First commit of geometry rewrite. Mesh and MeshElement traits have be…

.github/workflows/rustbca_compile_check.yml

@@ -26,7 +26,7 @@ jobs:
         sudo apt-get install python3-pip
     - name: Install Python libraries
       run: |
-        pip3 
+        pip3
         python3 -m pip install numpy shapely scipy
     - name: Install python TOML library from source
       run: |
@@ -42,4 +42,6 @@ jobs:
     - name: Run Examples
       run: |
         cargo run --release examples/boron_nitride.toml
+        cargo run --release 0D examples/boron_nitride_0D.toml
+        cargo run --release 0D examples/titanium_dioxide_0D.toml
         cargo run --release --features distributions examples/layered_geometry.toml

Cargo.toml

@@ -9,12 +9,13 @@ name="rustBCA"
 
 [dependencies]
 rand = "0.8.3"
-geo = "0.17.1"
+
 toml = "0.5.8"
 anyhow = "1.0.38"
 itertools = "0.10.0"
 rayon = "1.5.0"
-indicatif = {version="0.15.0", features=["rayon"]}
+geo = {version = "0.17.1", optional = false}
+indicatif = {version = "0.15.0", features=["rayon"]}
 serde = { version = "1.0.123", features = ["derive"] }
 hdf5 = {version = "0.7.1", optional = true}
 openblas-src = {version  = "0.9", optional = true}
@@ -39,3 +40,5 @@ cpr_rootfinder_netlib = ["rcpr", "netlib-src"]
 cpr_rootfinder_intel_mkl = ["rcpr", "intel-mkl-src"]
 distributions = ["ndarray"]
 no_list_output = []
+mesh_0D = []
+mesh_2D = []

examples/boron_nitride.toml

@@ -44,7 +44,7 @@ dir = [ [ 0.9999999999984769, 1.7453292519934434e-6, 0.0,], [ 0.9999999999984769
 interaction_index = [0, 0, 0, 0, 0, 0, 0, 0, 0, 0]
 particle_input_filename=""
 
