Add Parser

examples/blowout_wake/inputs_SI

@@ -4,6 +4,11 @@ hipace.predcorr_max_iterations = 1
 hipace.predcorr_B_mixing_factor = 0.12
 hipace.predcorr_B_error_tolerance = -1
 
+my_constants.kp_inv = 10.e-6
+my_constants.kp = 1. / kp_inv
+my_constants.wp = clight * kp
+my_constants.ne = wp^2 * m_e * epsilon0 / q_e^2
+
 amr.blocking_factor = 2
 amr.max_level = 0
 
@@ -16,25 +21,25 @@ hipace.numprocs_y = 1
 hipace.depos_order_xy = 2
 
 geometry.coord_sys   = 0                  # 0: Cartesian
-geometry.is_periodic = 1     1     0      # Is periodic?
-geometry.prob_lo     = -80.e-6   -80.e-6   -60.e-6    # physical domain
-geometry.prob_hi     =  80.e-6    80.e-6    60.e-6
+geometry.is_periodic = true  true  false  # Is periodic?
+geometry.prob_lo     = -8.*kp_inv -8.*kp_inv -6.*kp_inv  # physical domain
+geometry.prob_hi     =  8.*kp_inv  8.*kp_inv  6.*kp_inv
 
 beams.names = beam
 beam.injection_type = fixed_ppc
 beam.profile = gaussian
 beam.zmin = -59.e-6
 beam.zmax = 59.e-6
 beam.radius = 12.e-6
-beam.density = 8.47187610257747e23 # 3*ne
+beam.density = 3.*ne
 beam.u_mean = 0. 0. 2000
 beam.u_std = 0. 0. 0.
 beam.position_mean = 0. 0. 0
 beam.position_std = 3.e-6 3.e-6 14.1e-6
 beam.ppc = 1 1 1
 
 plasmas.names = plasma
-plasma.density =  2.8239587008591567e23 # at this density, 1/kp = 10um
+plasma.density = ne
 plasma.ppc = 1 1
 plasma.u_mean = 0.0 0.0 0.
 plasma.element = electron

examples/blowout_wake/inputs_ionization_SI

@@ -5,6 +5,11 @@ hipace.predcorr_max_iterations = 1
 hipace.predcorr_B_mixing_factor = 0.12
 hipace.predcorr_B_error_tolerance = -1
 
+my_constants.ne = 1.25e24
+my_constants.wp = sqrt(ne * q_e^2  / (epsilon0 * m_e))
+my_constants.kp = wp / clight
+my_constants.kp_inv = 1. / kp # =4.753069541um
+
 amr.blocking_factor = 2
 amr.max_level = 0
 
@@ -24,23 +29,23 @@ geometry.prob_hi     =  20.e-6    20.e-6    30.e-6
 beams.names = beam
 beam.injection_type = fixed_ppc
 beam.profile = flattop
-beam.zmin = 15.493860918e-6
-beam.zmax = 25e-6
-beam.radius = 2.376534771e-6
-beam.density = 5e24
+beam.zmin = 25.e-6 - 2. * kp_inv
+beam.zmax = 25.e-6
+beam.radius = kp_inv / 2
+beam.density = 4. * ne
 beam.u_mean = 0. 0. 2000
 beam.u_std = 0. 0. 0.
 beam.ppc = 1 1 1
 
 plasmas.names = elec ion
 
-elec.density = 1.25e24 # at this density, 1/kp = 4.753069541um
+elec.density = ne
 elec.ppc = 0 0
 elec.u_mean = 0.0 0.0 0.0
 elec.element = electron
-elec.neutralize_background = 0
+elec.neutralize_background = false
 
