V0.4.0 (#175)

* reexport Xtals; matter, box, crystal * finished (?) split of Xtals code * final source changes * won't build until Xtals v0.3.0 * re-attempt * easy access to long GCMC tests * registry lag workaround * release v0.4 * physical constants * GLOBALS, bugfixes
SimonEnsemble · Jun 11, 2021 · 913d0e5 · 913d0e5
1 parent e4e8ea2
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diff --git a/.gitignore b/.gitignore
@@ -8,4 +8,6 @@
 *.jld2
 docs/build/
 docs/site/
-*checkpoint.ipynb
+*checkpoint.ipynb
+.vscode
+Manifest.toml
diff --git a/.travis.yml b/.travis.yml
@@ -1,9 +1,9 @@
 language: julia
 
-coveralls: true
+codecov: true
 
 julia:
-    - 1.5
+  - 1.6
 
 addons:
   apt:
@@ -13,20 +13,13 @@ addons:
 sudo: enabled
 
 script:
-    - julia --project --check-bounds=yes -e 'import Pkg; Pkg.build(); Pkg.test("PorousMaterials")'
+  - julia --project -e 'ENV["JULIA_PKG_SERVER"] = ""; import Pkg; Pkg.update()'
+  - julia --project --check-bounds=yes -e 'import Pkg; Pkg.build(); Pkg.test("PorousMaterials")'
 
 after_success:
-    - julia --project -e 'import Pkg; Pkg.add("Documenter")'
-    - julia --project ./docs/make.jl
+  - julia --project -e 'import Pkg; Pkg.add("Documenter"); Pkg.add("Coverage")'
+  - julia --project -e 'using Coverage; Codecov.submit(process_folder())'
+  - julia --project ./docs/make.jl
 
 notifications:
   email: true
-  slack:
-    rooms:
-      - secure: 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
-    on_success: always
-    on_failure: always
-    template:
-      - "Repo `%{repository_slug}` *%{result}* build (<%{build_url}|#%{build_number}>) for commit (<%{compare_url}|%{commit}>) on branch `%{branch}`."
-      - "Execution time: *%{duration}*"
-      - "Message: %{message}"
diff --git a/Project.toml b/Project.toml
@@ -1,12 +1,13 @@
 name = "PorousMaterials"
 uuid = "68953c7c-a3c7-538e-83d3-73516288599e"
 authors = ["SimonEnsemble <[email protected]>"]
-version = "0.3.1"
+version = "0.4.0"
 
 [deps]
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 Distributed = "8ba89e20-285c-5b6f-9357-94700520ee1b"
+FIGlet = "3064a664-84fe-4d92-92c7-ed492f3d8fae"
 FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
 JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
 LightGraphs = "093fc24a-ae57-5d10-9952-331d41423f4d"
@@ -18,13 +19,17 @@ Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 ProgressMeter = "92933f4c-e287-5a05-a399-4b506db050ca"
 PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
+Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 Roots = "f2b01f46-fcfa-551c-844a-d8ac1e96c665"
 SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+Xtals = "ede5f01d-793e-4c47-9885-c447d1f18d6d"
 
 [compat]
+FIGlet = "^0.2.1"
+JLD2 = "^0.4.9"
 CSV = "^0.8.0"
 DataFrames = "^0.22.1"
 FileIO = "1.2.0"
@@ -36,7 +41,8 @@ ProgressMeter = "1.2.0"
 Roots = "0.8.4"
 SpecialFunctions = "0.10.0"
 StatsBase = "0.32.0,0.33.8"
-julia = "1.5,1.6"
+Xtals = "0.3.0"
+julia = "1.6"
 
 [extras]
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"

diff --git a/run_gcmc_long.sh b/run_gcmc_long.sh
@@ -0,0 +1,15 @@
+#!/bin/env bash
+
+julia -p 24 -e '
+    using Distributed
+    @everywhere begin
+        import Pkg
+        Pkg.activate(".")
+    end
+    #Pkg.test("PorousMaterials")
+    @info "Running test/gcmc_long.jl on $(length(workers())) workers."
+    @warn "This will take HOURS!"
+    cd("test")
+    include("gcmc_long.jl")
+    @info "Long GCMC tests complete!"
+'
diff --git a/src/PorousMaterials.jl b/src/PorousMaterials.jl
@@ -1,120 +1,19 @@
 module PorousMaterials
 
