C:\Program Files\iMaGE\iCP-1.3>java -Xss4m -Xms40m -Xmx8024m -XX:MaxPermSize=256m -cp ".\bin\*;.\lib\*;C:\Program Files\COMSOL\COMSOL52a\Multiphysics\plugins\*;" iCP.iCP "C:\Users\Agraw003\Documents\iCP_Examples\Benchmark 2 Calcite dissolution\iCPinput.json" Java HotSpot(TM) 64-Bit Server VM warning: ignoring option MaxPermSize=256m; support was removed in 8.0 Using input file C:\Users\Agraw003\Documents\iCP_Examples\Benchmark 2 Calcite dissolution\iCPinput.json 17/10 11:05:54 - [INFO] -> --------------------------------------------- iCP: interface COMSOL PHREEQC --------------------------------------------- iCP has been developed by AMPHOS 21 iCP is a project of the iMaGe initiative and is supported by the iCP partnership Visit www.image-modelling.net for details iCP v.1.3 contains: -> phreeqcRocks v.1.0 -> IPHREEQCLib embedded v.3.1 -> comsolRT v.1.0 -> Compatibility with COMSOL v.5.2 --------------------------------------------- 17/10 11:05:54 - [INFO] -> --------------------------------------------- This application is licensed to: -> First Name: Priyanka -> Last Name: Agrawal -> License Type: Trial -> Valid until: 04/01/2017 --------------------------------------------- 17/10 11:05:54 - [INFO] -> Reading input file C:\Users\Agraw003\Documents\iCP_Examples\Benchmark 2 Calcite dissolution\iCPinput.json 17/10 11:05:54 - [INFO] -> Restart option active 17/10 11:05:54 - [INFO] -> Starting loop of problems 17/10 11:05:54 - [INFO] -> Creating problem: problem1 17/10 11:05:54 - [INFO] -> Creating domains: [domainId1, BCwaterId1] 17/10 11:05:54 - [INFO] -> Creating variables -from Phreeqc to Comsol: selectedOutput 17/10 11:05:54 - [INFO] -> Creating variables -from Comsol to Phreeqc: 17/10 11:05:54 - [INFO] -> Creating variables -both directions: aqueousComponents 17/10 11:05:55 - [INFO] -> Unzipping variable -selectedOutput to 7 new variables t_Cl t_Mg t_C Calcite water t_Ca Dolomite(ord) 17/10 11:05:55 - [INFO] -> Unzipping variable -aqueousComponents to 7 new variables Ca_tr C_tr Cl_tr H_tr charge_tr O_tr Mg_tr 17/10 11:05:55 - [INFO] -> Initializing problem for problem1 17/10 11:05:55 - [INFO] -> Initializing phreeqcRocks 17/10 11:05:55 - [INFO] -> Initializing comsolRT 17/10 11:05:55 - [INFO] -> Connecting to COMSOL server: -> Port: 2036 -> Hostname: Geo00489 17/10 11:05:56 - [INFO] -> Connected to the COMSOL server! 17/10 11:05:56 - [INFO] -> Loading file C:\Users\Agraw003\Documents\iCP_Examples\Benchmark 2 Calcite dissolution\comsol\input.mph 17/10 11:06:03 - [INFO] -> Loading file done 17/10 11:06:03 - [INFO] -> initialize variables in COMSOL 17/10 11:06:04 - [INFO] -> Reactive transport domains are over mesh:Mesh 1 17/10 11:06:04 - [INFO] -> Calculating variable position in COMSOL (this may take a while) 17/10 11:06:08 - [INFO] -> Calculating compact numbering 17/10 11:06:08 - [INFO] -> Calculating global contribution 17/10 11:06:08 - [INFO] -> Set interpolation results 17/10 11:06:08 - [INFO] -> Initializing domain dimensions 17/10 11:06:08 - [INFO] -> ---------------------------------------------- Size of domains involved - BCwaterId1 1 nodes - domainId1 101 nodes ---------------------------------------------- 17/10 11:06:08 - [INFO] -> Restarting from problem: problem1 17/10 11:06:08 - [INFO] -> Loading file C:\Users\Agraw003\Documents\iCP_Examples\Benchmark 2 