diff --git a/src/configuration.c b/src/configuration.c
new file mode 100644
index 0000000000000000000000000000000000000000..b740bf6893c3c16268593792d5de7b1b3a190dd9
--- /dev/null
+++ b/src/configuration.c
@@ -0,0 +1,847 @@
+/** @file configuration.c
+ * @brief Module for input/output of parameters
+ */
+/* ----------------------------------------------------------------------------
+ libconfig - A library for processing structured configuration files
+ Copyright (C) 2005-2010 Mark A Lindner
+
+ This file is part of libconfig.
+
+ This library 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 2.1 of
+ the License, or (at your option) any later version.
+
+ This library 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
+ Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Library General Public
+ License along with this library; if not, see
+ .
+ ----------------------------------------------------------------------------
+*/
+
+#include
+#include
+#include
+#include
+#include
+
+#include
+#include
+#include
+#include
+#include
+
+/** @brief Looks in a libconfig file *.cfg for a parameter of type 'int', with
+ * name 'sstring' and add its value to the global variable with the same name.
+ * If already initialized, its value will be overwritten.
+ *
+ * @param[in] name name of the parameter (see e.g., input file default.cfg)
+ * @param[in] type type of parameter (see e.g., input file default.cfg)
+ * @param[in] comment comment to be added (see e.g., input file default.cfg)
+ * @param[in] sstring name to be found
+ * @param[out] *par global 'int' variable named 'name';
+ * on return *par will have value 'value'
+ * @param[in] value of type 'int'
+ * @param[in] count number of elements in array 'parameter_names' to examine
+ * @param[in] *change if TRUE then value in setting_default will be changed
+ * @param[in] setting_default related to default configuration file
+ * @param[out] i position in global array 'parameter_names'
+ * defined in configuration.h
+ *
+ */
+bool
+change_cfg_integer(const char* name,
+ const char *type,
+ const char *comment,
+ const char *sstring,
+ int *par,
+ int value,
+ int count,
+ bool *change,
+ config_setting_t *setting_default,
+ int i)
+{
+ int j;
+ config_setting_t *elem,*setting_value,*setting_comment;
+
+ if(!(strncmp(name,sstring,COMPARE_LIMIT))) {
+ if(!(strncmp(type,"int",COMPARE_LIMIT))) {
+ *par = value;
+ if(change) {
+ /* Find the corresponding index in the file default.cfg */
+ for(j=0; j You should use something smaller.
+ */
+ if(change_cfg_integer (name,type,comment,"max_disk_space_mb",&max_disk_space_mb,ivalue,count,change,setting,ii))
+ return;
+
+ /************************
+ * Numerical parameters *
+ ************************/
+
+ /* Number of gridpoints in r direction at level 0. */
+ if(change_cfg_integer (name,type,comment,"gridpoints_r",&gridpoints_r,ivalue,count,change,setting,ii))
+ return;
+
+ /* Number of gridpoints in z direction at level 0. */
+ if(change_cfg_integer (name,type,comment,"gridpoints_z",&gridpoints_z,ivalue,count,change,setting,ii))
+ return;
+
+ /* Number of azimuthal modes. */
+ if(change_cfg_integer (name,type,comment,"max_ntheta",&max_ntheta,ivalue,count,change,setting,ii))
+ return;
+
+ /* Initial time may be away from 0 */
+ if(change_cfg_double(name,type,comment,"start_t",&start_t,dvalue,count,change,setting,ii))
+ return;
+
+ /* End time of simulation, originally 500.0 */
+ if(change_cfg_double(name,type,comment,"end_t",&end_t,dvalue,count,change,setting,ii))
+ return;
+
+ /* The actual timestep may be smaller that this one, if it is needed
+ * to satisfy the Courant constraint.
+ */
+ if(change_cfg_double(name,type,comment,"attempt_dt",&attempt_dt,dvalue,count,change,setting,ii))
+ return;
+
+ /* Number of levels that are used for the Poisson equation
+ * but NOT for the cdr integrator.
+ */
+ if(change_cfg_integer (name,type,comment,"extra_pois_levels",&extra_pois_levels,ivalue,count,change,setting,ii))
+ return;
+
+ /* Maximum nesting depth */
+ if(change_cfg_integer (name,type,comment,"max_levels",&max_levels,ivalue,count,change,setting,ii))
+ return;
+
+ /* Total number of species */
+ if(change_cfg_integer (name,type,comment,"no_species",&no_species,ivalue,count,change,setting,ii))
+ return;
+
+ /* Maximum error allowed in the Poisson solver.
+ * Cells with larger errors will be further refined.
+ */
+ if(change_cfg_double(name,type,comment,"pois_max_error",&pois_max_error,dvalue,count,change,setting,ii))
+ return;
+
+ /* Maximum refinement level for the Poisson solver. */
+ if(change_cfg_integer(name,type,comment,"pois_max_level",&pois_max_level,ivalue,count,change,setting,ii))
+ return;
+
+ /* These are photo-ionization parameters equivalent to the Poisson ones.
+ * If extra_photo_levels < 0, then these parameters are ignored and the
+ * poisson-parameters are used. If extra_photo_levels_2 < 0 then the
+ * parameters for the second term are ignored and the parameters for the
+ * first term are used for both terms.
+ */
+
+ /* First photo-ionization term */
+ if(change_cfg_integer (name,type,comment,"extra_photo_levels",&extra_photo_levels,ivalue,count,change,setting,ii))
+ return;
+
+ /* Maximum level of refinement in the photo-ionization solver.*/
+ if(change_cfg_integer (name,type,comment,"photo_max_level",&photo_max_level,ivalue,count,change,setting,ii))
+ return;
+
+ /* Error threshold that leads to refinement in the photo-ionization code. */
+ if(change_cfg_double(name,type,comment,"photo_max_error",&photo_max_error,dvalue,count,change,setting,ii))
+ return;
+
+ /* Photo-ionization boundary condition at r = L_r
+ * 1 means homogeneous Neumann boundary conditions
+ * -1 means homogeneous Dirichlet boundary conditions.
+ */
+ if(change_cfg_integer(name,type,comment,"photo_bnd_right" ,&photo_bnd_right ,ivalue,count,change,setting,ii))
+ return;
+
+ if(change_cfg_integer(name,type,comment,"photo_bnd_bottom",&photo_bnd_bottom,ivalue,count,change,setting,ii))
+ return;
+
+ if(change_cfg_integer(name,type,comment,"photo_bnd_top" ,&photo_bnd_top ,ivalue,count,change,setting,ii))
+ return;
+
+
+ /* Second photo-ionization term: Extra levels for the photo-ionization solver. */
+ if(change_cfg_integer(name,type,comment,"extra_photo_levels_2",&extra_photo_levels_2,ivalue,count,change,setting,ii))
+ return;
+
+ /* Maximum level of refinement in the photo-ionization solver.*/
+ if(change_cfg_integer(name,type,comment,"photo_max_level_2",&photo_max_level_2,ivalue,count,change,setting,ii))
+ return;
+
+
+ /* Error threshold that leads to refinement in the photo-ionization code.*/
+ if(change_cfg_double(name,type,comment,"photo_max_error_2",&photo_max_error_2,dvalue,count,change,setting,ii))
+ return;
+
+ /* Photo-ionization boundary condition at r = L_r.
+ * 1 for homogeneous Neumann,
+ * -1 for homogeneous Dirichlet
+ */
+ if(change_cfg_integer(name,type,comment,"photo_bnd_right_2",&photo_bnd_right_2,ivalue,count,change,setting,ii))
+ return;
+
+ /* Photo-ionization boundary condition at z = 0.
+ * 1 for homogeneous Neumann,
+ * -1 for homogeneous Dirichlet
+ */
+ if(change_cfg_integer(name,type,comment,"photo_bnd_bottom_2",&photo_bnd_bottom_2,ivalue,count,change,setting,ii))
+ return;
+
+ /* Photo-ionization boundary condition at z = L_z.
+ * 1 for homogeneous Neumann,
+ * -1 for homogeneous Dirichlet
+ */
+ if(change_cfg_integer(name,type,comment,"photo_bnd_top_2",&photo_bnd_top_2,ivalue,count,change,setting,ii))
+ return;
+
+ /* Boundary conditions for the CDR system. */
+ if(change_cfg_integer(name,type,comment,"cdr_bnd_bottom",&cdr_bnd_bottom,ivalue,count,change,setting,ii))
+ return;
+
+ if(change_cfg_integer(name,type,comment,"cdr_bnd_top",&cdr_bnd_top,ivalue,count,change,setting,ii))
+ return;
+
+ if(change_cfg_integer(name,type,comment,"cdr_bnd_right",&cdr_bnd_right,ivalue,count,change,setting,ii))
+ return;
+
+ if(change_cfg_integer(name,type,comment,"pois_bnd_right",&pois_bnd_right,ivalue,count,change,setting,ii))
+ return;
+
+ if(change_cfg_integer(name,type,comment,"pois_bnd_bottom",&pois_bnd_bottom,ivalue,count,change,setting,ii))
+ return;
+
+ if(change_cfg_integer(name,type,comment,"pois_bnd_top",&pois_bnd_top,ivalue,count,change,setting,ii))
+ return;
+
+ /* Courant numbers. */
+ if(change_cfg_double(name,type,comment,"nu_a",&nu_a,dvalue,count,change,setting,ii))
+ return;
+
+ if(change_cfg_double(name,type,comment,"nu_d",&nu_d,dvalue,count,change,setting,ii))
+ return;
+
+ if(change_cfg_double(name,type,comment,"nu_rt",&nu_rt,dvalue,count,change,setting,ii))
+ return;
+
+ if(change_cfg_double(name,type,comment,"nu_f",&nu_f,dvalue,count,change,setting,ii))
+ return;
+
+ /* Refinement criteria for the CDR equation. */
+ if(change_cfg_double(name,type,comment,"ref_threshold_eabs",&ref_threshold_eabs,dvalue,count,change,setting,ii))
+ return;
+
+ /* Refinement criteria for the CDR equation. */
+ if(change_cfg_integer(name,type,comment,"ref_level_eabs",&ref_level_eabs,ivalue,count,change,setting,ii))
+ return;
+
+ if(change_cfg_double(name,type,comment,"ref_threshold_charge",&ref_threshold_charge,dvalue,count,change,setting,ii))
+ return;
+
+ if(change_cfg_double(name,type,comment,"ref_threshold_dens",&ref_threshold_dens,dvalue,count,change,setting,ii))
+ return;
+
+ if(change_cfg_double(name,type,comment,"ref_threshold_edge",&ref_threshold_edge,dvalue,count,change,setting,ii))
+ return;
+
+ /* r- and z-length of the minimal refinement area in the cdr equation*/
+ if(change_cfg_integer(name,type,comment,"cdr_brick_dr",&cdr_brick_dr,ivalue,count,change,setting,ii))
+ return;
+
+ if(change_cfg_integer(name,type,comment,"cdr_brick_dz",&cdr_brick_dz,ivalue,count,change,setting,ii))
+ return;
+
+ /* Maximum refinement level for the cdr solver. */
+ if(change_cfg_integer(name,type,comment,"cdr_max_level",&cdr_max_level,ivalue,count,change,setting,ii))
+ return;
+
+ /* Interpolation method. */
+ if(change_cfg_integer(name,type,comment,"cdr_interp_in",&cdr_interp_in,ivalue,count,change,setting,ii))
+ return;
+
+ if(change_cfg_integer(name,type,comment,"cdr_interp_bnd",&cdr_interp_bnd,ivalue,count,change,setting,ii))
+ return;
+
+ /***********************
+ * Physical parameters *
+ ***********************/
+ if(change_cfg_double(name,type,comment,"L_r",&L_r,dvalue,count,change,setting,ii))
+ return;
+
+ if(change_cfg_double(name,type,comment,"L_z",&L_z,dvalue,count,change,setting,ii))
+ return;
+
+ if(change_cfg_double(name,type,comment,"diffusion_coeff",&diffusion_coeff,dvalue,count,change,setting,ii))
+ return;
+
+ if(change_cfg_double(name,type,comment,"attachment_rate",&attachment_rate,dvalue,count,change,setting,ii))
+ return;
+
+ if(change_cfg_double(name,type,comment,"attachment_E0",&attachment_E0,dvalue,count,change,setting,ii))
+ return;
+
+ /* Constant external electric field. */
+ if(change_cfg_double(name,type,comment,"E0_x",&E0_x,dvalue,count,change,setting,ii))
+ return;
+
+ if(change_cfg_double(name,type,comment,"E0_y",&E0_y,dvalue,count,change,setting,ii))
+ return;
+