-ion.density = 1.25e24 # at this density, 1/kp = 4.753069541um
+ion.density = ne
 ion.ppc = 1 1
 ion.u_mean = 0.0 0.0 0.0
 ion.element = H

examples/blowout_wake/inputs_normalized

@@ -17,8 +17,8 @@ hipace.numprocs_y = 1
 hipace.depos_order_xy = 2
 
 geometry.coord_sys   = 0                  # 0: Cartesian
-geometry.is_periodic = 1     1     0      # Is periodic?
-geometry.prob_lo     = -8.   -8.   -6    # physical domain
+geometry.is_periodic = true  true  false  # Is periodic?
+geometry.prob_lo     = -8.   -8.   -6     # physical domain
 geometry.prob_hi     =  8.    8.    6
 
 beams.names = beam

examples/linear_wake/inputs_SI

@@ -1,5 +1,10 @@
 amr.n_cell = 32 32 200
 
+my_constants.kp_inv = 10.e-6
+my_constants.kp = 1. / kp_inv
+my_constants.wp = clight * kp
+my_constants.ne = wp^2 * m_e * epsilon0 / q_e^2
+
 amr.blocking_factor = 2
 amr.max_level = 0
 
@@ -12,7 +17,7 @@ hipace.numprocs_y = 1
 hipace.depos_order_xy = 2
 
 geometry.coord_sys   = 0                  # 0: Cartesian
-geometry.is_periodic = 1     1     0      # Is periodic?
+geometry.is_periodic = true  true  false  # Is periodic?
 geometry.prob_lo     = -100.e-6   -100.e-6   -75.e-6    # physical domain
 geometry.prob_hi     =  100.e-6    100.e-6    20.e-6
 
@@ -22,13 +27,13 @@ beam.profile = flattop
 beam.zmin = -10.e-6
 beam.zmax = 10.e-6
 beam.radius = 30.e-6
-beam.density = 2.8239587008591567e21
+beam.density = 0.01 * ne
 beam.u_mean = 0. 0. 2000
 beam.u_std = 0. 0. 0.
 beam.ppc = 1 1 1
 
 plasmas.names = plasma
-plasma.density =  2.8239587008591567e23 # at this density, 1/kp = 10um
+plasma.density = ne
 plasma.ppc = 1 1
 plasma.u_mean = 0.0 0.0 0.
 plasma.element = electron

src/Hipace.H

@@ -9,6 +9,7 @@
 #include "utils/AdaptiveTimeStep.H"
 #include "utils/GridCurrent.H"
 #include "utils/Constants.H"
+#include "utils/Parser.H"
 #include "diagnostics/Diagnostic.H"
 #include "diagnostics/OpenPMDWriter.H"
 
@@ -24,8 +25,21 @@
 
 #include <memory>
 
+
+/** \brief Helper struct to initialize m_phys_const and Parser before amrex::AmrCore */
+struct Hipace_early_init
+{
+    /** Constructor of m_phys_const, initialize Hipace::m_instance, Hipace::m_normalized_units
+     * and Parser Constants */
+    Hipace_early_init (Hipace* instance);
+
+    /** Struct containing physical constants (which values depends on the unit system, determined
+     * at runtime): SI or normalized units. */
+    PhysConst m_phys_const;
+};
+
 /** \brief Singleton class, that intialize, runs and finalizes the simulation */
-class Hipace final : public amrex::AmrCore
+class Hipace final : public Hipace_early_init, public amrex::AmrCore
 {
 public:
     /** Ctor: read general input parameters, call constructors of main member variables
@@ -190,15 +204,10 @@ public:
     /** status of the physical time send request */
     MPI_Request m_tsend_request = MPI_REQUEST_NULL;
 
-private:
     /** Pointer to current (and only) instance of class Hipace */
     static Hipace* m_instance;
-public:
     /** Whether to use normalized units */
     static bool m_normalized_units;
-    /** Struct containing physical constants (which values depends on the unit system, determined
-     * at runtime): SI or normalized units. */
-    PhysConst m_phys_const;
     /** All field data (3D array, slices) and field methods */
     Fields m_fields;
     /** Contains all beam species */

src/Hipace.cpp

@@ -51,6 +51,20 @@ bool Hipace::m_do_tiling = false;
 bool Hipace::m_do_tiling = true;
 #endif
 
