Package evaluation of ComplexMixtures on Julia 1.11.4 (a71dd056e0*) started at 2025-04-08T13:39:18.603 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 8.76s ################################################################################ # Installation # Installing ComplexMixtures... Resolving package versions... Updating `~/.julia/environments/v1.11/Project.toml` [6f35c628] + ComplexMixtures v2.12.1 Updating `~/.julia/environments/v1.11/Manifest.toml` [a963bdd2] + AtomsBase v0.5.1 [69e1c6dd] + CellListMap v0.9.8 [46823bd8] + Chemfiles v0.10.42 [ae650224] + ChunkSplitters v3.1.2 [34da2185] + Compat v4.16.0 [6f35c628] + ComplexMixtures v2.12.1 [187b0558] + ConstructionBase v1.5.8 [ffbed154] + DocStringExtensions v0.9.4 [1fa38f19] + Format v1.3.7 [c58ffaec] + FortranFiles v0.6.0 [842dd82b] + InlineStrings v1.4.3 [692b3bcd] + JLLWrappers v1.7.0 [0f8b85d8] + JSON3 v1.14.2 [1914dd2f] + MacroTools v0.5.15 [aea21201] + MolSimToolkitShared v1.1.3 [bac558e1] + OrderedCollections v1.8.0 [e29189f1] + PDBTools v2.8.0 [d96e819e] + Parameters v0.12.3 [69de0a69] + Parsers v2.8.1 [7b2266bf] + PeriodicTable v1.2.1 ⌅ [aea7be01] + PrecompileTools v1.2.1 [21216c6a] + Preferences v1.4.3 [92933f4c] + ProgressMeter v1.10.4 [e6cf234a] + RandomNumbers v1.6.0 [ae029012] + Requires v1.3.1 [efcf1570] + Setfield v1.1.2 [860ef19b] + StableRNGs v1.0.2 [90137ffa] + StaticArrays v1.9.13 [1e83bf80] + StaticArraysCore v1.4.3 [10745b16] + Statistics v1.11.1 [856f2bd8] + StructTypes v1.11.0 [1c621080] + TestItems v1.0.0 [3a884ed6] + UnPack v1.0.2 [1986cc42] + Unitful v1.22.0 [a7773ee8] + UnitfulAtomic v1.0.0 [78a364fa] + Chemfiles_jll v0.10.4+0 [0dad84c5] + ArgTools v1.1.2 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [8ba89e20] + Distributed v1.11.0 [f43a241f] + Downloads v1.6.0 [7b1f6079] + FileWatching v1.11.0 [9fa8497b] + Future v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [b27032c2] + LibCURL v0.6.4 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.11.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [ca575930] + NetworkOptions v1.2.0 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v0.7.0 [9e88b42a] + Serialization v1.11.0 [6462fe0b] + Sockets v1.11.0 [fa267f1f] + TOML v1.0.3 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.1.1+0 [deac9b47] + LibCURL_jll v8.6.0+0 [29816b5a] + LibSSH2_jll v1.11.0+1 [c8ffd9c3] + MbedTLS_jll v2.28.6+0 [14a3606d] + MozillaCACerts_jll v2023.12.12 [4536629a] + OpenBLAS_jll v0.3.27+1 [83775a58] + Zlib_jll v1.2.13+1 [8e850b90] + libblastrampoline_jll v5.11.0+0 [8e850ede] + nghttp2_jll v1.59.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Installation completed after 4.31s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 244.98s ################################################################################ # Testing # Testing ComplexMixtures Status `/tmp/jl_FLhDk8/Project.toml` [4c88cf16] Aqua v0.8.11 [6e4b80f9] BenchmarkTools v1.6.0 [69e1c6dd] CellListMap v0.9.8 [46823bd8] Chemfiles v0.10.42 [ae650224] ChunkSplitters v3.1.2 [6f35c628] ComplexMixtures v2.12.1 [8bb1440f] DelimitedFiles v1.9.1 [ffbed154] DocStringExtensions v0.9.4 [e30172f5] Documenter v1.10.1 [c58ffaec] FortranFiles v0.6.0 [0f8b85d8] JSON3 v1.14.2 [aea21201] MolSimToolkitShared v1.1.3 [e29189f1] PDBTools v2.8.0 [91a5bcdd] Plots v1.40.11 ⌅ [aea7be01] PrecompileTools v1.2.1 [92933f4c] ProgressMeter v1.10.4 [e6cf234a] RandomNumbers v1.6.0 [aed2ae9c] ShowMethodTesting v1.2.0 [860ef19b] StableRNGs v1.0.2 [90137ffa] StaticArrays v1.9.13 [10745b16] Statistics v1.11.1 [856f2bd8] StructTypes v1.11.0 [f8b46487] TestItemRunner v1.1.0 [1c621080] TestItems v1.0.0 [37e2e46d] LinearAlgebra v1.11.0 [de0858da] Printf 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LibGit2_jll v1.7.2+0 [29816b5a] LibSSH2_jll v1.11.0+1 [c8ffd9c3] MbedTLS_jll v2.28.6+0 [14a3606d] MozillaCACerts_jll v2023.12.12 [4536629a] OpenBLAS_jll v0.3.27+1 [05823500] OpenLibm_jll v0.8.5+0 [efcefdf7] PCRE2_jll v10.42.0+1 [bea87d4a] SuiteSparse_jll v7.7.0+0 [83775a58] Zlib_jll v1.2.13+1 [8e850b90] libblastrampoline_jll v5.11.0+0 [8e850ede] nghttp2_jll v1.59.0+0 [3f19e933] p7zip_jll v17.4.0+2 Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. Testing Running tests... Precompiling BenchmarkTools... 3009.9 ms ✓ BenchmarkTools 1 dependency successfully precompiled in 4 seconds. 15 already precompiled. ┌ Warning: │ │ Using default values for dbulk, cutoff and/or usecutoff: │ │ dbulk = 10.0 │ cutoff = 10.0 │ usecutoff = false │ │ It is recommended to set bulk_range manually, according to the │ system size and correlations of the distribution function with, │ for example: Options(bulk_range = (8.0, 12.0)) │ └ @ ComplexMixtures ┌ Warning: │ │ Using default values for dbulk, cutoff and/or usecutoff: │ │ dbulk = 10.0 │ cutoff = 10.0 │ usecutoff = false │ │ It is recommended to set bulk_range manually, according to the │ system size and correlations of the distribution function with, │ for example: Options(bulk_range = (8.0, 12.0)) │ └ @ ComplexMixtures ┌ Warning: │ │ Using default values for dbulk, cutoff and/or usecutoff: │ │ dbulk = 10.0 │ cutoff = 10.0 │ usecutoff = false │ │ It is recommended to set bulk_range manually, according to the │ system size and correlations of the distribution function with, │ for example: Options(bulk_range = (8.0, 12.0)) │ └ @ ComplexMixtures show methods: Error During Test at /home/pkgeval/.julia/packages/ComplexMixtures/8gsyg/test/show_methods.jl:63 Test threw exception Expression: parse_show(R; repl = Dict(r"Version.*" => "Version")) ≈ "--------------------------------------------------------------------------------\nMDDF Overview - ComplexMixtures - Version\n--------------------------------------------------------------------------------\n\nSolvent properties:\n-------------------\n\nSimulation concentration: 0.18450433782524045 mol L⁻¹\nMolar volume: 5419.9267713 cm³ mol⁻¹\n\nConcentration in bulk: 0.0 mol L⁻¹\nMolar volume in bulk: Inf cm³ mol⁻¹\n\nSolute properties:\n------------------\n\nSimulation Concentration: 0.061501445941746814 mol L⁻¹\nEstimated solute partial molar volume: -Inf cm³ mol⁻¹\n\nBulk range: >= 10.0 Å\nMolar volume of the solute domain: 0.0 cm³ mol⁻¹\n\nAuto-correlation: false\n\nTrajectory files and weights:\n\n /home/leandro/.julia/dev/ComplexMixtures/test/data/toy/cross.pdb - w = 1.0\n\nLong range MDDF mean (expected 1.0): 0.0 ± 0.0\nLong range RDF mean (expected 1.0): 0.0 ± 0.0\n\n--------------------------------------------------------------------------------\n" AssertionError: show method comparison failed for ComplexMixtures (String) == cross.pdb (String) full parsed show strings: ShowMethodTesting.ParsedShow("--------------------------------------------------------------------------------\nMDDF Overview - ComplexMixtures - Version\n--------------------------------------------------------------------------------\n\nSolvent properties:\n-------------------\n\nSimulation concentration: 0.18450433782524045 mol L⁻¹\nMolar volume: 5419.9267713 cm³ mol⁻¹\n\nConcentration in bulk: 0.0 mol L⁻¹\nMolar volume in bulk: Inf cm³ mol⁻¹\n\nSolute properties:\n------------------\n\nSimulation Concentration: 0.061501445941746814 mol L⁻¹\nEstimated solute partial molar volume: -Inf cm³ mol⁻¹\n\nBulk range: >= 10.0 Å\nMolar volume of the solute domain: 0.0 cm³ mol⁻¹\n\nAuto-correlation: false\n\nTrajectory files and weights:\n\n /home/pkgeval/.julia/packages/ComplexMixtures/ 8 gsyg/test/data/toy/cross.pdb - w = 1.0 \n\nLong range MDDF mean (expected 1.0 ): 0.0 ± 0.0 \nLong range RDF mean (expected 1.0 ): 0.0 ± 0.0 \n\n--------------------------------------------------------------------------------") ShowMethodTesting.ParsedShow("--------------------------------------------------------------------------------\nMDDF Overview - ComplexMixtures - Version\n--------------------------------------------------------------------------------\n\nSolvent properties:\n-------------------\n\nSimulation concentration: 0.18450433782524045 mol L⁻¹\nMolar volume: 5419.9267713 cm³ mol⁻¹\n\nConcentration in bulk: 0.0 mol L⁻¹\nMolar volume in bulk: Inf cm³ mol⁻¹\n\nSolute properties:\n------------------\n\nSimulation Concentration: 0.061501445941746814 mol L⁻¹\nEstimated solute partial molar volume: -Inf cm³ mol⁻¹\n\nBulk range: >= 10.0 Å\nMolar volume of the solute domain: 0.0 cm³ mol⁻¹\n\nAuto-correlation: false\n\nTrajectory files and weights:\n\n /home/leandro/.julia/dev/ComplexMixtures/test/data/toy/cross.pdb - w = 1.0 \n\nLong range MDDF mean (expected 1.0 ): 0.0 ± 0.0 \nLong range RDF mean (expected 1.0 ): 0.0 ± 0.0 \n\n--------------------------------------------------------------------------------\n") Stacktrace: [1] (::ShowMethodTesting.var"#match#10"{Bool, ShowMethodTesting.ParsedShow, ShowMethodTesting.ParsedShow})(f::ShowMethodTesting.var"#6#13", x1::String, x2::String) @ ShowMethodTesting ~/.julia/packages/ShowMethodTesting/vtI5I/src/ShowMethodTesting.jl:129 [2] isapprox(x::ShowMethodTesting.ParsedShow, y::ShowMethodTesting.ParsedShow; float_match::Function, int_match::Function, path_match::Function, assertion_error::Bool) @ ShowMethodTesting ~/.julia/packages/ShowMethodTesting/vtI5I/src/ShowMethodTesting.jl:164 [3] isapprox @ ~/.julia/packages/ShowMethodTesting/vtI5I/src/ShowMethodTesting.jl:118 [inlined] [4] isapprox(x::ShowMethodTesting.ParsedShow, y::String) @ ShowMethodTesting ~/.julia/packages/ShowMethodTesting/vtI5I/src/ShowMethodTesting.jl:171 [5] eval_test(evaluated::Expr, quoted::Expr, source::LineNumberNode, negate::Bool) @ Test /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:362 [6] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:676 [inlined] [7] top-level scope @ ~/.julia/packages/ComplexMixtures/8gsyg/test/show_methods.jl:515 ┌ Warning: │ │ Using default values for dbulk, cutoff and/or usecutoff: │ │ dbulk = 10.0 │ cutoff = 10.0 │ usecutoff = false │ │ It is recommended to set bulk_range manually, according to the │ system size and correlations of the distribution function with, │ for example: Options(bulk_range = (8.0, 12.0)) │ └ @ ComplexMixtures -------------------------------------------------------------------------------- Opening trajectory ... -------------------------------------------------------------------------------- Initializing data structures ... Evaluate trajectory length and go to first frame ... ┌ Warning: │ │ Using default values for dbulk, cutoff and/or usecutoff: │ │ dbulk = 10.0 │ cutoff = 10.0 │ usecutoff = false │ │ It is recommended to set bulk_range manually, according to the │ system size and correlations of the distribution function with, │ for example: Options(bulk_range = (8.0, 12.0)) │ └ @ ComplexMixtures -------------------------------------------------------------------------------- Opening trajectory ... -------------------------------------------------------------------------------- Initializing data structures ... Evaluate trajectory length and go to first frame ... -------------------------------------------------------------------------------- Starting MDDF calculation in parallel: 2 frames will be considered. Number of calculation threads: 1 Solute: 2 atoms belonging to 2 molecules. Solvent: 2 atoms belonging to 2 molecules. [ Info: From thread id: 1: stop_complexmixtures file found. Exiting. ┌ Warning: │ │ Ideal-gas histogram bins with zero samples. │ Increase n_random_samples, number of trajectory frames, and/or bin size. │ └ @ ComplexMixtures -------------------------------------------------------------------------------- ┌ Warning: │ │ Using default values for dbulk, cutoff and/or usecutoff: │ │ dbulk = 10.0 │ cutoff = 10.0 │ usecutoff = false │ │ It is recommended to set bulk_range manually, according to the │ system size and correlations of the distribution function with, │ for example: Options(bulk_range = (8.0, 12.0)) │ └ @ ComplexMixtures ┌ Warning: │ │ Using default values for dbulk, cutoff and/or usecutoff: │ │ dbulk = 10.0 │ cutoff = 10.0 │ usecutoff = false │ │ It is recommended to set bulk_range manually, according to the │ system size and correlations of the distribution function with, │ for example: Options(bulk_range = (8.0, 12.0)) │ └ @ ComplexMixtures -------------------------------------------------------------------------------- Opening trajectory ... -------------------------------------------------------------------------------- Initializing data structures ... Evaluate trajectory length and go to first frame ... -------------------------------------------------------------------------------- Starting MDDF calculation in parallel: 2 frames will be considered. Number of calculation threads: 1 Solute: 9 atoms belonging to 9 molecules. Solvent: 9 atoms belonging to 9 molecules. ┌ Warning: │ │ Ideal-gas histogram bins with zero samples. │ Increase n_random_samples, number of trajectory frames, and/or bin size. │ └ @ ComplexMixtures -------------------------------------------------------------------------------- ┌ Warning: │ │ Using default values for dbulk, cutoff and/or usecutoff: │ │ dbulk = 10.0 │ cutoff = 10.0 │ usecutoff = false │ │ It is recommended to set bulk_range manually, according to the │ system size and correlations of the distribution function with, │ for example: Options(bulk_range = (8.0, 12.0)) │ └ @ ComplexMixtures -------------------------------------------------------------------------------- Opening trajectory ... -------------------------------------------------------------------------------- Initializing data structures ... Evaluate trajectory length and go to first frame ... -------------------------------------------------------------------------------- Starting MDDF calculation in parallel: 2 frames will be considered. Number of calculation threads: 1 Solute: 9 atoms belonging to 9 molecules. Solvent: 9 atoms belonging to 9 molecules. ┌ Warning: │ │ Ideal-gas histogram bins with zero samples. │ Increase n_random_samples, number of trajectory frames, and/or bin size. │ └ @ ComplexMixtures -------------------------------------------------------------------------------- ┌ Warning: │ │ Using default values for dbulk, cutoff and/or usecutoff: │ │ dbulk = 10.0 │ cutoff = 10.0 │ usecutoff = false │ │ It is recommended to set bulk_range manually, according to the │ system size and correlations of the distribution function with, │ for example: Options(bulk_range = (8.0, 12.0)) │ └ @ ComplexMixtures -------------------------------------------------------------------------------- Opening trajectory ... -------------------------------------------------------------------------------- Initializing data structures ... Evaluate trajectory length and go to first frame ... -------------------------------------------------------------------------------- Starting MDDF calculation in parallel: 2 frames will be considered. Number of calculation threads: 1 Solute: 9 atoms belonging to 9 molecules. Solvent: 9 atoms belonging to 9 molecules. ┌ Warning: │ │ Ideal-gas histogram bins with zero samples. │ Increase n_random_samples, number of trajectory frames, and/or bin size. │ └ @ ComplexMixtures -------------------------------------------------------------------------------- ┌ Warning: │ │ Using default values for dbulk, cutoff and/or usecutoff: │ │ dbulk = 10.0 │ cutoff = 10.0 │ usecutoff = false │ │ It is recommended to set bulk_range manually, according to the │ system size and correlations of the distribution function with, │ for example: Options(bulk_range = (8.0, 12.0)) │ └ @ ComplexMixtures -------------------------------------------------------------------------------- Opening trajectory ... -------------------------------------------------------------------------------- Initializing data structures ... Evaluate trajectory length and go to first frame ... -------------------------------------------------------------------------------- Starting MDDF calculation in parallel: 2 frames will be considered. Number of calculation threads: 1 Solute: 9 atoms belonging to 9 molecules. Solvent: 9 atoms belonging to 9 molecules. ┌ Warning: │ │ Ideal-gas histogram bins with zero samples. │ Increase n_random_samples, number of trajectory frames, and/or bin size. │ └ @ ComplexMixtures -------------------------------------------------------------------------------- ┌ Warning: │ │ Using default values for dbulk, cutoff and/or usecutoff: │ │ dbulk = 10.0 │ cutoff = 10.0 │ usecutoff = false │ │ It is recommended to set bulk_range manually, according to the │ system size and correlations of the distribution function with, │ for example: Options(bulk_range = (8.0, 12.0)) │ └ @ ComplexMixtures -------------------------------------------------------------------------------- Initializing data structures ... Evaluate trajectory length and go to first frame ... -------------------------------------------------------------------------------- Starting MDDF calculation in parallel: 2 frames will be considered. Number of calculation threads: 1 Solute: 9 atoms belonging to 9 molecules. Solvent: 9 atoms belonging to 9 molecules. ┌ Warning: │ │ coordination_number_only was set to true, so the MDDF and KB integrals were not computed. │ (to remove this warning use `Options(silent=true)`) │ └ @ ComplexMixtures -------------------------------------------------------------------------------- ┌ Warning: │ │ Using default values for dbulk, cutoff and/or usecutoff: │ │ dbulk = 10.0 │ cutoff = 10.0 │ usecutoff = false │ │ It is recommended to set bulk_range manually, according to the │ system size and correlations of the distribution function with, │ for example: Options(bulk_range = (8.0, 12.0)) │ └ @ ComplexMixtures -------------------------------------------------------------------------------- Initializing data structures ... Evaluate trajectory length and go to first frame ... -------------------------------------------------------------------------------- Starting MDDF calculation in parallel: 2 frames will be considered. Number of calculation threads: 1 Solute: 9 atoms belonging to 9 molecules. Solvent: 9 atoms belonging to 9 molecules. ┌ Warning: │ │ coordination_number_only was set to true, so the MDDF and KB integrals were not computed. │ (to remove this warning use `Options(silent=true)`) │ └ @ ComplexMixtures -------------------------------------------------------------------------------- ┌ Warning: │ │ Using default values for dbulk, cutoff and/or usecutoff: │ │ dbulk = 10.0 │ cutoff = 10.0 │ usecutoff = false │ │ It is recommended to set bulk_range manually, according to the │ system size and correlations of the distribution function with, │ for example: Options(bulk_range = (8.0, 12.0)) │ └ @ ComplexMixtures -------------------------------------------------------------------------------- Initializing data structures ... Evaluate trajectory length and go to first frame ... -------------------------------------------------------------------------------- Starting MDDF calculation in parallel: 2 frames will be considered. Number of calculation threads: 1 Solute: 9 atoms belonging to 9 molecules. Solvent: 9 atoms belonging to 9 molecules. ┌ Warning: │ │ coordination_number_only was set to true, so the MDDF and KB integrals were not computed. │ (to remove this warning use `Options(silent=true)`) │ └ @ ComplexMixtures -------------------------------------------------------------------------------- ┌ Warning: │ │ Using default values for dbulk, cutoff and/or usecutoff: │ │ dbulk = 10.0 │ cutoff = 10.0 │ usecutoff = false │ │ It is recommended to set bulk_range manually, according to the │ system size and correlations of the distribution function with, │ for example: Options(bulk_range = (8.0, 12.0)) │ └ @ ComplexMixtures -------------------------------------------------------------------------------- Initializing data structures ... Evaluate trajectory length and go to first frame ... -------------------------------------------------------------------------------- Starting MDDF calculation in parallel: 2 frames will be considered. Number of calculation threads: 1 Solute: 9 atoms belonging to 9 molecules. Solvent: 9 atoms belonging to 9 molecules. ┌ Warning: │ │ coordination_number_only was set to true, so the MDDF and KB integrals were not computed. │ (to remove this warning use `Options(silent=true)`) │ └ @ ComplexMixtures -------------------------------------------------------------------------------- ┌ Warning: │ │ Using default values for dbulk, cutoff and/or usecutoff: │ │ dbulk = 10.0 │ cutoff = 10.0 │ usecutoff = false │ │ It is recommended to set bulk_range manually, according to the │ system size and correlations of the distribution function with, │ for example: Options(bulk_range = (8.0, 12.0)) │ └ @ ComplexMixtures ┌ Warning: │ │ Using default values for dbulk, cutoff and/or usecutoff: │ │ dbulk = 10.0 │ cutoff = 10.0 │ usecutoff = false │ │ It is recommended to set bulk_range manually, according to the │ system size and correlations of the distribution function with, │ for example: Options(bulk_range = (8.0, 12.0)) │ └ @ ComplexMixtures ┌ Warning: │ │ Using default values for dbulk, cutoff and/or usecutoff: │ │ dbulk = 10.0 │ cutoff = 10.0 │ usecutoff = false │ │ It is recommended to set bulk_range manually, according to the │ system size and correlations of the distribution function with, │ for example: Options(bulk_range = (8.0, 12.0)) │ └ @ ComplexMixtures -------------------------------------------------------------------------------- Opening trajectory ... -------------------------------------------------------------------------------- Initializing data structures ... Evaluate trajectory length and go to first frame ... ┌ Warning: │ │ The memory required for the computation is a large proportion of the total system's memory. │ Depending on resources used by other processes, this may lead to memory exhaustion and │ and the termination of the computation. │ │ - The Results data structure is 0.01 GiB, and 10000000000 copies are required │ for the parallel computation, thus requiring 5.677042529e7 GiB. │ - The total system memory is: 32.0 GiB. │ │ To reduce memory requirements, consider: │ │ - Use the `low_memory = true` option in the call to `mddf`. │ For example: `mddf(trajectory_file, solute, solvent, options; low_memory = true)` │ - Using the predefinition of custom groups of atoms in the solute and solvent. │ See: https://m3g.github.io/ComplexMixtures.jl/stable/selection/#predefinition-of-groups │ - Reducing the number of threads, with the `Options(nthreads=N)` parameter. │ Here, we suggest at most N=1127. │ └ @ ComplexMixtures ┌ Warning: │ │ Using default values for dbulk, cutoff and/or usecutoff: │ │ dbulk = 10.0 │ cutoff = 10.0 │ usecutoff = false │ │ It is recommended to set bulk_range manually, according to the │ system size and correlations of the distribution function with, │ for example: Options(bulk_range = (8.0, 12.0)) │ └ @ ComplexMixtures -------------------------------------------------------------------------------- Opening trajectory ... -------------------------------------------------------------------------------- Initializing data structures ... Evaluate trajectory length and go to first frame ... -------------------------------------------------------------------------------- Starting MDDF calculation in parallel: 3 frames will be considered. Number of calculation threads: 1 Solute: 2534 atoms belonging to 181 molecules. Solvent: 2534 atoms belonging to 181 molecules. Running with low-memory option: - Parallel CellListMap can be used. - Number of parallel minimum-distance computations: 1 - Each minimum-distance computation will use 1 threads. ┌ Warning: │ │ Ideal-gas histogram bins with zero samples. │ Increase n_random_samples, number of trajectory frames, and/or bin size. │ └ @ ComplexMixtures -------------------------------------------------------------------------------- ┌ Warning: │ │ Using default values for dbulk, cutoff and/or usecutoff: │ │ dbulk = 10.0 │ cutoff = 10.0 │ usecutoff = false │ │ It is recommended to set bulk_range manually, according to the │ system size and correlations of the distribution function with, │ for example: Options(bulk_range = (8.0, 12.0)) │ └ @ ComplexMixtures -------------------------------------------------------------------------------- Opening trajectory ... -------------------------------------------------------------------------------- Initializing data structures ... Evaluate trajectory length and go to first frame ... -------------------------------------------------------------------------------- Starting MDDF calculation in parallel: 2 frames will be considered. Number of calculation threads: 1 Solute: 2534 atoms belonging to 181 molecules. Solvent: 2534 atoms belonging to 181 molecules. Running with low-memory option: - Parallel CellListMap can be used. - Number of parallel minimum-distance computations: 1 - Each minimum-distance computation will use 1 threads. ┌ Warning: │ │ Ideal-gas histogram bins with zero samples. │ Increase n_random_samples, number of trajectory frames, and/or bin size. │ └ @ ComplexMixtures -------------------------------------------------------------------------------- ┌ Warning: │ │ Using default values for dbulk, cutoff and/or usecutoff: │ │ dbulk = 10.0 │ cutoff = 10.0 │ usecutoff = false │ │ It is recommended to set bulk_range manually, according to the │ system size and correlations of the distribution function with, │ for example: Options(bulk_range = (8.0, 12.0)) │ └ @ ComplexMixtures -------------------------------------------------------------------------------- Opening trajectory ... -------------------------------------------------------------------------------- Initializing data structures ... Evaluate trajectory length and go to first frame ... -------------------------------------------------------------------------------- Starting MDDF calculation in parallel: 2 frames will be considered. Number of calculation threads: 1 Solute: 2534 atoms belonging to 181 molecules. Solvent: 2534 atoms belonging to 181 molecules. Running with low-memory option: - Parallel CellListMap can be used. - Number of parallel minimum-distance computations: 1 - Each minimum-distance computation will use 1 threads. ┌ Warning: │ │ Ideal-gas histogram bins with zero samples. │ Increase n_random_samples, number of trajectory frames, and/or bin size. │ └ @ ComplexMixtures -------------------------------------------------------------------------------- ┌ Warning: │ │ Using default values for dbulk, cutoff and/or usecutoff: │ │ dbulk = 10.0 │ cutoff = 10.0 │ usecutoff = false │ │ It is recommended to set bulk_range manually, according to the │ system size and correlations of the distribution function with, │ for example: Options(bulk_range = (8.0, 12.0)) │ └ @ ComplexMixtures -------------------------------------------------------------------------------- Opening trajectory ... -------------------------------------------------------------------------------- Initializing data structures ... Evaluate trajectory length and go to first frame ... -------------------------------------------------------------------------------- Starting MDDF calculation in parallel: 2 frames will be considered. Number of calculation threads: 1 Solute: 2534 atoms belonging to 181 molecules. Solvent: 2534 atoms belonging to 181 