Merge branch 'development' into nse_neutrinos

EOS/gamma_law/_parameters

@@ -1,4 +1,4 @@
 @namespace: eos
 
 eos_gamma            real     5.d0/3.d0
-eos_assume_neutral   logical  .true.
+eos_assume_neutral   integer  1

EOS/helmholtz/_parameters

@@ -1,10 +1,10 @@
 @namespace: eos
 
 # use the Coulomb corrections
-use_eos_coulomb                     logical            .true.
+use_eos_coulomb                     integer            1
 
 # Force the EOS output quantities to match input
-eos_input_is_constant               logical            .true.
+eos_input_is_constant               integer            1
 
 # Tolerance for iterations with respect to temperature
 eos_ttol                            real               1.0d-8

Make.Microphysics

@@ -153,7 +153,6 @@ endif
 EXTERN_PARAMETERS := $(shell $(MICROPHYSICS_HOME)/util/build_scripts/findparams.py $(EXTERN_SEARCH))
 
 
-$(MICROPHYSICS_AUTO_SOURCE_DIR)/extern.F90: $(MICROPHYSICS_AUTO_SOURCE_DIR)/extern_parameters.H
 $(MICROPHYSICS_AUTO_SOURCE_DIR)/extern_parameters.cpp: $(MICROPHYSICS_AUTO_SOURCE_DIR)/extern_parameters.H
 
 $(MICROPHYSICS_AUTO_SOURCE_DIR)/extern_parameters.H: $(EXTERN_PARAMETERS) $(EXTERN_TEMPLATE)

integration/VODE/actual_integrator_simplified_sdc.H

@@ -177,14 +177,14 @@ void actual_integrator (BurnT& state, Real dt)
             std::cout << "temp start = " << std::setprecision(16) << T_in << std::endl;
             std::cout << "rhoe start = " << std::setprecision(16) << rhoe_in << std::endl;
             std::cout << "xn start = ";
-            for (int n = 0; n < NumSpec; ++n) {
-                std::cout << std::setprecision(16) << xn_in[n] << " ";
+            for (auto X : xn_in) {
+                std::cout << std::setprecision(16) << X << " ";
             }
             std::cout << std::endl;
 #ifdef AUX_THERMO
             std::cout << "aux start = ";
-            for (int n = 0; n < NumAux; ++n) {
-                std::cout << std::setprecision(16) << aux_in[n] << " ";
+            for (auto aux : aux_in) {
+                std::cout << std::setprecision(16) << aux << " ";
             }
             std::cout << std::endl;
 #endif

integration/_parameters

@@ -6,10 +6,10 @@
 # the current internal energy. This is done with an EOS call, which can
 # be turned off if desired. This will freeze the temperature and specific heat
 # to the values at the beginning of the burn, which is inaccurate but cheaper.
-call_eos_in_rhs          logical   .true.
+call_eos_in_rhs          integer   1
 
 # Allow the energy integration to be disabled by setting the RHS to zero.
-integrate_energy         logical   .true.
+integrate_energy         integer   1
 
 # Whether to use an analytical or numerical Jacobian.
 # 1 == Analytical
@@ -18,7 +18,7 @@ integrate_energy         logical   .true.
 jacobian                 integer   1
 
 # Should we print out diagnostic output after the solve?
-burner_verbose           logical   .false.
+burner_verbose           integer   0
 
 # Tolerances for the solver (relative and absolute), for the
 # species and energy equations.
@@ -30,7 +30,7 @@ atol_enuc                real      1.d-6
 
 # Whether to renormalize the mass fractions at each step in the evolution
 # so that they sum to unity.
-renormalize_abundances   logical   .false.
+renormalize_abundances   integer   0
 
 # The absolute cutoff for species -- note that this might be larger
 # than ``small_x``, but the issue is that we need to prevent underflow
@@ -51,7 +51,7 @@ ode_max_steps              integer      150000
 ode_max_dt                 real         1.d30
 
 # Whether to use Jacobian caching in VODE
-use_jacobian_caching    logical   .true.
+use_jacobian_caching    integer    1
 
 # Inputs for generating a Nonaka Plot (TM)
 nonaka_i                integer           0
@@ -65,10 +65,10 @@ nonaka_file             character         "nonaka_plot.dat"
 do_species_clip              integer          1
 