Calcite dissolution\checkPoint\checkpoint1.mph 17/10 11:06:10 - [INFO] -> Loading file done 17/10 11:06:10 - [INFO] -> Loading chemical domain C:\Users\Agraw003\Documents\iCP_Examples\Benchmark 2 Calcite dissolution\checkPoint\checkpoint1_BCwaterId1_0 17/10 11:06:10 - [INFO] -> Loading chemical domain C:\Users\Agraw003\Documents\iCP_Examples\Benchmark 2 Calcite dissolution\checkPoint\checkpoint1_domainId1_0 17/10 11:06:10 - [INFO] -> Loading chemical domain C:\Users\Agraw003\Documents\iCP_Examples\Benchmark 2 Calcite dissolution\checkPoint\checkpoint1_domainId1_1 17/10 11:06:10 - [INFO] -> Loading chemical domain C:\Users\Agraw003\Documents\iCP_Examples\Benchmark 2 Calcite dissolution\checkPoint\checkpoint1_domainId1_2 17/10 11:06:10 - [INFO] -> Loading chemical domain C:\Users\Agraw003\Documents\iCP_Examples\Benchmark 2 Calcite dissolution\checkPoint\checkpoint1_domainId1_3 17/10 11:06:10 - [INFO] -> Loading checkPoint File domain C:\Users\Agraw003\Documents\iCP_Examples\Benchmark 2 Calcite dissolution\checkPoint\checkpoint1_settings 17/10 11:06:10 - [INFO] -> Saving output file C:\Users\Agraw003\Documents\iCP_Examples\Benchmark 2 Calcite dissolution\results\myOutput.mph 17/10 11:06:10 - [INFO] -> Start run of problem1 17/10 11:06:10 - [INFO] -> CALCULATING TIME STEP step number: 4/50 from time 6.0 to 8.0 17/10 11:06:10 - [INFO] -> Solving transport step 17/10 11:06:10 - [INFO] -> - Solving solver masterSolver 17/10 11:06:11 - [INFO] -> Solving chemical step 17/10 11:06:12 - [INFO] -> --------------------------------------------------------------------------------------------------------- Id Domain Size Name of thread xCell Time IsCalc 1 BCwaterId1 1 pool-3-thread-1 0.00 0.00 false 3 domainId1 25 pool-3-thread-3 9.48 237.00 true 4 domainId1 25 pool-3-thread-4 10.28 257.00 true 5 domainId1 26 pool-3-thread-1 12.19 317.00 true 2 domainId1 25 pool-3-thread-2 13.44 336.00 true --------------------------------------------------------------------------------------------------------- serial time: 1147.00 parallel time: 336.00 speed up : 3.41 calculated domains: 4/5 --------------------------------------------------------------------------------------------------------- 17/10 11:06:12 - [INFO] -> Saving results to file 17/10 11:06:16 - [INFO] -> Saving output file C:\Users\Agraw003\Documents\iCP_Examples\Benchmark 2 Calcite dissolution\results\myOutput.mph 17/10 11:06:16 - [INFO] -> ******************************************************** TIME STEP RESUME -step number: 4/50 -from time 6.0 to 8.0 -transport step(msec): 902.0 -reactive step(msec): 340.0 -saving results(msec): 4703.0 -total (msec): 5945.0 ******************************************************** 17/10 11:06:16 - [INFO] -> CALCULATING TIME STEP step number: 5/50 from time 8.0 to 10.0 17/10 11:06:16 - [INFO] -> Solving transport step 17/10 11:06:16 - [INFO] -> - Solving solver masterSolver 17/10 11:06:17 - [INFO] -> Solving chemical step 17/10 11:06:17 - [INFO] -> --------------------------------------------------------------------------------------------------------- Id Domain Size Name of thread xCell Time IsCalc 1 BCwaterId1 1 pool-3-thread-3 0.00 0.00 false 3 domainId1 25 pool-3-thread-1 0.00 0.00 false 2 domainId1 25 pool-3-thread-4 0.04 1.00 false 4 domainId1 25 pool-3-thread-2 0.04 1.00 false 5 domainId1 26 