g16.ircinput.sh

#!/bin/bash

###
#
# tools-for-g16.bash -- 
#   A collection of tools for the help with Gaussian 16.
# Copyright (C) 2019-2020 Martin C Schwarzer
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program.  If not, see <https://www.gnu.org/licenses/>.
#
###

# 
# The help lines are distributed throughout the script and grepped for
#
#hlp   This script reads an input file of a frequency calculation, 
#hlp   extracts the route section,
#hlp   and writes new input files for a IRC runs.
#hlp
#hlp   tools-for-g16.bash  Copyright (C) 2019  Martin C Schwarzer
#hlp   This program comes with ABSOLUTELY NO WARRANTY; this is free software, 
#hlp   and you are welcome to redistribute it under certain conditions; 
#hlp   please see the license file distributed alongside this repository,
#hlp   which is available when you type 'g16.tools-info.sh -L',
#hlp   or at <https://github.com/polyluxus/tools-for-g16.bash>.
#hlp
#hlp   Usage: $scriptname [options] [--] <INPUT_FILE>
#hlp

#
# Generic functions to find the scripts 
# (Copy of ./resources/locations.sh)
#
# Let's know where the script is and how it is actually called
#

get_absolute_location ()
{
    # Resolves the absolute location of parameter and returns it
    # Taken from https://stackoverflow.com/a/246128/3180795
    local resolve_file="$1" description="$2" 
    local link_target directory_name filename resolve_dir_name 
    debug "Getting directory for '$resolve_file'."
    #  resolve $resolve_file until it is no longer a symlink
    while [[ -h "$resolve_file" ]]; do 
      link_target="$(readlink "$resolve_file")"
      if [[ $link_target == /* ]]; then
        debug "File '$resolve_file' is an absolute symlink to '$link_target'"
        resolve_file="$link_target"
      else
        directory_name="$(dirname "$resolve_file")" 
        debug "File '$resolve_file' is a relative symlink to '$link_target' (relative to '$directory_name')"
        #  If $resolve_file was a relative symlink, we need to resolve 
        #+ it relative to the path where the symlink file was located
        resolve_file="$directory_name/$link_target"
      fi
    done
    debug "File is '$resolve_file'" 
    filename="$(basename "$resolve_file")"
    debug "File name is '$filename'"
    resolve_dir_name="$(dirname "$resolve_file")"
    directory_name="$(cd -P "$(dirname "$resolve_file")" && pwd)"
    if [[ "$directory_name" != "$resolve_dir_name" ]]; then
      debug "$description '$directory_name' resolves to '$directory_name'."
    fi
    debug "$description is '$directory_name'"
    if [[ -z $directory_name ]] ; then
      directory_name="."
    fi
    echo "$directory_name/$filename"
}

get_absolute_filename ()
{
    # Returns only the filename
    local resolve_file="$1" description="$2" return_filename
    return_filename=$(get_absolute_location "$resolve_file" "$description")
    return_filename=${return_filename##*/}
    echo "$return_filename"
}

get_absolute_dirname ()
{
    # Returns only the directory
    local resolve_file="$1" description="$2" return_dirname
    return_dirname=$(get_absolute_location "$resolve_file" "$description")
    return_dirname=${return_dirname%/*}
    echo "$return_dirname"
}


get_scriptpath_and_source_files ()
{
    local error_count tmplog line
    tmplog=$(mktemp tmp.XXXXXXXX) 
    # Who are we and where are we?
    scriptname="$(get_absolute_filename "${BASH_SOURCE[0]}" "installname")"
    debug "Script is called '$scriptname'"
    # remove scripting ending (if present)
    scriptbasename=${scriptname%.sh} 
    debug "Base name of the script is '$scriptbasename'"
    scriptpath="$(get_absolute_dirname  "${BASH_SOURCE[0]}" "installdirectory")"
    debug "Script is located in '$scriptpath'"
    resourcespath="$scriptpath/resources"
    
    if [[ -d "$resourcespath" ]] ; then
      debug "Found library in '$resourcespath'."
    else
      (( error_count++ ))
    fi
    
    # Import default variables
    #shellcheck source=./resources/default_variables.sh
    source "$resourcespath/default_variables.sh" &> "$tmplog" || (( error_count++ ))
    
    # Set more default variables
    exit_status=0
    stay_quiet=0
    # Ensure that in/outputfile variables are empty
    unset inputfile
    unset outputfile
    