molecules. Running with low-memory option: - Parallel CellListMap can be used. - Number of parallel minimum-distance computations: 1 - Each minimum-distance computation will use 1 threads. ┌ Warning: │ │ Ideal-gas histogram bins with zero samples. │ Increase n_random_samples, number of trajectory frames, and/or bin size. │ └ @ ComplexMixtures -------------------------------------------------------------------------------- ┌ Warning: │ │ Using default values for dbulk, cutoff and/or usecutoff: │ │ dbulk = 10.0 │ cutoff = 10.0 │ usecutoff = false │ │ It is recommended to set bulk_range manually, according to the │ system size and correlations of the distribution function with, │ for example: Options(bulk_range = (8.0, 12.0)) │ └ @ ComplexMixtures -------------------------------------------------------------------------------- Opening trajectory ... -------------------------------------------------------------------------------- Initializing data structures ... Evaluate trajectory length and go to first frame ... -------------------------------------------------------------------------------- Starting MDDF calculation in parallel: 2 frames will be considered. Number of calculation threads: 1 Solute: 2534 atoms belonging to 181 molecules. Solvent: 2534 atoms belonging to 181 molecules. Running with low-memory option: - Parallel CellListMap can be used. - Number of parallel minimum-distance computations: 1 - Each minimum-distance computation will use 1 threads. ┌ Warning: │ │ Ideal-gas histogram bins with zero samples. │ Increase n_random_samples, number of trajectory frames, and/or bin size. │ └ @ ComplexMixtures -------------------------------------------------------------------------------- ┌ Warning: │ │ Using default values for dbulk, cutoff and/or usecutoff: │ │ dbulk = 10.0 │ cutoff = 10.0 │ usecutoff = false │ │ It is recommended to set bulk_range manually, according to the │ system size and correlations of the distribution function with, │ for example: Options(bulk_range = (8.0, 12.0)) │ └ @ ComplexMixtures -------------------------------------------------------------------------------- Opening trajectory ... -------------------------------------------------------------------------------- Initializing data structures ... Evaluate trajectory length and go to first frame ... -------------------------------------------------------------------------------- Starting MDDF calculation in parallel: 3 frames will be considered. Number of calculation threads: 1 Solute: 2534 atoms belonging to 181 molecules. Solvent: 2534 atoms belonging to 181 molecules. ┌ Warning: │ │ Ideal-gas histogram bins with zero samples. │ Increase n_random_samples, number of trajectory frames, and/or bin size. │ └ @ ComplexMixtures -------------------------------------------------------------------------------- ┌ Warning: │ │ Using default values for dbulk, cutoff and/or usecutoff: │ │ dbulk = 10.0 │ cutoff = 10.0 │ usecutoff = false │ │ It is recommended to set bulk_range manually, according to the │ system size and correlations of the distribution function with, │ for example: Options(bulk_range = (8.0, 12.0)) │ └ @ ComplexMixtures -------------------------------------------------------------------------------- Opening trajectory ... -------------------------------------------------------------------------------- Initializing data structures ... Evaluate trajectory length and go to first frame ... -------------------------------------------------------------------------------- Starting MDDF calculation in parallel: 2 frames will be considered. Number of calculation threads: 1 Solute: 2534 atoms belonging to 181 molecules. Solvent: 2534 atoms belonging to 181 molecules. ┌ Warning: │ │ Ideal-gas histogram bins with zero samples. │ Increase n_random_samples, number of trajectory frames, and/or bin size. │ └ @ ComplexMixtures -------------------------------------------------------------------------------- ┌ Warning: │ │ Using default values for dbulk, cutoff and/or usecutoff: │ │ dbulk = 10.0 │ cutoff = 10.0 │ usecutoff = false │ │ It is recommended to set bulk_range manually, according to the │ system size and correlations of the distribution function with, │ for example: Options(bulk_range = (8.0, 12.0)) │ └ @ ComplexMixtures -------------------------------------------------------------------------------- Opening trajectory ... -------------------------------------------------------------------------------- Initializing data structures ... Evaluate trajectory length and go to first frame ... -------------------------------------------------------------------------------- Starting MDDF calculation in parallel: 2 frames will be considered. Number of calculation threads: 1 Solute: 2534 atoms belonging to 181 molecules. Solvent: 2534 atoms belonging to 181 molecules. ┌ Warning: │ │ Ideal-gas histogram bins with zero samples. │ Increase n_random_samples, number of trajectory frames, and/or bin size. │ └ @ ComplexMixtures -------------------------------------------------------------------------------- ┌ Warning: │ │ Using default values for dbulk, cutoff and/or usecutoff: │ │ dbulk = 10.0 │ cutoff = 10.0 │ usecutoff = false │ │ It is recommended to set bulk_range manually, according to the │ system size and correlations of the distribution function with, │ for example: Options(bulk_range = (8.0, 12.0)) │ └ @ ComplexMixtures -------------------------------------------------------------------------------- Opening trajectory ... -------------------------------------------------------------------------------- Initializing data structures ... Evaluate trajectory length and go to first frame ... -------------------------------------------------------------------------------- Starting MDDF calculation in parallel: 2 frames will be considered. Number of calculation threads: 1 Solute: 2534 atoms belonging to 181 molecules. Solvent: 2534 atoms belonging to 181 molecules. ┌ Warning: │ │ Ideal-gas histogram bins with zero samples. │ Increase n_random_samples, number of trajectory frames, and/or bin size. │ └ @ ComplexMixtures -------------------------------------------------------------------------------- ┌ Warning: │ │ Using default values for dbulk, cutoff and/or usecutoff: │ │ dbulk = 10.0 │ cutoff = 10.0 │ usecutoff = false │ │ It is recommended to set bulk_range manually, according to the │ system size and correlations of the distribution function with, │ for example: Options(bulk_range = (8.0, 12.0)) │ └ @ ComplexMixtures -------------------------------------------------------------------------------- Opening trajectory ... -------------------------------------------------------------------------------- Initializing data structures ... Evaluate trajectory length and go to first frame ... -------------------------------------------------------------------------------- Starting MDDF calculation in parallel: 2 frames will be considered. Number of calculation threads: 1 Solute: 2534 atoms belonging to 181 molecules. Solvent: 2534 atoms belonging to 181 molecules. ┌ Warning: │ │ Ideal-gas histogram bins with zero samples. │ Increase n_random_samples, number of trajectory frames, and/or bin size. │ └ @ ComplexMixtures -------------------------------------------------------------------------------- ┌ Warning: │ │ Using default values for dbulk, cutoff and/or usecutoff: │ │ dbulk = 10.0 │ cutoff = 10.0 │ usecutoff = false │ │ It is recommended to set bulk_range manually, according to the │ system size and correlations of the distribution function with, │ for example: Options(bulk_range = (8.0, 12.0)) │ └ @ ComplexMixtures -------------------------------------------------------------------------------- Opening trajectory ... -------------------------------------------------------------------------------- Initializing data structures ... Evaluate trajectory length and go to first frame ... -------------------------------------------------------------------------------- Starting MDDF calculation in parallel: 3 frames will be considered. Number of calculation threads: 1 Solute: 2534 atoms belonging to 181 molecules. Solvent: 2534 atoms belonging to 181 molecules. Running with low-memory option: - Parallel CellListMap can be used. - Number of parallel minimum-distance computations: 1 - Each minimum-distance computation will use 1 threads. ┌ Warning: │ │ Ideal-gas histogram bins with zero samples. │ Increase n_random_samples, number of trajectory frames, and/or bin size. │ └ @ ComplexMixtures -------------------------------------------------------------------------------- ┌ Warning: │ │ Using default values for dbulk, cutoff and/or usecutoff: │ │ dbulk = 10.0 │ cutoff = 10.0 │ usecutoff = false │ │ It is recommended to set bulk_range manually, according to the │ system size and correlations of the distribution function with, │ for example: Options(bulk_range = (8.0, 12.0)) │ └ @ ComplexMixtures -------------------------------------------------------------------------------- Opening trajectory ... -------------------------------------------------------------------------------- Initializing