If you think that there is an error in how your package is being tested or represented, please file an issue at NewPkgEval.jl , making sure to read the FAQ first.
Results with Julia v1.2.0
Testing was successful .
Last evaluation was ago and took 28 minutes, 17 seconds.
Click here to download the log file.
Click here to show the log contents.
Resolving package versions...
Installed Missings ──────────────────── v0.4.3
Installed DataAPI ───────────────────── v1.1.0
Installed Inflate ───────────────────── v0.1.1
Installed TableTraits ───────────────── v1.0.0
Installed BinaryProvider ────────────── v0.5.8
Installed CSV ───────────────────────── v0.5.18
Installed DataFrames ────────────────── v0.19.4
Installed StatsBase ─────────────────── v0.32.0
Installed URIParser ─────────────────── v0.4.0
Installed JLD2 ──────────────────────── v0.1.9
Installed ArrayLayouts ──────────────── v0.1.5
Installed PooledArrays ──────────────── v0.5.2
Installed DataValueInterfaces ───────── v1.0.0
Installed Reexport ──────────────────── v0.2.0
Installed Polynomials ───────────────── v0.6.0
Installed Compat ────────────────────── v2.2.0
Installed InvertedIndices ───────────── v1.0.0
Installed OffsetArrays ──────────────── v0.11.2
Installed OrderedCollections ────────── v1.1.0
Installed Tables ────────────────────── v0.2.11
Installed FilePathsBase ─────────────── v0.7.0
Installed RecipesBase ───────────────── v0.7.0
Installed DataStructures ────────────── v0.17.6
Installed WeakRefStrings ────────────── v0.6.1
Installed Roots ─────────────────────── v0.8.3
Installed Parsers ───────────────────── v0.3.10
Installed LightGraphs ───────────────── v1.3.0
Installed FillArrays ────────────────── v0.8.2
Installed TranscodingStreams ────────── v0.9.5
Installed JSON ──────────────────────── v0.21.0
Installed SimpleTraits ──────────────── v0.9.1
Installed CodecZlib ─────────────────── v0.6.0
Installed StaticArrays ──────────────── v0.12.1
Installed IteratorInterfaceExtensions ─ v1.0.0
Installed CategoricalArrays ─────────── v0.7.3
Installed SortingAlgorithms ─────────── v0.3.1
Installed LazyArrays ────────────────── v0.14.10
Installed ArnoldiMethod ─────────────── v0.0.4
Installed MacroTools ────────────────── v0.5.2
Installed SpecialFunctions ──────────── v0.8.0
Installed BinDeps ───────────────────── v0.8.10
Installed FileIO ────────────────────── v1.1.0
Installed ProgressMeter ─────────────── v0.9.0
Installed PorousMaterials ───────────── v0.1.6
Updating `~/.julia/environments/v1.2/Project.toml`
[68953c7c] + PorousMaterials v0.1.6
Updating `~/.julia/environments/v1.2/Manifest.toml`
[ec485272] + ArnoldiMethod v0.0.4
[4c555306] + ArrayLayouts v0.1.5
[9e28174c] + BinDeps v0.8.10
[b99e7846] + BinaryProvider v0.5.8
[336ed68f] + CSV v0.5.18
[324d7699] + CategoricalArrays v0.7.3
[944b1d66] + CodecZlib v0.6.0
[34da2185] + Compat v2.2.0
[9a962f9c] + DataAPI v1.1.0
[a93c6f00] + DataFrames v0.19.4
[864edb3b] + DataStructures v0.17.6
[e2d170a0] + DataValueInterfaces v1.0.0
[5789e2e9] + FileIO v1.1.0
[48062228] + FilePathsBase v0.7.0
[1a297f60] + FillArrays v0.8.2
[d25df0c9] + Inflate v0.1.1
[41ab1584] + InvertedIndices v1.0.0
[82899510] + IteratorInterfaceExtensions v1.0.0
[033835bb] + JLD2 v0.1.9
[682c06a0] + JSON v0.21.0
[5078a376] + LazyArrays v0.14.10
[093fc24a] + LightGraphs v1.3.0
[1914dd2f] + MacroTools v0.5.2
[e1d29d7a] + Missings v0.4.3
[6fe1bfb0] + OffsetArrays v0.11.2
[bac558e1] + OrderedCollections v1.1.0
[69de0a69] + Parsers v0.3.10
[f27b6e38] + Polynomials v0.6.0
[2dfb63ee] + PooledArrays v0.5.2
[68953c7c] + PorousMaterials v0.1.6
[92933f4c] + ProgressMeter v0.9.0
[3cdcf5f2] + RecipesBase v0.7.0
[189a3867] + Reexport v0.2.0
[f2b01f46] + Roots v0.8.3
[699a6c99] + SimpleTraits v0.9.1
[a2af1166] + SortingAlgorithms v0.3.1
[276daf66] + SpecialFunctions v0.8.0
[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
[30578b45] + URIParser v0.4.0
[ea10d353] + WeakRefStrings v0.6.1
[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
[9abbd945] + Profile
[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`
Building SpecialFunctions → `~/.julia/packages/SpecialFunctions/ne2iw/deps/build.log`
Testing PorousMaterials
Status `/tmp/jl_E7xMYk/Manifest.toml`
[ec485272] ArnoldiMethod v0.0.4
[4c555306] ArrayLayouts v0.1.5
[9e28174c] BinDeps v0.8.10
[b99e7846] BinaryProvider v0.5.8
[336ed68f] CSV v0.5.18
[324d7699] CategoricalArrays v0.7.3
[944b1d66] CodecZlib v0.6.0
[34da2185] Compat v2.2.0
[9a962f9c] DataAPI v1.1.0
[a93c6f00] DataFrames v0.19.4
[864edb3b] DataStructures v0.17.6
[e2d170a0] DataValueInterfaces v1.0.0
[5789e2e9] FileIO v1.1.0
[48062228] FilePathsBase v0.7.0
[1a297f60] FillArrays v0.8.2
[d25df0c9] Inflate v0.1.1
[41ab1584] InvertedIndices v1.0.0
[82899510] IteratorInterfaceExtensions v1.0.0
[033835bb] JLD2 v0.1.9
[682c06a0] JSON v0.21.0
[5078a376] LazyArrays v0.14.10
[093fc24a] LightGraphs v1.3.0
[1914dd2f] MacroTools v0.5.2
[e1d29d7a] Missings v0.4.3
[6fe1bfb0] OffsetArrays v0.11.2
[bac558e1] OrderedCollections v1.1.0
[69de0a69] Parsers v0.3.10
[f27b6e38] Polynomials v0.6.0
[2dfb63ee] PooledArrays v0.5.2
[68953c7c] PorousMaterials v0.1.6
[92933f4c] ProgressMeter v0.9.0
[3cdcf5f2] RecipesBase v0.7.0
[189a3867] Reexport v0.2.0
[f2b01f46] Roots v0.8.3
[699a6c99] SimpleTraits v0.9.1
[a2af1166] SortingAlgorithms v0.3.1
[276daf66] SpecialFunctions v0.8.0
[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
[30578b45] URIParser v0.4.0
[ea10d353] WeakRefStrings v0.6.1
[2a0f44e3] Base64 [`@stdlib/Base64`]
[ade2ca70] Dates [`@stdlib/Dates`]
[8bb1440f] DelimitedFiles [`@stdlib/DelimitedFiles`]
[8ba89e20] Distributed [`@stdlib/Distributed`]
[9fa8497b] Future [`@stdlib/Future`]
[b77e0a4c] InteractiveUtils [`@stdlib/InteractiveUtils`]
[76f85450] LibGit2 [`@stdlib/LibGit2`]
[8f399da3] Libdl [`@stdlib/Libdl`]
[37e2e46d] LinearAlgebra [`@stdlib/LinearAlgebra`]
[56ddb016] Logging [`@stdlib/Logging`]
[d6f4376e] Markdown [`@stdlib/Markdown`]
[a63ad114] Mmap [`@stdlib/Mmap`]
[44cfe95a] Pkg [`@stdlib/Pkg`]
[de0858da] Printf [`@stdlib/Printf`]
[9abbd945] Profile [`@stdlib/Profile`]
[3fa0cd96] REPL [`@stdlib/REPL`]
[9a3f8284] Random [`@stdlib/Random`]
[ea8e919c] SHA [`@stdlib/SHA`]
[9e88b42a] Serialization [`@stdlib/Serialization`]
[1a1011a3] SharedArrays [`@stdlib/SharedArrays`]
[6462fe0b] Sockets [`@stdlib/Sockets`]
[2f01184e] SparseArrays [`@stdlib/SparseArrays`]
[10745b16] Statistics [`@stdlib/Statistics`]
[8dfed614] Test [`@stdlib/Test`]
[cf7118a7] UUIDs [`@stdlib/UUIDs`]
[4ec0a83e] Unicode [`@stdlib/Unicode`]
Test Summary: | Pass Total
Box 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/qkqKR/src/Crystal.jl:678
┌ Warning: Charges are already present in test_structure2.cif. Removing the current charges on the
│ framework and adding new ones...
