Add new entries in Physical Species properties (+ refactoring of the SpeciesPhysicalProperties file)

Docs/source/usage/parameters.rst

@@ -574,8 +574,19 @@ Particle initialization
 
 * ``<species_name>.species_type`` (`string`) optional (default `unspecified`)
     Type of physical species.
-    Currently, the accepted species are ``"electron"``, ``"positron"``, ``"photon"``, ``"hydrogen"`` (or equivalently ``"proton"``), ``"helium"`` (or equivalently ``"alpha"``), ``"boron"``, ``"carbon"``, ``"oxygen"``, ``"nitrogen"``, ``"argon"``, ``"copper"`` and ``"xenon"``.
-    Either this or both ``mass`` and ``charge`` have to be specified.
+    Currently, the accepted species are
+    ``"electron"``, ``"positron"``, ``"muon"``, ``"antimuon"``, ``"photon"``, ``"neutron"``, ``"proton"`` , ``"alpha"``,
+    ``"hydrogen1"`` (a.k.a. ``"protium"``), ``"hydrogen2"`` (a.k.a. ``"deuterium"``), ``"hydrogen3"`` (a.k.a.``"tritium"``),
+    ``"helium"``, ``"helium3"``, ``"helium4"``,
+    ``"lithium"``, ``"lithium6"``, ``"lithium7"``, ``"beryllium"``, ``"boron"``, ``"boron10"``, ``"boron11"``,
+    ``"carbon"``, ``"carbon12"``, ``"carbon13"``, ``"nitrogen"``, ``"nitrogen14"``, ``"nitrogen15"``,
+    ``"oxygen"``, ``"oxygen16"``, ``"oxygen17"``, ``"oxygen18"``, ``"fluorine"``, ``"neon"``, ``"neon20"``,
+    ``"neon21"``, ``"neon22"``, ``"aluminium"``, ``"argon"``, ``"copper"``, ``"xenon"`` and ``"gold"``.
+    The difference between ``"proton"`` and ``"hydrogen1"`` is that the mass of the latter includes also the mass
+    of the bound electron (same for ``"alpha"`` and ``"helium4"``). When only the name of an element is specified, the mass
+    is a weighted average of the masses of the stable isotopes. For all the elements with ``Z < 11`` we provide
+    also the stable isotopes as an option for ``species_type`` (e.g., ``"helium3"`` and ``"helium4"``).
+    Either ``species_type`` or both ``mass`` and ``charge`` have to be specified.
 
 * ``<species_name>.charge`` (`float`) optional (default `NaN`)
     The charge of one `physical` particle of this species.

Examples/Modules/nuclear_fusion/analysis_proton_boron_fusion.py

@@ -66,9 +66,9 @@
 MeV_to_Joule = scc.e*1e6
 barn_to_square_meter = 1.e-28
 m_p = scc.m_p # Proton mass
-m_b = 10.9298*m_p # Boron 11 mass
+m_b = 11.00930536*scc.m_u # Boron 11 mass
 m_reduced = m_p*m_b/(m_p+m_b)
-m_a = 3.97369*m_p # Alpha mass
+m_a = 4.002602*scc.m_u # Alpha mass
 m_be = 7.94748*m_p # Beryllium 8 mass
 Z_boron = 5.
 Z_proton = 1.
@@ -381,7 +381,7 @@ def p_sq_boron_frame_to_E_COM_frame(p_proton_sq):
     E_com = np.sqrt(E_lab**2 - p_proton_sq*scc.c**2)
     # Corresponding kinetic energy
     E_com_kin = E_com - (m_b+scc.m_p)*scc.c**2
-    return E_com_kin
+    return E_com_kin*(p_proton_sq>0.)
 
 def p_sq_to_kinetic_energy(p_sq, m):
     ## Returns the kinetic energy of a particle as a function of its squared momentum.

Examples/Modules/nuclear_fusion/inputs_3d

@@ -32,7 +32,7 @@ algo.particle_shape = 1
 particles.species_names = proton1 boron1 alpha1 proton2 boron2 alpha2 proton3 boron3 alpha3
                           proton4 boron4 alpha4 proton5 boron5 alpha5
 
-my_constants.m_b11 =  10.9298*m_p # Boron 11 mass
+my_constants.m_b11 = 11.00930536*m_u # Boron 11 mass
 my_constants.m_reduced = m_p*m_b11/(m_p+m_b11)
 my_constants.keV_to_J = 1.e3*q_e
 my_constants.Energy_step = 22. * keV_to_J
@@ -63,7 +63,7 @@ boron1.momentum_function_uz(x,y,z) = -sqrt(2*m_reduced*Energy_step*(floor(z)**2)
 boron1.do_not_push = 1
 boron1.do_not_deposit = 1
 
