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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
1 parent e4e8ea2 commit 913d0e5

30 files changed

+247
-3368
lines changed

‎.gitignore

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@@ -8,4 +8,6 @@
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*.jld2
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docs/build/
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docs/site/
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*checkpoint.ipynb
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*checkpoint.ipynb
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.vscode
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Manifest.toml

‎.travis.yml

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language: julia
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coveralls: true
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codecov: true
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julia:
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- 1.5
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- 1.6
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addons:
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apt:
@@ -13,20 +13,13 @@ addons:
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sudo: enabled
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script:
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- julia --project --check-bounds=yes -e 'import Pkg; Pkg.build(); Pkg.test("PorousMaterials")'
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- julia --project -e 'ENV["JULIA_PKG_SERVER"] = ""; import Pkg; Pkg.update()'
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- julia --project --check-bounds=yes -e 'import Pkg; Pkg.build(); Pkg.test("PorousMaterials")'
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after_success:
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- julia --project -e 'import Pkg; Pkg.add("Documenter")'
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- julia --project ./docs/make.jl
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- julia --project -e 'import Pkg; Pkg.add("Documenter"); Pkg.add("Coverage")'
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- julia --project -e 'using Coverage; Codecov.submit(process_folder())'
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- julia --project ./docs/make.jl
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notifications:
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email: true
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slack:
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rooms:
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- secure: 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on_success: always
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on_failure: always
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template:
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- "Repo `%{repository_slug}` *%{result}* build (<%{build_url}|#%{build_number}>) for commit (<%{compare_url}|%{commit}>) on branch `%{branch}`."
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- "Execution time: *%{duration}*"
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- "Message: %{message}"

‎Project.toml

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@@ -1,12 +1,13 @@
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name = "PorousMaterials"
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uuid = "68953c7c-a3c7-538e-83d3-73516288599e"
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authors = ["SimonEnsemble <[email protected]>"]
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version = "0.3.1"
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version = "0.4.0"
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[deps]
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CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
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DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
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Distributed = "8ba89e20-285c-5b6f-9357-94700520ee1b"
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FIGlet = "3064a664-84fe-4d92-92c7-ed492f3d8fae"
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FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
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JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
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LightGraphs = "093fc24a-ae57-5d10-9952-331d41423f4d"
@@ -18,13 +19,17 @@ Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
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ProgressMeter = "92933f4c-e287-5a05-a399-4b506db050ca"
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PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0"
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Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
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Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
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Roots = "f2b01f46-fcfa-551c-844a-d8ac1e96c665"
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SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
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Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
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StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
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Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
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Xtals = "ede5f01d-793e-4c47-9885-c447d1f18d6d"
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[compat]
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FIGlet = "^0.2.1"
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JLD2 = "^0.4.9"
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CSV = "^0.8.0"
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DataFrames = "^0.22.1"
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FileIO = "1.2.0"
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Roots = "0.8.4"
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SpecialFunctions = "0.10.0"
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StatsBase = "0.32.0,0.33.8"
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julia = "1.5,1.6"
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Xtals = "0.3.0"
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julia = "1.6"
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[extras]
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CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"

‎run_gcmc_long.sh

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#!/bin/env bash
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julia -p 24 -e '
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using Distributed
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@everywhere begin
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import Pkg
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Pkg.activate(".")
8+
end
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#Pkg.test("PorousMaterials")
10+
@info "Running test/gcmc_long.jl on $(length(workers())) workers."
11+
@warn "This will take HOURS!"
12+
cd("test")
13+
include("gcmc_long.jl")
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@info "Long GCMC tests complete!"
15+
'

‎src/PorousMaterials.jl

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module PorousMaterials
22

3-
using CSV
4-
using DataFrames
5-
using Roots # for fzero
6-
using OffsetArrays # used for Ewald sum
7-
using SpecialFunctions # for erfc
8-
using StatsBase
9-
using ProgressMeter
10-
using Polynomials
11-
using JLD2
12-
using Statistics
13-
using Printf
14-
using LinearAlgebra
15-
using LightGraphs
16-
using Distributed
17-
using Optim
18-
using PyCall
19-
# import Base.push!
20-
#
21-
22-
# atoms are considered to overlap if this close.
23-
const R²_OVERLAP = 0.1 # Units: Angstrom²
24-
25-
"""
26-
print_file_paths()
27-
28-
print off paths where PorousMaterials.jl looks for input files and writes output files.
29-
"""
30-
function print_file_paths()
31-
println("general data folder: ", PATH_TO_DATA)
32-
println("\tcrystal structures (.cif, .cssr): ", PATH_TO_CRYSTALS)
33-
println("\tforce field files (.csv): ", PATH_TO_FORCEFIELDS)
34-
println("\tmolecule input files: ", PATH_TO_MOLECULES)
35-
println("\tsimulation output files: ", PATH_TO_SIMS)
36-
println("\tgrids (.cube): ", PATH_TO_GRIDS)
37-
end
3+
using Roots, OffsetArrays, SpecialFunctions, StatsBase, ProgressMeter, Polynomials,
4+
JLD2, Statistics, Distributed, Optim, Printf, DataFrames, LightGraphs, CSV, LinearAlgebra
385