+Hipace_early_init::Hipace_early_init (Hipace* instance)
+{
+    Hipace::m_instance = instance;
+    amrex::ParmParse pph("hipace");
+    queryWithParser(pph ,"normalized_units", Hipace::m_normalized_units);
+    if (Hipace::m_normalized_units) {
+        m_phys_const = make_constants_normalized();
+    } else {
+        m_phys_const = make_constants_SI();
+    }
+    Parser::addConstantsToParser(m_phys_const);
+    Parser::replaceAmrexParamsWithParser();
+}
+
 Hipace&
 Hipace::GetInstance ()
 {
@@ -59,59 +73,52 @@ Hipace::GetInstance ()
 }
 
 Hipace::Hipace () :
-    m_phys_const([this](){
-        m_instance = this;
-        amrex::ParmParse pph("hipace");
-        pph.query("normalized_units", this->m_normalized_units);
-        if (this->m_normalized_units){
-            return make_constants_normalized();
-        } else {
-            return make_constants_SI();
-        }
-    }()),
+    Hipace_early_init(this),
+    amrex::AmrCore(),
     m_fields(this),
     m_multi_beam(this),
     m_multi_plasma(this),
     m_diags(this->maxLevel()+1)
 {
     amrex::ParmParse pp;// Traditionally, max_step and stop_time do not have prefix.
-    pp.query("max_step", m_max_step);
+    queryWithParser(pp, "max_step", m_max_step);
 
 #ifndef AMREX_USE_GPU
     int seed;
-    if (pp.query("random_seed", seed)) amrex::ResetRandomSeed(seed);
+    if (queryWithParser(pp, "random_seed", seed)) amrex::ResetRandomSeed(seed);
 #endif
 
     amrex::ParmParse pph("hipace");
-    pph.query("dt", m_dt);
-    pph.query("verbose", m_verbose);
-    pph.query("numprocs_x", m_numprocs_x);
-    pph.query("numprocs_y", m_numprocs_y);
+
+    queryWithParser(pph, "dt", m_dt);
+    queryWithParser(pph, "verbose", m_verbose);
+    queryWithParser(pph, "numprocs_x", m_numprocs_x);
+    queryWithParser(pph, "numprocs_y", m_numprocs_y);
     m_numprocs_z = amrex::ParallelDescriptor::NProcs() / (m_numprocs_x*m_numprocs_y);
     AMREX_ALWAYS_ASSERT_WITH_MESSAGE(m_numprocs_z <= m_max_step+1,
                                      "Please use more or equal time steps than number of ranks");
     AMREX_ALWAYS_ASSERT_WITH_MESSAGE(m_numprocs_x*m_numprocs_y*m_numprocs_z
                                      == amrex::ParallelDescriptor::NProcs(),
                                      "Check hipace.numprocs_x and hipace.numprocs_y");
-    pph.query("boxes_in_z", m_boxes_in_z);
+    queryWithParser(pph, "boxes_in_z", m_boxes_in_z);
     if (m_boxes_in_z > 1) AMREX_ALWAYS_ASSERT_WITH_MESSAGE( m_numprocs_z == 1,
                             "Multiple boxes per rank only implemented for one rank.");
-    pph.query("depos_order_xy", m_depos_order_xy);
-    pph.query("depos_order_z", m_depos_order_z);
-    pph.query("predcorr_B_error_tolerance", m_predcorr_B_error_tolerance);
-    pph.query("predcorr_max_iterations", m_predcorr_max_iterations);
-    pph.query("predcorr_B_mixing_factor", m_predcorr_B_mixing_factor);
-    pph.query("output_period", m_output_period);
+    queryWithParser(pph, "depos_order_xy", m_depos_order_xy);
+    queryWithParser(pph, "depos_order_z", m_depos_order_z);
+    queryWithParser(pph, "predcorr_B_error_tolerance", m_predcorr_B_error_tolerance);
+    queryWithParser(pph, "predcorr_max_iterations", m_predcorr_max_iterations);
+    queryWithParser(pph, "predcorr_B_mixing_factor", m_predcorr_B_mixing_factor);
+    queryWithParser(pph, "output_period", m_output_period);
     AMREX_ALWAYS_ASSERT_WITH_MESSAGE(m_output_period != 0,
                                      "To avoid output, please use output_period = -1.");
-    pph.query("beam_injection_cr", m_beam_injection_cr);
-    pph.query("do_beam_jx_jy_deposition", m_do_beam_jx_jy_deposition);
-    pph.query("do_device_synchronize", m_do_device_synchronize);
-    pph.query("external_ExmBy_slope", m_external_ExmBy_slope);
-    pph.query("external_Ez_slope", m_external_Ez_slope);
-    pph.query("external_Ez_uniform", m_external_Ez_uniform);
+    queryWithParser(pph, "beam_injection_cr", m_beam_injection_cr);
+    queryWithParser(pph, "do_beam_jx_jy_deposition", m_do_beam_jx_jy_deposition);
+    queryWithParser(pph, "do_device_synchronize", m_do_device_synchronize);
+    queryWithParser(pph, "external_ExmBy_slope", m_external_ExmBy_slope);
+    queryWithParser(pph, "external_Ez_slope", m_external_Ez_slope);
+    queryWithParser(pph, "external_Ez_uniform", m_external_Ez_uniform);
     std::string solver = "predictor-corrector";
-    pph.query("bxby_solver", solver);
+    queryWithParser(pph, "bxby_solver", solver);
     AMREX_ALWAYS_ASSERT_WITH_MESSAGE(
         solver == "predictor-corrector" ||
         solver == "explicit",
@@ -121,9 +128,9 @@ Hipace::Hipace () :
         !(m_explicit && !m_multi_plasma.AllSpeciesNeutralizeBackground()),
         "Ion motion with explicit solver is not implemented, need to use neutralize_background");
 