-alpha1.species_type = alpha
+alpha1.species_type = helium
 alpha1.do_not_push = 1
 alpha1.do_not_deposit = 1
 
@@ -94,7 +94,7 @@ boron2.momentum_distribution_type = "constant"
 boron2.do_not_push = 1
 boron2.do_not_deposit = 1
 
-alpha2.species_type = alpha
+alpha2.species_type = helium
 alpha2.do_not_push = 1
 alpha2.do_not_deposit = 1
 
@@ -120,7 +120,7 @@ boron3.theta = temperature/(m_b11*clight**2)
 boron3.do_not_push = 1
 boron3.do_not_deposit = 1
 
-alpha3.species_type = alpha
+alpha3.species_type = helium
 alpha3.do_not_push = 1
 alpha3.do_not_deposit = 1
 
@@ -145,7 +145,7 @@ boron4.momentum_distribution_type = "constant"
 boron4.do_not_push = 1
 boron4.do_not_deposit = 1
 
-alpha4.species_type = alpha
+alpha4.species_type = helium
 alpha4.do_not_push = 1
 alpha4.do_not_deposit = 1
 
@@ -168,7 +168,7 @@ boron5.momentum_distribution_type = "constant"
 boron5.do_not_push = 1
 boron5.do_not_deposit = 1
 
-alpha5.species_type = alpha
+alpha5.species_type = helium
 alpha5.do_not_push = 1
 alpha5.do_not_deposit = 1
 

Regression/Checksum/benchmarks_json/LaserIonAcc2d.json

@@ -2,37 +2,37 @@
   "electrons": {
     "particle_cpu": 0.0,
     "particle_id": 2101654260.0,
-    "particle_momentum_x": 3.8190076010374515e-19,
+    "particle_momentum_x": 3.819011093562328e-19,
     "particle_momentum_y": 0.0,
-    "particle_momentum_z": 1.6442919198257052e-18,
-    "particle_position_x": 0.008132686110435036,
-    "particle_position_y": 0.030529759951728817,
+    "particle_momentum_z": 1.6442909854275157e-18,
+    "particle_position_x": 0.008132686101590795,
+    "particle_position_y": 0.030529760810180325,
     "particle_weight": 2.641331189632942e+17
   },
   "hydrogen": {
     "particle_cpu": 0.0,
     "particle_id": 8663540542.0,
-    "particle_momentum_x": 2.2442930534191287e-18,
+    "particle_momentum_x": 2.2442952799834144e-18,
     "particle_momentum_y": 0.0,
-    "particle_momentum_z": 1.084110863159823e-18,
+    "particle_momentum_z": 1.0841140295639398e-18,
     "particle_orig_x": 0.008258544921875001,
     "particle_orig_z": 0.0366896337890625,
-    "particle_position_x": 0.008258183385255663,
-    "particle_position_y": 0.03668783554837751,
+    "particle_position_x": 0.008258183633694481,
+    "particle_position_y": 0.036687836783915156,
     "particle_weight": 2.701906737218416e+17
   },
   "lev=0": {
     "Bx": 0.0,
-    "By": 11393535.73084639,
+    "By": 11393530.864665572,
     "Bz": 0.0,
-    "Ex": 2033400430027297.5,
+    "Ex": 2033401599040428.8,
     "Ey": 0.0,
-    "Ez": 316047261967858.8,
-    "jx": 1.6346708093212e+19,
+    "Ez": 316047997346965.6,
+    "jx": 1.634666300264935e+19,
     "jy": 0.0,
-    "jz": 8.884557829033169e+18,
-    "rho": 61729754469.05863,
-    "rho_electrons": 17451988254912.61,
-    "rho_hydrogen": 17441820007044.357
+    "jz": 8.884561198935773e+18,
+    "rho": 61730016945.00626,
+    "rho_electrons": 17451988195798.281,
+    "rho_hydrogen": 17441819816491.93
   }
 }

