def run_bse_cli():
################################################################################################
# NOTE: I am deliberately not using the 'choices' argument in add_argument. I could use it
# for formats, etc, however I wouldn't want to use it for basis set names. Therefore, I handle
# all of that manually so that error output is consistent and clean
################################################################################################
########################################
# Main global options
########################################
parser = argparse.ArgumentParser(description='Description of your program')
parser.add_argument('-V',
action='version',
version='basis_set_exchange ' + version())
parser.add_argument('-d',
'--data-dir',
metavar='PATH',
help='Override which data directory to use')
parser.add_argument('-o',
'--output',
metavar='PATH',
help='Output to given file rather than stdout')
subparsers = parser.add_subparsers(metavar='subcommand', dest='subcmd')
subparsers.required = True # https://bugs.python.org/issue9253#msg186387
########################################
# Listing of data-independent info
########################################
# list-formats subcommand
subp = subparsers.add_parser(
'list-formats',
help=
'Output a list of basis set formats that can be used with obtaining a basis set'
)
subp.add_argument('-n',
'--no-description',
action='store_true',
help='Print only the format names')
# list-writer-formats subcommand
subp = subparsers.add_parser(
'list-writer-formats',
help='Output a list available basis set formats that can be written')
subp.add_argument('-n',
'--no-description',
action='store_true',
help='Print only the format names')
# list-reader-formats
subp = subparsers.add_parser(
'list-reader-formats',
help='Output a list of basis set formats that can be read')
subp.add_argument('-n',
'--no-description',
action='store_true',
help='Print only the format names')
# list-ref-formats subcommand
subp = subparsers.add_parser(
'list-ref-formats',
help='Output a list all available reference formats and descriptions')
subp.add_argument('-n',
'--no-description',
action='store_true',
help='Print only the reference format names')
# list-roles subcommand
subp = subparsers.add_parser(
'list-roles',
help='Output a list all available roles and descriptions')
subp.add_argument('-n',
'--no-description',
action='store_true',
help='Print only the role names')
########################################
# Listing of general info and metadata
########################################
# get-data-dir
subparsers.add_parser(
'get-data-dir',
help='Output the default data directory of this package')
# list-basis-sets subcommand
subp = subparsers.add_parser(
'list-basis-sets',
help='Output a list all available basis sets and descriptions')
subp.add_argument('-n',
'--no-description',
action='store_true',
help='Print only the basis set names')
subp.add_argument(
'-f',
'--family',
help='Limit the basis set list to only the specified family'
).completer = cli_family_completer
subp.add_argument(
'-r',
'--role',
help='Limit the basis set list to only the specified role'
).completer = cli_role_completer
subp.add_argument(
'-s',
'--substr',
help=
'Limit the basis set list to only basis sets whose name contains the specified substring'
)
subp.add_argument(
'-e',
'--elements',
help=
'Limit the basis set list to only basis sets that contain all the given elements'
)
# list-families subcommand
subparsers.add_parser(
'list-families', help='Output a list all available basis set families')
# lookup-by-role
subp = subparsers.add_parser(
'lookup-by-role',
help='Lookup a companion/auxiliary basis by primary basis and role')
subp.add_argument(
'basis',
help='Name of the primary basis we want the auxiliary basis for'
).completer = cli_bsname_completer
subp.add_argument('role', help='Role of the auxiliary basis to look for'
).completer = cli_role_completer
#################################
# Output of info
#################################
# get-basis subcommand
subp = subparsers.add_parser('get-basis',
help='Output a formatted basis set')
subp.add_argument('basis', help='Name of the basis set to output'
).completer = cli_bsname_completer
subp.add_argument('fmt', help='Which format to output the basis set as'
).completer = cli_write_fmt_completer
subp.add_argument(
'--elements',
help=
'Which elements of the basis set to output. Default is all defined in the given basis'
)
subp.add_argument(
'--version',
help=
'Which version of the basis set to output. Default is the latest version'
)
subp.add_argument('--noheader',
action='store_true',
help='Do not output the header at the top')
subp.add_argument('--unc-gen',
action='store_true',
help='Remove general contractions')
subp.add_argument('--unc-spdf',
action='store_true',
help='Remove combined sp, spd, ... contractions')
subp.add_argument('--unc-seg',
action='store_true',
help='Remove general contractions')
subp.add_argument('--rm-free',
action='store_true',
help='Remove free primitives')
subp.add_argument('--opt-gen',
action='store_true',
help='Optimize general contractions')
subp.add_argument(
'--make-gen',
action='store_true',
help='Make the basis set as generally-contracted as possible')
subp.add_argument('--aug-steep',
type=int,
default=0,
help='Augment with n steep functions')
subp.add_argument('--aug-diffuse',
type=int,
default=0,
help='Augment with n diffuse functions')
subp.add_argument(
'--get-aux',
type=int,
default=0,
help=
'Instead of the orbital basis, get an automatically formed auxiliary basis'
)
# get-refs subcommand
subp = subparsers.add_parser('get-refs',
help='Output references for a basis set')
subp.add_argument('basis',
help='Name of the basis set to output the references for'
).completer = cli_bsname_completer
subp.add_argument('reffmt',
help='Which format to output the references as'
).completer = cli_reffmt_completer
subp.add_argument(
'--elements',
help=
'Which elements to output the references for. Default is all defined in the given basis.'
