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Modified IO functions

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This commit is contained in:
rastogi 2025-10-17 15:37:49 +02:00
parent af6462409b
commit d1d6211c30
83 changed files with 493 additions and 62 deletions
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18
bin/dolo_fgcs_3.R
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@ -115,17 +115,21 @@ setup <- list(
Chemistry = chemistry_setup # Parameters related to the chemistry process
)
iterations <- 20
dt <- 100
control_iteration <- 10
species_epsilon <- rep(0.001, length(dht_species))
iterations <- 500
dt <- 200
checkpoint_interval <- 50
control_interval <- 100
mape_threshold <- c(.0, .0, 1e-12, 1e-1, 1e-1, 1e-2, 1e-2, 1e+1, 1e+1, 1e-3, 0, 1e-1, .0)
rrmse_threshold <- c(.0, .0, 1e-12, 1e-4, 1e-1, 1e-2, 1e-2, 1e+1, 1e+1, 1e-3, 0, 1e-1, .0)
#out_save <- seq(50, iterations, by = 50)
list(
timesteps = rep(dt, iterations),
store_result = TRUE,
store_result = FALSE,
#out_save = out_save,
control_iteration = control_iteration,
species_epsilon = species_epsilon
checkpoint_interval = checkpoint_interval,
control_interval = control_interval,
mape_threshold = mape_threshold,
rrmse_threshold = rrmse_threshold
)

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Iteration Rollback Species MAPE RRSME
---------------------------------------------------------------------------
100 0 cell_ID 0 0
100 0 ID 0 0
100 0 H 3.12231e-14 1.1509e-15
100 0 O 5.71631e-09 1.52456e-10
100 0 Charge 0.00277434 0.000180148
100 0 C 0.000123678 2.12884e-05
100 0 Ca 0.00012359 2.12719e-05
100 0 Cl 52.4183 0.723995
100 0 Mg 0.25793 0.0507445
100 0 Calcite 7.41077e-06 1.27769e-06
100 0 Calcite_p1 0 0
100 0 Dolomite 0 0
100 0 Dolomite_p1 0 0
200 1 cell_ID 0 0
200 1 ID 0 0
200 1 H 2.95859e-14 9.60014e-16
200 1 O 5.02824e-09 6.20613e-11
200 1 Charge 0.00161321 8.9929e-05
200 1 C 2.83375e-05 3.68986e-06
200 1 Ca 2.82814e-05 3.6869e-06
200 1 Cl 4.33261 0.208132
200 1 Mg 0.261454 0.0511126
200 1 Calcite 1.69344e-06 2.19948e-07
200 1 Calcite_p1 0 0
200 1 Dolomite 2.12138e-07 4.39278e-07
200 1 Dolomite_p1 0 0
300 1 cell_ID 0 0
300 1 ID 0 0
300 1 H 2.61483e-14 8.44115e-16
300 1 O 4.20912e-09 5.28953e-11
300 1 Charge 0.00111694 4.8082e-05
300 1 C 9.01588e-06 1.37917e-06
300 1 Ca 8.98915e-06 1.37725e-06
300 1 Cl 0.0250508 0.0158114
300 1 Mg 0.0368942 0.0192029
300 1 Calcite 5.42801e-07 8.23432e-08
300 1 Calcite_p1 0 0
300 1 Dolomite 1.34065e-05 1.50929e-05
300 1 Dolomite_p1 0 0
400 1 cell_ID 0 0
400 1 ID 0 0
400 1 H 2.52669e-14 7.70988e-16
400 1 O 3.13537e-09 4.41261e-11
400 1 Charge 0.00111045 4.73189e-05
400 1 C 5.21852e-06 4.67209e-07
400 1 Ca 5.28321e-06 4.7664e-07
400 1 Cl 1.88383e-08 1.72516e-08
400 1 Mg 1.6654e-07 7.23985e-08
400 1 Calcite 3.29709e-07 3.02443e-08
400 1 Calcite_p1 0 0
400 1 Dolomite 0.000108165 7.44989e-05
400 1 Dolomite_p1 0 0
500 1 cell_ID 0 0
500 1 ID 0 0
500 1 H 2.5648e-14 8.49637e-16
500 1 O 2.06816e-09 3.48582e-11
500 1 Charge 0.00117171 7.1904e-05
500 1 C 4.68561e-06 3.1246e-07
500 1 Ca 4.847e-06 3.29307e-07
500 1 Cl 8.19957e-11 4.15952e-11
500 1 Mg 2.88349e-07 1.01377e-07
500 1 Calcite 3.12577e-07 2.30026e-08
500 1 Calcite_p1 0 0
500 1 Dolomite 7.6329e-05 3.37797e-05
500 1 Dolomite_p1 0 0

