Merge branch 'master' into henry_fix

src/Forcefield.jl

@@ -176,7 +176,7 @@ function check_forcefield_coverage(f_or_m::Union{Framework, Molecule}, ljff::LJF
     all_covered = true
     for species in unique_species
         if !(species in keys(ljff.pure_ϵ))
-            @warn @sprintf("\t%s in %s missing from %s force field.", species, 
+            @warn @sprintf("\t%s in %s missing from %s force field.", species,
                 isa(f_or_m, Framework) ? f_or_m.name : f_or_m.species, ljff.name)
             all_covered = false
         end

src/Molecules.jl

@@ -40,7 +40,7 @@ function Molecule(species::AbstractString; assert_charge_neutrality::Bool=true)
         error(@sprintf("No directory created for %s in %s\n", species,
                        PATH_TO_DATA * "molecules/"))
     end
-    
+
     ###
     #  Read in Lennard Jones spheres
     ###
@@ -73,7 +73,7 @@ function Molecule(species::AbstractString; assert_charge_neutrality::Bool=true)
     x_com /= total_mass
     # construct atoms attribute of molecule
     atoms = Atoms(atom_species, atom_coords)
-    
+
     ###
     #  Read in point charges
     ###
@@ -94,7 +94,7 @@ function Molecule(species::AbstractString; assert_charge_neutrality::Bool=true)
     end
     # construct charges attribute of molecule
     charges = Charges(charge_vals, charge_coords)
-    
+
     # construct molecule
     molecule = Molecule(Symbol(species), atoms, charges, x_com)
 
@@ -399,5 +399,5 @@ end
 Ion(q::Float64, xf::Array{Float64, 1}, species::Symbol=:ion) = Molecule(
     species,
     Atoms(0, Symbol[], zeros(0, 0)),
-    Charges(1, [q], reshape(xf, (3, 1))), 
+    Charges(1, [q], reshape(xf, (3, 1))),
     xf)

src/PorousMaterials.jl

@@ -20,6 +20,60 @@ import Base.push!
 function __init__()
     # this is the directory where crystal structures, forcefields, and molecules data is stored
     global PATH_TO_DATA = pwd() * "/data/"
+    if ! isdir(PATH_TO_DATA)
+        @warn @sprintf("Directory for input data, \"/data/\", not found in present working directory, %s\nChange the PATH_TO_DATA variable to load input files from a different directory. See \"set_path_to_data()\".\n", pwd())
+    end
+end
+
+"""
+    set_path_to_data("user/path/to/data")
+    set_path_to_data()
+
+Sets PorousMaterials PATH_TO_DATA variable which dictates where crystal, forcefield,
+and molecule files are loaded from. This function allows the user to set PATH_TO_DATA
+manually to any directory or to a "/data/" folder within their current directory.
+This function WILL change the PATH_TO_DATA regardless of whether or not the path
+exists, but will give a warning alerting the user that PorousMaterials cannot load
+files from the chosen path.
+
+# Arguments
+- `new_path_to_data::String`: The desired PATH_TO_DATA in string form.
+"""
+function set_path_to_data(new_path_to_data::String)
+    if new_path_to_data[end] != '/'
+        new_path_to_data = new_path_to_data * "/"
+    end
+    global PATH_TO_DATA = new_path_to_data
+    if ! isdir(PATH_TO_DATA)
+        @warn @sprintf("The directory %s does not exist.\nChange the PATH_TO_DATA variable to load input files from a different directory. See \"set_path_to_data()\".\n", new_path_to_data)
+    end
+    @printf("PATH_TO_DATA set to %s\n", PATH_TO_DATA)
+end
+
+function set_path_to_data()
+    global PATH_TO_DATA = pwd() * "/data/"
+    if ! isdir(PATH_TO_DATA)
+        @warn @sprintf("Directory for input data, \"/data/\", not found in present working directory, %s\nChange the PATH_TO_DATA variable to load input files from a different directory. See \"set_path_to_data()\".\n", pwd())
+    end
+    @printf("PATH_TO_DATA set to %s\n", PATH_TO_DATA)
+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 = 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
+        @warn "PorousMaterials is now in Tutorial Mode. You have access to the testing data to experiment with PorousMaterials.\nTo get access to your own data use: reset_path_to_data()\n"
+    end
 end
 
 include("Box.jl")
@@ -39,54 +93,57 @@ include("Henry.jl")
 include("GCMC.jl")
 
 export
-       # Box.jl
-       Box, replicate, UnitCube, write_vtk,
+    # PorousMaterials.jl
+    set_path_to_data, set_tutorial_mode,
+
+    # Box.jl
+    Box, replicate, UnitCube, write_vtk,
 
-       # Matter.jl
-       Atoms, Charges,
+    # Matter.jl
+    Atoms, Charges,
 
-       # NearestImage.jl
-       nearest_image!, nearest_r², nearest_r,
+    # NearestImage.jl
+    nearest_image!, nearest_r², nearest_r,
 
-       # Misc.jl
-       read_xyz, read_cpk_colors, read_atomic_radii, write_xyz,
+    # Misc.jl
+    read_xyz, read_cpk_colors, read_atomic_radii, write_xyz,
 