    # Import other functions
    #shellcheck source=./resources/messaging.sh
    source "$resourcespath/messaging.sh" &> "$tmplog" || (( error_count++ ))
    #shellcheck source=./resources/rcfiles.sh
    source "$resourcespath/rcfiles.sh" &> "$tmplog" || (( error_count++ ))
    #shellcheck source=./resources/test_files.sh
    source "$resourcespath/test_files.sh" &> "$tmplog" || (( error_count++ ))
    #shellcheck source=./resources/process_gaussian.sh
    source "$resourcespath/process_gaussian.sh" &> "$tmplog" || (( error_count++ ))
    #shellcheck source=./resources/validate_numbers.sh
    source "$resourcespath/validate_numbers.sh" &> "$tmplog" || (( error_count++ ))

    if (( error_count > 0 )) ; then
      echo "ERROR: Unable to locate library functions. Check installation." >&2
      echo "ERROR: Expect functions in '$resourcespath'."
      debug "Errors caused by:"
      while read -r line || [[ -n "$line" ]] ; do
        debug "$line"
      done < "$tmplog"
      debug "$(rm -v -- "$tmplog")"
      exit 1
    else
      debug "$(rm -v -- "$tmplog")"
    fi
}

#
# Specific functions for this script only
#

process_inputfile ()
{
    local testfile="$1"
    debug "Processing Input: $testfile"
    read_g16_input_file "$testfile"
    if [[ -z "$route_section" ]] ; then
      warning "It appears that '$testfile' does not contain a valid (or recognised) route section."
      warning "Make sure this template file contains '#/#P/#N/#T' followed by a space."
      return 1
    else
      debug "Route (unmodified): $route_section"
    fi
    local modified_route="$route_section"
    local -a additional_keywords

    extract_jobname_inoutnames "$testfile"
    
    # The opt and irc keywords are mutually exclusive, therefore opt needs to be removed
    while ! modified_route=$(remove_opt_keyword      "$modified_route") ; do : ; done
    # IRC calculations build upon Freq calculations, hence the latter should be present in the source
    if check_freq_keyword "$modified_route" ; then
      message "Source input is frequency calculation, found 'FREQ' keyword."
    else
      warning "Keyword 'freq' was not found in input stream. Please check source input."
      warning "Running an IRC calculation makes only sense on a successful frequency calculation."
      warning "Please also check the created IRC inputfiles manually for errors."
    fi
    # remove the freq keyword, we don't need it anymore
    while ! modified_route=$(remove_freq_keyword     "$modified_route") ; do : ; done
    # The irc keyword will be added, therefore it should not be present
    while ! modified_route=$(remove_irc_keyword      "$modified_route") ; do : ; done
    # The guess/geom keyword will be added, it will clash if already present
    while ! modified_route=$(remove_guess_keyword    "$modified_route") ; do : ; done
    additional_keywords+=("guess(read)")
    message "Added '${additional_keywords[-1]}' to the route section."
    if check_allcheck_option "$modified_route" ; then 
      debug "Keyword 'AllCheck' detected in input stream."
    else 
      while ! modified_route=$(remove_geom_keyword     "$modified_route") ; do : ; done
      additional_keywords+=("geom(check)")
      message "Added '${additional_keywords[-1]}' to the route section."
    fi
    # Population analysis doesn't work well with irc runs
    while ! modified_route=$(remove_pop_keyword      "$modified_route") ; do : ; done
    # Writing additional output does not work well with irc runs
    while ! modified_route=$(remove_output_keyword   "$modified_route") ; do : ; done
    
    if modified_route=$(remove_gen_keyword "$modified_route") ; then
      debug "No gen keyword present."
    else
      warning "Additional basis set specifications have not been read,"
      warning "but will be retrieved from the checkpointfile."
      while ! modified_route=$(remove_gen_keyword "$modified_route") ; do : ; done
      additional_keywords+=('ChkBasis')
      message "Added '${additional_keywords[-1]}' to the route section."
      if check_denfit_keyword "$modified_route" ; then
        warning "Please check density fitting ('DenFit') settings are compatible with 'ChkBasis'."
      else
        debug "No 'DenFit' present."
      fi
    fi

    # Add the custom route options
    if (( ${#use_custom_route_keywords[@]} == 0 )) ; then
      debug "No custom route keywords specified."
    else
      additional_keywords+=("${use_custom_route_keywords[@]}")
      debug "Added the following custom keywords to route section:"
      debug "$(fold -w80 -s <<< "${use_custom_route_keywords[*]}")"
    fi

    debug "Added the following keywords to route section:"
    debug "$(fold -w80 -s <<< "${additional_keywords[*]}")"