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@ -0,0 +1,72 @@
Iteration Rollback Species MAPE RRSME
---------------------------------------------------------------------------
100 0 cell_ID 0 0
100 0 ID 0 0
100 0 H 3.47278e-14 1.28046e-15
100 0 O 3.91041e-09 1.46205e-10
100 0 Charge 0.00341346 0.000209852
100 0 C 0.00012351 2.10537e-05
100 0 Ca 0.00012342 2.10371e-05
100 0 Cl 51.8517 0.720026
100 0 Mg 0.0164251 0.0119904
100 0 Calcite 7.40172e-06 1.26365e-06
100 0 Calcite_p1 0 0
100 0 Dolomite 0 0
100 0 Dolomite_p1 0 0
200 1 cell_ID 0 0
200 1 ID 0 0
200 1 H 2.85412e-14 9.17937e-16
200 1 O 4.25235e-09 5.35197e-11
200 1 Charge 0.00115635 6.27422e-05
200 1 C 2.84308e-05 3.72039e-06
200 1 Ca 2.83753e-05 3.71755e-06
200 1 Cl 4.21085 0.205107
200 1 Mg 0.0583267 0.0238491
200 1 Calcite 1.6987e-06 2.21727e-07
200 1 Calcite_p1 0 0
200 1 Dolomite 1.4852e-07 2.49534e-07
200 1 Dolomite_p1 0 0
300 1 cell_ID 0 0
300 1 ID 0 0
300 1 H 3.09033e-14 1.04628e-15
300 1 O 3.61033e-09 4.49029e-11
300 1 Charge 0.00199629 0.000104649
300 1 C 8.92201e-06 1.3502e-06
300 1 Ca 8.88482e-06 1.34813e-06
300 1 Cl 0.0252149 0.0158115
300 1 Mg 0.0271398 0.0163938
300 1 Calcite 5.36046e-07 8.05148e-08
300 1 Calcite_p1 0 0
300 1 Dolomite 8.76776e-06 8.08383e-06
300 1 Dolomite_p1 0 0
400 1 cell_ID 0 0
400 1 ID 0 0
400 1 H 2.47784e-14 8.02966e-16
400 1 O 2.77372e-09 3.82347e-11
400 1 Charge 0.00109769 4.46829e-05
400 1 C 5.18807e-06 4.53038e-07
400 1 Ca 5.25706e-06 4.58743e-07
400 1 Cl 7.98413e-08 6.88159e-08
400 1 Mg 3.17154e-07 1.76467e-07
400 1 Calcite 3.28375e-07 2.88573e-08
400 1 Calcite_p1 0 0
400 1 Dolomite 9.74408e-05 5.10781e-05
400 1 Dolomite_p1 0 0
500 1 cell_ID 0 0
500 1 ID 0 0
500 1 H 2.58635e-14 8.70649e-16
500 1 O 1.81852e-09 2.99676e-11
500 1 Charge 0.00140547 7.9273e-05
500 1 C 4.61893e-06 3.09187e-07
500 1 Ca 4.79576e-06 3.21992e-07
500 1 Cl 2.35937e-10 1.70544e-10
500 1 Mg 3.04927e-07 9.42059e-08
500 1 Calcite 3.10603e-07 2.22112e-08
500 1 Calcite_p1 0 0
500 1 Dolomite 7.05202e-05 2.85239e-05
500 1 Dolomite_p1 0 0