Regression/Checksum/benchmarks_json/PlasmaAccelerationBoost2d.json

@@ -20,21 +20,21 @@
     "particle_weight": 93622636116911.45
   },
   "lev=0": {
-    "Bx": 0.3939499531816347,
-    "By": 9563.615022656986,
-    "Bz": 0.3591030695780064,
-    "Ex": 1057402535431.5992,
-    "Ey": 144244335.4692135,
-    "Ez": 3010491709181.335,
-    "jx": 3227914399.2203197,
-    "jy": 5068791609.127958,
-    "jz": 102420312561236.62
+    "Bx": 0.3939499531816364,
+    "By": 9563.615022656964,
+    "Bz": 0.3591030695780125,
+    "Ex": 1057402535431.6746,
+    "Ey": 144244335.46922195,
+    "Ez": 3010491709181.3467,
+    "jx": 3227914369.7171793,
+    "jy": 5068791609.12788,
+    "jz": 102420312561226.17
   },
   "plasma_e": {
     "particle_cpu": 504.0,
     "particle_id": 236124.0,
-    "particle_momentum_x": 1.2615128163446419e-23,
-    "particle_momentum_y": 1.5392234050947253e-27,
+    "particle_momentum_x": 1.2615128163589931e-23,
+    "particle_momentum_y": 1.5392234051130659e-27,
     "particle_momentum_z": 1.3694904132251956e-18,
     "particle_position_x": 0.01771877489382093,
     "particle_position_y": 0.020620065534187347,
@@ -43,11 +43,11 @@
   "plasma_p": {
     "particle_cpu": 504.0,
     "particle_id": 272412.0,
-    "particle_momentum_x": 1.2615099271970135e-23,
-    "particle_momentum_y": 1.5392492676794249e-27,
-    "particle_momentum_z": 2.514586739414616e-15,
-    "particle_position_x": 0.017718749986442184,
-    "particle_position_y": 0.02062006546318014,
+    "particle_momentum_x": 1.2615099272124483e-23,
+    "particle_momentum_y": 1.53924926768808e-27,
+    "particle_momentum_z": 2.51631809113383e-15,
+    "particle_position_x": 0.017718749986451513,
+    "particle_position_y": 0.020620065463180168,
     "particle_weight": 727797380314273.1
   }
 }