└ @ PorousMaterials ~/.julia/packages/PorousMaterials/qkqKR/src/Crystal.jl:678
# atoms removed: 2
# charges removed: 2
Test Summary: | Pass Total
Crystal Tests | 25 25
See random_vectors_on_sphere
see co2s.xyz for dist'n of rotations
atom dist [0.0 1.1599999999947173 1.159999999994656; 1.1599999999947173 0.0 2.319999999989373; 1.159999999994656 2.319999999989373 0.0]
charge dist [0.0 1.1599999999947173 1.159999999994656; 1.1599999999947173 0.0 2.319999999989373; 1.159999999994656 2.319999999989373 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/qkqKR/src/Forcefield.jl:181
┌ Warning: C in SBMOF-1.cif missing from bogus.csv force field.
└ @ PorousMaterials ~/.julia/packages/PorousMaterials/qkqKR/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.PengRobinsonGas(::Symbol) at EOS.jl:111
└ @ PorousMaterials ~/.julia/packages/PorousMaterials/qkqKR/src/EOS.jl:111
┌ Warning: `getindex(df::DataFrame, col_ind::ColumnIndex)` is deprecated, use `df[!, col_ind]` instead.
│ caller = PorousMaterials.PengRobinsonGas(::Symbol) at EOS.jl:114
└ @ PorousMaterials ~/.julia/packages/PorousMaterials/qkqKR/src/EOS.jl:114
┌ Warning: `getindex(df::DataFrame, col_ind::ColumnIndex)` is deprecated, use `df[!, col_ind]` instead.
│ caller = PorousMaterials.PengRobinsonGas(::Symbol) at EOS.jl:115
└ @ PorousMaterials ~/.julia/packages/PorousMaterials/qkqKR/src/EOS.jl:115
┌ Warning: `getindex(df::DataFrame, col_ind::ColumnIndex)` is deprecated, use `df[!, col_ind]` instead.
│ caller = PorousMaterials.PengRobinsonGas(::Symbol) at EOS.jl:116
└ @ PorousMaterials ~/.julia/packages/PorousMaterials/qkqKR/src/EOS.jl:116
Test Summary: | Pass Total
EOS Tests | 5 5
Test Summary: | Pass Total
GCMC Checkpoint Tests | 12 12
Simulating Henry coefficient of CO2 in FIQCEN_clean_min_charges.cif at 298.0 K, using UFF.csv force field with 0.16052649377009756 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_min_charges.cif have charges? true
Molecule CO2 has point charges? true
Ewald summation parameters:
k-replication factors: 7 7 7
Ewald convergence param. α = 0.219398
short-range cutoff radius (Å): 14.000000
1081 kvectors
(calculated with specified precision 1.000000e-06)
Ewald summation parameters:
k-replication factors: 7 7 7
Ewald convergence param. α = 0.219398
short-range cutoff radius (Å): 14.000000
1081 kvectors
(calculated with specified precision 1.000000e-06)
Ewald summation parameters:
k-replication factors: 7 7 7
Ewald convergence param. α = 0.219398
short-range cutoff radius (Å): 14.000000
1081 kvectors
(calculated with specified precision 1.000000e-06)
Ewald summation parameters:
k-replication factors: 7 7 7
Ewald convergence param. α = 0.219398
short-range cutoff radius (Å): 14.000000
1081 kvectors
(calculated with specified precision 1.000000e-06)
Ewald summation parameters:
k-replication factors: 7 7 7
Ewald convergence param. α = 0.219398
short-range cutoff radius (Å): 14.000000
1081 kvectors
(calculated with specified precision 1.000000e-06)
Block 1/5 statistics:
Henry coeff. [mmol/(g-bar)]: 1.9416602906535878
⟨U, vdw⟩ (K): -1636.4453344512622
⟨U, Coulomb⟩ (K): -353.9609402527154
Block 2/5 statistics:
Henry coeff. [mmol/(g-bar)]: 68.27462360087334
⟨U, vdw⟩ (K): -2570.802481913682
⟨U, Coulomb⟩ (K): -1067.2078824918337
Block 3/5 statistics:
Henry coeff. [mmol/(g-bar)]: 0.7145795687048162
⟨U, vdw⟩ (K): -1258.9200266059713
⟨U, Coulomb⟩ (K): -166.2725637993748
Block 4/5 statistics:
Henry coeff. [mmol/(g-bar)]: 1.089179363248315
⟨U, vdw⟩ (K): -1534.9629973227884
⟨U, Coulomb⟩ (K): -253.12974699613852
Block 5/5 statistics:
Henry coeff. [mmol/(g-bar)]: 1.9554312719854892
⟨U, vdw⟩ (K): -1446.181932738705
⟨U, Coulomb⟩ (K): -295.3000123563448
Results saved in: /root/.julia/packages/PorousMaterials/qkqKR/test/data/henry_sims/henry_sim_CO2_in_FIQCEN_clean_min_charges.cif_298.000000K_UFF.csv_ff_0_insertions_per_volume.jld2
Elapsed time (min): 2.122946365674337
----- final results ----
henry coefficient [mmol/(g-bar)] = 14.795095 +/- 26.744124
⟨U, vdw⟩ (kJ/mol) = -14.046968 +/- 3.806522
⟨U, Coulomb⟩ (kJ/mol) = -3.551723 +/- 2.708920
Qst (kJ/mol) = 20.076400 +/- 6.515442
Simulating Henry coefficient of CO2 in FIQCEN_clean_min_charges.cif at 298.0 K, using UFF.csv force field with 0.16052649377009756 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_min_charges.cif have charges? true
Molecule CO2 has point charges? true
Ewald summation parameters:
k-replication factors: 7 7 7
Ewald convergence param. α = 0.219398
short-range cutoff radius (Å): 14.000000
1081 kvectors
(calculated with specified precision 1.000000e-06)
Block 1: recovered previous, finished simulation results from checkpoint
Ewald summation parameters:
k-replication factors: 7 7 7
Ewald convergence param. α = 0.219398
short-range cutoff radius (Å): 14.000000
1081 kvectors
(calculated with specified precision 1.000000e-06)
Block 2: recovered previous, finished simulation results from checkpoint
Ewald summation parameters:
k-replication factors: 7 7 7
Ewald convergence param. α = 0.219398
short-range cutoff radius (Å): 14.000000
1081 kvectors
(calculated with specified precision 1.000000e-06)
Block 3: recovered previous, finished simulation results from checkpoint
Ewald summation parameters:
k-replication factors: 7 7 7
Ewald convergence param. α = 0.219398
short-range cutoff radius (Å): 14.000000
1081 kvectors
(calculated with specified precision 1.000000e-06)
Block 4: recovered previous, finished simulation results from checkpoint
Ewald summation parameters:
k-replication factors: 7 7 7
Ewald convergence param. α = 0.219398
short-range cutoff radius (Å): 14.000000
1081 kvectors
(calculated with specified precision 1.000000e-06)
Block 5: recovered previous, finished simulation results from checkpoint
Block 1/5 statistics:
Henry coeff. [mmol/(g-bar)]: 1.9416602906535878
⟨U, vdw⟩ (K): -1636.4453344512622
⟨U, Coulomb⟩ (K): -353.9609402527154
Block 2/5 statistics:
Henry coeff. [mmol/(g-bar)]: 68.27462360087334
⟨U, vdw⟩ (K): -2570.802481913682
⟨U, Coulomb⟩ (K): -1067.2078824918337
Block 3/5 statistics:
Henry coeff. [mmol/(g-bar)]: 0.7145795687048162
⟨U, vdw⟩ (K): -1258.9200266059713
⟨U, Coulomb⟩ (K): -166.2725637993748
Block 4/5 statistics:
Henry coeff. [mmol/(g-bar)]: 1.089179363248315
⟨U, vdw⟩ (K): -1534.9629973227884
⟨U, Coulomb⟩ (K): -253.12974699613852
Block 5/5 statistics:
Henry coeff. [mmol/(g-bar)]: 1.9554312719854892
⟨U, vdw⟩ (K): -1446.181932738705
⟨U, Coulomb⟩ (K): -295.3000123563448
Results saved in: /root/.julia/packages/PorousMaterials/qkqKR/test/data/henry_sims/henry_sim_CO2_in_FIQCEN_clean_min_charges.cif_298.000000K_UFF.csv_ff_0_insertions_per_volume.jld2
Elapsed time (min): 0.010786135991414389
----- final results ----
henry coefficient [mmol/(g-bar)] = 14.795095 +/- 26.744124
⟨U, vdw⟩ (kJ/mol) = -14.046968 +/- 3.806522
⟨U, Coulomb⟩ (kJ/mol) = -3.551723 +/- 2.708920
Qst (kJ/mol) = 20.076400 +/- 6.515442
Test Summary: | Pass Total
Henry Checkpoint Tests | 5 5
See /root/.julia/packages/PorousMaterials/qkqKR/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 /root/.julia/packages/PorousMaterials/qkqKR/test/data/grids/CH4_in_LTA_UFF_b4_pocket_blocking.cube
See /root/.julia/packages/PorousMaterials/qkqKR/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 /root/.julia/packages/PorousMaterials/qkqKR/test/data/grids/CH4_in_SOD_UFF_b4_pocket_blocking.cube
See /root/.julia/packages/PorousMaterials/qkqKR/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/qkqKR/src/Grid.jl:668
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 /root/.julia/packages/PorousMaterials/qkqKR/test/data/grids/CH4_in_LTA_UFF_b4_pocket_blocking.cube
See /root/.julia/packages/PorousMaterials/qkqKR/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 /root/.julia/packages/PorousMaterials/qkqKR/test/data/grids/CH4_in_LTA_UFF_b4_pocket_blocking.cube
See /root/.julia/packages/PorousMaterials/qkqKR/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 /root/.julia/packages/PorousMaterials/qkqKR/test/data/grids/CH4_in_SBMOF-1_UFF_b4_pocket_blocking.cube
See /root/.julia/packages/PorousMaterials/qkqKR/test/data/grids/CH4_in_SBMOF-1_UFF_after_pocket_blocking.cube
See /root/.julia/packages/PorousMaterials/qkqKR/test/data/grids/CH4_in_CAXVII_clean_UFF_b4_pocket_blocking.cube
See /root/.julia/packages/PorousMaterials/qkqKR/test/data/grids/CH4_in_CAXVII_clean_UFF_after_pocket_blocking.cube
Test Summary: | Pass Total
Grid Tests | 53 53
┌ Warning: PorousMaterials is now in Tutorial Mode. You have access to the testing data to experiment with PorousMaterials.
│ To get access to your own data use: reset_path_to_data()
└ @ PorousMaterials ~/.julia/packages/PorousMaterials/qkqKR/src/PorousMaterials.jl:74
PATH_TO_DATA set to /root/.julia/packages/PorousMaterials/qkqKR/test
PATH_TO_DATA set to /root/.julia/packages/PorousMaterials/qkqKR/test/data
Test Summary: | Pass Total
Path Tests | 3 3
Test Summary: | Pass Total
Generic Rotation Tests | 7 7
Testing PorousMaterials tests passed
Results with Julia v1.3.0
Testing was successful .
Last evaluation was ago and took 30 minutes, 3 seconds.
Click here to download the log file.
Click here to show the log contents.
Resolving package versions...