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bin/dolo_interp_rt.R
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@ -2,14 +2,14 @@ iterations <- 1000
dt <- 200
checkpoint_interval <- 100
control_interval <- 200
mape_threshold <- c(.0, .0, 1e-12, 1e-1, 1e-1, 1e-2, 1e-2, 1e+1, 1e+1, 1e-3, 0, 1e-1, .0, 0.12, .0)
rrmse_threshold <- c(.0, .0, 1e-12, 1e-4, 1e-1, 1e-2, 1e-2, 1e+1, 1e+1, 1e-3, 0, 1e-1, .0, 0.12, .0)
out_save <- seq(50, iterations, by = 50)
mape_threshold <- c(.0, .0, 1e-12, .0, 1e-1, 1e-2, 1e-2, 1e+1, 1e+1, 1e-3, 0, 1e-1, .0, .0, .0)
rrmse_threshold <- c(.0, .0, 1e-12, 1e-1, 1e-1, 1e-2, 1e-2, 1e+1, 1e+1, 1e-3, 0, 1e-1, .0, 1e-1, .0)
#out_save <- seq(50, iterations, by = 50)
list(
timesteps = rep(dt, iterations),
store_result = TRUE,
out_save = out_save,
store_result = FALSE,
#out_save = out_save,
checkpoint_interval = checkpoint_interval,
control_interval = control_interval,
mape_threshold = mape_threshold,

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@ -0,0 +1,18 @@
Iteration Rollback Species MAPE RRSME
---------------------------------------------------------------------------
40 0 cell_ID 0 0
40 0 ID 0 0
40 0 H 1.97536e-14 3.39767e-16
40 0 O 0.108667 0.00113058
40 0 Charge 0.0149527 0.000159859
40 0 C 0.000320855 3.77065e-05
40 0 Ca 0.000320918 3.77053e-05
40 0 Cl 2.94255 0.0564879
40 0 Mg 2.99364 0.058404
40 0 Calcite 0.000193155 2.27958e-05
40 0 Calcite_p1 0 0
40 0 Dolomite 5.53123e-06 7.32342e-06
40 0 Dolomite_p1 0 0
40 0 O2g_eq 0.292811 0.0030472
40 0 O2g_si 0 0