-using CSV
-using DataFrames
-using Roots # for fzero
-using OffsetArrays # used for Ewald sum
-using SpecialFunctions # for erfc
-using StatsBase
-using ProgressMeter
-using Polynomials
-using JLD2
-using Statistics
-using Printf
-using LinearAlgebra
-using LightGraphs
-using Distributed
-using Optim
-using PyCall
- # import Base.push!
- #
-
-# atoms are considered to overlap if this close.
-const R²_OVERLAP = 0.1 # Units: Angstrom²
-
-"""
-    print_file_paths()
-
-print off paths where PorousMaterials.jl looks for input files and writes output files.
-"""
-function print_file_paths()
-    println("general data folder: ", PATH_TO_DATA)
-    println("\tcrystal structures (.cif, .cssr): ", PATH_TO_CRYSTALS)
-    println("\tforce field files (.csv): ", PATH_TO_FORCEFIELDS)
-    println("\tmolecule input files: ", PATH_TO_MOLECULES)
-    println("\tsimulation output files: ", PATH_TO_SIMS)
-    println("\tgrids (.cube): ", PATH_TO_GRIDS)
-end
+using Roots, OffsetArrays, SpecialFunctions, StatsBase, ProgressMeter, Polynomials,
+JLD2, Statistics, Distributed, Optim, Printf, DataFrames, LightGraphs, CSV, LinearAlgebra
 
-"""
-    set_path_to_data(path; print_paths=true)
-
-Set the path variables: `PATH_TO_DATA`, `PATH_TO_CRYSTALS`, `PATH_TO_FORCEFIELDS`, `PATH_TO_MOLECULES`,
-`PATH_TO_GRIDS`, and `PATH_TO_SIMS`.  The latter five paths are set relative to the root data path.
-
-# Arguments
-- `path::String`: the absolute path to the root of the data directory.
-- `print_paths::Bool`: set false to suppress printing of path values.
-"""
-function set_path_to_data(path::String; print_paths::Bool=true)
-    global PATH_TO_DATA = path
-    global PATH_TO_CRYSTALS = joinpath(PATH_TO_DATA, "crystals")
-    global PATH_TO_FORCEFIELDS = joinpath(PATH_TO_DATA, "forcefields")
-    global PATH_TO_MOLECULES = joinpath(PATH_TO_DATA, "molecules")
-    global PATH_TO_GRIDS = joinpath(PATH_TO_DATA, "grids")
-    global PATH_TO_SIMS = joinpath(PATH_TO_DATA, "simulations")
-
-    if print_paths
-        print_file_paths()
-    end
-end
+# extend Xtals
+using Reexport
+@reexport using Xtals
+import Xtals.Cart, Xtals.Frac, Xtals.write_xyz
 
-"""
-    set_default_file_paths(print_paths=true)
-
-sets the default paths for where input files and some output files are stored.
-to see current set up, call [`print_file_paths`](@ref)
-"""
-function set_default_file_paths(;print_paths::Bool=true)
-    # this is the main directory where crystal structures, forcefields, and molecules data is stored
-    global PATH_TO_DATA = joinpath(pwd(), "data")
-
-    global PATH_TO_CRYSTALS = joinpath(PATH_TO_DATA, "crystals")
-    global PATH_TO_FORCEFIELDS = joinpath(PATH_TO_DATA, "forcefields")
-    global PATH_TO_MOLECULES = joinpath(PATH_TO_DATA, "molecules")
-    global PATH_TO_GRIDS = joinpath(PATH_TO_DATA, "grids")
-    global PATH_TO_SIMS = joinpath(PATH_TO_DATA, "simulations")
-
-    if print_paths
-        print_file_paths()
-    end
-end
+# physical constants
+const UNIV_GAS_CONST = 8.3144598e-5 # m³-bar/(K-mol)
+const K_TO_KJ_PER_MOL = 8.3144598e-3 # kJ/(mol-K)
+const BOLTZMANN = 1.38064852e7 # Boltmann constant (Pa-m3/K --> Pa-A3/K)
 
-# this runs everytime porousmaterials is loaded, so if the user changes directory
-#   then the path_to_data will change as well
-function __init__()
-    set_default_file_paths(print_paths=false)
-end
-
- # """
- #     set_tutorial_mode()
- #
- # places porousmaterials in "tutorial mode". it changes the `path_to_data` variable to
- # the directory where the porousmaterials test data is stored. it can be used to
- # follow examples shown in the readme. it displays a warning so that the user knows
- # they are no longer using their own data.
- # """
- # function set_tutorial_mode()
- #     new_path = joinpath(dirname(pathof(porousmaterials)), "..", "test", "data")
- #     if ! isdir(new_path)
- #         @error @sprintf("directory for testing data %s does not exist.\nnot entering tutorial mode.\n", new_path)
- #     else
- #         global path_to_data = new_path
- #         global path_to_crystals = joinpath(path_to_data, "crystals")
- #         global path_to_forcefields = joinpath(path_to_data, "forcefields")
- #         global path_to_molecules = joinpath(path_to_data, "molecules")
- #         global path_to_grids = joinpath(path_to_data, "grids")
- #         @warn "porousmaterials is now in tutorial mode. you have access to the testing data to experiment with porousmaterials.\nto reset to default file paths, call `set_default_file_paths()`\n"
- #     end
- # end
- #
-include("matter.jl")
-include("box.jl")
-include("distance.jl")
-include("misc.jl")
 include("isotherm_fitting.jl")
-include("crystal.jl")
-include("bonds.jl")
 include("forcefield.jl")
 include("molecule.jl")
 include("energy_utilities.jl")
@@ -125,48 +24,23 @@ include("grid.jl")
 include("eos.jl")
 include("henry.jl")
 include("gcmc.jl")
- # include("generic_rotations.jl")
 include("energy_min.jl")
+include("atomic_masses.jl")
 
