Add a select output test

tests/selectOutput.yml

+SelectOutput:
+  # Particle Type 0
+  Coordinates_Gas: 1   # check if written when specified
+  Velocities_Gas:  0   # check if not written when specified
+  Masses_Gas:     -5   # check warning if not 0 or 1 and if written
+  Pot_Gas:         1   # check warning if wrong name
+  # Density_Gas:   1   # check if written when not specified
+
+# Parameters for the hydrodynamics scheme
+SPH:
+  resolution_eta:        1.2348   # Target smoothing length in units of the mean inter-particle separation (1.2348 == 48Ngbs with the cubic spline kernel).
+  CFL_condition:         0.1      # Courant-Friedrich-Levy condition for time integration.

tests/testSelectOutput.c

+/*******************************************************************************
+ * This file is part of SWIFT.
+ * Copyright (C) 2015 Matthieu Schaller (matthieu.schaller@durham.ac.uk).
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published
+ * by the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program 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 Lesser General Public License
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ ******************************************************************************/
+
+/* Some standard headers. */
+#include <stdlib.h>
+
+/* Includes. */
+#include "swift.h"
+
+void select_output_engine_init(struct engine *e, struct space *s,
+			       struct cosmology *cosmo, struct swift_params *params,
+			       struct cooling_function_data *cooling,
+			       struct hydro_props *hydro_properties) {
+  /* set structures */
+  e->s = s;
+  e->cooling_func = cooling;
+  e->parameter_file = params;
+  e->cosmology = cosmo;
+  e->policy = engine_policy_hydro;
+  e->hydro_properties = hydro_properties;
+
+  /* initialization of threadpool */
+  threadpool_init(&e->threadpool, 1);
+
+  /* set parameters */
+  e->verbose = 1;
+  e->time = 0;
+  e->snapshotOutputCount = 0;
+  e->snapshotCompression = 0;  
+  
+};
+
+void select_output_space_init(struct space *s, double *dim, int periodic,
+			      size_t Ngas, size_t Nspart, size_t Ngpart,
+			      struct part *parts, struct spart *sparts,
+			      struct gpart *gparts) {
+  s->periodic = periodic;
+  for (int i=0; i<3; i++) {
+    s->dim[i] = dim[i];
+  }
+
+  /* init space particles */
+  s->nr_parts = Ngas;
+  s->nr_sparts = Nspart;
+  s->nr_gparts = Ngpart;
+
+  s->parts = parts;
+  s->gparts = gparts;
+  s->sparts = sparts;
+
+  /* Allocate the extra parts array for the gas particles. */
+  if (posix_memalign((void **)&s->xparts, xpart_align,
+		     Ngas * sizeof(struct xpart)) != 0)
+    error("Failed to allocate xparts.");
+  bzero(s->xparts, Ngas * sizeof(struct xpart));
+};
+
+void select_output_space_clean(struct space *s) {
+  free(s->xparts);
+};
+
+
+void select_output_engine_clean(struct engine *e) {
+  threadpool_clean(&e->threadpool);  
+}
+
+int main() {
+
+  char *base_name = "testSelectOutput";
+  size_t Ngas = 0, Ngpart = 0, Nspart = 0;
+  int periodic = -1;
+  int flag_entropy_ICs = -1;
+  double dim[3];
+  struct part *parts = NULL;
+  struct gpart *gparts = NULL;
+  struct spart *sparts = NULL;
+
+  /* parse parameters */
+  message("Reading parameters.");
+  struct swift_params param_file;
+  char *input_file = "selectOutput.yml";
+  parser_read_file(input_file, &param_file);
+
+  /* Default unit system */
+  message("Initialization of the unit system.");
+  struct unit_system us;
+  units_init_cgs(&us);
+
+  /* Default physical constants */
+  message("Initialization of the physical constants.");
+  struct phys_const prog_const;
+  phys_const_init(&us, &param_file, &prog_const);
+
+  /* Read data */
+  message("Reading initial conditions.");
+  read_ic_single("input.hdf5", &us, dim, &parts, &gparts, &sparts, &Ngas,
+                 &Ngpart, &Nspart, &periodic, &flag_entropy_ICs, 1, 0, 0, 0, 1.,
+                 1, 0);
+
+  /* pseudo initialization of the space */
+  message("Initialization of the space.");
+  struct space s;
+  select_output_space_init(&s, dim, periodic, Ngas, Nspart, Ngpart,
+			   parts, sparts, gparts);
+
+  /* initialization of cosmology */
+  message("Initialization of the cosmology.");
+  struct cosmology cosmo;
+  cosmology_init_no_cosmo(&cosmo);
+
+  /* pseudo initialization of cooling */
+  message("Initialization of the cooling.");
+  struct cooling_function_data cooling;
+
+  /* pseudo initialization of hydro */
+  message("Initialization of the hydro.");
+  struct hydro_props hydro_properties;
+  hydro_props_init(&hydro_properties, &prog_const, &us, &param_file);
+
+  /* pseudo initialization of the engine */
+  message("Initialization of the engine.");
+  struct engine e;
+  select_output_engine_init(&e, &s, &cosmo, &param_file,
+			    &cooling, &hydro_properties);
+
+  /* check output selection */
+  message("Checking output parameters.");
+  long long N_total[swift_type_count] = {Ngas, Ngpart, 0, 0, Nspart, 0};
+  io_check_output_fields(&param_file, &e, N_total);
+
+  /* write output file */
+  message("Writing output.");
+  write_output_single(&e, base_name, &us, &us);
+
+  /* Clean-up */
+  message("Cleaning memory.");
+  select_output_engine_clean(&e);
+  select_output_space_clean(&s);
+  cosmology_clean(&cosmo);
+  free(parts);
+  free(gparts);
+
+  return 0;
+}

