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1.5.0-DEV-ed177d17d6.log
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Julia Version 1.5.0-DEV.158
Commit ed177d17d6 (2020-01-27 16:45 UTC)
Platform Info:
OS: Linux (x86_64-pc-linux-gnu)
CPU: Intel(R) Xeon(R) Silver 4114 CPU @ 2.20GHz
WORD_SIZE: 64
LIBM: libopenlibm
LLVM: libLLVM-8.0.1 (ORCJIT, skylake)
Environment:
JULIA_DEPOT_PATH = ::/usr/local/share/julia
JULIA_NUM_THREADS = 2
Resolving package versions...
Installed PositiveFactorizations ────── v0.2.3
Installed SortingAlgorithms ─────────── v0.3.1
Installed Parsers ───────────────────── v0.3.10
Installed Compat ────────────────────── v3.2.0
Installed DiffResults ───────────────── v1.0.2
Installed ArrayInterface ────────────── v2.3.1
Installed Optim ─────────────────────── v0.19.7
Installed OpenSpecFun_jll ───────────── v0.5.3+1
Installed OffsetArrays ──────────────── v0.11.4
Installed Tables ────────────────────── v0.2.11
Installed BinaryProvider ────────────── v0.5.8
Installed OrderedCollections ────────── v1.1.0
Installed Calculus ──────────────────── v0.5.1
Installed NLSolversBase ─────────────── v7.6.0
Installed FilePathsBase ─────────────── v0.7.0
Installed WeakRefStrings ────────────── v0.6.2
Installed SpecialFunctions ──────────── v0.9.0
Installed IteratorInterfaceExtensions ─ v1.0.0
Installed Parameters ────────────────── v0.12.0
Installed StatsBase ─────────────────── v0.32.0
Installed CommonSubexpressions ──────── v0.2.0
Installed ForwardDiff ───────────────── v0.10.9
Installed FileIO ────────────────────── v1.2.1
Installed CodecZlib ─────────────────── v0.6.0
Installed DataStructures ────────────── v0.17.9
Installed LineSearches ──────────────── v7.0.1
Installed DiffEqDiffTools ───────────── v1.7.0
Installed DataValueInterfaces ───────── v1.0.0
Installed Missings ──────────────────── v0.4.3
Installed Polynomials ───────────────── v0.6.0
Installed Inflate ───────────────────── v0.1.1
Installed StaticArrays ──────────────── v0.12.1
Installed CSV ───────────────────────── v0.5.22
Installed Roots ─────────────────────── v0.8.4
Installed ArnoldiMethod ─────────────── v0.0.4
Installed JSON ──────────────────────── v0.21.0
Installed CategoricalArrays ─────────── v0.7.7
Installed LightGraphs ───────────────── v1.3.0
Installed TableTraits ───────────────── v1.0.0
Installed DataAPI ───────────────────── v1.1.0
Installed PooledArrays ──────────────── v0.5.3
Installed ProgressMeter ─────────────── v1.2.0
Installed FillArrays ────────────────── v0.8.4
Installed DataFrames ────────────────── v0.20.0
Installed InvertedIndices ───────────── v1.0.0
Installed TranscodingStreams ────────── v0.9.5
Installed MacroTools ────────────────── v0.5.3
Installed FiniteDiff ────────────────── v2.1.0
Installed DiffRules ─────────────────── v1.0.0
Installed Requires ──────────────────── v1.0.0
Installed NaNMath ───────────────────── v0.3.3
Installed SimpleTraits ──────────────── v0.9.1
Installed RecipesBase ───────────────── v0.7.0
Installed Reexport ──────────────────── v0.2.0
Installed PorousMaterials ───────────── v0.2.0
Installed JLD2 ──────────────────────── v0.1.11
Updating `~/.julia/environments/v1.5/Project.toml`
[68953c7c] + PorousMaterials v0.2.0
Updating `~/.julia/environments/v1.5/Manifest.toml`
[ec485272] + ArnoldiMethod v0.0.4
[4fba245c] + ArrayInterface v2.3.1
[b99e7846] + BinaryProvider v0.5.8
[336ed68f] + CSV v0.5.22
[49dc2e85] + Calculus v0.5.1
[324d7699] + CategoricalArrays v0.7.7
