diff --git a/README.md b/README.md index 348092c..98f9afa 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ # sum_dirac_dfcoef : SUMMARIZE DIRAC DFCOEF COEFFICIENTS -[![sum_dirac_dfcoef_test](https://github.com/kohei-noda-qcrg/sum_dirac_dfcoef/actions/workflows/test.yml/badge.svg)](https://github.com/kohei-noda-qcrg/sum_dirac_dfcoef/actions/workflows/test.yml) +[![sum_dirac_dfcoef_test](https://github.com/RQC-HU/sum_dirac_dfcoef/actions/workflows/test.yml/badge.svg)](https://github.com/RQC-HU/sum_dirac_dfcoef/actions/workflows/test.yml) This program provides a utility to summarize the contribution of each atomic orbital per molecular orbital from the [DIRAC](http://diracprogram.org/doku.php) output file that the [*PRIVEC and .VECPRI options](http://www.diracprogram.org/doc/release-22/manual/analyze/privec.html) are used. @@ -133,18 +133,19 @@ optional arguments (--input is required) - -o OUTPUT, --output OUTPUT - Output file name. Default: sum_dirac_dfcoef.out + Output file name. + Default: sum_dirac_dfcoef.out - -g, --for-generator - Automatically set the arguments for dcaspt2_input_generator. - This option is useful when you want to use the result of this program as input to dcaspt2_input_generator. + Automatically set the arguments for dcaspt2_input_generator. + This option is useful when you want to use the result of this program as input to dcaspt2_input_generator. This option is equivalent to set -c/--compress and not set -p/--positronic and --no-scf options. - -j [PARALLEL], --parallel [PARALLEL] - Number of parallel processes. - Default: 1 (single process). + Number of parallel processes. + Default: 1 (single process). If you set -j option without argument, the number of parallel processes is set to the number of CPU cores(=os.cpu_count()). - -c, --compress @@ -152,19 +153,17 @@ optional arguments (--input is required) Compress output. Display all coefficients on one line for each MO. This options is useful when you want to use the result in a spreadsheet like Microsoft Excel. -- --only-moltra - - Print only MOs that is included in the range of MOLTRA. You should activate this option when you want to get compressed output (-c/--compress option) but you don't want to get the output that is not included in the range of MOLTRA. - - -t THRESHOLD, --threshold THRESHOLD threshold. Default: 0.1 % - (e.g) --threshold=0.1 => print orbital with more than 0.1 % contribution + (e.g) --threshold=0.1 → print orbital with more than 0.1 % contribution - -d DECIMAL, --decimal DECIMAL - Set the decimal places. Default: 5 - (e.g) --decimal=3 => print orbital with 3 decimal places (0.123, 2.456, ...). range: 1-15 + Set the decimal places. + Default: 5 + (e.g) --decimal=3 → print orbital with 3 decimal places (0.123, 2.456, ...). + range: 1-15 - -a, --all-write @@ -172,7 +171,8 @@ optional arguments (--input is required) - -p, --positronic-write - Print only Positronic MOs. The output with this option cannot be used as input to dcaspt2_input_generator. + Print only Positronic MOs. + The output with this option cannot be used as input to dcaspt2_input_generator. - -v, --version @@ -180,7 +180,7 @@ optional arguments (--input is required) - --no-scf - If you don't activate .SCF keyword in your DIRAC input file, you must use this option. + If you don't activate .SCF keyword in your DIRAC input file, you must use this option. But you cannot use the output using this option to dcaspt2_input_generator program. - --debug diff --git a/src/sum_dirac_dfcoef/args.py b/src/sum_dirac_dfcoef/args.py index 46dbebd..d5e6be7 100644 --- a/src/sum_dirac_dfcoef/args.py +++ b/src/sum_dirac_dfcoef/args.py @@ -61,14 +61,7 @@ def parse_args() -> "argparse.Namespace": dest="compress", ) parser.add_argument( - "--only-moltra", - action="store_true", - help="Print only MOs that is included in the range of MOLTRA. You should activate this option when you want to get compressed output (-c/--compress option)\ - but you don't want to get the output that is not included in the range of MOLTRA.", - dest="only_moltra", - ) - parser.add_argument( - "-t", "--threshold", type=float, default=0.1, help="threshold. Default: 0.1 %% (e.g) --threshold=0.1 => print orbital with more than 0.1 %% contribution", dest="threshold" + "-t", "--threshold", type=float, default=0.1, help="threshold. Default: 0.1 %% (e.g) --threshold=0.1 → print orbital with more than 0.1 %% contribution", dest="threshold" ) parser.add_argument( "-d", @@ -76,7 +69,7 @@ def parse_args() -> "argparse.Namespace": type=int, default=5, choices=range(1, 16), - help="Set the decimal places. Default: 5 (e.g) --decimal=3 => print orbital with 3 decimal places (0.123, 2.456, ...). range: 1-15", + help="Set the decimal places. Default: 5 (e.g) --decimal=3 → print orbital with 3 decimal places (0.123, 2.456, ...). range: 1-15", dest="decimal", ) parser.add_argument("-a", "--all-write", action="store_true", help="Print all MOs(Positronic and Electronic).", dest="all_write") @@ -110,15 +103,9 @@ def parse_args() -> "argparse.Namespace": if not (args.no_scf or args.positronic_write) and args.compress: args.for_generator = True - if args.only_moltra and args.for_generator: - parser.error("--only-moltra option cannot be used with --for-generator option.\nUse either --only-moltra or --for-generator option.") - if args.all_write and args.positronic_write: parser.error("-a/--all-write and -p/--positronic-write options cannot be set at the same time.") - if args.only_moltra and not args.compress: - print("Warning: --only-moltra option is activated but --compress option is not activated. --only-moltra option will be ignored.") - return args diff --git a/src/sum_dirac_dfcoef/privec_reader.py b/src/sum_dirac_dfcoef/privec_reader.py index 5957e26..36b49f4 100644 --- a/src/sum_dirac_dfcoef/privec_reader.py +++ b/src/sum_dirac_dfcoef/privec_reader.py @@ -128,7 +128,7 @@ def check_start_vector_print(self, words: List[str]) -> bool: return False def check_end_vector_print(self, words: List[str]) -> bool: - # https://github.com/kohei-noda-qcrg/summarize_dirac_dfcoef_coefficients/issues/7#issuecomment-1377969626 + # https://github.com/RQC-HU/sum_dirac_dfcoef/issues/7#issuecomment-1377969626 if len(words) >= 2 and self.stage == STAGE.WAIT_END_READING_COEF: return True return False