-    pph.query("MG_tolerance_rel", m_MG_tolerance_rel);
-    pph.query("MG_tolerance_abs", m_MG_tolerance_abs);
-    pph.query("do_tiling", m_do_tiling);
+    queryWithParser(pph, "MG_tolerance_rel", m_MG_tolerance_rel);
+    queryWithParser(pph, "MG_tolerance_abs", m_MG_tolerance_abs);
+    queryWithParser(pph, "do_tiling", m_do_tiling);
 #ifdef AMREX_USE_GPU
     AMREX_ALWAYS_ASSERT_WITH_MESSAGE(m_do_tiling==0, "Tiling must be turned off to run on GPU.");
 #endif
@@ -133,14 +140,14 @@ Hipace::Hipace () :
         AMREX_ALWAYS_ASSERT_WITH_MESSAGE(!m_explicit, "Mesh refinement + explicit solver is not yet"
                                 " supported! Please use hipace.bxby_solver = predictor-corrector");
         amrex::Array<amrex::Real, AMREX_SPACEDIM> loc_array;
-        pph.get("patch_lo", loc_array);
+        getWithParser(pph, "patch_lo", loc_array);
         for (int idim=0; idim<AMREX_SPACEDIM; ++idim) patch_lo[idim] = loc_array[idim];
-        pph.get("patch_hi", loc_array);
+        getWithParser(pph, "patch_hi", loc_array);
         for (int idim=0; idim<AMREX_SPACEDIM; ++idim) patch_hi[idim] = loc_array[idim];
     }
 