[944b1d66] + CodecZlib v0.6.0
[bbf7d656] + CommonSubexpressions v0.2.0
[34da2185] + Compat v3.2.0
[9a962f9c] + DataAPI v1.1.0
[a93c6f00] + DataFrames v0.20.0
[864edb3b] + DataStructures v0.17.9
[e2d170a0] + DataValueInterfaces v1.0.0
[01453d9d] + DiffEqDiffTools v1.7.0
[163ba53b] + DiffResults v1.0.2
[b552c78f] + DiffRules v1.0.0
[5789e2e9] + FileIO v1.2.1
[48062228] + FilePathsBase v0.7.0
[1a297f60] + FillArrays v0.8.4
[6a86dc24] + FiniteDiff v2.1.0
[f6369f11] + ForwardDiff v0.10.9
[d25df0c9] + Inflate v0.1.1
[41ab1584] + InvertedIndices v1.0.0
[82899510] + IteratorInterfaceExtensions v1.0.0
[033835bb] + JLD2 v0.1.11
[682c06a0] + JSON v0.21.0
[093fc24a] + LightGraphs v1.3.0
[d3d80556] + LineSearches v7.0.1
[1914dd2f] + MacroTools v0.5.3
[e1d29d7a] + Missings v0.4.3
[d41bc354] + NLSolversBase v7.6.0
[77ba4419] + NaNMath v0.3.3
[6fe1bfb0] + OffsetArrays v0.11.4
[efe28fd5] + OpenSpecFun_jll v0.5.3+1
[429524aa] + Optim v0.19.7
[bac558e1] + OrderedCollections v1.1.0
[d96e819e] + Parameters v0.12.0
[69de0a69] + Parsers v0.3.10
[f27b6e38] + Polynomials v0.6.0
[2dfb63ee] + PooledArrays v0.5.3
[68953c7c] + PorousMaterials v0.2.0
[85a6dd25] + PositiveFactorizations v0.2.3
[92933f4c] + ProgressMeter v1.2.0
[3cdcf5f2] + RecipesBase v0.7.0
[189a3867] + Reexport v0.2.0
[ae029012] + Requires v1.0.0
[f2b01f46] + Roots v0.8.4
[699a6c99] + SimpleTraits v0.9.1
[a2af1166] + SortingAlgorithms v0.3.1
[276daf66] + SpecialFunctions v0.9.0
[90137ffa] + StaticArrays v0.12.1
[2913bbd2] + StatsBase v0.32.0
[3783bdb8] + TableTraits v1.0.0
[bd369af6] + Tables v0.2.11
[3bb67fe8] + TranscodingStreams v0.9.5
[ea10d353] + WeakRefStrings v0.6.2
[2a0f44e3] + Base64
[ade2ca70] + Dates
[8bb1440f] + DelimitedFiles
[8ba89e20] + Distributed
[9fa8497b] + Future
[b77e0a4c] + InteractiveUtils
[76f85450] + LibGit2
[8f399da3] + Libdl
[37e2e46d] + LinearAlgebra
[56ddb016] + Logging
[d6f4376e] + Markdown
[a63ad114] + Mmap
[44cfe95a] + Pkg
[de0858da] + Printf
[3fa0cd96] + REPL
[9a3f8284] + Random
[ea8e919c] + SHA
[9e88b42a] + Serialization
[1a1011a3] + SharedArrays
[6462fe0b] + Sockets
[2f01184e] + SparseArrays
[10745b16] + Statistics
[8dfed614] + Test
[cf7118a7] + UUIDs
[4ec0a83e] + Unicode
Building CodecZlib → `~/.julia/packages/CodecZlib/5t9zO/deps/build.log`
Updating `/tmp/jl_AvgRXg/Project.toml`
[no changes]
Updating `/tmp/jl_AvgRXg/Manifest.toml`
[no changes]
Testing PorousMaterials
Installed DocStringExtensions ─ v0.8.1
Installed Documenter ────────── v0.24.4
Updating `/tmp/jl_xFNhsn/Project.toml`
[e30172f5] + Documenter v0.24.4
Updating `/tmp/jl_xFNhsn/Manifest.toml`
[ffbed154] + DocStringExtensions v0.8.1
[e30172f5] + Documenter v0.24.4
Running sandbox
Status `/tmp/jl_xFNhsn/Project.toml`
[336ed68f] CSV v0.5.22
[a93c6f00] DataFrames v0.20.0
[e30172f5] Documenter v0.24.4
[5789e2e9] FileIO v1.2.1
[033835bb] JLD2 v0.1.11
[093fc24a] LightGraphs v1.3.0
[6fe1bfb0] OffsetArrays v0.11.4
[429524aa] Optim v0.19.7
[f27b6e38] Polynomials v0.6.0
[68953c7c] PorousMaterials v0.2.0
[92933f4c] ProgressMeter v1.2.0
[f2b01f46] Roots v0.8.4
[276daf66] SpecialFunctions v0.9.0
[2913bbd2] StatsBase v0.32.0
[8ba89e20] Distributed
[37e2e46d] LinearAlgebra
[de0858da] Printf
[9a3f8284] Random
[10745b16] Statistics
[8dfed614] Test
WARNING: Method definition vec(Number) in module FiniteDiff at /home/pkgeval/.julia/packages/FiniteDiff/EBys0/src/jacobians.jl:128 overwritten in module DiffEqDiffTools at /home/pkgeval/.julia/packages/DiffEqDiffTools/3mm8U/src/jacobians.jl:114.
** incremental compilation may be fatally broken for this module **
WARNING: Method definition vec(Number) in module FiniteDiff at /home/pkgeval/.julia/packages/FiniteDiff/EBys0/src/jacobians.jl:128 overwritten in module DiffEqDiffTools at /home/pkgeval/.julia/packages/DiffEqDiffTools/3mm8U/src/jacobians.jl:114.
** incremental compilation may be fatally broken for this module **
┌ Warning: Package PorousMaterials does not have Test in its dependencies:
│ - If you have PorousMaterials checked out for development and have
│ added Test as a dependency but haven't updated your primary
│ environment's manifest file, try `Pkg.resolve()`.
│ - Otherwise you may need to report an issue with PorousMaterials
└ Loading Test into PorousMaterials from project dependency, future warnings for PorousMaterials are suppressed.
Test Summary: | Pass Total
Box Tests | 16 16
Test Summary: | Pass Total
Matter Tests | 16 16
┌ Warning: Charges are already present in test_structure2.cif. Removing the current charges on the
│ framework and adding new ones...
└ @ PorousMaterials ~/.julia/packages/PorousMaterials/6i8Pq/src/Crystal.jl:1299
┌ Warning: Charges are already present in test_structure2.cif. Removing the current charges on the
│ framework and adding new ones...
└ @ PorousMaterials ~/.julia/packages/PorousMaterials/6i8Pq/src/Crystal.jl:1299
# atoms removed: 2
# charges removed: 2
┌ Warning: Framework symmetry_test_structure.cif has R -3 space group. We are converting it to P1 symmetry for use in molecular simulations.
│ To afrain from this, pass `convert_to_p1=false` to the `Framework` constructor.
└ @ PorousMaterials ~/.julia/packages/PorousMaterials/6i8Pq/src/Crystal.jl:438
┌ Warning: Framework symmetry_test_structure_cartn.cif has R -3 space group. We are converting it to P1 symmetry for use in molecular simulations.
│ To afrain from this, pass `convert_to_p1=false` to the `Framework` constructor.
└ @ PorousMaterials ~/.julia/packages/PorousMaterials/6i8Pq/src/Crystal.jl:438
┌ Warning: Framework symmetry_test_structure_P1.cif has space group. We are converting it to P1 symmetry for use in molecular simulations.
│ To afrain from this, pass `convert_to_p1=false` to the `Framework` constructor.
└ @ PorousMaterials ~/.julia/packages/PorousMaterials/6i8Pq/src/Crystal.jl:438
┌ Warning: Atoms 2 and 1 in framework 1_framework 2 are less than 0.100000 Å apart.
└ @ PorousMaterials ~/.julia/packages/PorousMaterials/6i8Pq/src/Crystal.jl:578
┌ Warning: Atoms 3 and 1 in framework 1_framework 2 are less than 0.100000 Å apart.
└ @ PorousMaterials ~/.julia/packages/PorousMaterials/6i8Pq/src/Crystal.jl:578
┌ Warning: Atoms 3 and 2 in framework 1_framework 2 are less than 0.100000 Å apart.
└ @ PorousMaterials ~/.julia/packages/PorousMaterials/6i8Pq/src/Crystal.jl:578
┌ Warning: Atoms 4 and 1 in framework 1_framework 2 are less than 0.100000 Å apart.
└ @ PorousMaterials ~/.julia/packages/PorousMaterials/6i8Pq/src/Crystal.jl:578
┌ Warning: Atoms 4 and 2 in framework 1_framework 2 are less than 0.100000 Å apart.
└ @ PorousMaterials ~/.julia/packages/PorousMaterials/6i8Pq/src/Crystal.jl:578
┌ Warning: Atoms 4 and 3 in framework 1_framework 2 are less than 0.100000 Å apart.
└ @ PorousMaterials ~/.julia/packages/PorousMaterials/6i8Pq/src/Crystal.jl:578
┌ Warning: This new framework has overlapping atoms, use:
│ `remove_overlapping_atoms_and_charges(framework)`
│ to remove them
└ @ PorousMaterials ~/.julia/packages/PorousMaterials/6i8Pq/src/Crystal.jl:1487
┌ Warning: Charges 2 and 1 in framework 1_framework 2 are less than 0.100000 Å apart.
└ @ PorousMaterials ~/.julia/packages/PorousMaterials/6i8Pq/src/Crystal.jl:598
┌ Warning: Charges 3 and 1 in framework 1_framework 2 are less than 0.100000 Å apart.
└ @ PorousMaterials ~/.julia/packages/PorousMaterials/6i8Pq/src/Crystal.jl:598
┌ Warning: Charges 3 and 2 in framework 1_framework 2 are less than 0.100000 Å apart.
└ @ PorousMaterials ~/.julia/packages/PorousMaterials/6i8Pq/src/Crystal.jl:598
┌ Warning: Charges 4 and 1 in framework 1_framework 2 are less than 0.100000 Å apart.
└ @ PorousMaterials ~/.julia/packages/PorousMaterials/6i8Pq/src/Crystal.jl:598
┌ Warning: Charges 4 and 2 in framework 1_framework 2 are less than 0.100000 Å apart.
└ @ PorousMaterials ~/.julia/packages/PorousMaterials/6i8Pq/src/Crystal.jl:598
┌ Warning: Charges 4 and 3 in framework 1_framework 2 are less than 0.100000 Å apart.
└ @ PorousMaterials ~/.julia/packages/PorousMaterials/6i8Pq/src/Crystal.jl:598
┌ Warning: This new framework has overlapping charges, use:
│ `remove_overlapping_atoms_and_charges(framework)`
│ to remove them
└ @ PorousMaterials ~/.julia/packages/PorousMaterials/6i8Pq/src/Crystal.jl:1491
┌ Warning: Atoms 2 and 1 in framework 1_framework 2 are less than 0.100000 Å apart.
└ @ PorousMaterials ~/.julia/packages/PorousMaterials/6i8Pq/src/Crystal.jl:578
┌ Warning: Atoms 3 and 1 in framework 1_framework 2 are less than 0.100000 Å apart.
└ @ PorousMaterials ~/.julia/packages/PorousMaterials/6i8Pq/src/Crystal.jl:578
┌ Warning: Atoms 3 and 2 in framework 1_framework 2 are less than 0.100000 Å apart.
└ @ PorousMaterials ~/.julia/packages/PorousMaterials/6i8Pq/src/Crystal.jl:578
┌ Warning: Atoms 4 and 1 in framework 1_framework 2 are less than 0.100000 Å apart.
└ @ PorousMaterials ~/.julia/packages/PorousMaterials/6i8Pq/src/Crystal.jl:578
┌ Warning: Atoms 4 and 2 in framework 1_framework 2 are less than 0.100000 Å apart.
└ @ PorousMaterials ~/.julia/packages/PorousMaterials/6i8Pq/src/Crystal.jl:578
┌ Warning: Atoms 4 and 3 in framework 1_framework 2 are less than 0.100000 Å apart.
└ @ PorousMaterials ~/.julia/packages/PorousMaterials/6i8Pq/src/Crystal.jl:578
┌ Warning: This new framework has overlapping atoms, use:
│ `remove_overlapping_atoms_and_charges(framework)`
│ to remove them
└ @ PorousMaterials ~/.julia/packages/PorousMaterials/6i8Pq/src/Crystal.jl:1487
┌ Warning: Charges 2 and 1 in framework 1_framework 2 are less than 0.100000 Å apart.