-[mesh_2d_input]
+[geometry_input]
 length_unit = "MICRON"
 energy_barrier_thickness = 1.7645653881793786e-4
 triangles = [ [ 0.0, 0.0, 0.0012558103905862675, 0.0, 0.02, 0.019960534568565433,], [ 0.0, 0.0012558103905862675, 0.0025066646712860853, 0.0, 0.019960534568565433, 0.019842294026289557,], [ 0.0, 0.0025066646712860853, 0.003747626291714493, 0.0, 0.019842294026289557, 0.019645745014573775,], [ 0.0, 0.003747626291714493, 0.004973797743297096, 0.0, 0.019645745014573775, 0.01937166322257262,], [ 0.0, 0.004973797743297096, 0.0061803398874989484, 0.0, 0.01937166322257262, 0.019021130325903073,], [ 0.0, 0.0061803398874989484, 0.00736249105369356, 0.0, 0.019021130325903073, 0.018595529717765027,], [ 0.0, 0.00736249105369356, 0.008515585831301454, 0.0, 0.018595529717765027, 0.01809654104932039,], [ 0.0, 0.008515585831301454, 0.009635073482034308, 0.0, 0.01809654104932039, 0.01752613360087727,], [ 0.0, 0.009635073482034308, 0.010716535899579934, 0.0, 0.01752613360087727, 0.0168865585100403,], [ 0.0, 0.010716535899579934, 0.011755705045849463, 0.0, 0.0168865585100403, 0.016180339887498948,], [ 0.0, 0.011755705045849463, 0.012748479794973795, 0.0, 0.016180339887498948, 0.015410264855515783,], [ 0.0, 0.012748479794973795, 0.013690942118573775, 0.0, 0.015410264855515783, 0.014579372548428232,], [ 0.0, 0.013690942118573775, 0.014579372548428232, 0.0, 0.014579372548428232, 0.013690942118573773,], [ 0.0, 0.014579372548428232, 0.015410264855515785, 0.0, 0.013690942118573773, 0.012748479794973793,], [ 0.0, 0.015410264855515785, 0.016180339887498948, 0.0, 0.012748479794973793, 0.011755705045849461,], [ 0.0, 0.016180339887498948, 0.0168865585100403, 0.0, 0.011755705045849461, 0.01071653589957993,], [ 0.0, 0.0168865585100403, 0.017526133600877274, 0.0, 0.01071653589957993, 0.009635073482034304,], [ 0.0, 0.017526133600877274, 0.018096541049320392, 0.0, 0.009635073482034304, 0.008515585831301454,], [ 0.0, 0.018096541049320392, 0.01859552971776503, 0.0, 0.008515585831301454, 0.007362491053693557,], [ 0.0, 0.01859552971776503, 0.019021130325903073, 0.0, 0.007362491053693557, 0.006180339887498949,], [ 0.0, 0.019021130325903073, 0.01937166322257262, 0.0, 0.006180339887498949, 0.004973797743297095,], [ 0.0, 0.01937166322257262, 0.019645745014573775, 0.0, 0.004973797743297095, 0.0037476262917144902,], [ 0.0, 0.019645745014573775, 0.019842294026289557, 0.0, 0.0037476262917144902, 0.0025066646712860853,], [ 0.0, 0.019842294026289557, 0.019960534568565433, 0.0, 0.0025066646712860853, 0.001255810390586266,], [ 0.0, 0.019960534568565433, 0.02, 0.0, 0.001255810390586266, -3.2162452993532734e-18,], [ 0.0, 0.02, 0.019960534568565433, 0.0, -3.2162452993532734e-18, -0.001255810390586268,], [ 0.0, 0.019960534568565433, 0.019842294026289557, 0.0, -0.001255810390586268, -0.0025066646712860875,], [ 0.0, 0.019842294026289557, 0.019645745014573772, 0.0, -0.0025066646712860875, -0.0037476262917144967,], [ 0.0, 0.019645745014573772, 0.01937166322257262, 0.0, -0.0037476262917144967, -0.004973797743297097,], [ 0.0, 0.01937166322257262, 0.019021130325903073, 0.0, -0.004973797743297097, -0.006180339887498951,], [ 0.0, 0.019021130325903073, 0.01859552971776503, 0.0, -0.006180339887498951, -0.00736249105369356,], [ 0.0, 0.01859552971776503, 0.01809654104932039, 0.0, -0.00736249105369356, -0.008515585831301454,], [ 0.0, 0.01809654104932039, 0.01752613360087727, 0.0, -0.008515585831301454, -0.00963507348203431,], [ 0.0, 0.01752613360087727, 0.0168865585100403, 0.0, -0.00963507348203431, -0.010716535899579938,], [ 0.0, 0.0168865585100403, 0.016180339887498948, 0.0, -0.010716535899579938, -0.011755705045849461,], [ 0.0, 0.016180339887498948, 0.015410264855515785, 0.0, -0.011755705045849461, -0.012748479794973795,], [ 0.0, 0.015410264855515785, 0.014579372548428228, 0.0, -0.012748479794973795, -0.013690942118573775,], [ 0.0, 0.014579372548428228, 0.01369094211857377, 0.0, -0.013690942118573775, -0.014579372548428234,], [ 0.0, 0.01369094211857377, 0.01274847979497379, 0.0, -0.014579372548428234, -0.015410264855515788,], [ 0.0, 0.01274847979497379, 0.011755705045849465, 0.0, -0.015410264855515788, -0.016180339887498948,], [ 0.0, 0.011755705045849465, 0.010716535899579934, 0.0, -0.016180339887498948, -0.0168865585100403,], [ 0.0, 0.010716535899579934, 0.009635073482034304, 0.0, -0.0168865585100403, -0.01752613360087727,], [ 0.0, 0.009635073482034304, 0.00851558583130145, 0.0, -0.01752613360087727, -0.018096541049320392,], [ 0.0, 0.00851558583130145, 0.007362491053693555, 0.0, -0.018096541049320392, -0.01859552971776503,], [ 0.0, 0.007362491053693555, 0.006180339887498942, 0.0, -0.01859552971776503, -0.019021130325903073,], [ 0.0, 0.006180339887498942, 0.004973797743297097, 0.0, -0.019021130325903073, -0.01937166322257262,], [ 0.0, 0.004973797743297097, 0.0037476262917144915, 0.0, -0.01937166322257262, -0.019645745014573775,], [ 0.0, 0.0037476262917144915, 0.002506664671286082, 0.0, -0.019645745014573775, -0.019842294026289557,], [ 0.0, 0.002506664671286082, 0.0012558103905862628, 0.0, -0.019842294026289557, -0.019960534568565433,], [ 0.0, 0.0012558103905862628, -6.432490598706547e-18, 0.0, -0.019960534568565433, -0.02,], [ 