Merge pull request #69 from Erastova-group/analysis_fixes

merging analysis fixes

package/ClayCode/plots/dataclasses.py

@@ -0,0 +1,37 @@
+from __future__ import annotations
+
+
+class Cutoff(str):
+    def __new__(cls, length):
+        string = f"{int(length):02}"
+        return super().__new__(cls, string)
+
+    def __init__(self, length):
+        self.num = float(length)
+
+    def __float__(self):
+        return float(self.num)
+
+    def __int__(self):
+        return int(self.num)
+
+    def __str__(self):
+        return self
+
+
+class Bins(str):
+    def __new__(cls, length):
+        string = f"{float(length):.02f}"[2:]
+        return super().__new__(cls, string)
+
+    def __init__(self, length):
+        self.num = float(length)
+
+    def __float__(self):
+        return float(self.num)
+
+    def __int__(self):
+        return int(self.num)
+
+    def __str__(self):
+        return self

pyproject.toml

@@ -22,19 +22,18 @@ dependencies = ['matplotlib>=3.6.2',
     'numba>=0.57',
     'pytest',
     "nglview>=3.0",
-    ]
-classifiers = [
-    "Programming Language :: Python :: 3",
-    "License :: OSI Approved :: BSD License",
-    "Operating System :: OS Independent"
+    "unicodeit"
 ]
+classifiers = ["Programming Language :: Python :: 3",
+    "License :: OSI Approved :: BSD License",
+    "Operating System :: OS Independent"]
 
 [project.scripts]
 ClayCode = "ClayCode:__main__.run"
 
 [tool.setuptools.packages.find]
 namespaces = true
-where=['package', 'tests']
+where = ['package', 'tests']
 
 [tool.setuptools]
 include-package-data = true
@@ -75,16 +74,14 @@ exclude = '''
 )/
 '''
 [project.optional-dependencies]
-test = [
-"pytest>=6.0",
-"pytest-xdist>=2.5",
-"pytest-cov>=3.0",
-
+test = ["pytest>=6.0",
+    "pytest-xdist>=2.5",
+    "pytest-cov>=3.0",
 ]
 
 [tool.pytest.ini_options]
+addopts = "-s"
 minversion = "6.0"
-testpaths = [
-"ClayCodeTests",
+testpaths = ["ClayCodeTests",
 ]
 python_files = ["test_*.py", "*_test.py", "test.py"]

tests/ClayCodeTests/builder/data/exp_clay.csv

@@ -0,0 +1,19 @@
+sheet,element,KGa-1,NAu-1-fe,NAu-2-fe,NG-1,SWa-1,SWy-1,IMt-1,LDH31,IMt-2,SWy-1-simplified,SWy-123,SWy-1-simplified-feo,IMt-1,SAz-1
+T,Si,3.83,6.98,7.55,7.08,7.09,7.98,6.77,,6.77,8,7.98,8,6.77,8
+T,Al,0.17,0.95,0.16,0.92,0.91,0.02,1.23,,1.23,,0.02,,1.23,
+T,Fe,,0.07,0.29,,,,,,,,,,,
+O,Fe,,3.61,3.54,3.75,3.08,0.41,,,0.82,,,,,
+O,Fe3,0.02,,,,,,0.76,,,,0.41,3,0.76,0.12
+O,Fe2,,,,,,,0.06,,,,,,0.06,
+O,Al,3.86,0.36,0.34,0.17,0.61,3.01,2.69,1,2.69,3,3.01,0,2.69,2.71
+O,Mg,,0.04,0.05,0.08,0.24,0.54,0.43,3,0.43,1,0.54,1,0.43,1.11
+O,Mn,,,,,,0.01,,,,,0.01,,,0.01
+O,Ti,0.11,,,,0.07,,,,,,,,,0.03
+I,Ca,0.01,0.525,0.36,0.32,0.36,0.12,0.06,,0.06,1,1,1,0.06,0.39
+I,Na,0.01,,,0.01,,0.32,,,,,,1,,0.36
+I,Mg,0.02,,,0.15,0.18,,0.09,,0.09,,,,0.09,
+I,K,0.01,,,0.03,0.01,0.05,1.37,,1.37,,,,1.37,0.02
+I,Cl,,,,,,,,1,,,,,,
+C,T,-0.17,-1.02,-0.45,-0.92,-0.91,-0.02,-1.23,,-1.23,0,-0.02,0,-1.23,0
+C,O,0.11,-0.03,-0.27,-0.08,-0.18,-0.53,-0.44,1,-0.44,-1,-0.53,-1,-0.44,-1.08
+C,tot,-0.06,-1.05,-0.72,-0.99,-1.09,-0.55,-1.68,1,-1.68,-1,-0.55,-1,-1.68,-1.08