 # flag for turning on the use of number densities for all species
-use_number_densities     logical          .false.
+use_number_densities     integer     0
 
 # flag for tuning on the subtraction of internal energy
-subtract_internal_energy   logical       .true.
+subtract_internal_energy   integer     1
 
 # SDC iteration tolerance adjustment factor
 sdc_burn_tol_factor          real         1.d0

integration/nse_update_simplified_sdc.H

@@ -183,13 +183,13 @@ void sdc_nse_burn(BurnT& state, const Real dt) {
     // the new mass fractions are just those that come from the table
     // make sure they are normalized
     Real sum_X{0.0_rt};
-    for (int n = 0; n < NumSpec; ++n) {
-        X[n] = amrex::max(small_x, amrex::min(1.0_rt, X[n]));
-        sum_X += X[n];
+    for (auto & xn : X) {
+        xn = amrex::max(small_x, amrex::min(1.0_rt, xn));
+        sum_X += xn;
     }
 
-    for (int n = 0; n < NumSpec; ++n) {
-        X[n] /= sum_X;
+    for (auto & xn : X) {
+        xn /= sum_X;
     }
 
     for (int n = 0; n < NumSpec; ++n) {

networks/CNO_extras/CNO_extras.py

@@ -19,7 +19,10 @@
 comp = pyna.Composition(rc.get_nuclei())
 comp.set_solar_like()
 
-rc.plot(outfile="cno_extras.png", rho=1.e6, T=1.e8, comp=comp, Z_range=[1,13], N_range=[1,13])
-rc.plot(outfile="cno_extras_hide_alpha.png", rho=1.e6, T=1.e8, comp=comp, Z_range=[1,13], N_range=[1,13],
-                    rotated=True, highlight_filter_function=lambda r: r.Q > 0,
-                    curved_edges=True, hide_xalpha=True)
+rho = 1.e6
+T = 1.e8
+
+rc.plot(rho, T, comp, outfile="cno_extras.png", Z_range=[1,13], N_range=[1,13])
+rc.plot(rho, T, comp, outfile="cno_extras_hide_alpha.png", Z_range=[1,13], N_range=[1,13],
+        rotated=True, highlight_filter_function=lambda r: r.Q > 0,
+        curved_edges=True, hide_xalpha=True)

networks/He-C-Fe-group/He-C-Fe-group.py

@@ -128,7 +128,7 @@
 comp.set_all(1.0)
 comp.normalize()
 
-fig = net.plot(rho=rho, T=T, comp=comp,
+fig = net.plot(rho, T, comp,
                rotated=True, curved_edges=True, hide_xalpha=True,
                size=(1800, 900),
                node_size=500, node_shape="s", node_font_size=10)

networks/_parameters

@@ -4,7 +4,7 @@
 small_x                              real               1.d-30
 
 # Should we use rate tables if they are present in the network?
-use_tables  logical   .false.
+use_tables                           integer            0
 
 # Should we use Deboer + 2017 rate for c12(a,g)o16?
-use_c12ag_deboer17  logical   .false.
+use_c12ag_deboer17                   integer            0

networks/ase/ase.py

@@ -113,7 +113,10 @@ def doit():
     comp.set_nuc("he4", 0.95)
     comp.normalize()
 
-    net.plot(outfile="ase.png", rho=1.e7, T=6.e9, comp=comp,
+    rho = 1.e7
+    T = 6.e9
+
+    net.plot(rho, T, comp, outfile="ase.png",
              rotated=True, hide_xalpha=True, curved_edges=True,
              size=(1500, 450),
              node_size=500, node_font_size=11, node_color="#337dff", node_shape="s",

networks/nova/network_plot.py

@@ -15,4 +15,7 @@
 comp = pyna.Composition(rc.get_nuclei())
 comp.set_solar_like()
 
-rc.plot(outfile="nova.png", rho=1.e4, T=9.e7, comp=comp)
+rho = 1.e4
+T = 9.e7
+
+rc.plot(rho, T, comp, outfile="nova.png")

networks/nova/nova.py

@@ -19,5 +19,7 @@
 comp = Composition(rc.get_nuclei())
 comp.set_solar_like()
 
-rc.plot(outfile="nova.png", rho=1.e4, T=9.e7, comp=comp)
+rho = 1.e4
+T = 9.e7
 
+rc.plot(rho, T, comp, outfile="nova.png")

networks/nova2/nova2.py

@@ -19,5 +19,7 @@
 comp = pyna.Composition(rc.get_nuclei())
 comp.set_solar_like()
 