0.0, -6.432490598706547e-18, -0.0012558103905862669, 0.0, -0.02, -0.019960534568565433,], [ 0.0, -0.0012558103905862669, -0.0025066646712860858, 0.0, -0.019960534568565433, -0.019842294026289557,], [ 0.0, -0.0025066646712860858, -0.0037476262917144954, 0.0, -0.019842294026289557, -0.019645745014573772,], [ 0.0, -0.0037476262917144954, -0.0049737977432971, 0.0, -0.019645745014573772, -0.01937166322257262,], [ 0.0, -0.0049737977432971, -0.0061803398874989545, 0.0, -0.01937166322257262, -0.019021130325903073,], [ 0.0, -0.0061803398874989545, -0.007362491053693567, 0.0, -0.019021130325903073, -0.018595529717765024,], [ 0.0, -0.007362491053693567, -0.008515585831301454, 0.0, -0.018595529717765024, -0.01809654104932039,], [ 0.0, -0.008515585831301454, -0.009635073482034308, 0.0, -0.01809654104932039, -0.01752613360087727,], [ 0.0, -0.009635073482034308, -0.010716535899579936, 0.0, -0.01752613360087727, -0.0168865585100403,], [ 0.0, -0.010716535899579936, -0.011755705045849468, 0.0, -0.0168865585100403, -0.016180339887498944,], [ 0.0, -0.011755705045849468, -0.0127484797949738, 0.0, -0.016180339887498944, -0.015410264855515781,], [ 0.0, -0.0127484797949738, -0.013690942118573775, 0.0, -0.015410264855515781, -0.014579372548428232,], [ 0.0, -0.013690942118573775, -0.014579372548428232, 0.0, -0.014579372548428232, -0.013690942118573773,], [ 0.0, -0.014579372548428232, -0.015410264855515788, 0.0, -0.013690942118573773, -0.01274847979497379,], [ 0.0, -0.015410264855515788, -0.016180339887498948, 0.0, -0.01274847979497379, -0.011755705045849465,], [ 0.0, -0.016180339887498948, -0.016886558510040308, 0.0, -0.011755705045849465, -0.010716535899579927,], [ 0.0, -0.016886558510040308, -0.01752613360087727, 0.0, -0.010716535899579927, -0.009635073482034306,], [ 0.0, -0.01752613360087727, -0.018096541049320396, 0.0, -0.009635073482034306, -0.008515585831301443,], [ 0.0, -0.018096541049320396, -0.01859552971776503, 0.0, -0.008515585831301443, -0.007362491053693556,], [ 0.0, -0.01859552971776503, -0.019021130325903073, 0.0, -0.007362491053693556, -0.006180339887498951,], [ 0.0, -0.019021130325903073, -0.019371663222572624, 0.0, -0.006180339887498951, -0.004973797743297089,], [ 0.0, -0.019371663222572624, -0.019645745014573775, 0.0, -0.004973797743297089, -0.003747626291714493,], [ 0.0, -0.019645745014573775, -0.019842294026289557, 0.0, -0.003747626291714493, -0.0025066646712860745,], [ 0.0, -0.019842294026289557, -0.019960534568565433, 0.0, -0.0025066646712860745, -0.001255810390586264,], [ 0.0, -0.019960534568565433, -0.02, 0.0, -0.001255810390586264, -3.673940397442059e-18,], [ 0.0, -0.02, -0.019960534568565433, 0.0, -3.673940397442059e-18, 0.0012558103905862745,], [ 0.0, -0.019960534568565433, -0.019842294026289557, 0.0, 0.0012558103905862745, 0.0025066646712860845,], [ 0.0, -0.019842294026289557, -0.019645745014573772, 0.0, 0.0025066646712860845, 0.003747626291714503,], [ 0.0, -0.019645745014573772, -0.01937166322257262, 0.0, 0.003747626291714503, 0.004973797743297099,], [ 0.0, -0.01937166322257262, -0.019021130325903073, 0.0, 0.004973797743297099, 0.006180339887498945,], [ 0.0, -0.019021130325903073, -0.018595529717765024, 0.0, 0.006180339887498945, 0.007362491053693565,], [ 0.0, -0.018595529717765024, -0.018096541049320392, 0.0, 0.007362491053693565, 0.008515585831301452,], [ 0.0, -0.018096541049320392, -0.017526133600877267, 0.0, 0.008515585831301452, 0.009635073482034314,], [ 0.0, -0.017526133600877267, -0.0168865585100403, 0.0, 0.009635073482034314, 0.010716535899579936,], [ 0.0, -0.0168865585100403, -0.01618033988749894, 0.0, 0.010716535899579936, 0.011755705045849473,], [ 0.0, -0.01618033988749894, -0.015410264855515781, 0.0, 0.011755705045849473, 0.0127484797949738,], [ 0.0, -0.015410264855515781, -0.014579372548428232, 0.0, 0.0127484797949738, 0.013690942118573773,], [ 0.0, -0.014579372548428232, -0.013690942118573766, 0.0, 0.013690942118573773, 0.014579372548428239,], [ 0.0, -0.013690942118573766, -0.012748479794973793, 0.0, 0.014579372548428239, 0.015410264855515788,], [ 0.0, -0.012748479794973793, -0.011755705045849453, 0.0, 0.015410264855515788, 0.016180339887498955,], [ 0.0, -0.011755705045849453, -0.010716535899579927, 0.0, 0.016180339887498955, 0.016886558510040305,], [ 0.0, -0.010716535899579927, -0.009635073482034308, 0.0, 0.016886558510040305, 0.01752613360087727,], [ 0.0, -0.009635073482034308, -0.008515585831301445, 0.0, 0.01752613360087727, 0.018096541049320396,], [ 0.0, -0.008515585831301445, -0.007362491053693557, 0.0, 0.018096541049320396, 0.01859552971776503,], [ 0.0, -0.007362491053693557, -0.006180339887498935, 0.0, 0.01859552971776503, 0.019021130325903076,], [ 0.0, -0.006180339887498935, -0.00497379774329709, 0.0, 0.019021130325903076, 0.019371663222572624,], [ 0.0, -0.00497379774329709, -0.0037476262917144937, 0.0, 0.019371663222572624, 0.019645745014573775,], [ 0.0, -0.0037476262917144937, -0.002506664671286076, 0.0, 0.019645745014573775, 0.019842294026289557,], [ 0.0, -0.002506664671286076, -0.0012558103905862654, 0.0, 0.019842294026289557, 0.019960534568565433,], [ 0.0, -0.0012558103905862654, -4.898587196589413e-18, 0.0, 0.019960534568565433, 0.02,],]