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Iteration Rollback Species MAPE RRSME
---------------------------------------------------------------------------
200 0 cell_ID 0 0
200 0 ID 0 0
200 0 H 4.24216e-14 7.93767e-16
200 0 O 0.266416 0.00345942
200 0 Charge 0.0108553 0.00016141
200 0 C 0.00105879 4.62528e-05
200 0 Ca 0.00106128 4.64714e-05
200 0 Cl 0.183638 0.0281206
200 0 Mg 0.357623 0.068502
200 0 Calcite 0.000660749 3.05684e-05
200 0 Calcite_p1 0 0
200 0 Dolomite 0.0377868 0.018717
200 0 Dolomite_p1 0 0
200 0 O2g_eq 0.727525 0.00942789
200 0 O2g_si 0 0
400 1 cell_ID 0 0
400 1 ID 0 0
400 1 H 4.96116e-14 1.03074e-15
400 1 O 0.0625096 0.00089073
400 1 Charge 0.00179685 5.81218e-05
400 1 C 0.00138513 4.19276e-05
400 1 Ca 0.00138939 4.22617e-05
400 1 Cl 2.01049e-10 1.12062e-11
400 1 Mg 1.73388e-05 1.58885e-06
400 1 Calcite 0.000887349 3.09872e-05
400 1 Calcite_p1 0 0
400 1 Dolomite 0.0508038 0.0422224
400 1 Dolomite_p1 0 0
400 1 O2g_eq 0.169632 0.00241576
400 1 O2g_si 0 0
600 2 cell_ID 0 0
600 2 ID 0 0
600 2 H 5.02907e-14 1.04743e-15
600 2 O 0.0339388 0.000529191
600 2 Charge 0.000872335 3.88643e-05
600 2 C 0.00161187 4.55169e-05
600 2 Ca 0.00161202 4.55691e-05
600 2 Cl 2.00968e-10 7.09682e-12
600 2 Mg 1.78737e-05 1.52671e-06
600 2 Calcite 0.00112915 5.57669e-05
600 2 Calcite_p1 0 0
600 2 Dolomite 0.0464188 0.020625
600 2 Dolomite_p1 0 0
600 2 O2g_eq 0.0916364 0.00144097
600 2 O2g_si 0 0
800 3 cell_ID 0 0
800 3 ID 0 0
800 3 H 5.02456e-14 1.07954e-15
800 3 O 0.0348835 0.000593709
800 3 Charge 0.000981333 4.59987e-05
800 3 C 0.00188335 5.51043e-05
800 3 Ca 0.00187866 5.48754e-05
800 3 Cl 1.91647e-10 6.80693e-12
800 3 Mg 1.99396e-05 1.4224e-06
800 3 Calcite 0.00133831 7.37938e-05
800 3 Calcite_p1 0 0
800 3 Dolomite 0.0122079 0.00910585
800 3 Dolomite_p1 0 0
800 3 O2g_eq 0.094699 0.00161554
800 3 O2g_si 0 0
1000 4 cell_ID 0 0
1000 4 ID 0 0
1000 4 H 4.58333e-14 9.19552e-16
1000 4 O 0.03928 0.000658637
1000 4 Charge 0.000850352 3.64268e-05
1000 4 C 0.00162933 4.32013e-05
1000 4 Ca 0.00162399 4.31629e-05
1000 4 Cl 1.78469e-10 6.32135e-12
1000 4 Mg 2.54679e-05 1.5059e-06
1000 4 Calcite 0.00110095 3.85726e-05
1000 4 Calcite_p1 0 0
1000 4 Dolomite 0.115066 0.0336203
1000 4 Dolomite_p1 0 0
1000 4 O2g_eq 0.10644 0.00178803
1000 4 O2g_si 0 0