-rc.plot(outfile="nova.png", rho=1.e4, T=9.e7, comp=comp)
+rho = 1.e4
+T = 9.e7
 
+rc.plot(rho, T, comp, outfile="nova.png")

networks/subch_approx/subch_approx.py

@@ -52,7 +52,10 @@ def doit():
     comp.set_nuc("he4", 0.95)
     comp.normalize()
 
-    net.plot(outfile="subch_approx.png", rho=1.e6, T=1.e9, comp=comp,
+    rho = 1.e6
+    T = 1.e9
+
+    net.plot(rho, T, comp, outfile="subch_approx.png",
              rotated=True, hide_xalpha=True, curved_edges=True,
              size=(1500, 450),
              node_size=500, node_font_size=11, node_color="#337dff", node_shape="s",

networks/subch_full/network_plot.py

@@ -12,6 +12,9 @@
 comp.set_nuc("he4", 0.95)
 comp.normalize()
 
-rc.plot(outfile="subch2.pdf", rho=1.e6, T=1.e9, comp=comp, hide_xalpha=True,
+rho = 1.e6
+T = 1.e9
+
+rc.plot(rho, T, comp, outfile="subch2.pdf", hide_xalpha=True,
         size=(1500, 650), node_size=500, node_font_size=11, node_color="#337dff", node_shape="s",
         Z_range=(1,29), rotated=True, curved_edges=True)

networks/subch_full/subch_full.py

@@ -44,7 +44,10 @@ def doit():
     comp.set_nuc("he4", 0.95)
     comp.normalize()
 
-    rc.plot(outfile="subch_full.png", rho=1.e6, T=1.e9, comp=comp,
+    rho = 1.e6
+    T = 1.e9
+
+    rc.plot(rho, T, comp, outfile="subch_full.png",
             rotated=True, hide_xalpha=True, curved_edges=True,
             size=(1500, 450),
             node_size=500, node_font_size=11, node_color="#337dff", node_shape="s",

networks/subch_simple/subch_simple.py

@@ -102,7 +102,10 @@ def doit():
     comp.set_nuc("he4", 0.95)
     comp.normalize()
 
-    net.plot(outfile="subch_simple.png", rho=1.e6, T=1.e9, comp=comp,
+    rho = 1.e6
+    T = 1.e9
+
+    net.plot(rho, T, comp, outfile="subch_simple.png",
              rotated=True, hide_xalpha=True, curved_edges=True,
              size=(1500, 450),
              node_size=500, node_font_size=11, node_color="#337dff", node_shape="s",

nse_solver/_parameters

@@ -3,7 +3,7 @@
 max_nse_iters           integer    500
 use_hybrid_solver       integer    1
 ase_tol                 real       0.1
-nse_dx_independent      logical    .false.
-nse_molar_independent   logical    .false.
-nse_skip_molar          logical    .false.
+nse_dx_independent      integer    0
+nse_molar_independent   integer    0
+nse_skip_molar          integer    0
 T_nse_net               real       -1.0

unit_test/burn_cell_sdc/burn_cell.H

@@ -334,8 +334,8 @@ void burn_cell_c()
     state_over_time << std::setw(10) << t;
     state_over_time << std::setw(12) << burn_state.rho;
     state_over_time << std::setw(12) << burn_state.T;
-    for (int x = 0; x < NumSpec; ++x){
-        state_over_time << std::setw(12) << burn_state.xn[x];
+    for (auto X : burn_state.xn) {
+        state_over_time << std::setw(12) << X;
     }
     state_over_time << std::endl;
 

util/build_scripts/write_probin.py

@@ -7,7 +7,6 @@
 max_step                            integer            1
 small_dt                            real               1.d-10
 xlo_boundary_type                   character          ""
-octant                              logical            .false.
 
 This specifies the runtime parameter name, datatype, and default
 value.
@@ -107,6 +106,11 @@ def parse_param_file(params_list, param_file, use_namespace=False):
         dtype = fields[1]
         default = fields[2]
 
+        if dtype == "logical":
+            print("write_probin.py: ERROR: logical type no longer supported in _parameter files.")
+            err = 1
+            continue
+
         if use_namespace:
             skip_namespace_in_declare = False
         else: