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1.5.0-DEV-4085873ec6.log
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Julia Version 1.5.0-DEV.431
Commit 4085873ec6 (2020-03-10 23:48 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-9.0.1 (ORCJIT, skylake)
Environment:
JULIA_DEPOT_PATH = ::/usr/local/share/julia
JULIA_NUM_THREADS = 2
Resolving package versions...
Installed PositiveFactorizations ─────── v0.2.3
Installed CodecZlib ──────────────────── v0.6.0
Installed CommonSubexpressions ───────── v0.2.0
Installed TableTraits ────────────────── v1.0.0
Installed DiffRules ──────────────────── v1.0.1
Installed BinaryProvider ─────────────── v0.5.8
Installed CategoricalArrays ──────────── v0.7.7
Installed OpenSpecFun_jll ────────────── v0.5.3+3
Installed Requires ───────────────────── v1.0.1
Installed CompilerSupportLibraries_jll ─ v0.2.0+1
Installed Reexport ───────────────────── v0.2.0
Installed SpecialFunctions ───────────── v0.9.0
Installed FillArrays ─────────────────── v0.8.5
Installed StaticArrays ───────────────── v0.12.1
Installed Optim ──────────────────────── v0.19.7
Installed DataStructures ─────────────── v0.17.10
Installed SortingAlgorithms ──────────── v0.3.1
Installed InvertedIndices ────────────── v1.0.0
Installed Roots ──────────────────────── v0.8.4
Installed TranscodingStreams ─────────── v0.9.5
Installed Tables ─────────────────────── v1.0.3
Installed JSON ───────────────────────── v0.21.0
Installed PorousMaterials ────────────── v0.2.0
Installed LightGraphs ────────────────── v1.3.1
Installed DataAPI ────────────────────── v1.1.0
Installed Compat ─────────────────────── v3.8.0
Installed MacroTools ─────────────────── v0.5.4
Installed ProgressMeter ──────────────── v1.2.0
Installed DiffEqDiffTools ────────────── v1.7.0
Installed OffsetArrays ───────────────── v0.11.4
Installed Parsers ────────────────────── v0.3.12
Installed DataFrames ─────────────────── v0.20.2
Installed WeakRefStrings ─────────────── v0.6.2
Installed Inflate ────────────────────── v0.1.1
Installed Parameters ─────────────────── v0.12.0
Installed ArnoldiMethod ──────────────── v0.0.4
Installed OrderedCollections ─────────── v1.1.0
Installed RecipesBase ────────────────── v0.8.0
Installed FilePathsBase ──────────────── v0.7.0
Installed Missings ───────────────────── v0.4.3
Installed DataValueInterfaces ────────── v1.0.0
Installed Calculus ───────────────────── v0.5.1
Installed PooledArrays ───────────────── v0.5.3
Installed DiffResults ────────────────── v1.0.2
Installed FiniteDiff ─────────────────── v2.2.1
Installed SimpleTraits ───────────────── v0.9.1
Installed StatsBase ──────────────────── v0.32.2
Installed NaNMath ────────────────────── v0.3.3
Installed ArrayInterface ─────────────── v2.5.1
Installed IteratorInterfaceExtensions ── v1.0.0
Installed JLD2 ───────────────────────── v0.1.12
Installed LineSearches ───────────────── v7.0.1
Installed FileIO ─────────────────────── v1.2.3
Installed ForwardDiff ────────────────── v0.10.9
Installed NLSolversBase ──────────────── v7.6.1
Installed CSV ────────────────────────── v0.5.26
Installed Polynomials ────────────────── v0.6.1
#=#=# ##O#- # ######################################################################## 100.0%