    # add the custom keywords
    modified_route="$modified_route ${additional_keywords[*]}"

    local verified_checkpoint
    if [[ -z $checkpoint ]] ; then
      checkpoint="${jobname}.chk"
      # Check if the guessed checkpointfile exists
      # (We'll trust the user if it was specified in the input file,
      #  after all the calculation might not be completed yet.)
      if verified_checkpoint=$(test_file_location "$checkpoint") ; then
        debug "verified_checkpoint=$verified_checkpoint"
        fatal "Cannot find '$verified_checkpoint'."
      else
        old_checkpoint="$checkpoint"
      fi
    else
      old_checkpoint="$checkpoint"
    fi

    # Throw away the body of the input file
    unset inputfile_body

    # declare a variable to hold the suffix
    local jobbasename use_file_suffix use_direction_suffix
    if [[ -n $inputfile_new ]] ; then
      jobbasename="${inputfile_new%.*}"
      use_file_suffix="${inputfile_new##*.}"
    else
      jobbasename="${jobname%.freq*}.irc"
      use_file_suffix="$g16_input_suffix"
    fi

    # create variables for irc keyword
    local concatenate_irc_opts irc_keyword

    if (( ${#use_irc_opts[@]} > 0 )) ; then
      concatenate_irc_opts=$(printf ',%s' "${use_irc_opts[@]}")
      concatenate_irc_opts=${concatenate_irc_opts:1}
    fi

    # Assign new checkpoint/inputfile in forward direction
    use_direction_suffix="fwd"
    jobname="${jobbasename}.$use_direction_suffix"
    checkpoint="${jobname}.chk"
    inputfile="${jobname}.$use_file_suffix"
    backup_if_exists "$inputfile"

    irc_keyword="IRC(RCFC,forward"
    [[ -n $concatenate_irc_opts ]] && irc_keyword+=",$concatenate_irc_opts"
    irc_keyword+=")"
    message "Added '$irc_keyword' to the route section."
    route_section="$modified_route $irc_keyword"

    write_g16_input_file > "$inputfile"
    message "Written modified inputfile '$inputfile'."
    unset irc_keyword

    # Assign new checkpoint/inputfile in reverse direction
    use_direction_suffix="rev"
    jobname="${jobbasename}.$use_direction_suffix"
    checkpoint="${jobname}.chk"
    inputfile="${jobname}.$use_file_suffix"
    backup_if_exists "$inputfile"

    irc_keyword="IRC(RCFC,reverse"
    [[ -n $concatenate_irc_opts ]] && irc_keyword+=",$concatenate_irc_opts"
    irc_keyword+=")"
    message "Added '$irc_keyword' to the route section."
    route_section="$modified_route $irc_keyword"

    write_g16_input_file > "$inputfile"
    message "Written modified inputfile '$inputfile'."
}

#
# Process Options
#

process_options ()
{
    #hlp   Options:
    #hlp    
    local OPTIND=1 

    while getopts :o:r:t:f:m:p:d:sh options ; do
        case $options in
          #hlp   -o <ARG>   Adds options <ARG> to the irc keyword.
          #hlp              May be specified multiple times.
          #hlp              The stack will be collated, but no sanity check will be performed.
          #hlp              Example Options: MaxPoints=<NUM>, StepSize=<NUM>, MaxCycle=<NUM>, ...
          #hlp
          o) 
            use_irc_opts+=("$OPTARG")
            ;;

          #hlp   -r <ARG>   Adds custom command <ARG> to the route section.
          #hlp              May be specified multiple times.
          #hlp              The stack will be collated, but no sanity check will be performed.
          #hlp 
          r) 
            use_custom_route_keywords+=("$OPTARG" )
            ;;

          #hlp   -t <ARG>   Adds <ARG> to the end (tail) of the new input file.
          #hlp              If specified multiple times, each argument goes to a new line.
          #hlp 
          t) 
            use_custom_tail[${#use_custom_tail[@]}]="$OPTARG" 
            ;;

          #hlp   -f <ARG>   Write inputfiles to <ARG>, where the argument should contain a dot,
          #hlp              e.g. the format like 'jobname.suffix' will produce two files
          #hlp              'jobname.fwd.suffix' and 'jobname.rev.suffix'.
          #hlp
          f)
            inputfile_new="$OPTARG"
            debug "Setting inputfile_new='$inputfile_new'."
            ;;