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Iteration Rollback Species MAPE RRSME
---------------------------------------------------------------------------
200 0 cell_ID 0 0
200 0 ID 0 0
200 0 H 4.35833e-14 7.81087e-16
200 0 O 0.265974 0.00345273
200 0 Charge 0.0139127 0.00021089
200 0 C 0.00106544 4.68727e-05
200 0 Ca 0.00106775 4.71101e-05
200 0 Cl 0.153803 0.0309734
200 0 Mg 0.259249 0.0557173
200 0 Calcite 0.000666058 3.09596e-05
200 0 Calcite_p1 0 0
200 0 Dolomite 0.0378628 0.0187185
200 0 Dolomite_p1 0 0
200 0 O2g_eq 0.726346 0.00940997
200 0 O2g_si 0 0
400 1 cell_ID 0 0
400 1 ID 0 0
400 1 H 4.96779e-14 1.02625e-15
400 1 O 0.0612117 0.000885574
400 1 Charge 0.00211885 7.23582e-05
400 1 C 0.0013936 4.246e-05
400 1 Ca 0.00139683 4.27607e-05
400 1 Cl 1.92492e-10 7.96912e-12
400 1 Mg 1.72798e-05 1.57044e-06
400 1 Calcite 0.000893972 3.23061e-05
400 1 Calcite_p1 0 0
400 1 Dolomite 0.0508392 0.0424705
400 1 Dolomite_p1 0 0
400 1 O2g_eq 0.166295 0.00240305
400 1 O2g_si 0 0
600 2 cell_ID 0 0
600 2 ID 0 0
600 2 H 4.98299e-14 1.03244e-15
600 2 O 0.0337469 0.000532858
600 2 Charge 0.000886747 3.95933e-05
600 2 C 0.00157754 4.32746e-05
600 2 Ca 0.0015787 4.33921e-05
600 2 Cl 1.99043e-10 6.97877e-12
600 2 Mg 1.78781e-05 1.51655e-06
600 2 Calcite 0.00112008 9.94027e-05
600 2 Calcite_p1 0 0
600 2 Dolomite 0.0440381 0.0200137
600 2 Dolomite_p1 0 0
600 2 O2g_eq 0.0911647 0.00145098
600 2 O2g_si 0 0
800 3 cell_ID 0 0
800 3 ID 0 0
800 3 H 4.95687e-14 1.04941e-15
800 3 O 0.0342771 0.000595825
800 3 Charge 0.000999783 4.79781e-05
800 3 C 0.00187815 5.36255e-05
800 3 Ca 0.00187373 5.34439e-05
800 3 Cl 1.90419e-10 6.73422e-12
800 3 Mg 2.00131e-05 1.42672e-06
800 3 Calcite 0.00127536 4.6846e-05
800 3 Calcite_p1 0 0
800 3 Dolomite 0.0116904 0.00900077
800 3 Dolomite_p1 0 0
800 3 O2g_eq 0.092918 0.00162017
800 3 O2g_si 0 0
1000 4 cell_ID 0 0
1000 4 ID 0 0
1000 4 H 4.46262e-14 8.84025e-16
1000 4 O 0.0393243 0.000668632
1000 4 Charge 0.000823168 3.55208e-05
1000 4 C 0.00163087 4.28808e-05
1000 4 Ca 0.00162568 4.28564e-05
1000 4 Cl 1.74767e-10 6.13816e-12
1000 4 Mg 2.51858e-05 1.49617e-06
1000 4 Calcite 0.00109436 3.63441e-05
1000 4 Calcite_p1 0 0
1000 4 Dolomite 0.115761 0.0351099
1000 4 Dolomite_p1 0 0
1000 4 O2g_eq 0.106644 0.00181596
1000 4 O2g_si 0 0