pool-3-thread-3 4.85 126.00 true --------------------------------------------------------------------------------------------------------- serial time: 128.00 parallel time: 127.00 speed up : 1.01 calculated domains: 1/5 --------------------------------------------------------------------------------------------------------- 17/10 11:06:17 - [INFO] -> Saving results to file 17/10 11:06:21 - [INFO] -> Saving output file C:\Users\Agraw003\Documents\iCP_Examples\Benchmark 2 Calcite dissolution\results\myOutput.mph 17/10 11:06:21 - [INFO] -> ******************************************************** TIME STEP RESUME -step number: 5/50 -from time 8.0 to 10.0 -transport step(msec): 642.0 -reactive step(msec): 128.0 -saving results(msec): 4177.0 -total (msec): 4947.0 ******************************************************** 17/10 11:06:21 - [INFO] -> CALCULATING TIME STEP step number: 6/50 from time 10.0 to 12.0 17/10 11:06:21 - [INFO] -> Solving transport step 17/10 11:06:21 - [INFO] -> - Solving solver masterSolver 17/10 11:06:22 - [INFO] -> Solving chemical step Oct 17, 2016 11:06:22 AM phreeqcRocks.chemistry.PhreeqcInterfaceLib runAccumulated SEVERE: unable to run phreeqc code Oct 17, 2016 11:06:22 AM phreeqcRocks.chemistry.PhreeqcInterfaceLib runAccumulated SEVERE: SOLUTION_MODIFY 0 -total_h 85.99017529945696 -total_o 30.48115936947478 -cb -25.02839035381863 -totals Cl 1.0E-14 Ca 1.0E-14 Mg 1.0E-14 C 1.0E-14 SOLUTION_MODIFY 1 -total_h 117.29907229593209 -total_o 61.789957859604506 -cb 6.280312468730655 -totals Cl 6.281701957816007 Ca 6.280416930382749 Mg 6.280991269281523 C 6.280400975575556 SOLUTION_MODIFY 2 -total_h 109.44509787718502 -total_o 53.93600135817818 -cb -1.5736107085047917 -totals Cl 1.0E-14 Ca 1.0E-14 Mg 1.0E-14 C 1.0E-14 SOLUTION_MODIFY 3 -total_h 111.41239561087794 -total_o 55.90329841990329 -cb 0.39367298881020846 -totals Cl 0.39438975630063106 Ca 0.3938841267528365 Mg 0.3939082884261228 C 0.3937610367120016 SOLUTION_MODIFY 4 -total_h 110.92041676146172 -total_o 55.411358601560444 -cb -0.09832082070017961 -totals Cl 1.0E-14 Ca 1.0E-14 Mg 1.0E-14 C 1.0E-14 SOLUTION_MODIFY 5 -total_h 111.04326456027792 -total_o 55.534235792686864 -cb 0.024511486462163824 -totals Cl 0.024748360718199653 Ca 0.02465830472428141 Mg 0.024599034069748046 C 0.02462741278838487 SOLUTION_MODIFY 6 -total_h 111.0126591878773 -total_o 55.50363951720991 -cb -0.006098798187607683 -totals Cl 1.0E-14 Ca 1.0E-14 Mg 1.0E-14 C 1.0E-14 SOLUTION_MODIFY 7 -total_h 111.02027504511508 -total_o 55.511260116813084 -cb 0.0015142400499761472 -totals Cl 0.001559412164869613 Ca 0.0016407456717540986 Mg 0.0015321476066484493 C 0.001636066152057176 SOLUTION_MODIFY 8 -total_h 111.01838671215998 -total_o 55.50937334700683 -cb -3.75095592347931E-4 -totals Cl 1.0E-14 Ca 1.0E-14 Mg 1.0E-14 C 1.0E-14 SOLUTION_MODIFY 9 -total_h 111.01885474734352 -total_o 55.50984167347945 -cb 9.26778140723779E-5 -totals Cl 9.730829932496889E-5 Ca 2.1567198581372605E-4 Mg 9.465420847365497E-5 C 2.153324133279723E-4 SOLUTION_MODIFY 10 -total_h 111.01873929412965 -total_o 55.5097262675184 -cb -2.2836969711019636E-5 -totals Cl 1.0E-14 Ca 9.991872044129725E-5 Mg 1.0E-14 C 9.984360918401546E-5 SOLUTION_MODIFY 11 -total_h 111.01876775057134 -total_o 55.509754724504056 -cb 5.6077857749017955E-6 -totals Cl 5.8863523928887825E-6 Ca 1.2830688140574476E-4 