39-
"""
40-
set_path_to_data(path; print_paths=true)
41-
42-
Set the path variables: `PATH_TO_DATA`, `PATH_TO_CRYSTALS`, `PATH_TO_FORCEFIELDS`, `PATH_TO_MOLECULES`,
43-
`PATH_TO_GRIDS`, and `PATH_TO_SIMS`. The latter five paths are set relative to the root data path.
44-
45-
# Arguments
46-
- `path::String`: the absolute path to the root of the data directory.
47-
- `print_paths::Bool`: set false to suppress printing of path values.
48-
"""
49-
function set_path_to_data(path::String; print_paths::Bool=true)
50-
global PATH_TO_DATA = path
51-
global PATH_TO_CRYSTALS = joinpath(PATH_TO_DATA, "crystals")
52-
global PATH_TO_FORCEFIELDS = joinpath(PATH_TO_DATA, "forcefields")
53-
global PATH_TO_MOLECULES = joinpath(PATH_TO_DATA, "molecules")
54-
global PATH_TO_GRIDS = joinpath(PATH_TO_DATA, "grids")
55-
global PATH_TO_SIMS = joinpath(PATH_TO_DATA, "simulations")
56-
57-
if print_paths
58-
print_file_paths()
59-
end
60-
end
6+
# extend Xtals
7+
using Reexport
8+
@reexport using Xtals
9+
import Xtals.Cart, Xtals.Frac, Xtals.write_xyz
6110

62-
"""
63-
set_default_file_paths(print_paths=true)
64-
65-
sets the default paths for where input files and some output files are stored.
66-
to see current set up, call [`print_file_paths`](@ref)
67-
"""
68-
function set_default_file_paths(;print_paths::Bool=true)
69-
# this is the main directory where crystal structures, forcefields, and molecules data is stored
70-
global PATH_TO_DATA = joinpath(pwd(), "data")
71-
72-
global PATH_TO_CRYSTALS = joinpath(PATH_TO_DATA, "crystals")
73-
global PATH_TO_FORCEFIELDS = joinpath(PATH_TO_DATA, "forcefields")
74-
global PATH_TO_MOLECULES = joinpath(PATH_TO_DATA, "molecules")
75-
global PATH_TO_GRIDS = joinpath(PATH_TO_DATA, "grids")
76-
global PATH_TO_SIMS = joinpath(PATH_TO_DATA, "simulations")
77-
78-
if print_paths
79-
print_file_paths()
80-
end
81-
end
11+
# physical constants
12+
const UNIV_GAS_CONST = 8.3144598e-5 # m³-bar/(K-mol)
13+
const K_TO_KJ_PER_MOL = 8.3144598e-3 # kJ/(mol-K)
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const BOLTZMANN = 1.38064852e7 # Boltmann constant (Pa-m3/K --> Pa-A3/K)
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# this runs everytime porousmaterials is loaded, so if the user changes directory
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# then the path_to_data will change as well
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function __init__()
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set_default_file_paths(print_paths=false)
87-
end
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# """
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# set_tutorial_mode()
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#
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# places porousmaterials in "tutorial mode". it changes the `path_to_data` variable to
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# the directory where the porousmaterials test data is stored. it can be used to
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# follow examples shown in the readme. it displays a warning so that the user knows
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# they are no longer using their own data.
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# """
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# function set_tutorial_mode()
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# new_path = joinpath(dirname(pathof(porousmaterials)), "..", "test", "data")
99-
# if ! isdir(new_path)
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# @error @sprintf("directory for testing data %s does not exist.\nnot entering tutorial mode.\n", new_path)
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# else
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# global path_to_data = new_path
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# global path_to_crystals = joinpath(path_to_data, "crystals")
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# global path_to_forcefields = joinpath(path_to_data, "forcefields")
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# global path_to_molecules = joinpath(path_to_data, "molecules")
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# global path_to_grids = joinpath(path_to_data, "grids")
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# @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"
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# end
109-
# end
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#
111-
include("matter.jl")
112-
include("box.jl")
113-
include("distance.jl")
114-
include("misc.jl")
11516
include("isotherm_fitting.jl")
116-
include("crystal.jl")
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include("bonds.jl")
11817
include("forcefield.jl")
11918
include("molecule.jl")
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include("energy_utilities.jl")
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12524
include("eos.jl")
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include("henry.jl")
12726
include("gcmc.jl")
128-
# include("generic_rotations.jl")
12927
include("energy_min.jl")
28+
include("atomic_masses.jl")
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30+
function __init__()
31+
rc[:paths][:forcefields] = joinpath(rc[:paths][:data], "forcefields")
32+
rc[:paths][:molecules] = joinpath(rc[:paths][:data], "molecules")
33+
rc[:paths][:grids] = joinpath(rc[:paths][:data], "grids")
34+
rc[:paths][:sims] = joinpath(rc[:paths][:data], "simulations")
35+
append_atomic_masses()
36+
@debug "Environment variables" rc
37+
end
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132-
export
133-
# porousmaterials.jl
134-
print_file_paths, set_path_to_data,
135-
136-
# matter.jl
137-
Coords, Frac, Cart, Atoms, Charges, wrap!, neutral, net_charge, translate_by!, origin,
138-
139-
# box.jl
140-
Box, replicate, unit_cube, write_vtk, inside, fractional_coords, cartesian_coords,
141-
142-
# distance.jl
143-
nearest_image!, distance, overlap, remove_duplicates,
144-
145-
# misc.jl
146-
read_xyz, read_cpk_colors, write_xyz, read_atomic_masses,
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40+
export
14841
# isotherm_fitting.jl
14942
fit_adsorption_isotherm,
15043