Installed SortingAlgorithms ─────────── v0.3.1
Installed JLD2 ──────────────────────── v0.1.9
Installed Roots ─────────────────────── v0.8.3
Installed DataStructures ────────────── v0.17.6
Installed StaticArrays ──────────────── v0.12.1
Installed LazyArrays ────────────────── v0.14.10
Installed CSV ───────────────────────── v0.5.18
Installed Compat ────────────────────── v3.0.0
Installed BinaryProvider ────────────── v0.5.8
Installed Missings ──────────────────── v0.4.3
Installed Parsers ───────────────────── v0.3.10
Installed ProgressMeter ─────────────── v0.9.0
Installed CategoricalArrays ─────────── v0.7.3
Installed FileIO ────────────────────── v1.1.0
Installed TableTraits ───────────────── v1.0.0
Installed OrderedCollections ────────── v1.1.0
Installed SpecialFunctions ──────────── v0.9.0
Installed MacroTools ────────────────── v0.5.1
Installed JSON ──────────────────────── v0.21.0
Installed ArrayLayouts ──────────────── v0.1.5
Installed LightGraphs ───────────────── v1.3.0
Installed RecipesBase ───────────────── v0.7.0
Installed DataAPI ───────────────────── v1.1.0
Installed Tables ────────────────────── v0.2.11
Installed Polynomials ───────────────── v0.6.0
Installed CSTParser ─────────────────── v1.1.0
Installed DataValueInterfaces ───────── v1.0.0
Installed OpenSpecFun_jll ───────────── v0.5.3+1
Installed ArnoldiMethod ─────────────── v0.0.4
Installed CodecZlib ─────────────────── v0.6.0
Installed FilePathsBase ─────────────── v0.7.0
Installed Inflate ───────────────────── v0.1.1
Installed SimpleTraits ──────────────── v0.9.1
Installed IteratorInterfaceExtensions ─ v1.0.0
Installed PooledArrays ──────────────── v0.5.2
Installed OffsetArrays ──────────────── v0.11.2
Installed TranscodingStreams ────────── v0.9.5
Installed WeakRefStrings ────────────── v0.6.1
Installed DataFrames ────────────────── v0.18.4
Installed FillArrays ────────────────── v0.8.2
Installed Reexport ──────────────────── v0.2.0
Installed StatsBase ─────────────────── v0.32.0
Installed Tokenize ──────────────────── v0.5.7
Installed PorousMaterials ───────────── v0.1.6
Updating `~/.julia/environments/v1.3/Project.toml`
[68953c7c] + PorousMaterials v0.1.6
Updating `~/.julia/environments/v1.3/Manifest.toml`
[ec485272] + ArnoldiMethod v0.0.4
[4c555306] + ArrayLayouts v0.1.5
[b99e7846] + BinaryProvider v0.5.8
[00ebfdb7] + CSTParser v1.1.0
[336ed68f] + CSV v0.5.18
[324d7699] + CategoricalArrays v0.7.3
[944b1d66] + CodecZlib v0.6.0
[34da2185] + Compat v3.0.0
[9a962f9c] + DataAPI v1.1.0
[a93c6f00] + DataFrames v0.18.4
[864edb3b] + DataStructures v0.17.6
[e2d170a0] + DataValueInterfaces v1.0.0
[5789e2e9] + FileIO v1.1.0
[48062228] + FilePathsBase v0.7.0
[1a297f60] + FillArrays v0.8.2
[d25df0c9] + Inflate v0.1.1
[82899510] + IteratorInterfaceExtensions v1.0.0
[033835bb] + JLD2 v0.1.9
[682c06a0] + JSON v0.21.0
[5078a376] + LazyArrays v0.14.10
[093fc24a] + LightGraphs v1.3.0
[1914dd2f] + MacroTools v0.5.1
[e1d29d7a] + Missings v0.4.3
[6fe1bfb0] + OffsetArrays v0.11.2
[efe28fd5] + OpenSpecFun_jll v0.5.3+1
[bac558e1] + OrderedCollections v1.1.0
[69de0a69] + Parsers v0.3.10
[f27b6e38] + Polynomials v0.6.0
[2dfb63ee] + PooledArrays v0.5.2
[68953c7c] + PorousMaterials v0.1.6
[92933f4c] + ProgressMeter v0.9.0
[3cdcf5f2] + RecipesBase v0.7.0
[189a3867] + Reexport v0.2.0
[f2b01f46] + Roots v0.8.3
[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
[0796e94c] + Tokenize v0.5.7
[3bb67fe8] + TranscodingStreams v0.9.5
[ea10d353] + WeakRefStrings v0.6.1
[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
[9abbd945] + Profile
[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_WbPbVd/Manifest.toml`
[ec485272] ArnoldiMethod v0.0.4
[4c555306] ArrayLayouts v0.1.5
[b99e7846] BinaryProvider v0.5.8
[00ebfdb7] CSTParser v1.1.0
[336ed68f] CSV v0.5.18
[324d7699] CategoricalArrays v0.7.3
[944b1d66] CodecZlib v0.6.0
[34da2185] Compat v3.0.0
[9a962f9c] DataAPI v1.1.0
[a93c6f00] DataFrames v0.18.4
[864edb3b] DataStructures v0.17.6
[e2d170a0] DataValueInterfaces v1.0.0
[5789e2e9] FileIO v1.1.0
[48062228] FilePathsBase v0.7.0
[1a297f60] FillArrays v0.8.2
[d25df0c9] Inflate v0.1.1
[82899510] IteratorInterfaceExtensions v1.0.0
[033835bb] JLD2 v0.1.9
[682c06a0] JSON v0.21.0
[5078a376] LazyArrays v0.14.10
[093fc24a] LightGraphs v1.3.0
[1914dd2f] MacroTools v0.5.1
[e1d29d7a] Missings v0.4.3
[6fe1bfb0] OffsetArrays v0.11.2
[efe28fd5] OpenSpecFun_jll v0.5.3+1
[bac558e1] OrderedCollections v1.1.0
[69de0a69] Parsers v0.3.10
[f27b6e38] Polynomials v0.6.0
[2dfb63ee] PooledArrays v0.5.2
[68953c7c] PorousMaterials v0.1.6
[92933f4c] ProgressMeter v0.9.0
[3cdcf5f2] RecipesBase v0.7.0
[189a3867] Reexport v0.2.0
[f2b01f46] Roots v0.8.3
[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
[0796e94c] Tokenize v0.5.7
[3bb67fe8] TranscodingStreams v0.9.5
[ea10d353] WeakRefStrings v0.6.1
[2a0f44e3] Base64 [`@stdlib/Base64`]
[ade2ca70] Dates [`@stdlib/Dates`]
[8bb1440f] DelimitedFiles [`@stdlib/DelimitedFiles`]
[8ba89e20] Distributed [`@stdlib/Distributed`]
[9fa8497b] Future [`@stdlib/Future`]
[b77e0a4c] InteractiveUtils [`@stdlib/InteractiveUtils`]
[76f85450] LibGit2 [`@stdlib/LibGit2`]
[8f399da3] Libdl [`@stdlib/Libdl`]
[37e2e46d] LinearAlgebra [`@stdlib/LinearAlgebra`]
[56ddb016] Logging [`@stdlib/Logging`]
[d6f4376e] Markdown [`@stdlib/Markdown`]
[a63ad114] Mmap [`@stdlib/Mmap`]
[44cfe95a] Pkg [`@stdlib/Pkg`]
[de0858da] Printf [`@stdlib/Printf`]
[9abbd945] Profile [`@stdlib/Profile`]
[3fa0cd96] REPL [`@stdlib/REPL`]
[9a3f8284] Random [`@stdlib/Random`]
[ea8e919c] SHA [`@stdlib/SHA`]
[9e88b42a] Serialization [`@stdlib/Serialization`]
[1a1011a3] SharedArrays [`@stdlib/SharedArrays`]
[6462fe0b] Sockets [`@stdlib/Sockets`]
[2f01184e] SparseArrays [`@stdlib/SparseArrays`]
[10745b16] Statistics [`@stdlib/Statistics`]
[8dfed614] Test [`@stdlib/Test`]
[cf7118a7] UUIDs [`@stdlib/UUIDs`]
[4ec0a83e] Unicode [`@stdlib/Unicode`]
WARNING: Compat.Statistics is deprecated, use Statistics instead.
likely near /root/.julia/packages/CategoricalArrays/U3LvJ/src/extras.jl:1
WARNING: Compat.Markdown is deprecated, use Markdown instead.
likely near /root/.julia/packages/MacroTools/ys44U/src/MacroTools.jl:4
WARNING: Compat.Random is deprecated, use Random instead.
likely near /root/.julia/packages/MacroTools/ys44U/src/MacroTools.jl:35
Test Summary: | Pass Total
Box 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/qkqKR/src/Crystal.jl:678
┌ Warning: Charges are already present in test_structure2.cif. Removing the current charges on the
│ framework and adding new ones...