#=#=# 0.7%#### 5.8%######## 11.5%############## 19.9%##################### 29.8%############################### 43.5%################################## 48.5%############################################# 63.2%############################################################## 86.6%######################################################################## 100.0%
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 v2.5.1
b99e7846 + BinaryProvider v0.5.8
336ed68f + CSV v0.5.26
49dc2e85 + Calculus v0.5.1
324d7699 + CategoricalArrays v0.7.7
944b1d66 + CodecZlib v0.6.0
bbf7d656 + CommonSubexpressions v0.2.0
34da2185 + Compat v3.8.0
e66e0078 + CompilerSupportLibraries_jll v0.2.0+1
9a962f9c + DataAPI v1.1.0
a93c6f00 + DataFrames v0.20.2
864edb3b + DataStructures v0.17.10
e2d170a0 + DataValueInterfaces v1.0.0
01453d9d + DiffEqDiffTools v1.7.0
163ba53b + DiffResults v1.0.2
b552c78f + DiffRules v1.0.1
5789e2e9 + FileIO v1.2.3
48062228 + FilePathsBase v0.7.0
1a297f60 + FillArrays v0.8.5
6a86dc24 + FiniteDiff v2.2.1
f6369f11 + ForwardDiff v0.10.9
d25df0c9 + Inflate v0.1.1
41ab1584 + InvertedIndices v1.0.0
82899510 + IteratorInterfaceExtensions v1.0.0
033835bb + JLD2 v0.1.12
682c06a0 + JSON v0.21.0
093fc24a + LightGraphs v1.3.1
d3d80556 + LineSearches v7.0.1
1914dd2f + MacroTools v0.5.4
e1d29d7a + Missings v0.4.3
d41bc354 + NLSolversBase v7.6.1
77ba4419 + NaNMath v0.3.3
6fe1bfb0 + OffsetArrays v0.11.4
efe28fd5 + OpenSpecFun_jll v0.5.3+3
429524aa + Optim v0.19.7
bac558e1 + OrderedCollections v1.1.0
d96e819e + Parameters v0.12.0
69de0a69 + Parsers v0.3.12
f27b6e38 + Polynomials v0.6.1
2dfb63ee + PooledArrays v0.5.3
68953c7c + PorousMaterials v0.2.0
85a6dd25 + PositiveFactorizations v0.2.3
92933f4c + ProgressMeter v1.2.0
3cdcf5f2 + RecipesBase v0.8.0
189a3867 + Reexport v0.2.0
ae029012 + Requires v1.0.1
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 v0.32.2
3783bdb8 + TableTraits v1.0.0
bd369af6 + Tables v1.0.3
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`
Testing PorousMaterials
Status `/tmp/jl_jlPawQ/Project.toml`
336ed68f CSV v0.5.26
a93c6f00 DataFrames v0.20.2
e30172f5 Documenter v0.24.5
5789e2e9 FileIO v1.2.3
033835bb JLD2 v0.1.12
093fc24a LightGraphs v1.3.1
6fe1bfb0 OffsetArrays v0.11.4
429524aa Optim v0.19.7
f27b6e38 Polynomials v0.6.1
68953c7c PorousMaterials v0.2.0
92933f4c ProgressMeter v1.2.0
f2b01f46 Roots v0.8.4
276daf66 SpecialFunctions v0.9.0
2913bbd2 StatsBase v0.32.2
8ba89e20 Distributed
37e2e46d LinearAlgebra
de0858da Printf
9a3f8284 Random
10745b16 Statistics
8dfed614 Test
Status `/tmp/jl_jlPawQ/Manifest.toml`
ec485272 ArnoldiMethod v0.0.4
4fba245c ArrayInterface v2.5.1
b99e7846 BinaryProvider v0.5.8
336ed68f CSV v0.5.26
49dc2e85 Calculus v0.5.1
324d7699 CategoricalArrays v0.7.7
944b1d66 CodecZlib v0.6.0
bbf7d656 CommonSubexpressions v0.2.0
34da2185 Compat v3.8.0
e66e0078 CompilerSupportLibraries_jll v0.2.0+1
9a962f9c DataAPI v1.1.0
a93c6f00 DataFrames v0.20.2
864edb3b DataStructures v0.17.10
e2d170a0 DataValueInterfaces v1.0.0
01453d9d DiffEqDiffTools v1.7.0
163ba53b DiffResults v1.0.2
b552c78f DiffRules v1.0.1
ffbed154 DocStringExtensions v0.8.1
e30172f5 Documenter v0.24.5
5789e2e9 FileIO v1.2.3
48062228 FilePathsBase v0.7.0
1a297f60 FillArrays v0.8.5
6a86dc24 FiniteDiff v2.2.1
