diff --git a/Tutorial/builder/IMt-1.yaml b/Tutorial/builder/IMt-1.yaml new file mode 100644 index 00000000..e17ad52c --- /dev/null +++ b/Tutorial/builder/IMt-1.yaml @@ -0,0 +1,121 @@ + +# ============================================================================= +# General specifications for clay model construction +# ============================================================================= + +# ============================================================================= +# Required Parameters +# ============================================================================= + +OUTPATH: IMt-1 + +# name of system to call according to CLAY_COMP (exp_clay.csv) +# compositions currently included are: 'NAu-1-fe' 'NAu-2-fe' 'NG-1' 'SWa-1' 'L31' 'IMt-1' 'KGa-1' +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: ./exp_clay.csv + +# clay type available options in 'clay_units' directory: +# 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: CD21 + + +# ============================================================================= +# Optional: Clay Sheet and Interlayer Specifications +# ============================================================================= + +# number of unit cells in x direction (Default 7) +X_CELLS: 7 + +# number of unit cells in y direction (Default 5) +Y_CELLS: 5 + +# number of unit cells in z direction (Default 3) +N_SHEETS: 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: 30 # 150.0 + +# ============================================================================= +# Optional: Solvation and Bulk Ions Specifications +# ============================================================================= + +# Bulk solvent added or not (Default: True) +BULK_SOLV: false + +# Ion species and concentration in mol/L name to add in bulk solvent +# (Default: BULK_IONS: +# Na: 0.1) + +BULK_IONS: + Na: 0.1 + Cl: 0.05 + +# ============================================================================= +# Optional: Simulation Runs Specifications +# ============================================================================= + +# ----------------------------------------------------------------------------- +# bash alias for used GROMACS version +# ----------------------------------------------------------------------------- + +GMX: gmx diff --git a/Tutorial/builder/KGa-1.yaml b/Tutorial/builder/KGa-1.yaml new file mode 100644 index 00000000..e6af65d0 --- /dev/null +++ b/Tutorial/builder/KGa-1.yaml @@ -0,0 +1,121 @@ + +# ============================================================================= +# General specifications for clay model construction +# ============================================================================= + +# ============================================================================= +# Required Parameters +# ============================================================================= + +OUTPATH: KGa-1 + +# name of system to call according to CLAY_COMP (exp_clay.csv) +# compositions currently included are: 'NAu-1-fe' 'NAu-2-fe' 'NG-1' 'SWa-1' 'L31' 'IMt-1' 'KGa-1' +SYSNAME: KGa-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: ./exp_clay.csv + +# clay type available options in 'clay_units' directory: +# 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: CD11 + + +# ============================================================================= +# Optional: Clay Sheet and Interlayer Specifications +# ============================================================================= + +# number of unit cells in x direction (Default 7) +X_CELLS: 7 + +# number of unit cells in y direction (Default 5) +Y_CELLS: 5 + +# number of unit cells in z direction (Default 3) +N_SHEETS: 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: 0 + +# 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: 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: 0.5 + Cl: 0.5 + +# ============================================================================= +# Optional: Simulation Runs Specifications +# ============================================================================= + +# ----------------------------------------------------------------------------- +# bash alias for used GROMACS version +# ----------------------------------------------------------------------------- + +GMX: gmx diff --git a/Tutorial/builder/NAu-1.yaml b/Tutorial/builder/NAu-1.yaml new file mode 100644 index 00000000..33ef5e88 --- /dev/null +++ b/Tutorial/builder/NAu-1.yaml @@ -0,0 +1,120 @@ + +# ============================================================================= +# General specifications for clay model construction +# ============================================================================= + +# ============================================================================= +# Required Parameters +# ============================================================================= + +OUTPATH: 'NAu-1-fe' + +# name of system to call according to CLAY_COMP (exp_clay.csv) +# compositions included are: 'NAu-1-fe' 'NAu-2-fe' 'NG-1' 'SWa-1' 'L31' 'IMt-1' 'KGa-1' +SYSNAME: NAu-1-fe + +# 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: ./exp_clay.csv + +# clay type available options in 'clay_units' directory: +# 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: TD21 + + +# ============================================================================= +# Optional: Clay Sheet and Interlayer Specifications +# ============================================================================= + +# number of unit cells in x direction (Default 7) +X_CELLS: 7 + +# number of unit cells in y direction (Default 5) +Y_CELLS: 5 + +# number of unit cells in z direction (Default 3) +N_SHEETS: 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: True + +# ----------------------------------------------------------------------------- +# 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: 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: + Ca: 0.25 + +# ============================================================================= +# Optional: Simulation Runs Specifications +# ============================================================================= + +# ----------------------------------------------------------------------------- +# bash alias for used GROMACS version +# ----------------------------------------------------------------------------- + +GMX: gmx diff --git a/Tutorial/builder/NAu-2.yaml b/Tutorial/builder/NAu-2.yaml new file mode 100644 index 00000000..5359f4a1 --- /dev/null +++ b/Tutorial/builder/NAu-2.yaml @@ -0,0 +1,150 @@ + +# ============================================================================= +# General specifications for clay model construction +# ============================================================================= + +# ============================================================================= +# Required