151-
# crystal.jl
152-
Crystal, strip_numbers_from_atom_labels!, assign_charges,
153-
chemical_formula, molecular_weight, crystal_density, write_cif, has_charges,
154-
apply_symmetry_operations,
155-
156-
# bonds.jl
157-
infer_bonds!, write_bond_information, BondingRule, bond_sanity_check, remove_bonds!,
158-
infer_geometry_based_bonds!, cordero_covalent_atomic_radii,
159-
160-
# construct_box,
161-
# replicate, read_atomic_masses, charged, write_cif, assign_charges,
162-
# is_symmetry_equal, apply_symmetry_rules, assert_p1_symmetry, infer_bonds!,
163-
# remove_bonds!, compare_bonds_in_framework, wrap_atoms_to_unit_cell!,
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# write_bond_information, is_bonded, default_bondingrules, has_same_sets_of_atoms_and_charges,
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# distance, bond_sanity_check,
166-
#
167-
# # FrameworkOperations.jl
168-
# partition_framework, subtract_atoms,
169-
#
17044
# molecule.jl
17145
Molecule, translate_by!, translate_to!, random_rotation!, random_rotation_matrix, ion, distortion,
17246

@@ -189,20 +63,17 @@ export
18963
# Grid.jl
19064
apply_periodic_boundary_condition!,
19165
Grid, write_cube, read_cube, energy_grid, compute_accessibility_grid, accessible,
192-
required_n_pts, xf_to_id, id_to_xf, update_density!, find_energy_minimum,
193-
#
66+
required_n_pts, xf_to_id, id_to_xf, update_density!, find_energy_minimum, origin,
67+
19468
# EOS.jl
19569
calculate_properties, PengRobinsonFluid, VdWFluid,
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# gcmc.jl
19872
μVT_sim, adsorption_isotherm, stepwise_adsorption_isotherm,
19973
μVT_output_filename, GCMCstats, MarkovCounts, isotherm_sim_results_to_dataframe,
200-
#
74+
20175
# henry.jl
20276
henry_coefficient, henry_result_savename,
203-
#
204-
# # generic_rotations.jl
205-
# rotation_matrix
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# energy_min.jl
20879
find_energy_minimum, find_energy_minimum_gridsearch

‎src/atomic_masses.jl

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# add atom types to rc[:atomic_masses] for contextual LJ potentials
2+
function append_atomic_masses()
3+
rc[:atomic_masses] = merge(rc[:atomic_masses], Dict(
4+
:N_in_N2 => 14.0067,
5+
:CH2 => 14.025,
6+
:CH3 => 15.035,
7+
:CH4 => 16.04,
8+
:C_b => 12.0107,
9+
:C_tol => 12.0107,
10+
:C_ac => 12.0107,
11+
:C_RCOO => 12.0107,
12+
:C_sp2 => 12.0107,
13+
:C_sp3 => 12.0107,
14+
:C_CO2 => 12.0107,
15+
:H_H2S => 1.00794,
16+
:H_b => 1.00794,
17+
:O_RCOO => 15.9994,
18+
:O_CO2 => 15.9994,
19+
:O_zeo => 15.9994,
20+
:S_H2S => 32.065,
21+
:Si_zeo => 28.0855,
22+
:X => 1.0
23+
))
24+
end

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