          # Link 0 related options
          #hlp   -m <ARG>   Define the total memory to be used in megabyte.
          #hlp              The total request will be larger to account for 
          #hlp              overhead which Gaussian may need. (Default: 512)
          #hlp
            m) 
               validate_integer "$OPTARG" "the memory"
               if (( OPTARG == 0 )) ; then
                 fatal "Memory limit must not be zero."
               fi
               requested_memory="$OPTARG" 
               ;;

          #hlp   -p <ARG>   Define number of professors to be used. (Default: 4)
          #hlp
            p) 
               validate_integer "$OPTARG" "the number of threads"
               if (( OPTARG == 0 )) ; then
                 fatal "Number of threads must not be zero."
               fi
               requested_numCPU="$OPTARG" 
               ;;

          #hlp   -d <ARG>   Define disksize via the MaxDisk keyword (MB).
          #hlp              This option does not set a parameter for the queueing system,
          #hlp              but will only modify the input file with the size specification.
          #hlp              
            d) 
               validate_integer "$OPTARG" "the 'MaxDisk' keyword"
               if (( OPTARG == 0 )) ; then
                 fatal "The keyword 'MaxDisk' must not be zero."
               fi
               requested_maxdisk="$OPTARG"
               ;;

          #hlp   -s         Suppress logging messages of the script.
          #hlp              (May be specified multiple times.)
          #hlp
          s) 
            (( stay_quiet++ )) 
            ;;

          #hlp   -h         this help.
          #hlp
          h) 
            helpme 
            ;;

          #hlp     --       Close reading options.
          # This is the standard closing argument for getopts, it needs no implemenation.

          \?) 
            fatal "Invalid option: -$OPTARG." 
            ;;

          :) 
            fatal "Option -$OPTARG requires an argument." 
            ;;

        esac
    done

    # Shift all variables processed to far
    shift $((OPTIND-1))

    if [[ -z "$1" ]] ; then 
      fatal "There is no inputfile specified"
    fi

    # If a filename is specified, it must exist, otherwise exit
    # different mode let's you only use the jobname
    requested_inputfile=$(is_readable_file_or_exit "$1") || exit 1 
    shift
    debug "Specified input: $requested_inputfile"

    # Issue a warning that the addidtional flag has no effect.
    warn_additional_args "$@"
}

#
# MAIN SCRIPT
#

# If this script is sourced, return before executing anything
if ( return 0 2>/dev/null ) ; then
  # [How to detect if a script is being sourced](https://stackoverflow.com/a/28776166/3180795)
  debug "Script is sourced. Return now."
  return 0
fi

# Save how script was called
printf -v script_invocation_spell "'%s' " "${0/#$HOME/<HOME>}" "$@"

# Sent logging information to stdout
exec 3>&1

# Need to define debug function if unknown
if ! command -v debug ; then
  debug () {
    echo "DEBUG  : " "$*" >&4
  }
fi

# Secret debugging switch
if [[ "$1" == "debug" ]] ; then
  exec 4>&1
  stay_quiet=0 
  shift 
else
  exec 4> /dev/null
fi

get_scriptpath_and_source_files || exit 1

# Check whether we have the right numeric format (set it if not)
warn_and_set_locale

# Check for settings in three default locations (increasing priority):
#   install path of the script, user's home directory, current directory
g16_tools_rc_searchlocations=( "$scriptpath" "$HOME" "$HOME/.config" "$PWD" )
g16_tools_rc_loc="$( get_rc "${g16_tools_rc_searchlocations[@]}" )"
debug "g16_tools_rc_loc=$g16_tools_rc_loc"

# Load custom settings from the rc

if [[ -n $g16_tools_rc_loc ]] ; then
  #shellcheck source=./g16.tools.rc 
  . "$g16_tools_rc_loc"
  message "Configuration file '${g16_tools_rc_loc/*$HOME/<HOME>}' applied."
  if [[ "${configured_version}" =~ ^${version%.*} ]] ; then 
    debug "Config: $configured_version ($configured_versiondate); Current: $version ($versiondate)."
  else
    warning "Configured version was ${configured_version:-unset} (${configured_versiondate:-unset}),"
    warning "and probably needs an update to $version ($versiondate)."
  fi
else
  debug "No custom settings found."
fi

# Initialise some variables

declare -a use_irc_opts
declare -a use_custom_route_keywords

# Evaluate Options

process_options "$@" || exit_status=$?
process_inputfile "$requested_inputfile" || exit_status=$?

#hlp   $scriptname is part of $softwarename $version ($versiondate) 
message "$scriptname is part of $softwarename $version ($versiondate)"
debug "$script_invocation_spell"
exit $exit_status