)
subp.add_argument(
'--version',
help='Which version of the basis set to get the references for')
# get-info subcommand
subp = subparsers.add_parser(
'get-info', help='Output general info and metadata for a basis set')
subp.add_argument('basis',
help='Name of the basis set to output the info for'
).completer = cli_bsname_completer
# get-notes subcommand
subp = subparsers.add_parser('get-notes',
help='Output the notes for a basis set')
subp.add_argument('basis',
help='Name of the basis set to output the notes for'
).completer = cli_bsname_completer
# get-family subcommand
subp = subparsers.add_parser('get-family',
help='Output the family of a basis set')
subp.add_argument('basis',
help='Name of the basis set to output the family for'
).completer = cli_bsname_completer
# get-versions subcommand
subp = subparsers.add_parser(
'get-versions',
help='Output a list all available versions of a basis set')
subp.add_argument('basis',
help='Name of the basis set to list the versions of'
).completer = cli_bsname_completer
subp.add_argument('-n',
'--no-description',
action='store_true',
help='Print only the version numbers')
# get-family-notes subcommand
subp = subparsers.add_parser(
'get-family-notes', help='Get the notes of a family of basis sets')
subp.add_argument('family',
type=str.lower,
help='The basis set family to the get the notes of'
).completer = cli_family_completer
#################################
# Converting basis sets
#################################
subp = subparsers.add_parser(
'convert-basis',
help='Convert basis set files from one format to another')
subp.add_argument('input_file', type=str, help='Basis set file to convert')
subp.add_argument('output_file', type=str, help='Converted basis set file')
subp.add_argument(
'--in-fmt',
type=str,
default=None,
help='Input format (default: autodetected from input filename'
).completer = cli_read_fmt_completer
subp.add_argument(
'--out-fmt',
type=str,
default=None,
help='Output format (default: autodetected from output filename'
).completer = cli_write_fmt_completer
subp.add_argument(
'--make-gen',
action='store_true',
help='Make the basis set as generally-contracted as possible')
#################################
# Auxiliary basis sets
#################################
subp = subparsers.add_parser('autoaux-basis',
help='Form AutoAux auxiliary basis')
subp.add_argument('input_file', type=str, help='Orbital basis to load')
subp.add_argument('output_file', type=str, help='AutoAux basis to write')
subp.add_argument(
'--in-fmt',
type=str,
default=None,
help='Input format (default: autodetected from input filename'
).completer = cli_read_fmt_completer
subp.add_argument(
'--out-fmt',
type=str,
default=None,
help='Output format (default: autodetected from output filename'
).completer = cli_write_fmt_completer
subp = subparsers.add_parser('autoabs-basis',
help='Form AutoABS auxiliary basis')
subp.add_argument('input_file', type=str, help='Orbital basis to load')
subp.add_argument('output_file', type=str, help='AutoABS basis to write')
subp.add_argument(
'--in-fmt',
type=str,
default=None,
help='Input format (default: autodetected from input filename'
).completer = cli_read_fmt_completer
subp.add_argument(
'--out-fmt',
type=str,
default=None,
help='Output format (default: autodetected from output filename'
).completer = cli_write_fmt_completer
#################################
# Creating bundles
#################################
subp = subparsers.add_parser('create-bundle',
help='Create a bundle of basis sets')
subp.add_argument('fmt', help='Which format to output the basis set as'
).completer = cli_write_fmt_completer
subp.add_argument('reffmt',
help='Which format to output the references as'
).completer = cli_reffmt_completer
subp.add_argument('bundle_file', help='Bundle/Archive file to create')
subp.add_argument(
'--archive-type',
help='Override the type of archive to create (zip or tbz)')
#############################
# DONE WITH SUBCOMMANDS
#############################
# setup autocomplete
argcomplete.autocomplete(parser, validator=cli_case_insensitive_validator)
# Now parse and handle the args
args = parser.parse_args()
# Check and make sure basis sets, roles, etc, are valid
args = cli_check_normalize_args(args)
# Actually generate the output
output = bse_cli_handle_subcmd(args)
if args.output:
with open(args.output, 'w', encoding='utf-8') as outfile:
outfile.write(output)
else:
print(output)
return 0
def run_bsecurate_cli():
################################################################################################
# NOTE: I am deliberately not using the 'choices' argument in add_argument. I could use it
# for formats, etc, however I wouldn't want to use it for basis set names. Therefore, I handle
# all of that manually so that error output is consistent and clean
################################################################################################