tests/ClayCodeTests/builder/data/input_empty.yaml

@@ -0,0 +1,152 @@
+
+# =============================================================================
+# General specifications for clay model construction
+# =============================================================================
+
+# =============================================================================
+# Required Parameters
+# =============================================================================
+
+OUTPATH: '/storage/clay_models'
+
+# name of system
+SYSNAME: IMt-1
+
+# specify whether new clay model should be constructed:
+# new - a new clay model is constructed
+# load - sheet coordinates or unit cell sequences are loaded from existent ._gro or .npy files
+# load: [X, Y]
+# with X - 'np' or '_gro', Y - '.npy' or '._gro' filename
+# False - no clay model is constructed
+
+BUILD: new
+
+# name of .csv file with target stoichiometry
+CLAY_COMP: package/ClayCode/builder/tests/data/exp_non.csv
+
+# clay type available options in 'clay_units' directory:
+# Dioctahedral 2:1 - D21
+# Trioctahedral 2:1 - T21
+# Dioctahedral 1:1 - D11
+# Trioctahedral 1:1 - T11
+# layered double hydroxide 3:1 - L31
+# layered double hydroxide 2:1 - L21
+# Sepiolite - SEP
+
+CLAY_TYPE: D21
+
+
+# =============================================================================
+# Optional: Clay Sheet and Interlayer Specifications
+# =============================================================================
+
+# number of unit cells in x direction (Default 7)
+X_CELLS: 6 #7
+
+# number of unit cells in y direction (Default 5)
+Y_CELLS: 4 # 5
+
+# number of unit cells in z direction (Default 3)
+N_SHEETS: 2 # 3
+
+# ----------------------------------------------------------------------------
+# Optional: Unit Cell Composition and Ratios input
+# if not given, these will be calculated from data in the CLAY_COMP .csv file
+# (Default UC_INDEX_LIST: [], UC_RATIOS_LIST: [])
+# -----------------------------------------------------------------------------
+
+# required UCs to builder system as list
+# UC_INDEX_LIST: [1]
+
+# probability list of unit cells in system
+# p(tot) = 1.00
+# UC_RATIOS_LIST: [1]
+
+# -----------------------------------------------------------------------------
+
+# interlayer solvent present or not (Default True)
+IL_SOLV: False
+
+# -----------------------------------------------------------------------------
+# Optional: Interlayer Ion Specification Options (comment the other options!)
+# (Default UC_WATERS: 20)
+# -----------------------------------------------------------------------------
+
+# 1. Number of water molecules that should be added per ion (ION_WATERS)
+# a. as ion species dictionary for hydration number
+# ION_WATERS = {'Ca': 12,
+#               'Na': 12
+#               }
+
+# b. as ion species int for hydration number
+# ION_WATERS = 12
+
+# 3. OR per unit cell
+UC_WATERS: 20
+
+# 4. OR for a target d-spacing value in A
+# SPACING_WATERS = 10.0
+
+# =============================================================================
+# Optional: Simulation Box Specifications
+# =============================================================================
+
+# full simulation box height in A (Default 150.0)
+BOX_HEIGHT: 50 # 150.0
+
+# =============================================================================
+# Optional: Solvation and Bulk Ions Specifications
+# =============================================================================
+
+# Bulk solvent added or not (Default: True)
+BULK_SOLV: True
+
+# Ion species and concentration in mol/L name to add in bulk solvent
+# (Default: BULK_IONS:
+#  Na: 0.1)
+
+BULK_IONS:
+  Na: 0
+  Cl: 0
+#  Na: 0.1
+#  Cl: 0.05
+
+# =============================================================================
+# Optional: Simulation Runs Specifications
+# =============================================================================
+
+# Generate scripts and '.mdp' files for simulation runs.
+# Available options:
+# EM - energy minimisation
+# EQ - equilibration
+# D-SPACE - d-spacing equilibration
+# P - production
+# SIMINP: [EM, D-SPACE]
+
+# select where EM and EQ should be run (Default: False)
+# MDRUNS_REMOTE: False
+
+# -----------------------------------------------------------------------------
+# d-spacing equilibration options
+# -----------------------------------------------------------------------------
+
+# Target d-spacing in A
+# D_SPACE: 19.5
+
+# Water molecules to be removed at a time during d-spacing equilibration runs
+# REMOVE_STEPS = 1000
+
+# Absolute number of water molecules per interlayer space
+# SHEET_WAT = 2
+
+# Number of water molecules per unit cell
+# UC_WAT = 0.1
+
+# Percentage of water molecules from interlayer
+# PERCENT_WAT = 5
+
+# -----------------------------------------------------------------------------
+# bash alias for used GROMACS version
+# -----------------------------------------------------------------------------
+
+GMX: gmx_mpi

tests/ClayCodeTests/core/test_core.py

@@ -0,0 +1,38 @@
+from pathlib import Path
+
+import pytest
+from ClayCode import ArgsFactory, parser
+from ClayCode.core.parsing import (
+    AddMolsArgs,
+    AnalysisArgs,
+    BuildArgs,
+    CheckArgs,
+    DataArgs,
+    EditArgs,
+    PlotArgs,
+    SiminpArgs,
+)
+
+
+@pytest.mark.parametrize(
+    ("submodule", "argclass"),
+    [
+        ("builder", BuildArgs),
+        # ("edit", EditArgs),
+        # ("check", CheckArgs),
+        ("analysis", AnalysisArgs),
+        ("siminp", SiminpArgs),
+        ("data", DataArgs),
+        # ("addmols", AddMolsArgs),
+        ("plot", PlotArgs),
+    ],
+)
+def test_args_factory(submodule, argclass):
+    args = ArgsFactory()
+    parse_args = parser.parse_args(
+        [f"{submodule}", "-f", str(Path(__file__).parent / f"data/empty.yaml")]
+    )
+    with pytest.raises(SystemExit, match="2"):
+        args = args.init_subclass(parse_args)
+        args.__class__ == argclass
+    return args