examples/boron_nitride_0D.toml

@@ -0,0 +1,50 @@
+[options]
+name = "boron_dust_grain_"
+track_trajectories = false
+track_recoils = true
+track_recoil_trajectories = false
+write_buffer_size = 8000
+weak_collision_order = 0
+suppress_deep_recoils = false
+high_energy_free_flight_paths = false
+num_threads = 1
+num_chunks = 1
+use_hdf5 = false
+electronic_stopping_mode = "LOW_ENERGY_NONLOCAL"
+mean_free_path_model = "LIQUID"
+interaction_potential = [["KR_C"]]
+scattering_integral = [["MENDENHALL_WELLER"]]
+root_finder = [[{"NEWTON"={max_iterations=100, tolerance=1E-3}}]]
+track_displacements = false
+track_energy_losses = false
+
+[material_parameters]
+energy_unit = "EV"
+mass_unit = "AMU"
+Eb = [ 0.0, 0.0,]
+Es = [ 5.76, 0.0,]
+Ec = [ 1.0, 1.0,]
+Z = [ 5, 7,]
+m = [ 10.811, 14,]
+interaction_index = [0, 0]
+surface_binding_model = "AVERAGE"
+
+[particle_parameters]
+length_unit = "MICRON"
+energy_unit = "EV"
+mass_unit = "AMU"
+N = [ 10000 ]
+m = [ 1.008 ]
+Z = [ 1 ]
+E = [ 1000.0 ]
+Ec = [ 1.0 ]
+Es = [ 10.0 ]
+pos = [ [ 0.0, 0.0, 0.0,] ]
+dir = [ [ 0.9999999999984769, 1.7453292519934434e-6, 0.0,] ]
+interaction_index = [ 0 ]
+particle_input_filename=""
+
+[geometry_input]
+length_unit = "ANGSTROM"
+electronic_stopping_correction_factor = 1.0
+densities = [0.065, 0.065]

examples/layered_geometry.toml

@@ -45,10 +45,10 @@ Ec = [ 1.0,]
 Es = [ 0.0,]
 interaction_index = [0]
 pos = [ [ -1.7453292519934434e-8, 0.0, 0.0,],]
-dir = [ [ 0.999, 0.0001, 0.0,],]
+dir = [ [ 0.999, 0.001, 0.0,],]
 particle_input_filename = ""
 