└ @ PorousMaterials ~/.julia/packages/PorousMaterials/qkqKR/src/Crystal.jl:678
# atoms removed: 2
# charges removed: 2
Test Summary: | Pass Total
Crystal Tests | 25 25
See random_vectors_on_sphere
see co2s.xyz for dist'n of rotations
atom dist [0.0 1.1599999999945143 1.159999999994286; 1.1599999999945143 0.0 2.319999999988801; 1.159999999994286 2.319999999988801 0.0]
charge dist [0.0 1.1599999999945143 1.159999999994286; 1.1599999999945143 0.0 2.319999999988801; 1.159999999994286 2.319999999988801 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/qkqKR/src/Forcefield.jl:181
┌ Warning: C in SBMOF-1.cif missing from bogus.csv force field.
└ @ PorousMaterials ~/.julia/packages/PorousMaterials/qkqKR/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
Test Summary: | Pass Total
EOS Tests | 5 5
Test Summary: | Pass Total
GCMC Checkpoint Tests | 12 12
Simulating Henry coefficient of CO2 in FIQCEN_clean_min_charges.cif at 298.0 K, using UFF.csv force field with 0.16052649377009756 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_min_charges.cif have charges? true
Molecule CO2 has point charges? true
Ewald summation parameters:
k-replication factors: 7 7 7
Ewald convergence param. α = 0.219398
short-range cutoff radius (Å): 14.000000
1081 kvectors
(calculated with specified precision 1.000000e-06)
Ewald summation parameters:
k-replication factors: 7 7 7
Ewald convergence param. α = 0.219398
short-range cutoff radius (Å): 14.000000
1081 kvectors
(calculated with specified precision 1.000000e-06)
Ewald summation parameters:
k-replication factors: 7 7 7
Ewald convergence param. α = 0.219398
short-range cutoff radius (Å): 14.000000
1081 kvectors
(calculated with specified precision 1.000000e-06)
Ewald summation parameters:
k-replication factors: 7 7 7
Ewald convergence param. α = 0.219398
short-range cutoff radius (Å): 14.000000
1081 kvectors
(calculated with specified precision 1.000000e-06)
Ewald summation parameters:
k-replication factors: 7 7 7
Ewald convergence param. α = 0.219398
short-range cutoff radius (Å): 14.000000
1081 kvectors
(calculated with specified precision 1.000000e-06)
Block 1/5 statistics:
Henry coeff. [mmol/(g-bar)]: 23.496443507516673
⟨U, vdw⟩ (K): -3080.1903703378844
⟨U, Coulomb⟩ (K): -95.26120026401733
Block 2/5 statistics:
Henry coeff. [mmol/(g-bar)]: 1.943945931251864
⟨U, vdw⟩ (K): -1245.7308115627754
⟨U, Coulomb⟩ (K): -620.8724350104906
Block 3/5 statistics:
Henry coeff. [mmol/(g-bar)]: 9.243861293818519
⟨U, vdw⟩ (K): -2885.743530040211
⟨U, Coulomb⟩ (K): 41.84512006300687
Block 4/5 statistics:
Henry coeff. [mmol/(g-bar)]: 14.239524566105464
⟨U, vdw⟩ (K): -2019.6675950995236
⟨U, Coulomb⟩ (K): -663.9976595781179
Block 5/5 statistics:
Henry coeff. [mmol/(g-bar)]: 2.048896681473122
⟨U, vdw⟩ (K): -1158.8794722709379
⟨U, Coulomb⟩ (K): -843.8411227215347
Results saved in: /root/.julia/packages/PorousMaterials/qkqKR/test/data/henry_sims/henry_sim_CO2_in_FIQCEN_clean_min_charges.cif_298.000000K_UFF.csv_ff_0_insertions_per_volume.jld2
Elapsed time (min): 1.9182583491007488
----- final results ----
henry coefficient [mmol/(g-bar)] = 10.194534 +/- 8.107159
⟨U, vdw⟩ (kJ/mol) = -17.277800 +/- 6.649169
⟨U, Coulomb⟩ (kJ/mol) = -3.628642 +/- 2.872843
Qst (kJ/mol) = 23.384151 +/- 9.522012
Simulating Henry coefficient of CO2 in FIQCEN_clean_min_charges.cif at 298.0 K, using UFF.csv force field with 0.16052649377009756 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_min_charges.cif have charges? true
Molecule CO2 has point charges? true
Ewald summation parameters:
k-replication factors: 7 7 7
Ewald convergence param. α = 0.219398
short-range cutoff radius (Å): 14.000000
1081 kvectors
(calculated with specified precision 1.000000e-06)
Block 1: recovered previous, finished simulation results from checkpoint
Ewald summation parameters:
k-replication factors: 7 7 7
Ewald convergence param. α = 0.219398
short-range cutoff radius (Å): 14.000000
1081 kvectors
(calculated with specified precision 1.000000e-06)
Block 2: recovered previous, finished simulation results from checkpoint
Ewald summation parameters:
k-replication factors: 7 7 7
Ewald convergence param. α = 0.219398
short-range cutoff radius (Å): 14.000000
1081 kvectors
(calculated with specified precision 1.000000e-06)
Block 3: recovered previous, finished simulation results from checkpoint
Ewald summation parameters:
k-replication factors: 7 7 7
Ewald convergence param. α = 0.219398
short-range cutoff radius (Å): 14.000000
1081 kvectors
(calculated with specified precision 1.000000e-06)
Block 4: recovered previous, finished simulation results from checkpoint
Ewald summation parameters:
k-replication factors: 7 7 7
Ewald convergence param. α = 0.219398
short-range cutoff radius (Å): 14.000000
1081 kvectors
(calculated with specified precision 1.000000e-06)
Block 5: recovered previous, finished simulation results from checkpoint
Block 1/5 statistics:
Henry coeff. [mmol/(g-bar)]: 23.496443507516673
⟨U, vdw⟩ (K): -3080.1903703378844
⟨U, Coulomb⟩ (K): -95.26120026401733
Block 2/5 statistics:
Henry coeff. [mmol/(g-bar)]: 1.943945931251864
⟨U, vdw⟩ (K): -1245.7308115627754
⟨U, Coulomb⟩ (K): -620.8724350104906
