#!/bin/bash
# runSimulation.sh
#
# Run a single ElasticPinchOff simulation from the repository root.
# The script creates simulationCases/c<CaseNo>-<mode>/, copies the parameter
# file and source file, compiles the selected case, and runs it.
#
# Usage:
#   bash runSimulation.sh [params_file] [--mode in|out] [--exec exec_code] [--threads N]

set -euo pipefail

SCRIPT_DIR="\$(cd "\$(dirname "\${BASH_SOURCE[0]}")" && pwd)"

usage() {
  cat <<'EOF'
Usage: bash runSimulation.sh [params_file] [--mode in|out] [--exec exec_code] [OPTIONS]

Arguments:
  params_file    Parameter file path (default: default.params)

Options:
  --mode X       Case mode: in or out (default: in)
  --exec FILE    C source in simulationCases/ (overrides --mode mapping)
  --threads N    Thread count; N=1 runs serial (default: 1)
  --CPUs N       Deprecated alias for --threads
  --mpi          Deprecated; ignored
  -h, --help     Show this help message
EOF
}

get_param_value() {
  local key="\$1"
  local file="\$2"
  awk -F '=' -v key="\$key" '
    /^[[:space:]]*#/ { next }
    {
      k = \$1
      gsub(/^[[:space:]]+|[[:space:]]+\$/, "", k)
      if (k == key) {
        v = \$2
        sub(/[[:space:]]*#.*/, "", v)
        gsub(/^[[:space:]]+|[[:space:]]+\$/, "", v)
        print v
        exit
      }
    }
  ' "\$file"
}

# Defaults
EXEC_CODE=""
EXEC_CODE_SET=0
MODE="in"
MODE_SET=0
PARAM_FILE="default.params"
PARAM_FILE_SET=0
OMP_THREADS=1
LEGACY_MPI_REQUESTED=0
LEGACY_CPUS_FLAG=0

while [[ \$# -gt 0 ]]; do
  case "\$1" in
    -h|--help)
      usage
      exit 0
      ;;
    --exec)
      if [[ -z "\${2:-}" ]]; then
        echo "ERROR: --exec requires a file name." >&2
        usage
        exit 1
      fi
      EXEC_CODE="\$2"
      EXEC_CODE_SET=1
      shift 2
      ;;
    --exec=*)
      EXEC_CODE="\${1#*=}"
      EXEC_CODE_SET=1
      shift
      ;;
    --mode)
      if [[ -z "\${2:-}" ]]; then
        echo "ERROR: --mode requires 'in' or 'out'." >&2
        usage
        exit 1
      fi
      MODE="\$2"
      MODE_SET=1
      shift 2
      ;;
    --mode=*)
      MODE="\${1#*=}"
      MODE_SET=1
      shift
      ;;
    --mpi)
      LEGACY_MPI_REQUESTED=1
      shift
      ;;
    --threads)
      if [[ -z "\${2:-}" ]]; then
        echo "ERROR: \$1 requires a positive integer value." >&2
        usage
        exit 1
      fi
      OMP_THREADS="\$2"
      shift 2
      ;;
    --threads=*)
      OMP_THREADS="\${1#*=}"
      shift
      ;;
    --CPUs|--cpus)
      if [[ -z "\${2:-}" ]]; then
        echo "ERROR: \$1 requires a positive integer value." >&2
        usage
        exit 1
      fi
      LEGACY_CPUS_FLAG=1
      OMP_THREADS="\$2"
      shift 2
      ;;
    --CPUs=*|--cpus=*)
      LEGACY_CPUS_FLAG=1
      OMP_THREADS="\${1#*=}"
      shift
      ;;
    --)
      shift
      break
      ;;
    -*)
      echo "ERROR: Unknown option: \$1" >&2
      usage
      exit 1
      ;;
    *)
      if [[ \$PARAM_FILE_SET -eq 0 ]]; then
        PARAM_FILE="\$1"
        PARAM_FILE_SET=1
        shift
      else
        echo "ERROR: Unexpected argument: \$1" >&2
        usage
        exit 1
      fi
      ;;
  esac
done

if [[ \$# -gt 0 ]]; then
  echo "ERROR: Unexpected trailing arguments: \$*" >&2
  usage
  exit 1
fi

if [[ ! "\$OMP_THREADS" =~ ^[1-9][0-9]*\$ ]]; then
  echo "ERROR: --threads must be a positive integer, got: \$OMP_THREADS" >&2
  exit 1
fi

MODE="\$(printf '%s' "\$MODE" | tr '[:upper:]' '[:lower:]')"
if [[ "\$MODE" != "in" && "\$MODE" != "out" ]]; then
  echo "ERROR: --mode must be either 'in' or 'out', got: \$MODE" >&2
  exit 1
fi

if [[ \$EXEC_CODE_SET -eq 0 ]]; then
  if [[ "\$MODE" == "in" ]]; then
    EXEC_CODE="LiquidInThinning.c"
  else
    EXEC_CODE="LiquidOutThinning.c"
  fi
fi

if [[ \$LEGACY_MPI_REQUESTED -eq 1 ]]; then
  echo "WARNING: --mpi is deprecated and ignored." >&2
fi
if [[ \$LEGACY_CPUS_FLAG -eq 1 ]]; then
  echo "WARNING: --CPUs/--cpus is deprecated; use --threads." >&2
fi