-       # Crystal.jl
-       Framework, read_crystal_structure_file, remove_overlapping_atoms,
-       strip_numbers_from_atom_labels!, chemical_formula, molecular_weight, crystal_density,
-       construct_box, replicate, read_atomic_masses, charged, write_cif, assign_charges,
+    # Crystal.jl
+    Framework, read_crystal_structure_file, remove_overlapping_atoms,
+    strip_numbers_from_atom_labels!, chemical_formula, molecular_weight, crystal_density,
+    construct_box, replicate, read_atomic_masses, charged, write_cif, assign_charges,
 
-       # Molecules.jl
-       Molecule, set_fractional_coords!, translate_by!, outside_box, set_fractional_coords_to_unit_cube!,
-       translate_to!, rotate!, rotation_matrix, rand_point_on_unit_sphere, charged,
-       pairwise_atom_distances, pairwise_charge_distances, Ion, bond_length_drift,
+    # Molecules.jl
+    Molecule, set_fractional_coords!, translate_by!, outside_box, set_fractional_coords_to_unit_cube!,
+    translate_to!, rotate!, rotation_matrix, rand_point_on_unit_sphere, charged,
+    pairwise_atom_distances, pairwise_charge_distances, Ion, bond_length_drift,
 
-       # Forcefield.jl
-       LJForceField, replication_factors, check_forcefield_coverage,
+    # Forcefield.jl
+    LJForceField, replication_factors, check_forcefield_coverage,
 
-       # Energetics_Util.jl
-       PotentialEnergy, SystemPotentialEnergy,
+    # Energetics_Util.jl
+    PotentialEnergy, SystemPotentialEnergy,
 
-       # VdWEnergetics.jl
-       lennard_jones, vdw_energy, vdw_energy_no_PBC,
+    # VdWEnergetics.jl
+    lennard_jones, vdw_energy, vdw_energy_no_PBC,
 
-       # ElectrostaticEnergetics.jl
-       electrostatic_potential, electrostatic_potential_energy, precompute_kvec_wts, setup_Ewald_sum, total, Eikr,
+    # ElectrostaticEnergetics.jl
+    electrostatic_potential, electrostatic_potential_energy, precompute_kvec_wts, setup_Ewald_sum, total, Eikr,
 
-       # MChelpers.jl
-       insert_molecule!, delete_molecule!, translate_molecule!, reinsert_molecule!, rotatable,
+    # MChelpers.jl
+    insert_molecule!, delete_molecule!, translate_molecule!, reinsert_molecule!, rotatable,
 
-       # Grid.jl
-       apply_periodic_boundary_condition!,
-       Grid, write_cube, read_cube, energy_grid,
+    # Grid.jl
+    apply_periodic_boundary_condition!,
+    Grid, write_cube, read_cube, energy_grid,
 
-       # EOS.jl
-       calculate_properties, PengRobinsonGas,
+    # EOS.jl
+    calculate_properties, PengRobinsonGas,
 
-       # GCMC.jl
-       gcmc_simulation, adsorption_isotherm, stepwise_adsorption_isotherm,
-       gcmc_result_savename, GCMCstats, MarkovCounts,
+    # GCMC.jl
+    gcmc_simulation, adsorption_isotherm, stepwise_adsorption_isotherm,
+    gcmc_result_savename, GCMCstats, MarkovCounts,
 
-       # Henry.jl
-       henry_coefficient, henry_result_savename
+    # Henry.jl
+    henry_coefficient, henry_result_savename
 end

test/gcmc_test.jl

@@ -101,7 +101,7 @@ if co2_tests
 
     # make sure bond lenghts are preserved
     bls = pairwise_atom_distances(co2, UnitCube())
-    results, molecules = gcmc_simulation(zif71, co2, 298.0, 1.0, ff, 
+    results, molecules = gcmc_simulation(zif71, co2, 298.0, 1.0, ff,
                         n_burn_cycles=25, n_sample_cycles=25, verbose=false)
     @printf("Testing that bond lenghts are preserved for %d molecules.\n", length(molecules))
     for m in molecules

test/path_test.jl

@@ -0,0 +1,19 @@
+module Path_Test
+
+using PorousMaterials
+using OffsetArrays
+using LinearAlgebra
+using Test
+using JLD2
+using Statistics
+using Random
+
+@testset "Path Tests" begin
+    set_tutorial_mode()
+    @test PorousMaterials.PATH_TO_DATA == dirname(pathof(PorousMaterials)) * "/../test/data/"
+    set_path_to_data(pwd())
+    @test PorousMaterials.PATH_TO_DATA == pwd() * "/"
+    set_path_to_data()
+    @test PorousMaterials.PATH_TO_DATA == pwd() * "/data/"
+end
+end

test/runtests.jl

@@ -14,3 +14,4 @@ include("guest_guest_energetics_test.jl")
 include("eos_test.jl")
 include("gcmc_checkpoints_test.jl")
 include("grid_test.jl")
+include("path_test.jl")