+ if(change_cfg_double(name,type,comment,"E0_z",&E0_z,dvalue,count,change,setting,ii))
+ return;
+
+ /* Constant external electric field. */
+ if(change_cfg_double(name,type,comment,"rise_time",&rise_time,dvalue,count,change,setting,ii))
+ return;
+
+ if(change_cfg_double(name,type,comment,"off_time",&off_time,dvalue,count,change,setting,ii))
+ return;
+
+ if(change_cfg_integer(name,type,comment,"has_photoionization",&has_photoionization,ivalue,count,change,setting,ii))
+ return;
+
+ /* Width of the initial seed in x-, y- and z-direction */
+ if(change_cfg_double(name,type,comment,"seed_sigma_x",&seed_sigma_x,dvalue,count,change,setting,ii))
+ return;
+
+ if(change_cfg_double(name,type,comment,"seed_sigma_y",&seed_sigma_y,dvalue,count,change,setting,ii))
+ return;
+
+ if(change_cfg_double(name,type,comment,"seed_sigma_z",&seed_sigma_z,dvalue,count,change,setting,ii))
+ return;
+
+ if(change_cfg_double(name,type,comment,"seed_N",&seed_N,dvalue,count,change,setting,ii))
+ return;
+
+ /* Initial background ionization */
+ if(change_cfg_double(name,type,comment,"background_ionization",&background_ionization,dvalue,count,change,setting,ii))
+ return;
+
+ /* Length of exponential increase of the pre-ionization for atmospherical
+ * models
+ */
+ if(change_cfg_double(name,type,comment,"background_increase_length",&background_increase_length,
+ dvalue,count,change,setting,ii))
+ return;
+
+ /* Use the point-plane geometry? */
+ if(change_cfg_integer(name,type,comment,"pois_inhom",&pois_inhom,ivalue,count,change,setting,ii))
+ return;
+
+ /* Number of mirror charges to use*/
+ if(change_cfg_integer(name,type,comment,"pois_inhom_reflections",&pois_inhom_reflections,ivalue,count,change,setting,ii))
+ return;
+
+ /* Length of the needle */
+ if(change_cfg_double(name,type,comment,"needle_length",&needle_length,dvalue,count,change,setting,ii))
+ return;
+
+ /* Radius of the needle */
+ if(change_cfg_double(name,type,comment,"needle_radius",&needle_radius,dvalue,count,change,setting,ii))
+ return;
+
+ /* If nonzero, the charge is fixed, not floating
+ * Simulation of charged clouds close to the earth surface.
+ */
+ if(change_cfg_double(name,type,comment,"pois_inhom_fixed_q",&pois_inhom_fixed_q,dvalue,count,change,setting,ii))
+ return;
+
+ /* Constant ionization rate. */
+ if(change_cfg_double(name,type,comment,"constant_source",&constant_source,dvalue,count,change,setting,ii))
+ return;
+
+ /* Random perturbations for stability analysis. */
+ if(change_cfg_double(name,type,comment,"perturb_epsilon",&perturb_epsilon,dvalue,count,change,setting,ii))
+ return;
+
+ /* Perturb only modes up to perturb_max_k, i.e. large number to perturb all */
+ if(change_cfg_integer(name,type,comment,"perturb_max_k",&perturb_max_k,ivalue,count,change,setting,ii))
+ return;
+
+ /******************
+ * Sprites module *
+ ******************/
+ if(change_cfg_integer(name,type,comment,"sprite_module",&sprite_module,ivalue,count,change,setting,ii))
+ return;
+
+ if(change_cfg_double(name,type,comment,"dens_decay_len",&dens_decay_len,dvalue,count,change,setting,ii))
+ return;
+
+ if(change_cfg_double(name,type,comment,"sprite_dens_0",&sprite_dens_0,dvalue,count,change,setting,ii))
+ return;
+
+ if(change_cfg_double(name,type,comment,"sprite_dens_q",&sprite_dens_q,dvalue,count,change,setting,ii))
+ return;
+
+ if(change_cfg_integer(name,type,comment,"sprite_sign",&sprite_sign,ivalue,count,change,setting,ii))
+ return;
+
+}
+
+/* @brief Read just one parameter from configuration file connected
+ * to setting2.
+ *
+ * In case setting1 and setting2 are different then
+ * the value in setting1 will be overwritten by the value of setting2.
+ *
+ * In case setting1 and setting2 are the same then
+ * the value in setting1 will be added.