Block 3/5 statistics:
Henry coeff. [mmol/(g-bar)]: 9.243861293818519
⟨U, vdw⟩ (K): -2885.743530040211
⟨U, Coulomb⟩ (K): 41.84512006300687
Block 4/5 statistics:
Henry coeff. [mmol/(g-bar)]: 14.239524566105464
⟨U, vdw⟩ (K): -2019.6675950995236
⟨U, Coulomb⟩ (K): -663.9976595781179
Block 5/5 statistics:
Henry coeff. [mmol/(g-bar)]: 2.048896681473122
⟨U, vdw⟩ (K): -1158.8794722709379
⟨U, Coulomb⟩ (K): -843.8411227215347
Results saved in: /root/.julia/packages/PorousMaterials/qkqKR/test/data/henry_sims/henry_sim_CO2_in_FIQCEN_clean_min_charges.cif_298.000000K_UFF.csv_ff_0_insertions_per_volume.jld2
Elapsed time (min): 0.010553983847300212
----- final results ----
henry coefficient [mmol/(g-bar)] = 10.194534 +/- 8.107159
⟨U, vdw⟩ (kJ/mol) = -17.277800 +/- 6.649169
⟨U, Coulomb⟩ (kJ/mol) = -3.628642 +/- 2.872843
Qst (kJ/mol) = 23.384151 +/- 9.522012
Test Summary: | Pass Total
Henry Checkpoint Tests | 5 5
See /root/.julia/packages/PorousMaterials/qkqKR/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 /root/.julia/packages/PorousMaterials/qkqKR/test/data/grids/CH4_in_LTA_UFF_b4_pocket_blocking.cube
See /root/.julia/packages/PorousMaterials/qkqKR/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 /root/.julia/packages/PorousMaterials/qkqKR/test/data/grids/CH4_in_SOD_UFF_b4_pocket_blocking.cube
See /root/.julia/packages/PorousMaterials/qkqKR/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/qkqKR/src/Grid.jl:668
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 /root/.julia/packages/PorousMaterials/qkqKR/test/data/grids/CH4_in_LTA_UFF_b4_pocket_blocking.cube
See /root/.julia/packages/PorousMaterials/qkqKR/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 /root/.julia/packages/PorousMaterials/qkqKR/test/data/grids/CH4_in_LTA_UFF_b4_pocket_blocking.cube
See /root/.julia/packages/PorousMaterials/qkqKR/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 /root/.julia/packages/PorousMaterials/qkqKR/test/data/grids/CH4_in_SBMOF-1_UFF_b4_pocket_blocking.cube
See /root/.julia/packages/PorousMaterials/qkqKR/test/data/grids/CH4_in_SBMOF-1_UFF_after_pocket_blocking.cube
See /root/.julia/packages/PorousMaterials/qkqKR/test/data/grids/CH4_in_CAXVII_clean_UFF_b4_pocket_blocking.cube
See /root/.julia/packages/PorousMaterials/qkqKR/test/data/grids/CH4_in_CAXVII_clean_UFF_after_pocket_blocking.cube
Test Summary: | Pass Total
Grid Tests | 53 53
┌ Warning: PorousMaterials is now in Tutorial Mode. You have access to the testing data to experiment with PorousMaterials.
│ To get access to your own data use: reset_path_to_data()
└ @ PorousMaterials ~/.julia/packages/PorousMaterials/qkqKR/src/PorousMaterials.jl:74
PATH_TO_DATA set to /root/.julia/packages/PorousMaterials/qkqKR/test
PATH_TO_DATA set to /root/.julia/packages/PorousMaterials/qkqKR/test/data
Test Summary: | Pass Total
Path Tests | 3 3
Test Summary: | Pass Total
Generic Rotation Tests | 7 7
Testing PorousMaterials tests passed
Results with Julia v1.3.1-pre-7704df0a5a
Testing was successful .
Last evaluation was ago and took 33 minutes, 13 seconds.
Click here to download the log file.
Click here to show the log contents.
Resolving package versions...
Installed WeakRefStrings ────────────── v0.6.1
Installed OpenSpecFun_jll ───────────── v0.5.3+1
Installed ArrayLayouts ──────────────── v0.1.5
Installed Tables ────────────────────── v0.2.11
Installed SpecialFunctions ──────────── v0.9.0
Installed DataStructures ────────────── v0.17.6
Installed LightGraphs ───────────────── v1.3.0
Installed LazyArrays ────────────────── v0.14.10
Installed Compat ────────────────────── v3.0.0
Installed Polynomials ───────────────── v0.6.0
Installed StaticArrays ──────────────── v0.12.1
Installed DataFrames ────────────────── v0.18.4
Installed Inflate ───────────────────── v0.1.1
Installed Roots ─────────────────────── v0.8.3
Installed MacroTools ────────────────── v0.5.1
Installed OffsetArrays ──────────────── v0.11.2
Installed StatsBase ─────────────────── v0.32.0
Installed FillArrays ────────────────── v0.8.2
Installed CodecZlib ─────────────────── v0.6.0
Installed CSTParser ─────────────────── v1.1.0
Installed Missings ──────────────────── v0.4.3
Installed FileIO ────────────────────── v1.1.0
Installed TableTraits ───────────────── v1.0.0
Installed FilePathsBase ─────────────── v0.7.0
Installed PooledArrays ──────────────── v0.5.2
Installed BinaryProvider ────────────── v0.5.8
Installed ProgressMeter ─────────────── v0.9.0
Installed Tokenize ──────────────────── v0.5.7
Installed SimpleTraits ──────────────── v0.9.1
Installed TranscodingStreams ────────── v0.9.5
Installed Reexport ──────────────────── v0.2.0
Installed DataValueInterfaces ───────── v1.0.0
Installed CategoricalArrays ─────────── v0.7.3
Installed RecipesBase ───────────────── v0.7.0
Installed IteratorInterfaceExtensions ─ v1.0.0
Installed JSON ──────────────────────── v0.21.0
Installed DataAPI ───────────────────── v1.1.0
Installed JLD2 ──────────────────────── v0.1.9
Installed ArnoldiMethod ─────────────── v0.0.4
Installed OrderedCollections ────────── v1.1.0
Installed Parsers ───────────────────── v0.3.10
Installed SortingAlgorithms ─────────── v0.3.1