 #ifdef AMREX_USE_MPI
-    pph.query("skip_empty_comms", m_skip_empty_comms);
+    queryWithParser(pph, "skip_empty_comms", m_skip_empty_comms);
     int myproc = amrex::ParallelDescriptor::MyProc();
     m_rank_z = myproc/(m_numprocs_x*m_numprocs_y);
     MPI_Comm_split(amrex::ParallelDescriptor::Communicator(), m_rank_z, myproc, &m_comm_xy);

src/diagnostics/Diagnostic.cpp

@@ -9,7 +9,7 @@ Diagnostic::Diagnostic (int nlev)
 {
     amrex::ParmParse ppd("diagnostic");
     std::string str_type;
-    ppd.get("diag_type", str_type);
+    getWithParser(ppd, "diag_type", str_type);
     if        (str_type == "xyz"){
         m_diag_type = DiagType::xyz;
         m_slice_dir = -1;
@@ -26,7 +26,7 @@ Diagnostic::Diagnostic (int nlev)
     for(int ilev = 0; ilev<nlev; ++ilev) {
         amrex::Array<int,3> diag_coarsen_arr{1,1,1};
         // set all levels the same for now
-        ppd.query("coarsening", diag_coarsen_arr);
+        queryWithParser(ppd, "coarsening", diag_coarsen_arr);
         if(m_slice_dir == 0 || m_slice_dir == 1) {
             diag_coarsen_arr[m_slice_dir] = 1;
         }
@@ -35,7 +35,7 @@ Diagnostic::Diagnostic (int nlev)
             "Coarsening ratio must be >= 1");
     }
 
-    ppd.queryarr("field_data", m_comps_output);
+    queryWithParser(ppd, "field_data", m_comps_output);
     const amrex::Vector<std::string> all_field_comps
             {"ExmBy", "EypBx", "Ez", "Bx", "By", "Bz", "jx", "jx_beam", "jy", "jy_beam", "jz",
              "jz_beam", "rho", "Psi"};
@@ -68,9 +68,9 @@ Diagnostic::Diagnostic (int nlev)
     amrex::ParmParse ppb("beams");
     // read in all beam names
     amrex::Vector<std::string> all_beam_names;
-    ppb.queryarr("names", all_beam_names);
+    queryWithParser(ppb, "names", all_beam_names);
     // read in which beam should be written to file
-    ppd.queryarr("beam_data", m_output_beam_names);
+    queryWithParser(ppd, "beam_data", m_output_beam_names);
 
     if(m_output_beam_names.empty()) {
         m_output_beam_names = all_beam_names;

src/diagnostics/OpenPMDWriter.cpp

@@ -12,12 +12,12 @@ OpenPMDWriter::OpenPMDWriter ()
     AMREX_ALWAYS_ASSERT_WITH_MESSAGE(m_real_names.size() == BeamIdx::nattribs,
         "List of real names in openPMD Writer class do not match BeamIdx::nattribs");
     amrex::ParmParse pp("hipace");
-    pp.query("file_prefix", m_file_prefix);
-    pp.query("openpmd_backend", m_openpmd_backend);
+    queryWithParser(pp, "file_prefix", m_file_prefix);
+    queryWithParser(pp, "openpmd_backend", m_openpmd_backend);
 
     // temporary workaround until openPMD-viewer gets fixed
     amrex::ParmParse ppd("diagnostic");
-    ppd.query("openpmd_viewer_u_workaround", m_openpmd_viewer_workaround);
+    queryWithParser(ppd, "openpmd_viewer_u_workaround", m_openpmd_viewer_workaround);
 }
 
 void

src/fields/Fields.cpp

@@ -12,7 +12,7 @@ Fields::Fields (Hipace const* a_hipace)
     : m_slices(a_hipace->maxLevel()+1)
 {
     amrex::ParmParse ppf("fields");
-    ppf.query("do_dirichlet_poisson", m_do_dirichlet_poisson);
+    queryWithParser(ppf, "do_dirichlet_poisson", m_do_dirichlet_poisson);
 }
 
 void

src/fields/fft_poisson_solver/fft/WrapCuDST.cpp

@@ -233,7 +233,7 @@ namespace AnyDST
 
         amrex::ParmParse pp("hipace");
         dst_plan.use_small_dst = (std::max(real_size[0], real_size[1]) >= 511);
-        pp.query("use_small_dst", dst_plan.use_small_dst);
+        queryWithParser(pp, "use_small_dst", dst_plan.use_small_dst);
 
         if(!dst_plan.use_small_dst) {
             const int nx = real_size[0];