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bin/poet_dolo_interp_iter1000_n4_roll/stats_overview Normal file
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@ -0,0 +1,82 @@
Iteration Rollback Species MAPE RRSME
---------------------------------------------------------------------------
200 0 cell_ID 0 0
200 0 ID 0 0
200 0 H 4.40607e-14 7.90085e-16
200 0 O 0.26477 0.0034449
200 0 Charge 0.0152426 0.000228736
200 0 C 0.00106749 4.69434e-05
200 0 Ca 0.00106988 4.71795e-05
200 0 Cl 0.19963 0.0417236
200 0 Mg 0.302507 0.109754
200 0 Calcite 0.000668562 3.12626e-05
200 0 Calcite_p1 0 0
200 0 Dolomite 0.022869 0.0141522
200 0 Dolomite_p1 0 0
200 0 O2g_eq 0.723052 0.0093885
200 0 O2g_si 0 0
400 1 cell_ID 0 0
400 1 ID 0 0
400 1 H 5.10132e-14 1.04621e-15
400 1 O 0.0620153 0.000909136
400 1 Charge 0.00227654 7.76102e-05
400 1 C 0.00140883 4.26784e-05
400 1 Ca 0.00141118 4.30019e-05
400 1 Cl 1.98506e-10 6.90649e-12
400 1 Mg 1.76159e-05 1.60076e-06
400 1 Calcite 0.000905335 3.16292e-05
400 1 Calcite_p1 0 0
400 1 Dolomite 0.0596336 0.0492175
400 1 Dolomite_p1 0 0
400 1 O2g_eq 0.168173 0.00246656
400 1 O2g_si 0 0
600 2 cell_ID 0 0
600 2 ID 0 0
600 2 H 5.0337e-14 1.03769e-15
600 2 O 0.0321049 0.000508398
600 2 Charge 0.000888608 3.9048e-05
600 2 C 0.00157038 4.35036e-05
600 2 Ca 0.00157147 4.36029e-05
600 2 Cl 2.03573e-10 7.1497e-12
600 2 Mg 1.78228e-05 1.51293e-06
600 2 Calcite 0.00110004 5.90231e-05
600 2 Calcite_p1 0 0
600 2 Dolomite 0.0444966 0.0200246
600 2 Dolomite_p1 0 0
600 2 O2g_eq 0.0867418 0.00138316
600 2 O2g_si 0 0
800 3 cell_ID 0 0
800 3 ID 0 0
800 3 H 5.07032e-14 1.07836e-15
800 3 O 0.0304553 0.000543198
800 3 Charge 0.000987327 4.5855e-05
800 3 C 0.00189037 5.46494e-05
800 3 Ca 0.00188634 5.4454e-05
800 3 Cl 1.9489e-10 6.83318e-12
800 3 Mg 2.04861e-05 1.45815e-06
800 3 Calcite 0.00129733 5.02191e-05
800 3 Calcite_p1 0 0
800 3 Dolomite 0.0132718 0.0097894
800 3 Dolomite_p1 0 0
800 3 O2g_eq 0.0823463 0.00147483
800 3 O2g_si 0 0
1000 4 cell_ID 0 0
1000 4 ID 0 0
1000 4 H 4.5926e-14 8.98972e-16
1000 4 O 0.0346924 0.000605097
1000 4 Charge 0.000854348 3.62669e-05
1000 4 C 0.00165366 4.37053e-05
1000 4 Ca 0.00164887 4.36839e-05
1000 4 Cl 1.81984e-10 6.37135e-12
1000 4 Mg 2.50557e-05 1.50812e-06
1000 4 Calcite 0.0011238 4.37014e-05
1000 4 Calcite_p1 0 0
1000 4 Dolomite 0.111075 0.0348126
1000 4 Dolomite_p1 0 0
1000 4 O2g_eq 0.0937111 0.00164022
1000 4 O2g_si 0 0

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18
bin/run_poet.sh
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@ -1,16 +1,20 @@
#!/bin/bash
#SBATCH --job-name=poet_dolo_interp
#SBATCH --output=poet_dolo_interp_%j.out
#SBATCH --error=poet_dolo_interp_%j.err
#SBATCH --nodes=2
#SBATCH --job-name=poet_dolo_interp_NOroll
#SBATCH --output=poet_dolo_interp_NOroll%j.out
#SBATCH --error=poet_dolo_interp_NOroll%j.err
#SBATCH --partition=long
#SBATCH --nodes=4
#SBATCH --ntasks=48
#SBATCH --ntasks-per-node=24
#SBATCH --ntasks-per-node=12
#SBATCH --time=02:00:00
#SBATCH --exclusive
#SBATCH --mail-user=vasudha.rastogi@uni-potsdam.de
#SBATCH --mail-type=END,FAIL
module load cmake gcc openmpi
source /etc/profile.d/modules.sh
module purge
module load cmake gcc openmpi R
mpirun -n 48 ./poet --interp dolo_interp_rt.R dolo_interp.qs2 dolo_interp
mpirun -n 48 ./poet --interp dolo_interp_rt.R dolo_interp.qs2 poet_dolo_interp_iter1000_n4_NOroll
#mpirun -n 48 ./poet --interp dolo_fgcs_3.R dolo_fgcs_3.qs2 dolo_fgcs_3_iter500_n2_roll