Installed CSV ───────────────────────── v0.5.18
Installed PorousMaterials ───────────── v0.1.6
Updating `~/.julia/environments/v1.3/Project.toml`
[68953c7c] + PorousMaterials v0.1.6
Updating `~/.julia/environments/v1.3/Manifest.toml`
[ec485272] + ArnoldiMethod v0.0.4
[4c555306] + ArrayLayouts v0.1.5
[b99e7846] + BinaryProvider v0.5.8
[00ebfdb7] + CSTParser v1.1.0
[336ed68f] + CSV v0.5.18
[324d7699] + CategoricalArrays v0.7.3
[944b1d66] + CodecZlib v0.6.0
[34da2185] + Compat v3.0.0
[9a962f9c] + DataAPI v1.1.0
[a93c6f00] + DataFrames v0.18.4
[864edb3b] + DataStructures v0.17.6
[e2d170a0] + DataValueInterfaces v1.0.0
[5789e2e9] + FileIO v1.1.0
[48062228] + FilePathsBase v0.7.0
[1a297f60] + FillArrays v0.8.2
[d25df0c9] + Inflate v0.1.1
[82899510] + IteratorInterfaceExtensions v1.0.0
[033835bb] + JLD2 v0.1.9
[682c06a0] + JSON v0.21.0
[5078a376] + LazyArrays v0.14.10
[093fc24a] + LightGraphs v1.3.0
[1914dd2f] + MacroTools v0.5.1
[e1d29d7a] + Missings v0.4.3
[6fe1bfb0] + OffsetArrays v0.11.2
[efe28fd5] + OpenSpecFun_jll v0.5.3+1
[bac558e1] + OrderedCollections v1.1.0
[69de0a69] + Parsers v0.3.10
[f27b6e38] + Polynomials v0.6.0
[2dfb63ee] + PooledArrays v0.5.2
[68953c7c] + PorousMaterials v0.1.6
[92933f4c] + ProgressMeter v0.9.0
[3cdcf5f2] + RecipesBase v0.7.0
[189a3867] + Reexport v0.2.0
[f2b01f46] + Roots v0.8.3
[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
[0796e94c] + Tokenize v0.5.7
[3bb67fe8] + TranscodingStreams v0.9.5
[ea10d353] + WeakRefStrings v0.6.1
[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
[9abbd945] + Profile
[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_ZMbHQT/Manifest.toml`
[ec485272] ArnoldiMethod v0.0.4
[4c555306] ArrayLayouts v0.1.5
[b99e7846] BinaryProvider v0.5.8
[00ebfdb7] CSTParser v1.1.0
[336ed68f] CSV v0.5.18
[324d7699] CategoricalArrays v0.7.3
[944b1d66] CodecZlib v0.6.0
[34da2185] Compat v3.0.0
[9a962f9c] DataAPI v1.1.0
[a93c6f00] DataFrames v0.18.4
[864edb3b] DataStructures v0.17.6
[e2d170a0] DataValueInterfaces v1.0.0
[5789e2e9] FileIO v1.1.0
[48062228] FilePathsBase v0.7.0
[1a297f60] FillArrays v0.8.2
[d25df0c9] Inflate v0.1.1
[82899510] IteratorInterfaceExtensions v1.0.0
[033835bb] JLD2 v0.1.9
[682c06a0] JSON v0.21.0
[5078a376] LazyArrays v0.14.10
[093fc24a] LightGraphs v1.3.0
[1914dd2f] MacroTools v0.5.1
[e1d29d7a] Missings v0.4.3
[6fe1bfb0] OffsetArrays v0.11.2
[efe28fd5] OpenSpecFun_jll v0.5.3+1
[bac558e1] OrderedCollections v1.1.0
[69de0a69] Parsers v0.3.10
[f27b6e38] Polynomials v0.6.0
[2dfb63ee] PooledArrays v0.5.2
[68953c7c] PorousMaterials v0.1.6
[92933f4c] ProgressMeter v0.9.0
[3cdcf5f2] RecipesBase v0.7.0
[189a3867] Reexport v0.2.0
[f2b01f46] Roots v0.8.3
[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
[0796e94c] Tokenize v0.5.7
[3bb67fe8] TranscodingStreams v0.9.5
[ea10d353] WeakRefStrings v0.6.1
[2a0f44e3] Base64 [`@stdlib/Base64`]
[ade2ca70] Dates [`@stdlib/Dates`]
[8bb1440f] DelimitedFiles [`@stdlib/DelimitedFiles`]
[8ba89e20] Distributed [`@stdlib/Distributed`]
[9fa8497b] Future [`@stdlib/Future`]
[b77e0a4c] InteractiveUtils [`@stdlib/InteractiveUtils`]
[76f85450] LibGit2 [`@stdlib/LibGit2`]
[8f399da3] Libdl [`@stdlib/Libdl`]
[37e2e46d] LinearAlgebra [`@stdlib/LinearAlgebra`]
[56ddb016] Logging [`@stdlib/Logging`]
[d6f4376e] Markdown [`@stdlib/Markdown`]
[a63ad114] Mmap [`@stdlib/Mmap`]
[44cfe95a] Pkg [`@stdlib/Pkg`]
[de0858da] Printf [`@stdlib/Printf`]
[9abbd945] Profile [`@stdlib/Profile`]
[3fa0cd96] REPL [`@stdlib/REPL`]
[9a3f8284] Random [`@stdlib/Random`]
[ea8e919c] SHA [`@stdlib/SHA`]
[9e88b42a] Serialization [`@stdlib/Serialization`]
[1a1011a3] SharedArrays [`@stdlib/SharedArrays`]
[6462fe0b] Sockets [`@stdlib/Sockets`]
[2f01184e] SparseArrays [`@stdlib/SparseArrays`]
[10745b16] Statistics [`@stdlib/Statistics`]
[8dfed614] Test [`@stdlib/Test`]
[cf7118a7] UUIDs [`@stdlib/UUIDs`]
[4ec0a83e] Unicode [`@stdlib/Unicode`]
WARNING: Compat.Statistics is deprecated, use Statistics instead.
likely near /root/.julia/packages/CategoricalArrays/U3LvJ/src/extras.jl:1
WARNING: Compat.Markdown is deprecated, use Markdown instead.
likely near /root/.julia/packages/MacroTools/ys44U/src/MacroTools.jl:4
WARNING: Compat.Random is deprecated, use Random instead.
likely near /root/.julia/packages/MacroTools/ys44U/src/MacroTools.jl:35
Test Summary: | Pass Total
Box 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/qkqKR/src/Crystal.jl:678
┌ Warning: Charges are already present in test_structure2.cif. Removing the current charges on the
│ framework and adding new ones...
└ @ PorousMaterials ~/.julia/packages/PorousMaterials/qkqKR/src/Crystal.jl:678
# atoms removed: 2
# charges removed: 2
Test Summary: | Pass Total
Crystal Tests | 25 25
See random_vectors_on_sphere
see co2s.xyz for dist'n of rotations
atom dist [0.0 1.1599999999948585 1.1599999999946622; 1.1599999999948585 0.0 2.3199999999895207; 1.1599999999946622 2.3199999999895207 0.0]
charge dist [0.0 1.1599999999948585 1.1599999999946622; 1.1599999999948585 0.0 2.3199999999895207; 1.1599999999946622 2.3199999999895207 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/qkqKR/src/Forcefield.jl:181
┌ Warning: C in SBMOF-1.cif missing from bogus.csv force field.