data structures ... Evaluate trajectory length and go to first frame ... -------------------------------------------------------------------------------- Starting MDDF calculation in parallel: 2 frames will be considered. Number of calculation threads: 1 Solute: 2534 atoms belonging to 181 molecules. Solvent: 2534 atoms belonging to 181 molecules. Running with low-memory option: - Parallel CellListMap can be used. - Number of parallel minimum-distance computations: 1 - Each minimum-distance computation will use 1 threads. ┌ Warning: │ │ Ideal-gas histogram bins with zero samples. │ Increase n_random_samples, number of trajectory frames, and/or bin size. │ └ @ ComplexMixtures -------------------------------------------------------------------------------- ┌ Warning: │ │ Using default values for dbulk, cutoff and/or usecutoff: │ │ dbulk = 10.0 │ cutoff = 10.0 │ usecutoff = false │ │ It is recommended to set bulk_range manually, according to the │ system size and correlations of the distribution function with, │ for example: Options(bulk_range = (8.0, 12.0)) │ └ @ ComplexMixtures -------------------------------------------------------------------------------- Opening trajectory ... -------------------------------------------------------------------------------- Initializing data structures ... Evaluate trajectory length and go to first frame ... -------------------------------------------------------------------------------- Starting MDDF calculation in parallel: 2 frames will be considered. Number of calculation threads: 1 Solute: 2534 atoms belonging to 181 molecules. Solvent: 2534 atoms belonging to 181 molecules. Running with low-memory option: - Parallel CellListMap can be used. - Number of parallel minimum-distance computations: 1 - Each minimum-distance computation will use 1 threads. ┌ Warning: │ │ Ideal-gas histogram bins with zero samples. │ Increase n_random_samples, number of trajectory frames, and/or bin size. │ └ @ ComplexMixtures -------------------------------------------------------------------------------- ┌ Warning: │ │ Using default values for dbulk, cutoff and/or usecutoff: │ │ dbulk = 10.0 │ cutoff = 10.0 │ usecutoff = false │ │ It is recommended to set bulk_range manually, according to the │ system size and correlations of the distribution function with, │ for example: Options(bulk_range = (8.0, 12.0)) │ └ @ ComplexMixtures -------------------------------------------------------------------------------- Opening trajectory ... -------------------------------------------------------------------------------- Initializing data structures ... Evaluate trajectory length and go to first frame ... -------------------------------------------------------------------------------- Starting MDDF calculation in parallel: 2 frames will be considered. Number of calculation threads: 1 Solute: 2534 atoms belonging to 181 molecules. Solvent: 2534 atoms belonging to 181 molecules. Running with low-memory option: - Parallel CellListMap can be used. - Number of parallel minimum-distance computations: 1 - Each minimum-distance computation will use 1 threads. ┌ Warning: │ │ Ideal-gas histogram bins with zero samples. │ Increase n_random_samples, number of trajectory frames, and/or bin size. │ └ @ ComplexMixtures -------------------------------------------------------------------------------- ┌ Warning: │ │ Using default values for dbulk, cutoff and/or usecutoff: │ │ dbulk = 10.0 │ cutoff = 10.0 │ usecutoff = false │ │ It is recommended to set bulk_range manually, according to the │ system size and correlations of the distribution function with, │ for example: Options(bulk_range = (8.0, 12.0)) │ └ @ ComplexMixtures -------------------------------------------------------------------------------- Opening trajectory ... -------------------------------------------------------------------------------- Initializing data structures ... Evaluate trajectory length and go to first frame ... -------------------------------------------------------------------------------- Starting MDDF calculation in parallel: 2 frames will be considered. Number of calculation threads: 1 Solute: 2534 atoms belonging to 181 molecules. Solvent: 2534 atoms belonging to 181 molecules. Running with low-memory option: - Parallel CellListMap can be used. - Number of parallel minimum-distance computations: 1 - Each minimum-distance computation will use 1 threads. ┌ Warning: │ │ Ideal-gas histogram bins with zero samples. │ Increase n_random_samples, number of trajectory frames, and/or bin size. │ └ @ ComplexMixtures -------------------------------------------------------------------------------- ┌ Warning: │ │ Using default values for dbulk, cutoff and/or usecutoff: │ │ dbulk = 10.0 │ cutoff = 10.0 │ usecutoff = false │ │ It is recommended to set bulk_range manually, according to the │ system size and correlations of the distribution function with, │ for example: Options(bulk_range = (8.0, 12.0)) │ └ @ ComplexMixtures -------------------------------------------------------------------------------- Opening trajectory ... -------------------------------------------------------------------------------- Initializing data structures ... Evaluate trajectory length and go to first frame ... -------------------------------------------------------------------------------- Starting MDDF calculation in parallel: 3 frames will be considered. Number of calculation threads: 1 Solute: 2534 atoms belonging to 181 molecules. Solvent: 2534 atoms belonging to 181 molecules. ┌ Warning: │ │ Ideal-gas histogram bins with zero samples. │ Increase n_random_samples, number of trajectory frames, and/or bin size. │ └ @ ComplexMixtures -------------------------------------------------------------------------------- ┌ Warning: │ │ Using default values for dbulk, cutoff and/or usecutoff: │ │ dbulk = 10.0 │ cutoff = 10.0 │ usecutoff = false │ │ It is recommended to set bulk_range manually, according to the │ system size and correlations of the distribution function with, │ for example: Options(bulk_range = (8.0, 12.0)) │ └ @ ComplexMixtures -------------------------------------------------------------------------------- Opening trajectory ... -------------------------------------------------------------------------------- Initializing data structures ... Evaluate trajectory length and go to first frame ... -------------------------------------------------------------------------------- Starting MDDF calculation in parallel: 2 frames will be considered. Number of calculation threads: 1 Solute: 2534 atoms belonging to 181 molecules. Solvent: 2534 atoms belonging to 181 molecules. ┌ Warning: │ │ Ideal-gas histogram bins with zero samples. │ Increase n_random_samples, number of trajectory frames, and/or bin size. │ └ @ ComplexMixtures -------------------------------------------------------------------------------- ┌ Warning: │ │ Using default values for dbulk, cutoff and/or usecutoff: │ │ dbulk = 10.0 │ cutoff = 10.0 │ usecutoff = false │ │ It is recommended to set bulk_range manually, according to the │ system size and correlations of the distribution function with, │ for example: Options(bulk_range = (8.0, 12.0)) │ └ @ ComplexMixtures -------------------------------------------------------------------------------- Opening trajectory ... -------------------------------------------------------------------------------- Initializing data structures ... Evaluate trajectory length and go to first frame ... -------------------------------------------------------------------------------- Starting MDDF calculation in parallel: 2 frames will be considered. Number of calculation threads: 1 Solute: 2534 atoms belonging to 181 molecules. Solvent: 2534 atoms belonging to 181 molecules. ┌ Warning: │ │ Ideal-gas histogram bins with zero samples. │ Increase n_random_samples, number of trajectory frames, and/or bin size. │ └ @ ComplexMixtures -------------------------------------------------------------------------------- ┌ Warning: │ │ Using default values for dbulk, cutoff and/or usecutoff: │ │ dbulk = 10.0 │ cutoff = 10.0 │ usecutoff = false │ │ It is recommended to set bulk_range manually, according to the │ system size and correlations of the distribution function with, │ for example: Options(bulk_range = (8.0, 12.0)) │ └ @ ComplexMixtures -------------------------------------------------------------------------------- Opening trajectory ... -------------------------------------------------------------------------------- Initializing data structures ... Evaluate trajectory length and go to first frame ... -------------------------------------------------------------------------------- Starting MDDF calculation in parallel: 2 frames will be considered. Number of calculation threads: 1 Solute: 2534 atoms belonging to 181 molecules. Solvent: 2534 atoms belonging to 181 molecules. ┌ Warning: │ │ Ideal-gas histogram bins with zero samples. │ Increase n_random_samples, number of trajectory frames, and/or bin size. │ └ @ ComplexMixtures -------------------------------------------------------------------------------- ┌ Warning: │ │ Using default values for dbulk, cutoff and/or usecutoff: │ │ dbulk = 10.0 │ cutoff = 10.0 │ usecutoff = false │ │ It is recommended to set bulk_range manually, according to the │ system size and correlations of the distribution function with, │ for example: Options(bulk_range = (8.0, 12.0)) │ └ @ ComplexMixtures -------------------------------------------------------------------------------- Opening trajectory ... -------------------------------------------------------------------------------- Initializing data structures ... Evaluate trajectory length and go to first frame ... -------------------------------------------------------------------------------- Starting MDDF calculation in parallel: 2 frames will be considered. Number of calculation threads: 1 Solute: 2534 atoms belonging to 181 molecules. Solvent: 2534 atoms belonging to 181 molecules. ┌ Warning: │ │ Ideal-gas histogram bins with zero samples. │ Increase n_random_samples, number of trajectory frames, and/or bin size. │ └ @ ComplexMixtures -------------------------------------------------------------------------------- ┌ Warning: │ │ Using default values for dbulk, cutoff and/or usecutoff: │ │ dbulk = 10.0 │ cutoff = 10.0 │ usecutoff = false │ │ It is recommended to set bulk_range manually, according to the │ system size and correlations of the distribution function with, │ for example: Options(bulk_range = (8.0, 12.0)) │ └ @ ComplexMixtures -------------------------------------------------------------------------------- Initializing data structures ... Evaluate trajectory length and go to first frame ... -------------------------------------------------------------------------------- Starting MDDF calculation in parallel: 20 frames will be considered. Number of calculation threads: 1 Solute: 1463 atoms belonging to 1 molecule. Solvent: 2534 atoms belonging to 181 molecules. ┌ Warning: │ │ coordination_number_only was set to true, so the MDDF and KB integrals were not computed. │ (to remove this warning use `Options(silent=true)`) │ └ @ ComplexMixtures -------------------------------------------------------------------------------- OUTPUT FILES: Wrote total MDDF to output file: /tmp/jl_UVYViHSJG9.dat Wrote solute group MDDF contributions to file: /tmp/jl_UVYViHSJG9-GROUP_CONTRIBUTIONS_SOLUTE.dat Wrote solute group MDDF contributions to file: /tmp/jl_UVYViHSJG9-GROUP_CONTRIBUTIONS_SOLVENT.dat OUTPUT FILES: Wrote total MDDF to output file: /tmp/jl_y1uxm3gfWR.dat Wrote solute group MDDF contributions to file: /tmp/jl_y1uxm3gfWR-GROUP_CONTRIBUTIONS_SOLUTE.dat Wrote solute group MDDF contributions to file: /tmp/jl_y1uxm3gfWR-GROUP_CONTRIBUTIONS_SOLVENT.dat OUTPUT FILES: Wrote total MDDF to output file: /tmp/jl_iRIvSlEZmd.dat Wrote solute group MDDF contributions to file: /tmp/jl_iRIvSlEZmd-GROUP_CONTRIBUTIONS_SOLUTE.dat Wrote solute group MDDF contributions to file: /tmp/jl_iRIvSlEZmd-GROUP_CONTRIBUTIONS_SOLVENT.dat ┌ Warning: │ │ Using default values for dbulk, cutoff and/or usecutoff: │ │ dbulk = 10.0 │ cutoff = 10.0 │ usecutoff = false │ │ It is recommended to set bulk_range manually, according to the │ system size and correlations of the distribution function with, │ for example: Options(bulk_range = (8.0, 12.0)) │ └ @ ComplexMixtures -------------------------------------------------------------------------------- Initializing data structures ... Evaluate trajectory length and go to first frame ... ┌ Warning: │ │ Using default values for dbulk, cutoff and/or usecutoff: │ │ dbulk = 10.0 │ cutoff = 10.0 │ usecutoff = false │ │ It is recommended to set bulk_range manually, according to the │ system size and correlations of the distribution function with, │ for example: Options(bulk_range = (8.0, 12.0)) │ └ @ ComplexMixtures -------------------------------------------------------------------------------- Initializing data structures ... Evaluate trajectory length and go to first frame ... ┌ Warning: │ │ Using default values for dbulk, cutoff and/or usecutoff: │ │ dbulk = 10.0 │ cutoff = 10.0 │ usecutoff = false │ │ It is recommended to set bulk_range manually, according to the │ system size and correlations of the distribution function with, │ for example: Options(bulk_range = (8.0, 12.0)) │ └ @ ComplexMixtures -------------------------------------------------------------------------------- Initializing data structures ... Evaluate trajectory length and go to first frame ... ┌ Warning: │ │ Using default values for dbulk, cutoff and/or usecutoff: │ │ dbulk = 10.0 │ cutoff = 10.0 │ usecutoff = false │ │ It is recommended to set bulk_range manually, according to the │ system size and correlations of the distribution function with, │ for example: Options(bulk_range = (8.0, 12.0)) │ └ @ ComplexMixtures -------------------------------------------------------------------------------- Initializing data structures ... Evaluate trajectory length and go to first frame ... ┌ Warning: │ │ Using default values for dbulk, cutoff and/or usecutoff: │ │ dbulk = 10.0 │ cutoff = 10.0 │ usecutoff = false │ │ It is recommended to set bulk_range manually, according to the │ system size and correlations of the distribution function with, │ for example: Options(bulk_range = (8.0, 12.0)) │ └ @ ComplexMixtures -------------------------------------------------------------------------------- Initializing data structures ... Evaluate trajectory length and go to first frame ... -------------------------------------------------------------------------------- Starting MDDF calculation in parallel: 1 frames will be considered. Number of calculation threads: 1 Solute: 1 atom belonging to 1 molecule. Solvent: 1 atom belonging to 1 molecule. ┌ Warning: │ │ Ideal-gas histogram bins with zero samples. │ Increase n_random_samples, number of trajectory frames, and/or bin size. │ └ @ ComplexMixtures -------------------------------------------------------------------------------- ┌ Warning: │ │ Using default values for dbulk, cutoff and/or usecutoff: │ │ dbulk = 10.0 │ cutoff = 10.0 │ usecutoff = false │ │ It is recommended to set bulk_range manually, according to the │ system size and correlations of the distribution function with, │ for example: Options(bulk_range = (8.0, 12.0)) │ └ @ ComplexMixtures -------------------------------------------------------------------------------- Initializing data structures ... Evaluate trajectory length and go to first frame ... -------------------------------------------------------------------------------- Starting MDDF calculation in parallel: 1 frames will be considered. Number of calculation threads: 1 Solute: 1 atom belonging to 1 molecule. Solvent: 1 atom belonging to 1 molecule. ┌ Warning: │ │ Ideal-gas histogram bins with zero samples. │ Increase n_random_samples, number of trajectory frames, and/or bin size. │ └ @ ComplexMixtures -------------------------------------------------------------------------------- ┌ Warning: │ │ Using default values for dbulk, cutoff and/or usecutoff: │ │ dbulk = 10.0 │ cutoff = 10.0 │ usecutoff = false │ │ It is recommended to set bulk_range manually, according to the │ system size and correlations of the distribution function with, │ for example: Options(bulk_range = (8.0, 12.0)) │ └ @ ComplexMixtures -------------------------------------------------------------------------------- Initializing data structures ... Evaluate trajectory length and go to first frame ... -------------------------------------------------------------------------------- Starting MDDF calculation in parallel: 1 frames will be considered. Number of calculation threads: 1 Solute: 1 atom belonging to 1 molecule. Solvent: 1 atom belonging to 1 molecule. ┌ Warning: │ │ Ideal-gas histogram bins with zero samples. │ Increase n_random_samples, number of trajectory frames, and/or bin size. │ └ @ ComplexMixtures -------------------------------------------------------------------------------- ┌ Warning: │ │ Frame weights and file weights differ, because crustom frame weights were provided. │ └ @ ComplexMixtures ┌ Warning: │ │ Using default values for dbulk, cutoff and/or usecutoff: │ │ dbulk = 10.0 │ cutoff = 10.0 │ usecutoff = false │ │ It is recommended to set bulk_range manually, according to the │ system size and correlations of the distribution function with, │ for example: Options(bulk_range = (8.0, 12.0)) │ └ @ ComplexMixtures ┌ Warning: │ │ Using default values for dbulk, cutoff and/or usecutoff: │ │ dbulk = 10.0 │ cutoff = 10.0 │ usecutoff = false │ │ It is recommended to set bulk_range manually, according to the │ system size and correlations of the distribution function with, │ for example: Options(bulk_range = (8.0, 12.0)) │ └ @ ComplexMixtures Precompiling Plotting... 16668.7 ms ✓ Plots → UnitfulExt 15399.0 ms ✓ PDBTools → Plotting 2 dependencies successfully precompiled in 34 seconds. 