└ @ PorousMaterials ~/.julia/packages/PorousMaterials/6i8Pq/src/Crystal.jl:598
┌ Warning: Charges 3 and 1 in framework 1_framework 2 are less than 0.100000 Å apart.
└ @ PorousMaterials ~/.julia/packages/PorousMaterials/6i8Pq/src/Crystal.jl:598
┌ Warning: Charges 3 and 2 in framework 1_framework 2 are less than 0.100000 Å apart.
└ @ PorousMaterials ~/.julia/packages/PorousMaterials/6i8Pq/src/Crystal.jl:598
┌ Warning: Charges 4 and 1 in framework 1_framework 2 are less than 0.100000 Å apart.
└ @ PorousMaterials ~/.julia/packages/PorousMaterials/6i8Pq/src/Crystal.jl:598
┌ Warning: Charges 4 and 2 in framework 1_framework 2 are less than 0.100000 Å apart.
└ @ PorousMaterials ~/.julia/packages/PorousMaterials/6i8Pq/src/Crystal.jl:598
┌ Warning: Charges 4 and 3 in framework 1_framework 2 are less than 0.100000 Å apart.
└ @ PorousMaterials ~/.julia/packages/PorousMaterials/6i8Pq/src/Crystal.jl:598
┌ Warning: This new framework has overlapping charges, use:
│ `remove_overlapping_atoms_and_charges(framework)`
│ to remove them
└ @ PorousMaterials ~/.julia/packages/PorousMaterials/6i8Pq/src/Crystal.jl:1491
┌ Warning: Atoms 2 and 1 in framework 1_framework 2 are less than 0.100000 Å apart.
└ @ PorousMaterials ~/.julia/packages/PorousMaterials/6i8Pq/src/Crystal.jl:578
┌ Warning: Atoms 3 and 1 in framework 1_framework 2 are less than 0.100000 Å apart.
└ @ PorousMaterials ~/.julia/packages/PorousMaterials/6i8Pq/src/Crystal.jl:578
┌ Warning: Atoms 3 and 2 in framework 1_framework 2 are less than 0.100000 Å apart.
└ @ PorousMaterials ~/.julia/packages/PorousMaterials/6i8Pq/src/Crystal.jl:578
┌ Warning: Atoms 4 and 1 in framework 1_framework 2 are less than 0.100000 Å apart.
└ @ PorousMaterials ~/.julia/packages/PorousMaterials/6i8Pq/src/Crystal.jl:578
┌ Warning: Atoms 4 and 2 in framework 1_framework 2 are less than 0.100000 Å apart.
└ @ PorousMaterials ~/.julia/packages/PorousMaterials/6i8Pq/src/Crystal.jl:578
┌ Warning: Atoms 4 and 3 in framework 1_framework 2 are less than 0.100000 Å apart.
└ @ PorousMaterials ~/.julia/packages/PorousMaterials/6i8Pq/src/Crystal.jl:578
┌ Warning: This new framework has overlapping atoms, use:
│ `remove_overlapping_atoms_and_charges(framework)`
│ to remove them
└ @ PorousMaterials ~/.julia/packages/PorousMaterials/6i8Pq/src/Crystal.jl:1487
┌ Warning: Charges 2 and 1 in framework 1_framework 2 are less than 0.100000 Å apart.
└ @ PorousMaterials ~/.julia/packages/PorousMaterials/6i8Pq/src/Crystal.jl:598
┌ Warning: Charges 3 and 1 in framework 1_framework 2 are less than 0.100000 Å apart.
└ @ PorousMaterials ~/.julia/packages/PorousMaterials/6i8Pq/src/Crystal.jl:598
┌ Warning: Charges 3 and 2 in framework 1_framework 2 are less than 0.100000 Å apart.
└ @ PorousMaterials ~/.julia/packages/PorousMaterials/6i8Pq/src/Crystal.jl:598
┌ Warning: Charges 4 and 1 in framework 1_framework 2 are less than 0.100000 Å apart.
└ @ PorousMaterials ~/.julia/packages/PorousMaterials/6i8Pq/src/Crystal.jl:598
┌ Warning: Charges 4 and 2 in framework 1_framework 2 are less than 0.100000 Å apart.
└ @ PorousMaterials ~/.julia/packages/PorousMaterials/6i8Pq/src/Crystal.jl:598
┌ Warning: Charges 4 and 3 in framework 1_framework 2 are less than 0.100000 Å apart.