56
bin/stats_overview
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@ -1,34 +1,30 @@
Iteration Rollback Species MAPE RRSME
---------------------------------------------------------------------------
20 0 cell_ID 0 0
20 0 ID 0 0
20 0 H 1.77731e-14 2.7095e-16
20 0 O 0.0553364 0.000567638
20 0 Charge 0.0138864 0.000147021
20 0 C 8.81221e-05 1.41354e-05
20 0 Ca 8.8185e-05 1.41354e-05
20 0 Cl 6.02029 0.0873663
20 0 Mg 6.08272 0.0883807
20 0 Calcite 5.26812e-05 8.46394e-06
20 0 Calcite_p1 0 0
20 0 Dolomite 5.3721e-07 1.14804e-06
20 0 Dolomite_p1 0 0
20 0 O2g_eq 0.145109 0.00148947
20 0 O2g_si 0 0
100 0 cell_ID 0 0
100 0 ID 0 0
100 0 H 6.12118e-14 2.16243e-15
100 0 O 1.82053e-09 1.46339e-10
100 0 Charge 0.00858644 0.000361839
100 0 C 0.00012588 2.14455e-05
100 0 Ca 0.000125782 2.14299e-05
100 0 Cl 52.1566 0.722171
100 0 Mg 0.490336 0.0697317
100 0 Calcite 7.54079e-06 1.28674e-06
100 0 Calcite_p1 0 0
100 0 Dolomite 3.89779e-08 1.55912e-07
100 0 Dolomite_p1 0 0
40 1 cell_ID 0 0
40 1 ID 0 0
40 1 H 1.70761e-14 3.24997e-16
40 1 O 0.0285341 0.000295504
40 1 Charge 0.012912 0.000140398
40 1 C 0.000332495 3.36477e-05
40 1 Ca 0.000332544 3.36467e-05
40 1 Cl 4.03557 0.0764422
40 1 Mg 4.11227 0.0777245
40 1 Calcite 0.000199586 2.02213e-05
40 1 Calcite_p1 0 0
40 1 Dolomite 1.50815e-06 1.98748e-06
40 1 Dolomite_p1 0 0
40 1 O2g_eq 0.0708157 0.000734877
40 1 O2g_si 0 0
200 1 cell_ID 0 0
200 1 ID 0 0
200 1 H 3.48099e-14 1.01368e-15
200 1 O 3.22418e-09 4.60101e-11
200 1 Charge 0.00171817 0.000117133
200 1 C 3.02114e-05 4.34024e-06
200 1 Ca 3.01505e-05 4.33741e-06
200 1 Cl 4.29804 0.207274
200 1 Mg 0.367412 0.0605187
200 1 Calcite 1.80463e-06 2.58645e-07
200 1 Calcite_p1 0 0
200 1 Dolomite 0 0
200 1 Dolomite_p1 0 0

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src/IO/HDF5Functions.hpp
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@ -3,7 +3,7 @@
#include <string>
#include "Datatypes.hpp"
int write_checkpoint(const std::string &file_path, struct Checkpoint_s &&checkpoint);
int read_checkpoint(const std::string &file_path, struct Checkpoint_s &checkpoint);
int write_checkpoint(const std::string &dir_path, const std::string &file_name, struct Checkpoint_s &&checkpoint);
int read_checkpoint(const std::string &dir_path, const std::string &file_name, struct Checkpoint_s &checkpoint);

12
src/IO/StatsIO.cpp
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@ -2,15 +2,19 @@
#include <fstream>
#include <iostream>
#include <string>
#include <iomanip> // for std::setw and std::setprecision
#include <iomanip>
#include <filesystem>
namespace poet
{
void writeStatsToCSV(const std::vector<ChemistryModule::SimulationErrorStats> &all_stats,
const std::vector<std::string> &species_names,
const std::string &out_dir,
const std::string &filename)
{
std::ofstream out(filename);
std::filesystem::path full_path = std::filesystem::path(out_dir) / filename;
std::ofstream out(full_path);
if (!out.is_open())
{
std::cerr << "Could not open " << filename << " !" << std::endl;
@ -24,7 +28,7 @@ namespace poet
<< std::setw(15) << "MAPE"
<< std::setw(15) << "RRSME" << "\n";
out << std::string(75, '-') << "\n"; // separator line
out << std::string(75, '-') << "\n";
// data rows
for (size_t i = 0; i < all_stats.size(); ++i)
@ -39,7 +43,7 @@ namespace poet
<< std::setw(15) << all_stats[i].rrmse[j]
<< "\n";
}
out << "\n"; // blank line between iterations
out << "\n";
}
out.close();