216 already precompiled. Progress: 8%|███▏ | ETA: 0:00:30 Progress: 100%|█████████████████████████████████████████| Time: 0:00:03 ┌ Warning: One-letter code for residue(s) not found. Using full residue name. └ @ Plotting ┌ Warning: │ │ Using default values for dbulk, cutoff and/or usecutoff: │ │ dbulk = 10.0 │ cutoff = 10.0 │ usecutoff = false │ │ It is recommended to set bulk_range manually, according to the │ system size and correlations of the distribution function with, │ for example: Options(bulk_range = (8.0, 12.0)) │ └ @ ComplexMixtures ┌ Warning: │ │ Using default values for dbulk, cutoff and/or usecutoff: │ │ dbulk = 10.0 │ cutoff = 10.0 │ usecutoff = false │ │ It is recommended to set bulk_range manually, according to the │ system size and correlations of the distribution function with, │ for example: Options(bulk_range = (8.0, 12.0)) │ └ @ ComplexMixtures -------------------------------------------------------------------------------- Initializing data structures ... Evaluate trajectory length and go to first frame ... -------------------------------------------------------------------------------- Starting MDDF calculation in parallel: 5 frames will be considered. Number of calculation threads: 1 Solute: 1463 atoms belonging to 1 molecule. Solvent: 2534 atoms belonging to 181 molecules. Progress: 80%|████████████████████████████████▊ | ETA: 0:00:00 Progress: 100%|█████████████████████████████████████████| Time: 0:00:01 ┌ Warning: │ │ Ideal-gas histogram bins with zero samples. │ Increase n_random_samples, number of trajectory frames, and/or bin size. │ └ @ ComplexMixtures -------------------------------------------------------------------------------- ┌ Warning: │ │ Using default values for dbulk, cutoff and/or usecutoff: │ │ dbulk = 10.0 │ cutoff = 10.0 │ usecutoff = false │ │ It is recommended to set bulk_range manually, according to the │ system size and correlations of the distribution function with, │ for example: Options(bulk_range = (8.0, 12.0)) │ └ @ ComplexMixtures -------------------------------------------------------------------------------- Initializing data structures ... Evaluate trajectory length and go to first frame ... -------------------------------------------------------------------------------- Starting MDDF calculation in parallel: 5 frames will be considered. Number of calculation threads: 1 Solute: 1463 atoms belonging to 1 molecule. Solvent: 2534 atoms belonging to 181 molecules. ┌ Warning: │ │ Ideal-gas histogram bins with zero samples. │ Increase n_random_samples, number of trajectory frames, and/or bin size. │ └ @ ComplexMixtures -------------------------------------------------------------------------------- ┌ Warning: │ │ Using default values for dbulk, cutoff and/or usecutoff: │ │ dbulk = 10.0 │ cutoff = 10.0 │ usecutoff = false │ │ It is recommended to set bulk_range manually, according to the │ system size and correlations of the distribution function with, │ for example: Options(bulk_range = (8.0, 12.0)) │ └ @ ComplexMixtures -------------------------------------------------------------------------------- Initializing data structures ... Evaluate trajectory length and go to first frame ... -------------------------------------------------------------------------------- Starting MDDF calculation in parallel: 5 frames will be considered. Number of calculation threads: 1 Solute: 72 atoms belonging to 1 molecule. Solvent: 2534 atoms belonging to 181 molecules. ┌ Warning: │ │ Ideal-gas histogram bins with zero samples. │ Increase n_random_samples, number of trajectory frames, and/or bin size. │ └ @ ComplexMixtures -------------------------------------------------------------------------------- ┌ Warning: │ │ Using default values for dbulk, cutoff and/or usecutoff: │ │ dbulk = 10.0 │ cutoff = 10.0 │ usecutoff = false │ │ It is recommended to set bulk_range manually, according to the │ system size and correlations of the distribution function with, │ for example: Options(bulk_range = (8.0, 12.0)) │ └ @ ComplexMixtures -------------------------------------------------------------------------------- Initializing data structures ... Evaluate trajectory length and go to first frame ... -------------------------------------------------------------------------------- Starting MDDF calculation in parallel: 20 frames will be considered. Number of calculation threads: 1 Solute: 3 atoms belonging to 1 molecule. Solvent: 58011 atoms belonging to 19337 molecules. Progress: 10%|████▏ | ETA: 0:00:10 Progress: 25%|██████████▎ | ETA: 0:00:07 Progress: 40%|████████████████▍ | ETA: 0:00:06 Progress: 55%|██████████████████████▌ | ETA: 0:00:04 Progress: 70%|████████████████████████████▊ | ETA: 0:00:03 Progress: 85%|██████████████████████████████████▉ | ETA: 0:00:01 Progress: 100%|█████████████████████████████████████████| Time: 0:00:08 ┌ Warning: │ │ Ideal-gas histogram bins with zero samples. │ Increase n_random_samples, number of trajectory frames, and/or bin size. │ └ @ ComplexMixtures -------------------------------------------------------------------------------- ┌ Warning: │ │ Group indices are not sorted. The array will be sorted for faster search. │ └ @ ComplexMixtures ┌ Warning: │ │ Group indices are not sorted. The array will be sorted for faster search. │ └ @ ComplexMixtures ┌ Warning: │ │ Group indices are not sorted. The array will be sorted for faster search. │ └ @ ComplexMixtures ┌ Warning: │ │ Using default values for dbulk, cutoff and/or usecutoff: │ │ dbulk = 10.0 │ cutoff = 10.0 │ usecutoff = false │ │ It is recommended to set bulk_range manually, according to the │ system size and correlations of the distribution function with, │ for example: Options(bulk_range = (8.0, 12.0)) │ └ @ ComplexMixtures -------------------------------------------------------------------------------- Initializing data structures ... Evaluate trajectory length and go to first frame ... -------------------------------------------------------------------------------- Starting MDDF calculation in parallel: 20 frames will be considered. Number of calculation threads: 1 Solute: 3 atoms belonging to 1 molecule. Solvent: 58011 atoms belonging to 19337 molecules. Progress: 20%|████████▎ | ETA: 0:00:05 Progress: 35%|██████████████▍ | ETA: 0:00:05 Progress: 50%|████████████████████▌ | ETA: 0:00:04 Progress: 65%|██████████████████████████▋ | ETA: 0:00:03 Progress: 80%|████████████████████████████████▊ | ETA: 0:00:02 Progress: 95%|███████████████████████████████████████ | ETA: 0:00:00 Progress: 100%|█████████████████████████████████████████| Time: 0:00:08 ┌ Warning: │ │ Ideal-gas histogram bins with zero samples. │ Increase n_random_samples, number of trajectory frames, and/or bin size. │ └ @ ComplexMixtures -------------------------------------------------------------------------------- ┌ Warning: │ │ Group indices are not sorted. The array will be sorted for faster search. │ └ @ ComplexMixtures ┌ Warning: │ │ Group indices are not sorted. The array will be sorted for faster search. │ └ @ ComplexMixtures ┌ Warning: │ │ Group indices are not sorted. The array will be sorted for faster search. │ └ @ ComplexMixtures ┌ Warning: │ │ Group indices are not sorted. The array will be sorted for faster search. │ └ @ ComplexMixtures ┌ Warning: │ │ Group indices are not sorted. The array will be sorted for faster search. │ └ @ ComplexMixtures ┌ Warning: │ │ Vector of group atom indices was provided but vector of group names is empty. │ The group contributions will be only retrieved by the group indices. │ └ @ ComplexMixtures Building grid... 0%| | ETA: 6:08:57 Building grid... 37%|█████████████ | ETA: 0:00:04 Building grid... 100%|███████████████████████████████████| Time: 0:00:02 Grid written to /tmp/jl_EtQTklwP4p.pdb ┌ Warning: │ │ Vector of group atom indices was provided but vector of group names is empty. │ The group contributions will be only retrieved by the group indices. │ └ @ ComplexMixtures ┌ Warning: │ │ Group indices are not sorted. The array will be sorted for faster search. │ └ @ ComplexMixtures ┌ Warning: │ │ Vector of group atom indices was provided but vector of group names is empty. │ The group contributions will be only retrieved by the group indices. │ └ @ ComplexMixtures ┌ Warning: │ │ Vector of group atom indices was provided but vector of group names is empty. │ The group contributions will be only retrieved by the group indices. │ └ @ ComplexMixtures ┌ Warning: │ │ Vector of group atom indices was provided but vector of group names is empty. │ The group contributions will be only retrieved by the group indices. │ └ @ ComplexMixtures ┌ Warning: │ │ Using default values for dbulk, cutoff and/or usecutoff: │ │ dbulk = 10.0 │ cutoff = 10.0 │ usecutoff = false │ │ It is recommended to set bulk_range manually, according to the │ system size and correlations of the distribution function with, │ for example: Options(bulk_range = (8.0, 12.0)) │ └ @ ComplexMixtures ┌ Warning: │ │ Using default values for dbulk, cutoff and/or usecutoff: │ │ dbulk = 10.0 │ cutoff = 10.0 │ usecutoff = false │ │ It is recommended to set bulk_range manually, according to the │ system size and correlations of the distribution function with, │ for example: Options(bulk_range = (8.0, 12.0)) │ └ @ ComplexMixtures ┌ Warning: │ │ Using default values for dbulk, cutoff