tests/testSelectOutput.py

+###############################################################################
+ # This file is part of SWIFT.
+ # Copyright (c) 2015 Bert Vandenbroucke (bert.vandenbroucke@ugent.be)
+ #                    Matthieu Schaller (matthieu.schaller@durham.ac.uk)
+ # 
+ # This program is free software: you can redistribute it and/or modify
+ # it under the terms of the GNU Lesser General Public License as published
+ # by the Free Software Foundation, either version 3 of the License, or
+ # (at your option) any later version.
+ # 
+ # This program 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 Lesser General Public License
+ # along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ # 
+ ##############################################################################
+
+# Check the output done with swift
+
+import h5py
+
+filename = "testSelectOutput_0000.hdf5"
+log_filename = "testSelectOutput.sh.log"
+
+# Read the simulation data
+sim = h5py.File(filename, "r")
+part0 = sim["/PartType0"]
+
+# check presence / absence fields
+if "Velocities" in part0:
+    raise Exception("`Velocities` present in HDF5 but should not be written")
+
+if "Coordinates" not in part0:
+    raise Exception("`Coordinates` not present in HDF5 but should be written")
+
+if "Masses" not in part0:
+    raise Exception("`Masses` not present in HDF5 but should be written")
+
+if "Density" not in part0:
+    raise Exception("`Density` not present in HDF5 but should be written")
+
+
+# check error detection
+with open(log_filename, "r") as f:
+    data = f.read()
+
+if "SelectOutput:Masses_Gas" not in data:
+    raise Exception("Input error in `SelectOuput:Masses_Gas` not detected")
+
+if "SelectOutput:Pot_Gas" not in data:
+    raise Exception("Parameter name error not detected for `SelectOutput:Pot_Gas`")

tests/testSelectOutput.sh.in

+#!/bin/bash
+
+echo "Creating initial conditions"
+python @srcdir@/makeInput.py
+
+echo "Generating output"
+./testSelectOutput 
+
+echo "Checking output"
+python @srcdir@/testSelectOutput.py
+