########################################
# Main global options
########################################
parser = argparse.ArgumentParser(description='Description of your program')
parser.add_argument('-V',
action='version',
version='basis_set_exchange ' + version())
parser.add_argument('-d',
'--data-dir',
metavar='PATH',
help='Override which data directory to use')
parser.add_argument('-o',
'--output',
metavar='PATH',
help='Output to given file rather than stdout')
subparsers = parser.add_subparsers(metavar='subcommand', dest='subcmd')
subparsers.required = True # https://bugs.python.org/issue9253#msg186387
########################################
# Listing of general info and metadata
########################################
# elements-in-files
subp = subparsers.add_parser(
'elements-in-files',
help='For a list of JSON files, output what elements are in each file')
subp.add_argument('files', nargs='+', help='List of files to inspect')
# elements-in-files
subp = subparsers.add_parser(
'component-file-refs',
help=
'For a list of component JSON files, output what elements/references are in each file'
)
subp.add_argument('files', nargs='+', help='List of files to inspect')
########################################
# Updating metadata
########################################
subparsers.add_parser('update-metadata',
help='Update the metadata in the repository')
########################################
# Printing data
########################################
subp = subparsers.add_parser(
'print-component-file',
help='(Pretty) print the contents of a component file')
subp.add_argument('file', help='File to print')
subp.add_argument(
'--elements',
help=
'Which elements of the basis set to output. Default is all defined in the given basis'
)
########################################
# Manipulating basis set data
########################################
# make-diff
subp = subparsers.add_parser(
'make-diff',
help='Find/Store the differences between two groups of files')
subp.add_argument('-l',
'--left',
nargs='+',
required=True,
help='Base JSON files')
subp.add_argument(
'-r',
'--right',
nargs='+',
required=True,
help='JSON files with data to subtract from the base files')
########################################
# Comparing
########################################
# compare-basis-sets
subp = subparsers.add_parser(
'compare-basis-sets',
help='Compare two basis sets in the data directory')
subp.add_argument(
'basis1',
help='First basis set to compare').completer = cli_bsname_completer
subp.add_argument(
'basis2',
help='Second basis set to compare').completer = cli_bsname_completer
subp.add_argument(
'--version1',
help='Version of the first basis set to compare with. Default is latest'
)
subp.add_argument(
'--version2',
help=
'Version of the second basis set to compare with. Default is latest')
subp.add_argument('--uncontract-general',
action='store_true',
help='Remove general contractions before comparing')
# compare-basis-files
subp = subparsers.add_parser('compare-basis-files',
help='Compare two formatted basis set files')
subp.add_argument('file1', help='First basis set file to compare')
subp.add_argument('file2', help='Second basis set file to compare')
subp.add_argument('--readfmt1', help='Override the file format of file 1'
).completer = cli_readerfmt_completer
subp.add_argument('--readfmt2', help='Override the file format of file 2'
).completer = cli_readerfmt_completer
subp.add_argument('--uncontract-general',
action='store_true',
help='Remove general contractions before comparing')
# compare-basis-to-file
subp = subparsers.add_parser(
'compare-basis-to-file',
help='Compare basis set in data directory to file')
subp.add_argument('basis', help='Basis set to compare')
subp.add_argument('file', help='Basis set file to compare to')
subp.add_argument(
'--readfmt',
help='Override the file format').completer = cli_readerfmt_completer
subp.add_argument(
'--version',
help='Version of the basis set to compare with. Default is latest')
subp.add_argument('--uncontract-general',
action='store_true',
help='Remove general contractions before comparing')
########################################
# Making graphs
########################################
# view-graph
subp = subparsers.add_parser('view-graph',
help='View a file graph for a basis set')
subp.add_argument(
'basis',
help='Name of the basis set inspect').completer = cli_bsname_completer
subp.add_argument(
'--version',
help=
'Which version of the basis set to inspect. Default is the latest version'
)
# make-graph-file
subp = subparsers.add_parser(
'make-graph-file',
help='Make a dot file (and png file) for a basis set file graph')
