdf5" %i
     f = h5.File(filename,'r')
     coords_dset = f["PartType0/Coordinates"]
     coords = np.array(coords_dset)

examples/HydrostaticHalo/test_energy_conservation.py

@@ -38,7 +38,7 @@ H_0_cgs = 100. * h * KM_PER_SEC_IN_CGS / (1.0e6 * PARSEC_IN_CGS)
 
 #read some header/parameter information from the first snapshot
 
-filename = "Hydrostatic_000.hdf5"
+filename = "Hydrostatic_0000.hdf5"
 f = h5.File(filename,'r')
 params = f["Parameters"]
 unit_mass_cgs = float(params.attrs["InternalUnitSystem:UnitMass_in_cgs"])
@@ -62,7 +62,7 @@ time_array_cgs = []
 
 for i in range(n_snaps):
 
-    filename = "Hydrostatic_%03d.hdf5" %i
+    filename = "Hydrostatic_%04d.hdf5" %i
     f = h5.File(filename,'r')
     coords_dset = f["PartType0/Coordinates"]
     coords = np.array(coords_dset)

examples/HydrostaticHalo/velocity_profile.py

@@ -60,7 +60,7 @@ H_0_cgs = 100. * h * KM_PER_SEC_IN_CGS / (1.0e6 * PARSEC_IN_CGS)
 
 #read some header/parameter information from the first snapshot
 
-filename = "Hydrostatic_000.hdf5"
+filename = "Hydrostatic_0000.hdf5"
 f = h5.File(filename,'r')
 params = f["Parameters"]
 unit_mass_cgs = float(params.attrs["InternalUnitSystem:UnitMass_in_cgs"])
@@ -79,7 +79,7 @@ M_vir_cgs = r_vir_cgs * v_c_cgs**2 / CONST_G_CGS
 
 for i in range(n_snaps):
 
-    filename = "Hydrostatic_%03d.hdf5" %i
+    filename = "Hydrostatic_%04d.hdf5" %i
     f = h5.File(filename,'r')
     coords_dset = f["PartType0/Coordinates"]
     coords = np.array(coords_dset)

examples/IsothermalPotential/energy_plot.py

@@ -34,7 +34,7 @@ import sys
 stats_filename = "./energy.txt"
 
 # First snapshot
-snap_filename = "Isothermal_000.hdf5"
+snap_filename = "Isothermal_0000.hdf5"
 f = h5.File(snap_filename,'r')
 
 # Read the units parameters from the snapshot
@@ -70,7 +70,7 @@ Lz_snap = np.zeros(402)
 
 # Read all the particles from the snapshots
 for i in range(402):
-    snap_filename = "Isothermal_%0.3d.hdf5"%i
+    snap_filename = "Isothermal_%0.4d.hdf5"%i
     f = h5.File(snap_filename,'r')
 
     pos_x = f["PartType1/Coordinates"][:,0]

examples/KelvinHelmholtz_2D/plotSolution.py

@@ -63,7 +63,7 @@ rc('font',**{'family':'sans-serif','sans-serif':['Times']})
 snap = int(sys.argv[1])
 
 # Read the simulation data
-sim = h5py.File("kelvinHelmholtz_%03d.hdf5"%snap, "r")
+sim = h5py.File("kelvinHelmholtz_%04d.hdf5"%snap, "r")
 boxSize = sim["/Header"].attrs["BoxSize"][0]
 time = sim["/Header"].attrs["Time"][0]
 scheme = sim["/HydroScheme"].attrs["Scheme"]

examples/Noh_1D/plotSolution.py

@@ -58,7 +58,7 @@ snap = int(sys.argv[1])
 
 
 # Read the simulation data
-sim = h5py.File("noh_%03d.hdf5"%snap, "r")
+sim = h5py.File("noh_%04d.hdf5"%snap, "r")
 boxSize = sim["/Header"].attrs["BoxSize"][0]
 time = sim["/Header"].attrs["Time"][0]
 scheme = sim["/HydroScheme"].attrs["Scheme"]

examples/Noh_2D/plotSolution.py

@@ -58,7 +58,7 @@ rc('font',**{'family':'sans-serif','sans-serif':['Times']})
 snap = int(sys.argv[1])
 
