#!/bin/bash
# =============================================================================
# BOMLIP-CSP Configuration File
# =============================================================================
# This file contains all configurable parameters for the crystal structure
# search and generation pipeline. Modify the values below to customize
# your run.
# =============================================================================

# -----------------------------------------------------------------------------
# [Molecular Parameters]
# SMILES string of the input molecule(s).
# Use '.' (dot) to separate multiple molecules for co-crystal generation.
# Example single molecule:  "C1CC2=COC=C12"
# Example co-crystal:       "C1CC2=COC=C12.CCO"
SMILES="C1CC2=COC=C12"

# Number of conformers to generate during the conformer search step.
# Higher values explore more conformational space but take longer.
# Set to 0 to skip generation and only load existing conformers.
GENERATE_CONFORMERS=10

# Number of conformers to actually use for crystal structure generation.
# Must be <= the number of generated conformers.
# Set to 0 to skip structure generation.
USE_CONFORMERS=4

# Number of molecules in the unit cell (Z').
# Use comma-separated values for multiple molecule types (co-crystal),
# e.g. "1,1" means 1 copy of each molecule in the asymmetric unit.
# Use space-separated values for multiple packings, e.g. "1 2".
MOLECULE_NUM_IN_CELL=1

# -----------------------------------------------------------------------------
# [Crystal Structure Parameters]
# Space group numbers for structure generation.
# Use comma-separated values within a packing, and space-separated
# values for multiple packings.
# Example: "14,61" means search space groups P21/c and Pbca in one packing.
# Example: "14 61" means P21/c in packing 1, Pbca in packing 2.
SPACE_GROUP_LIST="14,61"

# Prefix name added to the output CIF files.
# Use space-separated values for multiple packings.
ADD_NAME="XULDUD"

# Number of crystal structures to generate per (space group, conformer) combination.
# Use space-separated values for multiple packings.
NUM_GENERATION=100

# -----------------------------------------------------------------------------
# [Compute Parameters]
# Maximum number of parallel workers for structure generation.
# Should not exceed the number of available CPU cores.
MAX_WORKERS=16

# -----------------------------------------------------------------------------
# [Run Mode]
# Execution mode controlling which steps are performed.
# Available options:
#   all              - Run conformer search followed by structure generation (default)
#   conformer_only   - Only perform conformer search
#   structure_only   - Skip conformer search, use existing conformers to generate structures
MODE="all"

# -----------------------------------------------------------------------------
# [Path Parameters]
# Directory for storing intermediate conformers and output CIF structures.
# Relative to the project root directory.
OUTPUT_DIR="csp_results"