diff --git a/bench/barite/README.org b/bench/barite/README.org index cc42b8c32..e7b316052 100644 --- a/bench/barite/README.org +++ b/bench/barite/README.org @@ -77,7 +77,7 @@ benchmarks the surface areas are set to A starting seed for barite is given at 0.001 mol in each domain element. -* TODO Nucleation +* Nucleation (TODO) Geochemical benchmark inspired by Tranter et al. (2021) without nucleation. @@ -97,13 +97,8 @@ transported species: H, O, Charge, Ba, Cl, S(6), Sr. - Diffusion coefficients: isotropic homogeneous \alpha = 1E-06 - Time steps & iterations: 20 iteration with \Delta t = 250 s - *DHT* parameters: -| H | 10 | -| O | 10 | -| Charge | 3 | -| Ba | 5 | -| Cl | 5 | -| S(6) | 5 | -| Sr | 5 | + | H | O | Charge | Ba | Cl | S(6) | Sr | + | 10 | 10 | 3 | 5 | 5 | 5 | 5 | @@ -115,14 +110,9 @@ transported species: H, O, Charge, Ba, Cl, S(6), Sr. BaCl_{2} - Diffusion coefficients: isotropic homogeneous \alpha = 1E-06 - Time steps & iterations: 200 iterations with \Delta t = 250 s -- *PHT* parameters: -| H | 10 | -| O | 10 | -| Charge | 3 | -| Ba | 5 | -| Cl | 5 | -| S(6) | 5 | -| Sr | 5 | +- *DHT* parameters: + | H | O | Charge | Ba | Cl | S(6) | Sr | + | 10 | 10 | 3 | 5 | 5 | 5 | 5 | * References diff --git a/bench/dolo/README.org b/bench/dolo/README.org index 72259f1db..67caf6e12 100644 --- a/bench/dolo/README.org +++ b/bench/dolo/README.org @@ -1,4 +1,4 @@ -#+TITLE: Description of =barite= benchmark +#+TITLE: Description of =dolo= benchmark #+AUTHOR: MDL #+DATE: 2023-08-26 #+STARTUP: inlineimages @@ -12,22 +12,22 @@ * Quick start #+begin_src sh :language sh :frame single -mpirun -np 4 ./poet dolomite.R dolomite_results -mpirun -np 4 ./poet --interp dolomite_interp_eval.R dolomite_results +mpirun -np 4 ./poet dolo_diffu_inner.R dolo_diffu_inner_res +mpirun -np 4 ./poet --dht --interp dolo_interp_long.R dolo_interp_long_res #+end_src * List of Files -- =dolo.R=: POET input script for a 20x20 simulation grid -- =dolo_diffu_inner.R=: POET input script for a 400x200 simulation +- =dolo_diffu_inner.R=: POET input script for a 100x100 simulation grid -- =dolo_diffu_inner_large.R=: POET input script for a 400x200 - simulation grid - =dolo_interp_long.R=: POET input script for a 400x200 simulation grid - =phreeqc_kin.dat=: PHREEQC database containing the kinetic expressions for dolomite and celestite, stripped down from =phreeqc.dat= - =dol.pqi=: PHREEQC input script for the chemical system +# - =dolo.R=: POET input script for a 20x20 simulation grid +# - =dolo_diffu_inner_large.R=: POET input script for a 400x200 +# simulation grid * Chemical system @@ -119,15 +119,8 @@ implicit total H, total O and Charge as required by PHREEQC_RM. - Diffusion coefficients: isotropic homogeneous \alpha = 1E-06 - Time steps & iterations: 10 iterations with \Delta t of 200 s - *DHT* parameters: - | H | 10 | - | O | 10 | - | Charge | 3 | - | C(4) | 5 | - | Ca | 5 | - | Cl | 5 | - | Mg | 5 | - | Calcite | 5 | - | Dolomite | 5 | + | H | O | Charge | C(4) | Ca | Cl | Mg | Calcite | Dolomite | + | 10 | 10 | 3 | 5 | 5 | 5 | 5 | 5 | 5 | - Hooks: the following hooks are defined: 1. =dht_fill=: 2. =dht_fuzz=: @@ -146,15 +139,8 @@ implicit total H, total O and Charge as required by PHREEQC_RM. - Diffusion coefficients: isotropic homogeneous \alpha = 1E-06 - Time steps & iterations: 20000 iterations with \Delta t of 200 s - *DHT* parameters: - | H | 10 | - | O | 10 | - | Charge | 3 | - | C(4) | 5 | - | Ca | 5 | - | Cl | 5 | - | Mg | 5 | - | Calcite | 5 | - | Dolomite | 5 | + | H | O | Charge | C(4) | Ca | Cl | Mg | Calcite | Dolomite | + | 10 | 10 | 3 | 5 | 5 | 5 | 5 | 5 | 5 | - Hooks: the following hooks are defined: 1. =dht_fill=: 2. =dht_fuzz=: diff --git a/src/DiffusionModule.cpp b/src/DiffusionModule.cpp index e02c42e03..ba7a60e62 100644 --- a/src/DiffusionModule.cpp +++ b/src/DiffusionModule.cpp @@ -177,11 +177,11 @@ void DiffusionModule::simulate(double dt) { t_field = field_2d; - std::cout << " done!\n"; sim_a_transport = MPI_Wtime(); transport_t += sim_a_transport - sim_b_transport; + std::cout << " done in "<< sim_a_transport - sim_b_transport << "sec" << std::endl; } void DiffusionModule::end() {