f6369f11 ForwardDiff v0.10.9
d25df0c9 Inflate v0.1.1
41ab1584 InvertedIndices v1.0.0
82899510 IteratorInterfaceExtensions v1.0.0
033835bb JLD2 v0.1.12
682c06a0 JSON v0.21.0
093fc24a LightGraphs v1.3.1
d3d80556 LineSearches v7.0.1
1914dd2f MacroTools v0.5.4
e1d29d7a Missings v0.4.3
d41bc354 NLSolversBase v7.6.1
77ba4419 NaNMath v0.3.3
6fe1bfb0 OffsetArrays v0.11.4
efe28fd5 OpenSpecFun_jll v0.5.3+3
429524aa Optim v0.19.7
bac558e1 OrderedCollections v1.1.0
d96e819e Parameters v0.12.0
69de0a69 Parsers v0.3.12
f27b6e38 Polynomials v0.6.1
2dfb63ee PooledArrays v0.5.3
68953c7c PorousMaterials v0.2.0
85a6dd25 PositiveFactorizations v0.2.3
92933f4c ProgressMeter v1.2.0
3cdcf5f2 RecipesBase v0.8.0
189a3867 Reexport v0.2.0
ae029012 Requires v1.0.1
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 v0.32.2
3783bdb8 TableTraits v1.0.0
bd369af6 Tables v1.0.3
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
WARNING: Method definition vec(Number) in module FiniteDiff at /home/pkgeval/.julia/packages/FiniteDiff/IZ61j/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/IZ61j/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 1.159999999994294 1.1599999999938506; 1.159999999994294 0.0 2.3199999999881444; 1.1599999999938506 2.3199999999881444 0.0]
charge dist [0.0 1.159999999994294 1.1599999999938506; 1.159999999994294 0.0 2.3199999999881444; 1.1599999999938506 2.3199999999881444 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)]: 16.3478367402905
⟨U, vdw⟩ (K): -3148.799065139264
⟨U, Coulomb⟩ (K): 0.0
Block 2/5 statistics:
Henry coeff. [mmol/(g-bar)]: 0.8698886460628208
⟨U, vdw⟩ (K): -1397.5338103522756
⟨U, Coulomb⟩ (K): 0.0
Block 3/5 statistics:
Henry coeff. [mmol/(g-bar)]: 0.6232678919064979
⟨U, vdw⟩ (K): -1419.8531995216615
⟨U, Coulomb⟩ (K): 0.0
Block 4/5 statistics:
Henry coeff. [mmol/(g-bar)]: 0.9444283221408374
⟨U, vdw⟩ (K): -1557.4868592161515
⟨U, Coulomb⟩ (K): 0.0
Block 5/5 statistics:
Henry coeff. [mmol/(g-bar)]: 13.444474615186856
⟨U, vdw⟩ (K): -3079.4827975398207
⟨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): 0.08629830280939738
----- final results ----
henry coefficient [mmol/(g-bar)] = 6.445979 +/- 6.961171
⟨U, vdw⟩ (kJ/mol) = -17.631902 +/- 6.762490
⟨U, Coulomb⟩ (kJ/mol) = 0.000000 +/- 0.000000
Qst (kJ/mol) = 20.109611 +/- 6.762490
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)]: 16.3478367402905
⟨U, vdw⟩ (K): -3148.799065139264
⟨U, Coulomb⟩ (K): 0.0
Block 2/5 statistics:
Henry coeff. [mmol/(g-bar)]: 0.8698886460628208
⟨U, vdw⟩ (K): -1397.5338103522756
⟨U, Coulomb⟩ (K): 0.0
Block 3/5 statistics:
Henry coeff. [mmol/(g-bar)]: 0.6232678919064979
⟨U, vdw⟩ (K): -1419.8531995216615
⟨U, Coulomb⟩ (K): 0.0
Block 4/5 statistics:
Henry coeff. [mmol/(g-bar)]: 0.9444283221408374
⟨U, vdw⟩ (K): -1557.4868592161515
⟨U, Coulomb⟩ (K): 0.0
Block 5/5 statistics:
Henry coeff. [mmol/(g-bar)]: 13.444474615186856
⟨U, vdw⟩ (K): -3079.4827975398207
⟨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): 0.00963764985402425
----- final results ----
henry coefficient [mmol/(g-bar)] = 6.445979 +/- 6.961171
⟨U, vdw⟩ (kJ/mol) = -17.631902 +/- 6.762490
⟨U, Coulomb⟩ (kJ/mol) = 0.000000 +/- 0.000000
Qst (kJ/mol) = 20.109611 +/- 6.762490
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