└ @ PorousMaterials ~/.julia/packages/PorousMaterials/qkqKR/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
Test Summary: | Pass Total
EOS Tests | 5 5
Test Summary: | Pass Total
GCMC Checkpoint Tests | 12 12
Simulating Henry coefficient of CO2 in FIQCEN_clean_min_charges.cif at 298.0 K, using UFF.csv force field with 0.16052649377009756 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_min_charges.cif have charges? true
Molecule CO2 has point charges? true
Ewald summation parameters:
k-replication factors: 7 7 7
Ewald convergence param. α = 0.219398
short-range cutoff radius (Å): 14.000000
1081 kvectors
(calculated with specified precision 1.000000e-06)
Ewald summation parameters:
k-replication factors: 7 7 7
Ewald convergence param. α = 0.219398
short-range cutoff radius (Å): 14.000000
1081 kvectors
(calculated with specified precision 1.000000e-06)
Ewald summation parameters:
k-replication factors: 7 7 7
Ewald convergence param. α = 0.219398
short-range cutoff radius (Å): 14.000000
1081 kvectors
(calculated with specified precision 1.000000e-06)
Ewald summation parameters:
k-replication factors: 7 7 7
Ewald convergence param. α = 0.219398
short-range cutoff radius (Å): 14.000000
1081 kvectors
(calculated with specified precision 1.000000e-06)
Ewald summation parameters:
k-replication factors: 7 7 7
Ewald convergence param. α = 0.219398
short-range cutoff radius (Å): 14.000000
1081 kvectors
(calculated with specified precision 1.000000e-06)
Block 1/5 statistics:
Henry coeff. [mmol/(g-bar)]: 6.834607330502543
⟨U, vdw⟩ (K): -2227.9083978343533
⟨U, Coulomb⟩ (K): -234.96841688761367
Block 2/5 statistics:
Henry coeff. [mmol/(g-bar)]: 8.80246111939153
⟨U, vdw⟩ (K): -1708.3495112928133
⟨U, Coulomb⟩ (K): -1016.5287433993327
Block 3/5 statistics:
Henry coeff. [mmol/(g-bar)]: 75.83134588311621
⟨U, vdw⟩ (K): -1919.7641327494264
⟨U, Coulomb⟩ (K): -1757.865615337094
Block 4/5 statistics:
Henry coeff. [mmol/(g-bar)]: 617.2652730600911
⟨U, vdw⟩ (K): -2913.2227267623234
⟨U, Coulomb⟩ (K): -1318.4106816502997
Block 5/5 statistics:
Henry coeff. [mmol/(g-bar)]: 12.337604180891159
⟨U, vdw⟩ (K): -2141.4739548188154
⟨U, Coulomb⟩ (K): -767.125595113529
Results saved in: /root/.julia/packages/PorousMaterials/qkqKR/test/data/henry_sims/henry_sim_CO2_in_FIQCEN_clean_min_charges.cif_298.000000K_UFF.csv_ff_0_insertions_per_volume.jld2
Elapsed time (min): 2.964477713902791
----- final results ----
henry coefficient [mmol/(g-bar)] = 144.214258 +/- 237.930435
⟨U, vdw⟩ (kJ/mol) = -18.143346 +/- 3.390728
⟨U, Coulomb⟩ (kJ/mol) = -8.472267 +/- 4.261875
Qst (kJ/mol) = 29.093322 +/- 7.652603
Simulating Henry coefficient of CO2 in FIQCEN_clean_min_charges.cif at 298.0 K, using UFF.csv force field with 0.16052649377009756 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_min_charges.cif have charges? true
Molecule CO2 has point charges? true
Ewald summation parameters:
k-replication factors: 7 7 7
Ewald convergence param. α = 0.219398
short-range cutoff radius (Å): 14.000000
1081 kvectors
(calculated with specified precision 1.000000e-06)
Block 1: recovered previous, finished simulation results from checkpoint
Ewald summation parameters:
k-replication factors: 7 7 7
Ewald convergence param. α = 0.219398
short-range cutoff radius (Å): 14.000000
1081 kvectors
(calculated with specified precision 1.000000e-06)
Block 2: recovered previous, finished simulation results from checkpoint
Ewald summation parameters:
k-replication factors: 7 7 7
Ewald convergence param. α = 0.219398
short-range cutoff radius (Å): 14.000000
1081 kvectors
(calculated with specified precision 1.000000e-06)
Block 3: recovered previous, finished simulation results from checkpoint
Ewald summation parameters:
k-replication factors: 7 7 7
Ewald convergence param. α = 0.219398
short-range cutoff radius (Å): 14.000000
1081 kvectors
(calculated with specified precision 1.000000e-06)
Block 4: recovered previous, finished simulation results from checkpoint
Ewald summation parameters:
k-replication factors: 7 7 7
Ewald convergence param. α = 0.219398
short-range cutoff radius (Å): 14.000000
1081 kvectors
(calculated with specified precision 1.000000e-06)
Block 5: recovered previous, finished simulation results from checkpoint
Block 1/5 statistics:
Henry coeff. [mmol/(g-bar)]: 6.834607330502543
⟨U, vdw⟩ (K): -2227.9083978343533
⟨U, Coulomb⟩ (K): -234.96841688761367
Block 2/5 statistics:
Henry coeff. [mmol/(g-bar)]: 8.80246111939153
⟨U, vdw⟩ (K): -1708.3495112928133
⟨U, Coulomb⟩ (K): -1016.5287433993327
Block 3/5 statistics:
Henry coeff. [mmol/(g-bar)]: 75.83134588311621
⟨U, vdw⟩ (K): -1919.7641327494264
⟨U, Coulomb⟩ (K): -1757.865615337094
Block 4/5 statistics:
Henry coeff. [mmol/(g-bar)]: 617.2652730600911
⟨U, vdw⟩ (K): -2913.2227267623234
⟨U, Coulomb⟩ (K): -1318.4106816502997
Block 5/5 statistics:
Henry coeff. [mmol/(g-bar)]: 12.337604180891159
⟨U, vdw⟩ (K): -2141.4739548188154
⟨U, Coulomb⟩ (K): -767.125595113529
Results saved in: /root/.julia/packages/PorousMaterials/qkqKR/test/data/henry_sims/henry_sim_CO2_in_FIQCEN_clean_min_charges.cif_298.000000K_UFF.csv_ff_0_insertions_per_volume.jld2
Elapsed time (min): 0.018201684951782225
----- final results ----
henry coefficient [mmol/(g-bar)] = 144.214258 +/- 237.930435
⟨U, vdw⟩ (kJ/mol) = -18.143346 +/- 3.390728
⟨U, Coulomb⟩ (kJ/mol) = -8.472267 +/- 4.261875
Qst (kJ/mol) = 29.093322 +/- 7.652603
Test Summary: | Pass Total
Henry Checkpoint Tests | 5 5
See /root/.julia/packages/PorousMaterials/qkqKR/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 /root/.julia/packages/PorousMaterials/qkqKR/test/data/grids/CH4_in_LTA_UFF_b4_pocket_blocking.cube
See /root/.julia/packages/PorousMaterials/qkqKR/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 /root/.julia/packages/PorousMaterials/qkqKR/test/data/grids/CH4_in_SOD_UFF_b4_pocket_blocking.cube
See /root/.julia/packages/PorousMaterials/qkqKR/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/qkqKR/src/Grid.jl:668
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 /root/.julia/packages/PorousMaterials/qkqKR/test/data/grids/CH4_in_LTA_UFF_b4_pocket_blocking.cube
See /root/.julia/packages/PorousMaterials/qkqKR/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 /root/.julia/packages/PorousMaterials/qkqKR/test/data/grids/CH4_in_LTA_UFF_b4_pocket_blocking.cube
See /root/.julia/packages/PorousMaterials/qkqKR/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 /root/.julia/packages/PorousMaterials/qkqKR/test/data/grids/CH4_in_SBMOF-1_UFF_b4_pocket_blocking.cube
See /root/.julia/packages/PorousMaterials/qkqKR/test/data/grids/CH4_in_SBMOF-1_UFF_after_pocket_blocking.cube
See /root/.julia/packages/PorousMaterials/qkqKR/test/data/grids/CH4_in_CAXVII_clean_UFF_b4_pocket_blocking.cube
See /root/.julia/packages/PorousMaterials/qkqKR/test/data/grids/CH4_in_CAXVII_clean_UFF_after_pocket_blocking.cube
Test Summary: | Pass Total
Grid Tests | 53 53
┌ Warning: PorousMaterials is now in Tutorial Mode. You have access to the testing data to experiment with PorousMaterials.
│ To get access to your own data use: reset_path_to_data()
└ @ PorousMaterials ~/.julia/packages/PorousMaterials/qkqKR/src/PorousMaterials.jl:74
PATH_TO_DATA set to /root/.julia/packages/PorousMaterials/qkqKR/test
PATH_TO_DATA set to /root/.julia/packages/PorousMaterials/qkqKR/test/data
Test Summary: | Pass Total
Path Tests | 3 3
Test Summary: | Pass Total
Generic Rotation Tests | 7 7
Testing PorousMaterials tests passed