Mg 5.731366018452558E-6 C 1.2829048515446373E-4 SOLUTION_MODIFY 12 -total_h 111.0187607705687 -total_o 55.509747743626754 -cb -1.3744492902786785E-6 -totals Cl 1.0E-14 Ca 1.2131175434185561E-4 Mg 1.0E-14 C 1.2130832875154485E-4 SOLUTION_MODIFY 13 -total_h 111.0187624789041 -total_o 55.50974945159529 -cb 3.334355773019976E-7 -totals Cl 3.482051130268861E-7 Ca 1.2301686487498618E-4 Mg 3.408129782768592E-7 C 1.230161660832654E-4 SOLUTION_MODIFY 14 -total_h 111.01876206287076 -total_o 55.50974903543985 -cb -8.267258861310135E-8 -totals Cl 1.0E-14 Ca 1.2260016859360544E-4 Mg 1.0E-14 C 1.2260002960434567E-4 SOLUTION_MODIFY 15 -total_h 111.01876216381311 -total_o 55.509749136348034 -cb 1.8255897634455555E-8 -totals Cl 2.0228276995652415E-8 Ca 1.227009770196388E-4 Mg 1.990541020623988E-8 C 1.2270094899629333E-4 SOLUTION_MODIFY 16 -total_h 111.01876213945938 -total_o 55.509749111986736 -cb -6.100130694434787E-9 -totals Cl 1.0E-14 Ca 1.226765960932176E-4 Mg 1.0E-14 C 1.2267659081582587E-4 SOLUTION_MODIFY 17 -total_h 111.01876214530287 -total_o 55.50974911782814 -cb -2.569762846016184E-10 -totals Cl 1.1508528650763736E-9 Ca 1.2268243441127143E-4 Mg 1.13720267451496E-9 C 1.2268243333203512E-4 SOLUTION_MODIFY 18 -total_h 111.01876214391073 -total_o 55.50974911643555 -cb -1.6492089387477463E-9 -totals Cl 1.0E-14 Ca 1.2268104116211652E-4 Mg 1.0E-14 C 1.2268104096946775E-4 SOLUTION_MODIFY 19 -total_h 111.01876214423984 -total_o 55.509749116764496 -cb -1.3201616288600805E-9 -totals Cl 6.356518455153474E-11 Ca 1.2268137001939425E-4 Mg 6.300558945197771E-11 C 1.2268136997911787E-4 SOLUTION_MODIFY 20 -total_h 111.01876214416296 -total_o 55.50974911668745 -cb -1.3971770384784548E-9 -totals Cl 1.0E-14 Ca 1.2268129296369868E-4 Mg 1.0E-14 C 1.2268129295680693E-4 SOLUTION_MODIFY 21 -total_h 111.01876214418094 -total_o 55.50974911670525 -cb -1.3793648163802186E-9 -totals Cl 3.3667611038459636E-12 Ca 1.2268131076847034E-4 Mg 3.344027555714092E-12 C 1.2268131076705011E-4 SOLUTION_MODIFY 22 -total_h 111.01876214417702 -total_o 55.509749116701194 -cb -1.3834232438949498E-9 -totals Cl 1.0E-14 Ca 1.2268130670842816E-4 Mg 1.0E-14 C 1.2268130670822083E-4 SOLUTION_MODIFY 23 -total_h 111.01876214417844 -total_o 55.5097491167021 -cb -1.3825162583025083E-9 -totals Cl 1.7461681372968263E-13 Ca 1.2268130761517067E-4 Mg 1.7371971091017547E-13 C 1.2268130761507203E-4 SOLUTION_MODIFY 24 -total_h 111.01876214417824 -total_o 55.509749116701904 -cb -1.382713748370361E-9 -totals Cl 1.0E-14 Ca 1.2268130741760507E-4 Mg 1.0E-14 C 1.2268130741760155E-4 SOLUTION_MODIFY 25 -total_h 111.01876214417817 -total_o 55.50974911670195 -cb -1.3826723137540832E-9 -totals Cl 1.687955072428891E-14 Ca 1.2268130745904496E-4 Mg 1.688157058520399E-14 C 1.2268130745904585E-4 DUMP -file myfile3.dmp -append false -cells 0-25 -all END RUN_CELLS -cells 0-25 -start_time 10.0 -time_step 2.0 END Oct 17, 2016 11:06:22 AM phreeqcRocks.chemistry.PhreeqcInterfaceLib runAccumulated SEVERE: ERROR: A(H2O) Activity of water has not converged. Residual: 7.527291e-001 ERROR: Numerical method failed on all combinations of convergence parameters java.lang.Exception: Problem in RunAccumulated at phreeqcRocks.chemistry.PhreeqcInterfaceLib.runAccumulated(PhreeqcInterfaceLib.java:269) at phreeqcRocks.chemistry.PhreeqcInterfaceLib.runCells(PhreeqcInterfaceLib.java:247) at