Regression/Checksum/benchmarks_json/Proton_Boron_Fusion_3D.json

@@ -2,55 +2,55 @@
   "alpha1": {
     "particle_cpu": 60780.0,
     "particle_id": 1351279015596.0,
-    "particle_momentum_x": 4.659632892446219e-15,
-    "particle_momentum_y": 4.617309311289228e-15,
-    "particle_momentum_z": 4.617390264429112e-15,
+    "particle_momentum_x": 4.659631949650719e-15,
+    "particle_momentum_y": 4.617308377231923e-15,
+    "particle_momentum_z": 4.617389330519975e-15,
     "particle_position_x": 453219.3436004627,
-    "particle_position_y": 457393.4211433249,
+    "particle_position_y": 457393.42114332493,
     "particle_position_z": 970481.0580153911,
-    "particle_weight": 1.904380063679924e-27
+    "particle_weight": 1.9043802455895325e-27
   },
   "alpha2": {
     "particle_cpu": 54528.0,
     "particle_id": 1211463810981.0,
-    "particle_momentum_x": 4.071679285778659e-15,
-    "particle_momentum_y": 4.119641921839256e-15,
-    "particle_momentum_z": 4.181785619797154e-15,
+    "particle_momentum_x": 4.071678402460901e-15,
+    "particle_momentum_y": 4.1196410276880726e-15,
+    "particle_momentum_z": 4.181784710058622e-15,
     "particle_position_x": 405848.1200755021,
-    "particle_position_y": 408011.5319128882,
+    "particle_position_y": 408011.53191288817,
     "particle_position_z": 866330.5923068221,
-    "particle_weight": 1.926173353413784e+19
+    "particle_weight": 1.9261737121655108e+19
   },
   "alpha3": {
     "particle_cpu": 6252.0,
     "particle_id": 153642773313.0,
-    "particle_momentum_x": 4.853583107582054e-16,
-    "particle_momentum_y": 4.797298533911113e-16,
-    "particle_momentum_z": 4.759502498651132e-16,
+    "particle_momentum_x": 4.853582081563116e-16,
+    "particle_momentum_y": 4.797297548379446e-16,
+    "particle_momentum_z": 4.759501504671248e-16,
     "particle_position_x": 51342.57223394147,
     "particle_position_y": 50913.6612890173,
-    "particle_position_z": 101306.340590083,
-    "particle_weight": 1.036014694926736e+28
+    "particle_position_z": 101306.34059008301,
+    "particle_weight": 1.0360147595748265e+28
   },
   "alpha4": {
     "particle_cpu": 307200.0,
     "particle_id": 7431218688000.0,
-    "particle_momentum_x": 2.337391296198344e-14,
-    "particle_momentum_y": 2.343942459367338e-14,
-    "particle_momentum_z": 2.355941676163024e-14,
-    "particle_position_x": 2457367.458278153,
+    "particle_momentum_x": 2.3373908106523292e-14,
+    "particle_momentum_y": 2.3439419725501755e-14,
+    "particle_momentum_z": 2.3559411845892612e-14,
+    "particle_position_x": 2457367.4582781526,
     "particle_position_y": 2457512.044373058,
     "particle_position_z": 4914475.776513073,
     "particle_weight": 3072.000000000002
   },
   "alpha5": {
     "particle_cpu": 307200.0,
     "particle_id": 7619962368000.0,
-    "particle_momentum_x": 2.333624736682437e-14,
-    "particle_momentum_y": 2.345594456920183e-14,
-    "particle_momentum_z": 2.357453114426799e-14,
+    "particle_momentum_x": 2.333624251961068e-14,
+    "particle_momentum_y": 2.3455939695798916e-14,
+    "particle_momentum_z": 2.3574526216382372e-14,
     "particle_position_x": 2457556.857163842,
-    "particle_position_y": 2457059.635379324,
+    "particle_position_y": 2457059.6353793237,
     "particle_position_z": 4915847.043341331,
     "particle_weight": 3.0719999999999984e-18
   },
@@ -59,7 +59,7 @@
     "particle_id": 78643205120000.0,
     "particle_momentum_x": 0.0,
     "particle_momentum_y": 0.0,
-    "particle_momentum_z": 2.524243076150406e-13,
+    "particle_momentum_z": 2.524242836246531e-13,
     "particle_position_x": 40958301.591654316,
     "particle_position_y": 40961136.14476712,
     "particle_position_z": 81920546.19181262,
@@ -74,26 +74,26 @@
     "particle_position_x": 409798.0158217681,
     "particle_position_y": 409670.9858143465,
     "particle_position_z": 819255.8152412223,
-    "particle_weight": 1.0239999999360338e+29
+    "particle_weight": 1.0239999999357942e+29
   },
   "boron3": {
     "particle_cpu": 512000.0,
     "particle_id": 11639194112000.0,
-    "particle_momentum_x": 9.277703190700158e-15,
-    "particle_momentum_y": 9.268420145552847e-15,
-    "particle_momentum_z": 9.279457128810487e-15,
-    "particle_position_x": 4096178.166422465,
-    "particle_position_y": 4096499.706038672,
+    "particle_momentum_x": 9.277692671587846e-15,
+    "particle_momentum_y": 9.268409636965691e-15,
+    "particle_momentum_z": 9.279446607709548e-15,
+    "particle_position_x": 4096178.1664224654,
+    "particle_position_y": 4096499.7060386725,
     "particle_position_z": 8191465.586938233,
-    "particle_weight": 5.119654661768357e+31
+    "particle_weight": 5.119654661746806e+31
   },
   "boron5": {
     "particle_cpu": 51200.0,
     "particle_id": 1208483891200.0,
     "particle_momentum_x": 0.0,
     "particle_momentum_y": 0.0,
     "particle_momentum_z": 0.0,
-    "particle_position_x": 409547.3312927569,
+    "particle_position_x": 409547.33129275695,
     "particle_position_y": 409518.5558814353,
     "particle_position_z": 819306.5006950963,
     "particle_weight": 1023.9999999999999
@@ -106,7 +106,7 @@
     "particle_id": 26214405120000.0,
     "particle_momentum_x": 0.0,
     "particle_momentum_y": 0.0,
-    "particle_momentum_z": 2.524243076150406e-13,
+    "particle_momentum_z": 2.524242836246531e-13,
     "particle_position_x": 40960140.72983793,
     "particle_position_y": 40959772.69310104,
     "particle_position_z": 81919021.52308556,
@@ -121,18 +121,18 @@
     "particle_position_x": 4095630.698135355,
     "particle_position_y": 4096073.5517983637,
     "particle_position_z": 8191737.5566503005,
-    "particle_weight": 1.022781024071589e+29
+    "particle_weight": 1.0227810240713489e+29
   },
   "proton3": {
     "particle_cpu": 307181.0,
     "particle_id": 6731321892958.0,
-    "particle_momentum_x": 1.684351051519872e-15,
-    "particle_momentum_y": 1.682381896868337e-15,
-    "particle_momentum_z": 1.679996145653965e-15,
+    "particle_momentum_x": 1.6843510515198723e-15,
+    "particle_momentum_y": 1.6823818968683368e-15,
+    "particle_momentum_z": 1.6799961456539653e-15,
     "particle_position_x": 2457338.899376694,
     "particle_position_y": 2457069.647393952,
     "particle_position_z": 4914642.288898885,
-    "particle_weight": 1.023654661768358e+31
+    "particle_weight": 1.0236546617468092e+31
   },
   "proton4": {
     "particle_cpu": 51200.0,
@@ -151,8 +151,8 @@
     "particle_momentum_x": 0.0,
     "particle_momentum_y": 0.0,
     "particle_momentum_z": 1.7581275870306353e-15,
-    "particle_position_x": 409638.287761857,
-    "particle_position_y": 409501.3225783394,
+    "particle_position_x": 409638.28776185703,
+    "particle_position_y": 409501.32257833943,
     "particle_position_z": 819309.1804186807,
     "particle_weight": 1.0240000000000003e+38
   }