+ *
+ * @param[in] config_setting_t *setting1 represents s configuration setting
+ * @param[in] config_setting_t *setting2 represents s configuration setting
+ * @param[in] ii position in array 'parameter_names'
+ * @param[in] count number of elements in parameter array to examine
+ * @param[in] *change if TRUE then value in setting_default will be changed
+ *
+ */
+bool
+read_parameter(config_setting_t *setting1,
+ config_setting_t *setting2,
+ int ii,
+ int count,
+ bool *change)
+{
+ const char *type,*name,*comment;
+ double dvalue;
+ int ivalue;
+ int bbool;
+ const char* astring;
+ config_setting_t *elem = config_setting_get_elem(setting2,ii);
+
+ /* Only output the record if all of the expected fields are present. */
+ if(config_setting_lookup_string(elem, "type", &type) &&
+ config_setting_lookup_string(elem, "name", &name) &&
+ config_setting_lookup_string(elem, "comment",&comment) &&
+ (config_setting_lookup_float (elem,"value", &dvalue) ||
+ config_setting_lookup_int (elem,"value", &ivalue) ||
+ config_setting_lookup_bool (elem,"value", &bbool ) ||
+ config_setting_lookup_string(elem,"value", &astring))
+ ) {
+ printf("\n# %s\n",comment);
+ if(!(strncmp(type,"string",COMPARE_LIMIT)))
+ printf("(%s) %s=%s\n",type,name,astring);
+ if(!(strncmp(type,"double",COMPARE_LIMIT)))
+ printf("(%s) %s=%g\n",type,name,dvalue);
+ if(!(strncmp(type,"int",COMPARE_LIMIT)))
+ printf("(%s) %s=%i\n",type,name,ivalue);
+ if(!(strncmp(type,"bool",COMPARE_LIMIT)))
+ printf("(%s) %s=%i\n",type,name,bbool);
+ } else {
+ printf("read_parameter: type is no string, double, int or bool but something else\n");
+ return(FALSE);
+ }
+
+ change_cfg_parameters(name,type,comment,ii,ivalue,dvalue,bbool,astring,
+ setting1,count,change);
+ return(TRUE);
+}
+
+/* @brief Reads the specifications of specie number 'ii' in the configuration
+ * file related to *setting. Initializes the fields of *temp_s.
+ *
+ * @param[in] *setting Of type config_setting_t. It represents a configuration
+ * setting
+ * @param[in] ii position in global 'parameter_names' array
+ * @param[out] *temp_s Of type 'species_t'. Its fields will be initialized
+ * with values "name","mass" and "charge" read
+ * from setting connected to configuration file
+ */
+bool
+read_specie(config_setting_t *setting,
+ int ii,
+ species_t *temp_s)
+{
+ config_setting_t *elem = config_setting_get_elem(setting,ii);
+
+ /* Only output the record if all of the expected fields are present. */
+ if (!(config_setting_lookup_string(elem,"name",&temp_s->name) &&
+ config_setting_lookup_float (elem,"mass",&temp_s->mass) &&
+ config_setting_lookup_float (elem,"charge",&temp_s->charge)))
+ {
+ printf("wrong types in kinetic file for species\n");
+ return(FALSE);
+ }
+ return(TRUE);
+}
+
+/* @brief Read the specifications of seed number 'ii' in the configuration
+ * file related to *setting. Initialize *temp_se.
+ *
+ * @param[in] *setting of type config_setting_t. It represents a configuration
+ * setting
+ * @param[in] ii position in global array '*seed_index'
+ * @param[out] *temp_se of type 'seed_t' describing a seed
+ */
+bool
+read_seed(config_setting_t *setting,
+ int ii,
+ seed_t *temp_se)
+{
+ config_setting_t *elem = config_setting_get_elem(setting,ii);
+
+ /* Only output the record if all of the expected fields are present. */
+ if (!(config_setting_lookup_string(elem,"species",&temp_se->kind_species) &&
+ config_setting_lookup_float (elem,"value",&temp_se->value) &&
+ config_setting_lookup_string(elem,"type",&temp_se->kind_type)))
+ {
+ printf("wrong types in kinetic file for seed: species,value or type\n");
+ return(FALSE);
+ }
+
+ /* Find the position in the species-array of a given species */
+ temp_se->species = find_species_by_name(temp_se->kind_species);
+
+ /* Translate string 'kind_type' into integer value,
+ * temp_se->type = -1 denotes unknown */
+ if (strcmp(temp_se->kind_type,"gaussian") == 0)
+ temp_se->type = 0;
+ else if (strcmp(temp_se->kind_type,"constant") == 0)
+ temp_se->type = 1;
+ else
+ temp_se->type = -1;
+
+ if (!(config_setting_lookup_float(elem,"x0",&temp_se->x0)))
+ { temp_se->x0=0.0; }
+ if (!(config_setting_lookup_float(elem,"y0",&temp_se->y0)))
+ { temp_se->y0=0.0; }
+ if (!(config_setting_lookup_float(elem,"z0",&temp_se->z0)))
+ { temp_se->z0=0.0; }
+
+ if (!(config_setting_lookup_float (elem,"sigma_x",&temp_se->sigma_x)))
+ { temp_se->sigma_x=0.0; }
+ if (!(config_setting_lookup_float(elem,"sigma_y",&temp_se->sigma_y)))
+ { temp_se->sigma_y=0.0; }
+ if (!(config_setting_lookup_float(elem,"sigma_z",&temp_se->sigma_z)))
+ { temp_se->sigma_z=0.0; }
+
+ return(TRUE);
+}
+
+/* @brief Read the specifications of reaction number 'ii' in the configuration
+ * file related to *setting. Initialize *temp_r.