 # Read the simulation data
-sim = h5py.File("noh_%03d.hdf5"%snap, "r")
+sim = h5py.File("noh_%04d.hdf5"%snap, "r")
 boxSize = sim["/Header"].attrs["BoxSize"][0]
 time = sim["/Header"].attrs["Time"][0]
 scheme = sim["/HydroScheme"].attrs["Scheme"]

examples/Noh_3D/plotSolution.py

@@ -59,7 +59,7 @@ snap = int(sys.argv[1])
 
 
 # Read the simulation data
-sim = h5py.File("noh_%03d.hdf5"%snap, "r")
+sim = h5py.File("noh_%04d.hdf5"%snap, "r")
 boxSize = sim["/Header"].attrs["BoxSize"][0]
 time = sim["/Header"].attrs["Time"][0]
 scheme = sim["/HydroScheme"].attrs["Scheme"]

examples/SedovBlast_1D/plotSolution.py

@@ -64,7 +64,7 @@ snap = int(sys.argv[1])
 
 
 # Read the simulation data
-sim = h5py.File("sedov_%03d.hdf5"%snap, "r")
+sim = h5py.File("sedov_%04d.hdf5"%snap, "r")
 boxSize = sim["/Header"].attrs["BoxSize"][0]
 time = sim["/Header"].attrs["Time"][0]
 scheme = sim["/HydroScheme"].attrs["Scheme"]

examples/SedovBlast_2D/plotSolution.py

@@ -65,7 +65,7 @@ snap = int(sys.argv[1])
 
 
 # Read the simulation data
-sim = h5py.File("sedov_%03d.hdf5"%snap, "r")
+sim = h5py.File("sedov_%04d.hdf5"%snap, "r")
 boxSize = sim["/Header"].attrs["BoxSize"][0]
 time = sim["/Header"].attrs["Time"][0]
 scheme = sim["/HydroScheme"].attrs["Scheme"]

examples/SedovBlast_3D/plotSolution.py

@@ -65,7 +65,7 @@ snap = int(sys.argv[1])
 
 
 # Read the simulation data
-sim = h5py.File("sedov_%03d.hdf5"%snap, "r")
+sim = h5py.File("sedov_%04d.hdf5"%snap, "r")
 boxSize = sim["/Header"].attrs["BoxSize"][0]
 time = sim["/Header"].attrs["Time"][0]
 scheme = sim["/HydroScheme"].attrs["Scheme"]

examples/SodShock_1D/plotSolution.py

@@ -67,7 +67,7 @@ snap = int(sys.argv[1])
 
 
 # Read the simulation data
-sim = h5py.File("sodShock_%03d.hdf5"%snap, "r")
+sim = h5py.File("sodShock_%04d.hdf5"%snap, "r")
 boxSize = sim["/Header"].attrs["BoxSize"][0]
 time = sim["/Header"].attrs["Time"][0]
 scheme = sim["/HydroScheme"].attrs["Scheme"]

examples/SodShock_2D/plotSolution.py

@@ -68,7 +68,7 @@ snap = int(sys.argv[1])
 
 
 # Read the simulation data
-sim = h5py.File("sodShock_%03d.hdf5"%snap, "r")
+sim = h5py.File("sodShock_%04d.hdf5"%snap, "r")
 boxSize = sim["/Header"].attrs["BoxSize"][0]
 time = sim["/Header"].attrs["Time"][0]
 scheme = sim["/HydroScheme"].attrs["Scheme"]

examples/SodShock_3D/plotSolution.py

@@ -68,7 +68,7 @@ snap = int(sys.argv[1])
 