USE_OPENMP=0
if [[ "\$OMP_THREADS" -gt 1 ]]; then
  USE_OPENMP=1
fi

if [[ "\$EXEC_CODE" != *.c ]]; then
  EXEC_CODE="\${EXEC_CODE}.c"
fi

if [[ \$MODE_SET -eq 0 ]]; then
  case "\$EXEC_CODE" in
    LiquidInThinning.c)
      MODE="in"
      ;;
    LiquidOutThinning.c)
      MODE="out"
      ;;
  esac
fi

if [[ ! "\$PARAM_FILE" = /* ]]; then
  PARAM_FILE="\${SCRIPT_DIR}/\${PARAM_FILE}"
fi

if [[ -f "\${SCRIPT_DIR}/.project_config" ]]; then
  # shellcheck disable=SC1091
  source "\${SCRIPT_DIR}/.project_config"
fi

if ! command -v qcc >/dev/null 2>&1; then
  echo "ERROR: qcc not found in PATH." >&2
  echo "Hint: source your Basilisk environment or provide .project_config." >&2
  exit 1
fi

if [[ ! -f "\$PARAM_FILE" ]]; then
  echo "ERROR: Parameter file not found: \$PARAM_FILE" >&2
  exit 1
fi

SRC_FILE_ORIG="\${SCRIPT_DIR}/simulationCases/\${EXEC_CODE}"
if [[ ! -f "\$SRC_FILE_ORIG" ]]; then
  echo "ERROR: Source file not found: \$SRC_FILE_ORIG" >&2
  exit 1
fi

CASE_NO="\$(get_param_value "CaseNo" "\$PARAM_FILE")"
if [[ -z "\$CASE_NO" ]]; then
  echo "ERROR: CaseNo not found in parameter file: \$PARAM_FILE" >&2
  exit 1
fi

if [[ ! "\$CASE_NO" =~ ^[0-9]+\$ ]]; then
  echo "ERROR: CaseNo must be numeric, got: \$CASE_NO" >&2
  exit 1
fi

if [[ "\$CASE_NO" -lt 1000 ]]; then
  echo "ERROR: CaseNo must be >= 1000 for consistent sorting, got: \$CASE_NO" >&2
  exit 1
fi

CASE_TAG="c\${CASE_NO}-\${MODE}"
CASE_DIR="\${SCRIPT_DIR}/simulationCases/\${CASE_TAG}"
SRC_FILE_LOCAL="\${EXEC_CODE}"
EXECUTABLE_NAME="\${EXEC_CODE%.c}"
CASE_LOG_FILE="c\${CASE_NO}-log"

echo "========================================="
echo "ElasticPinchOff - Single Case Runner"
echo "========================================="
echo "Source file: \${EXEC_CODE}"
echo "Mode: \${MODE}"
echo "Parameter file: \${PARAM_FILE}"
echo "CaseNo: \${CASE_NO}"
echo "Case directory: \${CASE_DIR}"
if [[ \$USE_OPENMP -eq 1 ]]; then
  echo "Run mode: OpenMP (threads=\${OMP_THREADS})"
else
  echo "Run mode: Serial"
fi
echo "Expected log file: \${CASE_LOG_FILE}"
echo "========================================="
echo ""

mkdir -p "\$CASE_DIR"
cp "\$PARAM_FILE" "\$CASE_DIR/case.params"
cp "\$SRC_FILE_ORIG" "\$CASE_DIR/\$SRC_FILE_LOCAL"

cd "\$CASE_DIR"

echo "Compiling \${SRC_FILE_LOCAL} ..."
QCC_FLAGS=(-I../../src-local -O2 -Wall -disable-dimensions)
if [[ \$USE_OPENMP -eq 1 ]]; then
  QCC_FLAGS+=(-fopenmp)
fi
if ! qcc "\${QCC_FLAGS[@]}" "\$SRC_FILE_LOCAL" -o "\$EXECUTABLE_NAME" -lm; then
  if [[ \$USE_OPENMP -eq 1 ]]; then
    echo "ERROR: OpenMP build failed. Re-run with --threads 1 for serial mode." >&2
  fi
  exit 1
fi
echo "Compilation successful: \$EXECUTABLE_NAME"
echo ""

if [[ -f "restart" ]]; then
  echo "Restart file found - simulation will resume from checkpoint."
fi

if [[ \$USE_OPENMP -eq 1 ]]; then
  echo "Running: OMP_NUM_THREADS=\${OMP_THREADS} ./\${EXECUTABLE_NAME} case.params"
  if OMP_NUM_THREADS="\$OMP_THREADS" ./"\$EXECUTABLE_NAME" case.params; then
    EXIT_CODE=0
  else
    EXIT_CODE=\$?
  fi
else
  echo "Running (serial): ./\${EXECUTABLE_NAME} case.params"
  if ./"\$EXECUTABLE_NAME" case.params; then
    EXIT_CODE=0
  else
    EXIT_CODE=\$?
  fi
fi

echo ""
if [[ \$EXIT_CODE -eq 0 ]]; then
  echo "Simulation completed successfully."
  echo "Output location: simulationCases/\${CASE_TAG}/"
  if [[ -f "\${CASE_LOG_FILE}" ]]; then
    echo "Log file: simulationCases/\${CASE_TAG}/\${CASE_LOG_FILE}"
  fi
else
  echo "Simulation failed with exit code: \$EXIT_CODE"
fi

exit "\$EXIT_CODE"