+ *
+ * @param[in] *setting of type config_setting_t. It represents a configuration
+ * setting
+ * @param[in] ii position in global array '*reaction_index'
+ * @param[out] *temp_r of type 'reaction_t' describing a reaction
+ */
+bool
+read_reaction(config_setting_t *setting,
+ int ii,
+ reaction_t *temp_r)
+{
+ config_setting_t *elem = config_setting_get_elem(setting,ii);
+ const char *table;
+ const char *error;
+ int cnt;
+
+ /* Only output the record if fields nin and nout are present. */
+ if (!(config_setting_lookup_string(elem,"reacttable",&table)))
+ {
+ printf("wrong types in kinetic file for reaction.reacttable\n");
+ return(FALSE);
+ } else
+ temp_r->tablefile = (char *) table;
+
+ /* Only output the record if fields nin and nout are present. */
+ if (!(config_setting_lookup_int(elem,"nin",&temp_r->nin) &&
+ config_setting_lookup_int(elem,"nout",&temp_r->nout)))
+ {
+ printf("wrong types in kinetic file for reactions\n");
+ return(FALSE);
+ }
+
+ error="not_init";
+ for(cnt = 0; cnt < REACTION_MAX_IN; ++cnt) {
+ temp_r->input[cnt] = -1;
+ temp_r->inname[cnt]=error;
+ }
+
+ config_setting_lookup_string(elem,"specin0",&temp_r->inname[0]);
+ config_setting_lookup_string(elem,"specin1",&temp_r->inname[1]);
+ config_setting_lookup_string(elem,"specin2",&temp_r->inname[2]);
+ config_setting_lookup_string(elem,"specin3",&temp_r->inname[3]);
+
+ /* Find the position in the species-array of a given species */
+ for(cnt = 0; cnt < temp_r->nin; cnt++) {
+ if(strcmp(temp_r->inname[cnt],error)==0)
+ {
+ printf("NOT all reaction.specin initialized for reaction %d and specie %d\n",ii,cnt);
+ exit(1);
+ }
+ else
+ temp_r->input[cnt] = find_species_by_name(temp_r->inname[cnt]);
+ }
+
+ for(cnt = 0; cnt < REACTION_MAX_OUT; ++cnt) {
+ temp_r->output[cnt] = -1;
+ temp_r->outname[cnt]=error;
+ }
+
+ config_setting_lookup_string(elem,"specout0",&temp_r->outname[0]);
+ config_setting_lookup_string(elem,"specout1",&temp_r->outname[1]);
+ config_setting_lookup_string(elem,"specout2",&temp_r->outname[2]);
+ config_setting_lookup_string(elem,"specout3",&temp_r->outname[3]);
+ config_setting_lookup_string(elem,"specout4",&temp_r->outname[4]);
+ config_setting_lookup_string(elem,"specout5",&temp_r->outname[5]);
+
+ /* Find the position in the species-array of a given species */
+ for(cnt = 0; cnt < temp_r->nout; cnt++) {
+ if(strcmp(temp_r->outname[cnt],error)==0)
+ {
+ debug(1,"temp_r->outname[%d]=%s; error=%s\n",cnt,temp_r->outname[cnt],error);
+ printf("NOT all reaction.specout initialized for reaction %d and specie %d\n",ii,cnt);
+ exit(1);
+ }
+ else
+ temp_r->output[cnt] = find_species_by_name(temp_r->outname[cnt]);
+ }
+
+ return(TRUE);
+}