 
 # Read the simulation data
-sim = h5py.File("sodShock_%03d.hdf5"%snap, "r")
+sim = h5py.File("sodShock_%04d.hdf5"%snap, "r")
 boxSize = sim["/Header"].attrs["BoxSize"][0]
 time = sim["/Header"].attrs["Time"][0]
 scheme = sim["/HydroScheme"].attrs["Scheme"]

examples/SquareTest_2D/plotSolution.py

@@ -63,7 +63,7 @@ rc('font',**{'family':'sans-serif','sans-serif':['Times']})
 snap = int(sys.argv[1])
 
 # Read the simulation data
-sim = h5py.File("square_%03d.hdf5"%snap, "r")
+sim = h5py.File("square_%04d.hdf5"%snap, "r")
 boxSize = sim["/Header"].attrs["BoxSize"][0]
 time = sim["/Header"].attrs["Time"][0]
 scheme = sim["/HydroScheme"].attrs["Scheme"]

examples/main.c

@@ -27,6 +27,7 @@
 
 /* Some standard headers. */
 #include <fenv.h>
+#include <libgen.h>
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
@@ -633,6 +634,21 @@ int main(int argc, char *argv[]) {
   /* Initialise the particles */
   engine_init_particles(&e, flag_entropy_ICs, clean_h_values);
 
+  /* Check if output directory exists */
+  char dir[200];
+  int test;
+  /* get output directory */
+  strcpy(dir, e.snapshotBaseName);
+  dirname(dir);
+  /* test if directory is current directory and update name if yes */
+  test = strchr(e.snapshotBaseName, '/') == NULL;
+  if (test) strcpy(dir, "./");
+  /* Check if user has write permission */
+  test = access(dir, W_OK);
+  if (-1 == test)
+    error("Directory %s does not exist or you do not have write permission",
+          dir);
+
   /* Write the state of the system before starting time integration. */
   engine_dump_snapshot(&e);
 

src/parallel_io.c

@@ -667,7 +667,7 @@ void write_output_parallel(struct engine* e, const char* baseName,
 
   /* File name */
   char fileName[FILENAME_BUFFER_SIZE];
-  snprintf(fileName, FILENAME_BUFFER_SIZE, "%s_%03i.hdf5", baseName,
+  snprintf(fileName, FILENAME_BUFFER_SIZE, "%s_%04i.hdf5", baseName,
            outputCount);
 
   /* First time, we need to create the XMF file */

src/serial_io.c

@@ -738,7 +738,7 @@ void write_output_serial(struct engine* e, const char* baseName,
 
   /* File name */
   char fileName[FILENAME_BUFFER_SIZE];
-  snprintf(fileName, FILENAME_BUFFER_SIZE, "%s_%03i.hdf5", baseName,
+  snprintf(fileName, FILENAME_BUFFER_SIZE, "%s_%04i.hdf5", baseName,
            outputCount);
 
   /* Compute offset in the file and total number of particles */

src/single_io.c

@@ -606,7 +606,7 @@ void write_output_single(struct engine* e, const char* baseName,
 
   /* File name */
   char fileName[FILENAME_BUFFER_SIZE];
-  snprintf(fileName, FILENAME_BUFFER_SIZE, "%s_%03i.hdf5", baseName,
+  snprintf(fileName, FILENAME_BUFFER_SIZE, "%s_%04i.hdf5", baseName,
            outputCount);
 
   /* First time, we need to create the XMF file */

src/xmf.c

@@ -135,7 +135,7 @@ void xmf_write_outputfooter(FILE* xmfFile, int output, float time) {
   /* Write end of the section of this time step */
 
   fprintf(xmfFile,
-          "\n</Grid> <!-- End of meta-data for output=%03i, time=%f -->\n",
+          "\n</Grid> <!-- End of meta-data for output=%04i, time=%f -->\n",
           output, time);
   fprintf(xmfFile, "\n</Grid> <!-- timeSeries -->\n");
   fprintf(xmfFile, "</Domain>\n");