└ @ PorousMaterials ~/.julia/packages/PorousMaterials/6i8Pq/src/Crystal.jl:598
┌ Warning: This new framework has overlapping charges, use:
│ `remove_overlapping_atoms_and_charges(framework)`
│ to remove them
└ @ PorousMaterials ~/.julia/packages/PorousMaterials/6i8Pq/src/Crystal.jl:1491
Test Summary: | Pass Total
Crystal Tests | 72 72
See random_vectors_on_sphere
see co2s.xyz for dist'n of rotations
atom dist [0.0 1.1599999999939123 1.1599999999953292; 1.1599999999939123 0.0 2.319999999989242; 1.1599999999953292 2.319999999989242 0.0]
charge dist [0.0 1.1599999999939123 1.1599999999953292; 1.1599999999939123 0.0 2.319999999989242; 1.1599999999953292 2.319999999989242 0.0]
Test Summary: | Pass Total
Molecules Tests | 75 75
Test Summary: | Pass Total
NearestImage Tests | 2 2
┌ Warning: O_CO2 in CO2 missing from bogus.csv force field.
└ @ PorousMaterials ~/.julia/packages/PorousMaterials/6i8Pq/src/Forcefield.jl:181
┌ Warning: C in SBMOF-1.cif missing from bogus.csv force field.
└ @ PorousMaterials ~/.julia/packages/PorousMaterials/6i8Pq/src/Forcefield.jl:181
Test Summary: | Pass Total
Forcefield Tests | 12 12
Test Summary: | Pass Total
VdwEnergetics Tests | 8 8
Test Summary: | Pass Total
Energetics_Util Tests | 18 18
Test Summary: | Pass Total
ElectrostaticEnergetics Tests | 41 41
Test Summary: | Pass Total
MCHelpers Tests | 14 14
Test Summary: | Pass Total
Guest-guest Energetics Tests | 20 20
┌ Warning: `getindex(df::DataFrame, col_ind::ColumnIndex)` is deprecated, use `df[!, col_ind]` instead.
│ caller = PorousMaterials.VdWFluid(::Symbol) at EOS.jl:151
└ @ PorousMaterials ~/.julia/packages/PorousMaterials/6i8Pq/src/EOS.jl:151
┌ Warning: `getindex(df::DataFrame, col_ind::ColumnIndex)` is deprecated, use `df[!, col_ind]` instead.
│ caller = PorousMaterials.VdWFluid(::Symbol) at EOS.jl:154
└ @ PorousMaterials ~/.julia/packages/PorousMaterials/6i8Pq/src/EOS.jl:154
┌ Warning: `getindex(df::DataFrame, col_ind::ColumnIndex)` is deprecated, use `df[!, col_ind]` instead.
│ caller = PorousMaterials.VdWFluid(::Symbol) at EOS.jl:155
└ @ PorousMaterials ~/.julia/packages/PorousMaterials/6i8Pq/src/EOS.jl:155
Test Summary: | Pass Total
EOS Tests | 10 10
Test Summary: | Pass Total
Simulation Rules Tests | 8 8
Test Summary: | Pass Total
GCMC Checkpoint Tests | 12 12
Simulating Henry coefficient of CO2 in FIQCEN_clean.cif at 298.0 K, using UFF.csv force field with 0.16410678370168813 insertions per ų.