and/or usecutoff: │ │ dbulk = 10.0 │ cutoff = 10.0 │ usecutoff = false │ │ It is recommended to set bulk_range manually, according to the │ system size and correlations of the distribution function with, │ for example: Options(bulk_range = (8.0, 12.0)) │ └ @ ComplexMixtures ┌ Warning: │ │ Using default values for dbulk, cutoff and/or usecutoff: │ │ dbulk = 10.0 │ cutoff = 12.0 │ usecutoff = true │ │ It is recommended to set bulk_range manually, according to the │ system size and correlations of the distribution function with, │ for example: Options(bulk_range = (8.0, 12.0)) │ └ @ ComplexMixtures ┌ Warning: │ │ Using default values for dbulk, cutoff and/or usecutoff: │ │ dbulk = 10.0 │ cutoff = 14.0 │ usecutoff = true │ │ It is recommended to set bulk_range manually, according to the │ system size and correlations of the distribution function with, │ for example: Options(bulk_range = (8.0, 12.0)) │ └ @ ComplexMixtures ┌ Warning: │ │ Using default values for dbulk, cutoff and/or usecutoff: │ │ dbulk = 10.0 │ cutoff = 10.0 │ usecutoff = false │ │ It is recommended to set bulk_range manually, according to the │ system size and correlations of the distribution function with, │ for example: Options(bulk_range = (8.0, 12.0)) │ └ @ ComplexMixtures ┌ Warning: │ │ The residue tick labels in the two ResidueContributions objects differ. │ The resulting tick labels will be from the first object. │ └ @ ComplexMixtures ┌ Warning: │ │ The residue tick labels in the two ResidueContributions objects differ. │ The resulting tick labels will be from the first object. │ └ @ ComplexMixtures ┌ Warning: │ │ The residue tick labels in the two ResidueContributions objects differ. │ The resulting tick labels will be from the first object. │ └ @ ComplexMixtures ┌ Warning: │ │ The residue tick labels in the two ResidueContributions objects differ. │ The resulting tick labels will be from the first object. │ └ @ ComplexMixtures ┌ Warning: │ │ The residue tick labels in the two ResidueContributions objects differ. │ The resulting tick labels will be from the first object. │ └ @ ComplexMixtures ┌ Warning: │ │ The residue tick labels in the two ResidueContributions objects differ. │ The resulting tick labels will be from the first object. │ └ @ ComplexMixtures ┌ Warning: │ │ The residue tick labels in the two ResidueContributions objects differ. │ The resulting tick labels will be from the first object. │ └ @ ComplexMixtures ┌ Warning: │ │ The residue tick labels in the two ResidueContributions objects differ. │ The resulting tick labels will be from the first object. │ └ @ ComplexMixtures ┌ Warning: │ │ The residue tick labels in the two ResidueContributions objects differ. │ The resulting tick labels will be from the first object. │ └ @ ComplexMixtures ┌ Warning: │ │ The residue tick labels in the two ResidueContributions objects differ. │ The resulting tick labels will be from the first object. │ └ @ ComplexMixtures ┌ Warning: │ │ The residue tick labels in the two ResidueContributions objects differ. │ The resulting tick labels will be from the first object. │ └ @ ComplexMixtures ┌ Warning: │ │ The residue tick labels in the two ResidueContributions objects differ. │ The resulting tick labels will be from the first object. │ └ @ ComplexMixtures ┌ Warning: │ │ The residue tick labels in the two ResidueContributions objects differ. │ The resulting tick labels will be from the first object. │ └ @ ComplexMixtures ┌ Warning: │ │ The residue tick labels in the two ResidueContributions objects differ. │ The resulting tick labels will be from the first object. │ └ @ ComplexMixtures ┌ Warning: │ │ The residue tick labels in the two ResidueContributions objects differ. │ The resulting tick labels will be from the first object. │ └ @ ComplexMixtures ┌ Warning: │ │ The residue tick labels in the two ResidueContributions objects differ. │ The resulting tick labels will be from the first object. │ └ @ ComplexMixtures ┌ Warning: │ │ The residue tick labels in the two ResidueContributions objects differ. │ The resulting tick labels will be from the first object. │ └ @ ComplexMixtures ┌ Warning: │ │ The residue tick labels in the two ResidueContributions objects differ. │ The resulting tick labels will be from the first object. │ └ @ ComplexMixtures ┌ Warning: │ │ The residue tick labels in the two ResidueContributions objects differ. │ The resulting tick labels will be from the first object. │ └ @ ComplexMixtures ┌ Warning: │ │ The residue tick labels in the two ResidueContributions objects differ. │ The resulting tick labels will be from the first object. │ └ @ ComplexMixtures ┌ Warning: │ │ The residue tick labels in the two ResidueContributions objects differ. │ The resulting tick labels will be from the first object. │ └ @ ComplexMixtures ┌ Warning: │ │ The residue tick labels in the two ResidueContributions objects differ. │ The resulting tick labels will be from the first object. │ └ @ ComplexMixtures ┌ Warning: │ │ The residue tick labels in the two ResidueContributions objects differ. │ The resulting tick labels will be from the first object. │ └ @ ComplexMixtures ┌ Warning: │ │ The residue tick labels in the two ResidueContributions objects differ. │ The resulting tick labels will be from the first object. │ └ @ ComplexMixtures ┌ Warning: │ │ The residue tick labels in the two ResidueContributions objects differ. │ The resulting tick labels will be from the first object. │ └ @ ComplexMixtures ┌ Warning: │ │ The residue tick labels in the two ResidueContributions objects differ. │ The resulting tick labels will be from the first object. │ └ @ ComplexMixtures ┌ Warning: │ │ The residue tick labels in the two ResidueContributions objects differ. │ The resulting tick labels will be from the first object. │ └ @ ComplexMixtures ┌ Warning: │ │ The residue tick labels in the two ResidueContributions objects differ. │ The resulting tick labels will be from the first object. │ └ @ ComplexMixtures ┌ Warning: │ │ The residue tick labels in the two ResidueContributions objects differ. │ The resulting tick labels will be from the first object. │ └ @ ComplexMixtures ┌ Warning: │ │ Using default values for dbulk, cutoff and/or usecutoff: │ │ dbulk = 10.0 │ cutoff = 10.0 │ usecutoff = false │ │ It is recommended to set bulk_range manually, according to the │ system size and correlations of the distribution function with, │ for example: Options(bulk_range = (8.0, 12.0)) │ └ @ ComplexMixtures -------------------------------------------------------------------------------- Initializing data structures ... Evaluate trajectory length and go to first frame ... -------------------------------------------------------------------------------- Starting MDDF calculation in parallel: 2 frames will be considered. Number of calculation threads: 1 Solute: 1463 atoms belonging to 1 molecule. Solvent: 58014 atoms belonging to 19338 molecules. ┌ Warning: │ │ Ideal-gas histogram bins with zero samples. │ Increase n_random_samples, number of trajectory frames, and/or bin size. │ └ @ ComplexMixtures -------------------------------------------------------------------------------- Test Summary: | Pass Error Total Time Package | 3776 1 3777 13m01.7s test/allocations.jl | 10 10 45.6s src/tools/gr.jl | 3 3 1m50.8s src/Trajectory.jl | 35 35 9.4s test/show_methods.jl | 7 1 8 12.5s show methods | 7 1 8 12.5s src/mddf.jl | 337 337 1m22.4s test/namd_chemfiles.jl | 6 6 1m37.2s src/tools/write.jl | 2979 2979 21.1s src/results.jl | 66 66 16.3s ext/Plotting.jl | 14 14 1m54.3s test/runtests.jl | 11 11 1m12.6s src/rigid_body.jl | 15 15 10.9s src/minimum_distances.jl | 17 17 2.0s test/gromacs.jl | 3 3 5.0s src/tools/contributions.jl | 69 69 1m00.2s src/tools/grid3D.jl | 14 14 16.1s src/update_counters.jl | 5 5 0.0s test/pdb.jl | 2 2 5.5s src/AtomSelection.jl | 73 73 9.2s src/Options.jl | 32 32 0.9s src/tools/coordination_number.jl | 6 6 1.6s src/tools/residue_contributions.jl | 60 60 58.8s src/io.jl | 4 4 0.0s src/trajectory_formats/ChemFiles.jl | 1 1 0.4s test/namd.jl | 7 7 28.9s ERROR: LoadError: Some tests did not pass: 3776 passed, 0 failed, 1 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/ComplexMixtures/8gsyg/test/runtests.jl:20 Testing failed after 844.3s ERROR: LoadError: Package ComplexMixtures errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.11/Pkg/src/Types.jl:68 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:2124 [3] test @ /opt/julia/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:2007 [inlined] [4] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@Kwargs{io::IOContext{IO}}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.11/Pkg/src/API.jl:481 [5] test(pkgs::Vector{Pkg.Types.PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.11/Pkg/src/API.jl:159 [6] test @ /opt/julia/share/julia/stdlib/v1.11/Pkg/src/API.jl:147 [inlined] [7] #test#74 @ /opt/julia/share/julia/stdlib/v1.11/Pkg/src/API.jl:146 [inlined] [8] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:219 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 1122.03s: package tests unexpectedly errored