Parameters +# ============================================================================= + +OUTPATH: NAu-2-fe + +# name of system to call according to CLAY_COMP (exp_clay.csv) +# compositions included are: 'NAu-1-fe' 'NAu-2-fe' 'NG-1' 'SWa-1' 'L31' 'IMt-1' 'KGa-1' +SYSNAME: NAu-2-fe + +# 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: ./exp_clay.csv + +# clay type available options in 'clay_units' directory: +# 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: TD21 + + +# ============================================================================= +# Optional: Clay Sheet and Interlayer Specifications +# ============================================================================= + +# number of unit cells in x direction (Default 7) +X_CELLS: 7 + +# number of unit cells in y direction (Default 5) +Y_CELLS: 5 + +# number of unit cells in z direction (Default 3) +N_SHEETS: 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: True + +# ----------------------------------------------------------------------------- +# 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: 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: + Ca: 0.25 + +# ============================================================================= +# 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 diff --git a/Tutorial/builder/SWy-1-simplified.yaml b/Tutorial/builder/SWy-1-simplified.yaml new file mode 100644 index 00000000..d039a48f --- /dev/null +++ b/Tutorial/builder/SWy-1-simplified.yaml @@ -0,0 +1,119 @@ + +# ============================================================================= +# General specifications for clay model construction +# ============================================================================= + +# ============================================================================= +# Required Parameters +# ============================================================================= + +OUTPATH: SWy-1-simplified + +# name of system to call according to CLAY_COMP (exp_clay.csv) +# compositions currently included are: 'NAu-1-fe' 'NAu-2-fe' 'NG-1' 'SWa-1' 'L31' 'IMt-1' 'KGa-1' +SYSNAME: SWy-1-simplified + +# 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: exp_clay.csv + +# clay type available options in internal database: +# trans-Dioctahedral 2:1 - TD21 +# cis-Diioctahedral 2:1 - TD21 +# Trioctahedral 2:1 - T21 +# cis-Dioctahedral 1:1 - CD11 +# Trioctahedral 1:1 - T11 +# old dioctaedral 2:1 unit cells - D21 + +CLAY_TYPE: D21 + + +# ============================================================================= +# Optional: Clay Sheet and Interlayer Specifications +# ============================================================================= + +# number of unit cells in x direction (Default 7) +X_CELLS: 7 + +# number of unit cells in y direction (Default 5) +Y_CELLS: 5 + +# number of unit cells in z direction (Default 3) +N_SHEETS: 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: True + +# ----------------------------------------------------------------------------- +# 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 : 22 + +# 3. OR per unit cell +UC_WATERS: 20 + +# 4. OR for a target d-spacing value in A +#SPACING_WATERS: 20 + +# ============================================================================= +# Optional: Simulation Box Specifications +# ============================================================================= + +# full simulation box height in A (Default 150.0) +BOX_HEIGHT: 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: 0.1 + Cl: 0.1 + +# ============================================================================= +# Optional: Simulation Runs Specifications +# ============================================================================= + +# ----------------------------------------------------------------------------- +# bash alias for used GROMACS version +# ----------------------------------------------------------------------------- + +GMX: gmx diff --git a/Tutorial/builder/SWy-1.yaml b/Tutorial/builder/SWy-1.yaml new file mode 100644 index 00000000..aa55a6c2 --- /dev/null +++ b/Tutorial/builder/SWy-1.yaml @@ -0,0 +1,122 @@ + +# ============================================================================= +# General specifications for clay model construction +# ============================================================================= + +# ============================================================================= +# Required Parameters +# ============================================================================= + +OUTPATH: SWy-1 + +# name of system to call according to CLAY_COMP (exp_clay.csv) +# compositions currently included are: 'NAu-1-fe' 'NAu-2-fe' 'NG-1' 'SWa-1' 'L31' 'IMt-1' 'KGa-1' +SYSNAME: SWy-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: exp_clay.csv + +# clay type available options in internal database: +# trans-Dioctahedral 2:1 - TD21 +# cis-Diioctahedral 2:1 - TD21 +# Trioctahedral 2:1 - T21 +# cis-Dioctahedral 1:1 - CD11 +# Trioctahedral 1:1 - T11 +# old dioctaedral 2:1 unit cells - D21 + +CLAY_TYPE: CD21 + + +# ============================================================================= +# Optional: Clay Sheet and Interlayer Specifications +# ============================================================================= + +# number of unit cells in x direction (Default 7) +X_CELLS: 7 + +# number of unit cells in y direction (Default 5) +Y_CELLS: 5 + +# number of unit cells in z direction (Default 3) +N_SHEETS: 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: [0] + +# probability list of unit cells in system +# p(tot): 1.00 +#UC_RATIOS_LIST: [1] +#UC_INDEX_RATIOS: +# 1: 0.5 +# 9: 0.5 + +# ----------------------------------------------------------------------------- + +# interlayer solvent present or not (Default True) +IL_SOLV: True + +# ----------------------------------------------------------------------------- +# 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: 20 + +# ============================================================================= +# Optional: Simulation Box Specifications +# ============================================================================= + +# full simulation box height in A (Default 150.0) +BOX_HEIGHT: 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: 0.1 + Cl: 0.1 + +# ============================================================================= +# Optional: Simulation Runs Specifications +# ============================================================================= + +# ----------------------------------------------------------------------------- +# bash alias for used GROMACS version +# ----------------------------------------------------------------------------- + +GMX: gmx