750 total # particle insertions
Replicating framework 2 by 2 by 2 for short-range cutoff 14.00
Framework atoms of FIQCEN_clean.cif have charges? false
Molecule CO2 has point charges? true
Block 1/5 statistics:
Henry coeff. [mmol/(g-bar)]: 2.1354448177713388
⟨U, vdw⟩ (K): -2190.9210130344345
⟨U, Coulomb⟩ (K): 0.0
Block 2/5 statistics:
Henry coeff. [mmol/(g-bar)]: 0.6137466083249268
⟨U, vdw⟩ (K): -1381.648244745274
⟨U, Coulomb⟩ (K): 0.0
Block 3/5 statistics:
Henry coeff. [mmol/(g-bar)]: 1.3975147192385555
⟨U, vdw⟩ (K): -1715.4896521619994
⟨U, Coulomb⟩ (K): 0.0
Block 4/5 statistics:
Henry coeff. [mmol/(g-bar)]: 1.5114134406894788
⟨U, vdw⟩ (K): -1810.1086342978888
⟨U, Coulomb⟩ (K): 0.0
Block 5/5 statistics:
Henry coeff. [mmol/(g-bar)]: 10.595394622854014
⟨U, vdw⟩ (K): -2792.468955184487
⟨U, Coulomb⟩ (K): 0.0
Results saved in: /home/pkgeval/.julia/packages/PorousMaterials/6i8Pq/test/data/henry_sims/henry_sim_CO2_in_FIQCEN_clean.cif_298.000000K_UFF.csv_ff_0_insertions_per_volume.jld2
Elapsed time (min): 0.09652888377507528
----- final results ----
henry coefficient [mmol/(g-bar)] = 3.250703 +/- 3.704086
⟨U, vdw⟩ (kJ/mol) = -16.447060 +/- 4.007241
⟨U, Coulomb⟩ (kJ/mol) = 0.000000 +/- 0.000000
Qst (kJ/mol) = 18.924769 +/- 4.007241
Simulating Henry coefficient of CO2 in FIQCEN_clean.cif at 298.0 K, using UFF.csv force field with 0.16410678370168813 insertions per ų.
750 total # particle insertions
Replicating framework 2 by 2 by 2 for short-range cutoff 14.00
Framework atoms of FIQCEN_clean.cif have charges? false
Molecule CO2 has point charges? true
Block 1: recovered previous, finished simulation results from checkpoint
Block 2: recovered previous, finished simulation results from checkpoint
Block 3: recovered previous, finished simulation results from checkpoint
Block 4: recovered previous, finished simulation results from checkpoint
Block 5: recovered previous, finished simulation results from checkpoint
Block 1/5 statistics:
Henry coeff. [mmol/(g-bar)]: 2.1354448177713388
⟨U, vdw⟩ (K): -2190.9210130344345
⟨U, Coulomb⟩ (K): 0.0
Block 2/5 statistics:
Henry coeff. [mmol/(g-bar)]: 0.6137466083249268
⟨U, vdw⟩ (K): -1381.648244745274
⟨U, Coulomb⟩ (K): 0.0
Block 3/5 statistics:
Henry coeff. [mmol/(g-bar)]: 1.3975147192385555
⟨U, vdw⟩ (K): -1715.4896521619994
⟨U, Coulomb⟩ (K): 0.0
Block 4/5 statistics:
Henry coeff. [mmol/(g-bar)]: 1.5114134406894788
⟨U, vdw⟩ (K): -1810.1086342978888
⟨U, Coulomb⟩ (K): 0.0
Block 5/5 statistics:
Henry coeff. [mmol/(g-bar)]: 10.595394622854014
⟨U, vdw⟩ (K): -2792.468955184487
⟨U, Coulomb⟩ (K): 0.0
Results saved in: /home/pkgeval/.julia/packages/PorousMaterials/6i8Pq/test/data/henry_sims/henry_sim_CO2_in_FIQCEN_clean.cif_298.000000K_UFF.csv_ff_0_insertions_per_volume.jld2
Elapsed time (min): 0.01171814997990926
----- final results ----
henry coefficient [mmol/(g-bar)] = 3.250703 +/- 3.704086
⟨U, vdw⟩ (kJ/mol) = -16.447060 +/- 4.007241
⟨U, Coulomb⟩ (kJ/mol) = 0.000000 +/- 0.000000
Qst (kJ/mol) = 18.924769 +/- 4.007241
Test Summary: | Pass Total
Henry Checkpoint Tests | 5 5
See /home/pkgeval/.julia/packages/PorousMaterials/6i8Pq/test/data/grids/test_grid.cube
Computing energy grid of CH4 in LTA.cif
Regular grid (in fractional space) of 10 by 10 by 10 points superimposed over the unit cell.
See /home/pkgeval/.julia/packages/PorousMaterials/6i8Pq/test/data/grids/CH4_in_LTA_UFF_b4_pocket_blocking.cube
See /home/pkgeval/.julia/packages/PorousMaterials/6i8Pq/test/data/grids/CH4_in_LTA_UFF_after_pocket_blocking.cube
8 pockets in LTA.cif were found to be inaccessible to CH4 and blocked.