-[mesh_2d_input]
+[geometry_input]
 length_unit = "MICRON"
 triangles = [ [ 0.0, 0.01, 0.0, 0.5, 0.5, -0.5,], [ 0.0, 0.01, 0.01, -0.5, 0.5, -0.5,], [ 0.01, 0.01, 0.04, -0.5, 0.5, -0.5,], [ 0.01, 0.04, 0.04, 0.5, 0.5, -0.5,], [ 0.04, 0.5, 0.04, 0.5, 0.5, -0.5,], [ 0.04, 0.5, 0.5, -0.5, 0.5, -0.5,],]
 densities = [ [ 3.0e+10, 6.0e+10, 0.0, 0.0,], [ 3.0e+10, 6.0e+10, 0.0, 0.0,], [ 0.0, 0.0, 6.026e+10, 0.0,], [ 0.0, 0.0, 6.026e+10, 0.0,], [ 0.0, 0.0, 0.0, 4.996e+10,], [ 0.0, 0.0, 0.0, 4.996e+10,],]

examples/multiple_interaction_potentials.toml

@@ -42,7 +42,7 @@ pos = [ [ -1.7453292519934434e-8, 0.0, 0.0,], [ -1.7453292519934434e-8, 0.0, 0.0
 dir = [ [ 0.9999999999984769, 1.7453292519934434e-6, 0.0,], [ 0.9999999999984769, 1.7453292519934434e-6, 0.0,],]
 particle_input_filename =
 
-[mesh_2d_input]
+[geometry_input]
 energy_barrier_thickness = 2.2E-4
 length_unit = "MICRON"
 triangles = [ [ 0.0, 0.01, 0.0, 0.5, 0.5, -0.5,], [ 0.0, 0.01, 0.01, -0.5, 0.5, -0.5,], [ 0.01, 0.01, 0.04, -0.5, 0.5, -0.5,], [ 0.01, 0.04, 0.04, 0.5, 0.5, -0.5,], [ 0.04, 0.5, 0.04, 0.5, 0.5, -0.5,], [ 0.04, 0.5, 0.5, -0.5, 0.5, -0.5,],]

examples/titanium_dioxide_0D.toml

@@ -0,0 +1,65 @@
+[options]
+name = "2000.0eV_0.0001deg_He_TiO2"
+track_trajectories = false
+track_recoils = true
+track_recoil_trajectories = false
+write_buffer_size = 8000
+weak_collision_order = 3
+suppress_deep_recoils = false
+high_energy_free_flight_paths = false
+electronic_stopping_mode = "LOW_ENERGY_NONLOCAL"
+mean_free_path_model = "LIQUID"
+interaction_potential = [["KR_C"]]
+scattering_integral = [["MENDENHALL_WELLER"]]
+use_hdf5 = false
+root_finder = [[{"NEWTON"={max_iterations=100, tolerance=1E-6}}]]
+num_threads = 4
+num_chunks = 10
+track_displacements = false
+track_energy_losses = false
+energy_min = 0.0
+energy_max = 2000.0
+energy_num = 20
+angle_min = 0.0
+angle_max = 90.0
+angle_num = 20
+x_min = 0.0
+y_min = -0.1
+z_min = -0.1
+x_max = 0.1
+y_max = 0.1
+z_max = 0.1
+x_num = 20
+y_num = 20
+z_num = 20
+
+[particle_parameters]
+length_unit = "1e-6"
+energy_unit = "EV"
+mass_unit = "AMU"
+N = [ 100000,]
+m = [ 4.002602,]
+Z = [ 2,]
+E = [ 2000.0,]
+Ec = [ 1.0,]
+Es = [ 0.0,]
+interaction_index = [0]
+pos = [ [ 0.0, 0.0, 0.0,],]
+dir = [ [ 0.5, 0.5, 0.0,],]
+particle_input_filename = ""
+
+[geometry_input]
+length_unit = "MICRON"
+densities = [ 3.0e+10, 6.0e+10, 0.0, 0.0 ]
+electronic_stopping_correction_factor = 1.0
+
+[material_parameters]
+energy_unit = "EV"
+mass_unit = "AMU"
+Eb = [ 3.0, 2.58, 3.0, 0.0,]
+Es = [ 4.84, 2.58, 3.39, 4.72,]
+Ec = [ 3.5, 2.0, 3.0, 1.5,]
+Z = [ 22, 8, 13, 14,]
+m = [ 47.867, 15.9994, 26.98, 28.08553,]
+interaction_index = [0, 0, 0, 0]
+surface_binding_model = "TARGET"