phreeqcRocks.chemistry.DomainChemistry.calculateChemicalStep(DomainChemistry.java:229) at phreeqcRocks.ParallelChemicalStep.call(ParallelChemicalStep.java:36) at phreeqcRocks.ParallelChemicalStep.call(ParallelChemicalStep.java:15) at java.util.concurrent.FutureTask.run(Unknown Source) at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source) at java.util.concurrent.FutureTask.run(Unknown Source) at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.lang.Thread.run(Unknown Source) Oct 17, 2016 11:06:22 AM phreeqcRocks.chemistry.PhreeqcInterfaceLib runCells SEVERE: Problem in RunAccumulated java.lang.Exception: Problem in runCells in 3 at phreeqcRocks.chemistry.PhreeqcInterfaceLib.runCells(PhreeqcInterfaceLib.java:256) at phreeqcRocks.chemistry.DomainChemistry.calculateChemicalStep(DomainChemistry.java:229) at phreeqcRocks.ParallelChemicalStep.call(ParallelChemicalStep.java:36) at phreeqcRocks.ParallelChemicalStep.call(ParallelChemicalStep.java:15) at java.util.concurrent.FutureTask.run(Unknown Source) at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source) at java.util.concurrent.FutureTask.run(Unknown Source) at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.lang.Thread.run(Unknown Source) 17/10 11:06:22 - [SEVERE] -> Problem in runCells in 3 java.util.concurrent.ExecutionException: java.lang.Exception: Problem in calculateChemicalStep in domainId1 at java.util.concurrent.FutureTask.report(Unknown Source) at java.util.concurrent.FutureTask.get(Unknown Source) at phreeqcRocks.Study.chemicalStep(Study.java:202) at phreeqcRocks.PhreeqcRocks.chemicalStep(PhreeqcRocks.java:347) at iCP.Problem.run(Problem.java:243) at iCP.iCPRunner.run(iCPRunner.java:68) at iCP.iCP.iCP_main(iCP.java:104) at iCP.iCP.main(iCP.java:31) Caused by: java.lang.Exception: Problem in calculateChemicalStep in domainId1 at phreeqcRocks.chemistry.DomainChemistry.calculateChemicalStep(DomainChemistry.java:269) at phreeqcRocks.ParallelChemicalStep.call(ParallelChemicalStep.java:36) at phreeqcRocks.ParallelChemicalStep.call(ParallelChemicalStep.java:15) at java.util.concurrent.FutureTask.run(Unknown Source) at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source) at java.util.concurrent.FutureTask.run(Unknown Source) at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.lang.Thread.run(Unknown Source) 17/10 11:06:22 - [SEVERE] -> java.lang.Exception: Problem in calculateChemicalStep in domainId1 17/10 11:06:22 - [SEVERE] -> error chemicalStep in PhreeqcRocks java.lang.Exception: error chemicalStep in PhreeqcRocks at phreeqcRocks.PhreeqcRocks.chemicalStep(PhreeqcRocks.java:351) at iCP.Problem.run(Problem.java:243) at iCP.iCPRunner.run(iCPRunner.java:68) at iCP.iCP.iCP_main(iCP.java:104) at iCP.iCP.main(iCP.java:31) 17/10 11:06:22 - [SEVERE] -> error RUNNING problem problem1 17/10 11:06:22 - [SEVERE] -> Saving error file at your input file folder: C:\Users\Agraw003\Documents\iCP_Examples\Benchmark 2 Calcite dissolution 17/10 11:06:22 - [INFO] -> Saving output file C:\Users\Agraw003\Documents\iCP_Examples\Benchmark 2 Calcite dissolution\error.mph 17/10 11:06:22 - [SEVERE] -> C:\Users\Agraw003\Documents\iCP_Examples\Benchmark 2 Calcite dissolution\error.mph saved 17/10 11:06:22 - [SEVERE] -> problem running the loop of problems 17/10 11:06:22 - [SEVERE] -> Execution aborted