Porosity of LTA.cif b4 pocket blocking is 0.169280
Porosity of LTA.cif after pocket blocking is 0.153920
potential energy barrier used to determine accessibility: 0.000000 kJ_mol
See LTAaccessible_inertions.xyz
Computing energy grid of CH4 in SOD.cif
Regular grid (in fractional space) of 10 by 10 by 10 points superimposed over the unit cell.
See /home/pkgeval/.julia/packages/PorousMaterials/6i8Pq/test/data/grids/CH4_in_SOD_UFF_b4_pocket_blocking.cube
See /home/pkgeval/.julia/packages/PorousMaterials/6i8Pq/test/data/grids/CH4_in_SOD_UFF_after_pocket_blocking.cube
┌ Warning: CH4 cannot enter the pores of SOD.cif with 0.000000 K energy tolerance.
└ @ PorousMaterials ~/.julia/packages/PorousMaterials/6i8Pq/src/Grid.jl:686
9 pockets in SOD.cif were found to be inaccessible to CH4 and blocked.
Porosity of SOD.cif b4 pocket blocking is 0.075072
Porosity of SOD.cif after pocket blocking is 0.000000
potential energy barrier used to determine accessibility: 0.000000 kJ_mol
See /home/pkgeval/.julia/packages/PorousMaterials/6i8Pq/test/data/grids/CH4_in_LTA_UFF_b4_pocket_blocking.cube
See /home/pkgeval/.julia/packages/PorousMaterials/6i8Pq/test/data/grids/CH4_in_LTA_UFF_after_pocket_blocking.cube
8 pockets in LTA.cif were found to be inaccessible to CH4 and blocked.
Porosity of LTA.cif b4 pocket blocking is 0.174000
Porosity of LTA.cif after pocket blocking is 0.154000
potential energy barrier used to determine accessibility: 0.000000 kJ_mol
See /home/pkgeval/.julia/packages/PorousMaterials/6i8Pq/test/data/grids/CH4_in_LTA_UFF_b4_pocket_blocking.cube
See /home/pkgeval/.julia/packages/PorousMaterials/6i8Pq/test/data/grids/CH4_in_LTA_UFF_after_pocket_blocking.cube
24 pockets in LTA.cif were found to be inaccessible to CH4 and blocked.
Porosity of LTA.cif b4 pocket blocking is 0.179310
Porosity of LTA.cif after pocket blocking is 0.162776
potential energy barrier used to determine accessibility: 0.000000 kJ_mol
See /home/pkgeval/.julia/packages/PorousMaterials/6i8Pq/test/data/grids/CH4_in_SBMOF-1_UFF_b4_pocket_blocking.cube
See /home/pkgeval/.julia/packages/PorousMaterials/6i8Pq/test/data/grids/CH4_in_SBMOF-1_UFF_after_pocket_blocking.cube
See /home/pkgeval/.julia/packages/PorousMaterials/6i8Pq/test/data/grids/CH4_in_CAXVII_clean_UFF_b4_pocket_blocking.cube
See /home/pkgeval/.julia/packages/PorousMaterials/6i8Pq/test/data/grids/CH4_in_CAXVII_clean_UFF_after_pocket_blocking.cube
Test Summary: | Pass Total
Grid Tests | 56 56
┌ Warning: PorousMaterials is now in Tutorial Mode. You have access to the testing data to experiment with PorousMaterials.
│ To reset to default file paths, call `set_default_file_paths()`
└ @ PorousMaterials ~/.julia/packages/PorousMaterials/6i8Pq/src/PorousMaterials.jl:78
General data folder: /home/pkgeval/.julia/packages/PorousMaterials/6i8Pq/test/data
crystal structures (.cif, .cssr): /home/pkgeval/.julia/packages/PorousMaterials/6i8Pq/test/data/crystals
force field files (.csv): /home/pkgeval/.julia/packages/PorousMaterials/6i8Pq/test/data/forcefields
molecule input files: /home/pkgeval/.julia/packages/PorousMaterials/6i8Pq/test/data/molecules
grids (.cube): /home/pkgeval/.julia/packages/PorousMaterials/6i8Pq/test/data/grids
Test Summary: | Pass Total
Path Tests | 5 5
Test Summary: | Pass Total
Misc Tests | 5 5
Test Summary: | Pass Total
Generic Rotation Tests | 7 7
Testing PorousMaterials tests passed