+function __init__()
+    rc[:paths][:forcefields] = joinpath(rc[:paths][:data], "forcefields")
+    rc[:paths][:molecules] = joinpath(rc[:paths][:data], "molecules")
+    rc[:paths][:grids] = joinpath(rc[:paths][:data], "grids")
+    rc[:paths][:sims] = joinpath(rc[:paths][:data], "simulations")
+    append_atomic_masses()
+    @debug "Environment variables" rc
+end
 
-export
-    # porousmaterials.jl
-    print_file_paths, set_path_to_data,
-
-    # matter.jl
-    Coords, Frac, Cart, Atoms, Charges, wrap!, neutral, net_charge, translate_by!, origin,
-
-    # box.jl
-    Box, replicate, unit_cube, write_vtk, inside, fractional_coords, cartesian_coords,
-
-    # distance.jl
-    nearest_image!, distance, overlap, remove_duplicates,
-
-    # misc.jl
-    read_xyz, read_cpk_colors, write_xyz, read_atomic_masses,
 
+export
     # isotherm_fitting.jl
     fit_adsorption_isotherm,
 
-    # crystal.jl
-    Crystal, strip_numbers_from_atom_labels!, assign_charges,
-    chemical_formula, molecular_weight, crystal_density, write_cif, has_charges,
-    apply_symmetry_operations,
-
-    # bonds.jl
-    infer_bonds!, write_bond_information, BondingRule, bond_sanity_check, remove_bonds!,
-    infer_geometry_based_bonds!, cordero_covalent_atomic_radii,
-
- #     construct_box,
- #     replicate, read_atomic_masses, charged, write_cif, assign_charges,
- #     is_symmetry_equal, apply_symmetry_rules, assert_p1_symmetry, infer_bonds!,
- #     remove_bonds!, compare_bonds_in_framework, wrap_atoms_to_unit_cell!,
- #     write_bond_information, is_bonded, default_bondingrules, has_same_sets_of_atoms_and_charges,
- #     distance, bond_sanity_check,
- #
- #     # FrameworkOperations.jl
- #     partition_framework, subtract_atoms,
- #
     # molecule.jl
     Molecule, translate_by!, translate_to!, random_rotation!, random_rotation_matrix, ion, distortion,
 
@@ -189,20 +63,17 @@ export
     # Grid.jl
     apply_periodic_boundary_condition!,
     Grid, write_cube, read_cube, energy_grid, compute_accessibility_grid, accessible,
-    required_n_pts, xf_to_id, id_to_xf, update_density!, find_energy_minimum,
- #
+    required_n_pts, xf_to_id, id_to_xf, update_density!, find_energy_minimum, origin,
+
     # EOS.jl
     calculate_properties, PengRobinsonFluid, VdWFluid,
 
     # gcmc.jl
     μVT_sim, adsorption_isotherm, stepwise_adsorption_isotherm,
     μVT_output_filename, GCMCstats, MarkovCounts, isotherm_sim_results_to_dataframe,
- #
+
     # henry.jl
     henry_coefficient, henry_result_savename,
- #
- #     # generic_rotations.jl
- #     rotation_matrix
 
     # energy_min.jl
     find_energy_minimum, find_energy_minimum_gridsearch

diff --git a/src/atomic_masses.jl b/src/atomic_masses.jl
@@ -0,0 +1,24 @@
+# add atom types to rc[:atomic_masses] for contextual LJ potentials
+function append_atomic_masses()
+    rc[:atomic_masses] = merge(rc[:atomic_masses], Dict(
+        :N_in_N2 => 14.0067,
+        :CH2 => 14.025,
+        :CH3 => 15.035,
+        :CH4 => 16.04,
+        :C_b => 12.0107,
+        :C_tol => 12.0107,
+        :C_ac => 12.0107,
+        :C_RCOO => 12.0107,
+        :C_sp2 => 12.0107,
+        :C_sp3 => 12.0107,
+        :C_CO2 => 12.0107,
+        :H_H2S => 1.00794,
+        :H_b => 1.00794,
+        :O_RCOO => 15.9994,
+        :O_CO2 => 15.9994,
+        :O_zeo => 15.9994,
+        :S_H2S => 32.065,
+        :Si_zeo => 28.0855,
+        :X => 1.0
+    ))
+end