1
src/IO/StatsIO.hpp
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@ -5,5 +5,6 @@ namespace poet
{
void writeStatsToCSV(const std::vector<ChemistryModule::SimulationErrorStats> &all_stats,
const std::vector<std::string> &species_names,
const std::string &out_dir,
const std::string &filename);
} // namespace poet

22
src/IO/checkpoint.cpp
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@ -1,13 +1,20 @@
#include "IO/Datatypes.hpp"
#include <cstdint>
#include <highfive/H5Easy.hpp>
#include <filesystem>
int write_checkpoint(const std::string &file_path, struct Checkpoint_s &&checkpoint){
namespace fs = std::filesystem;
int write_checkpoint(const std::string &dir_path, const std::string &file_name, struct Checkpoint_s &&checkpoint){
if (!fs::exists(dir_path)) {
std::cerr << "Directory does not exist: " << dir_path << std::endl;
return -1;
}
fs::path file_path = fs::path(dir_path) / file_name;
// TODO: errorhandling
H5Easy::File file(file_path, H5Easy::File::Overwrite);
H5Easy::dump(file, "/MetaParam/Iterations", checkpoint.iteration);
H5Easy::dump(file, "/Grid/Names", checkpoint.field.GetProps());
H5Easy::dump(file, "/Grid/Chemistry", checkpoint.field.As2DVector());
@ -15,9 +22,16 @@ int write_checkpoint(const std::string &file_path, struct Checkpoint_s &&checkpo
return 0;
}
int read_checkpoint(const std::string &file_path, struct Checkpoint_s &checkpoint){
int read_checkpoint(const std::string &dir_path, const std::string &file_name, struct Checkpoint_s &checkpoint){
fs::path file_path = fs::path(dir_path) / file_name;
H5Easy::File file(file_path, H5Easy::File::ReadOnly);
if (!fs::exists(file_path)) {
std::cerr << "File does not exist: " << file_path << std::endl;
return -1;
}
H5Easy::File file(file_path, H5Easy::File::ReadOnly);
checkpoint.iteration = H5Easy::load<uint32_t>(file, "/MetaParam/Iterations");

6
src/poet.cpp
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@ -330,7 +330,7 @@ bool triggerRollbackIfExceeded(ChemistryModule &chem, RuntimeParameters &params,
" → rolling back to iteration " + std::to_string(rollback_iter));
Checkpoint_s checkpoint_read{.field = chem.getField()};
read_checkpoint("checkpoint" + std::to_string(rollback_iter) + ".hdf5", checkpoint_read);
read_checkpoint(params.out_dir, "checkpoint" + std::to_string(rollback_iter) + ".hdf5", checkpoint_read);
current_iteration = checkpoint_read.iteration;
return true; // rollback happened
}
@ -490,13 +490,13 @@ static Rcpp::List RunMasterLoop(RInsidePOET &R, RuntimeParameters &params,
if(iter % params.checkpoint_interval == 0){
MSG("Writing checkpoint of iteration " + std::to_string(iter));
write_checkpoint("checkpoint" + std::to_string(iter) + ".hdf5",
write_checkpoint(params.out_dir, "checkpoint" + std::to_string(iter) + ".hdf5",
{.field = chem.getField(), .iteration = iter});
}
if (params.control_interval_enabled && !params.rollback_enabled)
{
writeStatsToCSV(chem.error_history, chem.getField().GetProps(), "stats_overview");
writeStatsToCSV(chem.error_history, chem.getField().GetProps(), params.out_dir,"stats_overview");
if(triggerRollbackIfExceeded(chem, params, iter)){
params.rollback_enabled = true;