subp.add_argument(
'basis',
help='Name of the basis set inspect').completer = cli_bsname_completer
subp.add_argument('outfile', help='Output DOT file to create')
subp.add_argument('--render',
action='store_true',
help='Render the DOT file into a corresponding png file')
subp.add_argument(
'--version',
help=
'Which version of the basis set to inspect. Default is the latest version'
)
#############################
# DONE WITH SUBCOMMANDS
#############################
# setup autocomplete
argcomplete.autocomplete(parser, validator=cli_case_insensitive_validator)
# Now parse and handle the args
args = parser.parse_args()
# Check and make sure basis sets, roles, etc, are valid
args = cli_check_normalize_args(args)
# Actually generate the output
output = bsecurate_cli_handle_subcmd(args)
if args.output:
with open(args.output, 'w', encoding='utf-8') as outfile:
outfile.write(output)
elif output:
# Don't print if output is empty
print(output)
return 0
#get version and list of elements
version_bs = md[bas_name]['latest_version']
elements_list = md[bas_name]['versions'][version_bs]['elements']
#open file
# get rid of asterisks
file_name = bas_name.replace("*", "s")
#get rid of parenthesis
file_name = file_name.replace("(", "")
file_name = file_name.replace(")", "")
#replace commas with underscore
file_name = file_name.replace(",", "_")
#replace whitespace with underscore
file_name = file_name.replace(" ", "_")
print(' file name is ' + file_name + "\n")
output_file = open(file_name, 'w')
output_file.write('# BSE Version ' + bse.version() + '\n')
output_file.write('# Data downloaded at ' + today + '\n')
output_file.write('# ' + bas_name + ' version number ' + version_bs + '\n')
output_file.write('# Description: ' + md[bas_name]['description'] + '\n')
output_file.write('# Role: ' + md[bas_name]['role'] + '\n')
output_file.write(
'# ' + bse.get_references(bas_name, fmt='txt').replace('\n', '\n# '))
output_file.write('# \n')
for element in elements_list:
#element='h'
try:
bs_str = bse.get_basis(bas_name,
header=False,
elements=element,
fmt='nwchem',
optimize_general=True)
def writebs(md, bas_name, summary_file, get_aux=0):
md_bas_name = bas_name.lower()
md_bas_name = md_bas_name.replace("*", "_st_")
md_bas_name = md_bas_name.replace("/", "_sl_")
print(' md_bas_name ' + md_bas_name + "\n")
print(' bas_name ' + bas_name + "\n")
version_bs = md[md_bas_name]['latest_version']
elements_list = md[md_bas_name]['versions'][version_bs]['elements']
#open file
# get rid of asterisks
file_name = bas_name.replace("*", "s")
#get rid of parenthesis
file_name = file_name.replace("(", "")
file_name = file_name.replace(")", "")
#replace commas with underscore
file_name = file_name.replace(",", "_")
#replace whitespace with underscore
file_name = file_name.replace(" ", "_")
#replace forward slash with underscore
file_name = file_name.replace("/", "_")
#lowercase
file_name = file_name.lower()
if get_aux == 1:
file_name = file_name + "-autoaux"
print(' file name is ' + file_name + "\n")
output_file = open(file_name, 'w')
output_file.write('# BSE Version ' + bse.version() + '\n')
output_file.write('# Data downloaded on ' + today + '\n')
if get_aux == 0:
output_file.write('# ' + bas_name + ' version number ' + version_bs +
'\n')
output_file.write('# Description: ' + md[md_bas_name]['description'] +
'\n')
output_file.write('# Role: ' + md[md_bas_name]['role'] + '\n')
output_file.write(
'# ' +
bse.get_references(bas_name, fmt='txt').replace('\n', '\n# '))
output_file.write('# \n')
elif get_aux == 1:
output_file.write('# ' + bas_name + ' version number ' + version_bs +
' AutoAux \n')
output_file.write('# Role: JK Fitting \n')
output_file.write(
'# Stoychev GL, Auer AA, Neese F. \n# Automatic Generation of Auxiliary Basis Sets.\n# J Chem Theory Comput. 2017 Feb 14;13(2):554-562.\n# doi: 10.1021/acs.jctc.6b01041.\n'
)
output_file.write('# \n')
n_elements = 0
for element in elements_list:
n_elements = n_elements + 1
if get_aux == 1:
summary_file.write('Basis set \"' + bas_name +
'-autoaux\" (number of atoms ' + str(n_elements) +
')\n')
else:
summary_file.write('Basis set \"' + bas_name + '\" (number of atoms ' +
str(n_elements) + ')\n')
for element in elements_list:
#element='h'
try:
bs_str = bse.get_basis(bas_name,
header=False,
elements=element,
fmt='nwchem',
optimize_general=True,
uncontract_general=True,
get_aux=get_aux)
except:
# print("failed for"+element)
pass
else:
bs_str = bs_str.replace("BASIS", "basis")
bs_str = bs_str.replace("END", "end")
bs_str = bs_str.replace("PRINT", "")
element_str = bse.misc.compact_elements([element])
if get_aux == 1:
bs_str = bs_str.replace(
"ao basis", element_str + "_" + bas_name + "-autoaux")
else:
bs_str = bs_str.replace("ao basis",
element_str + "_" + bas_name)
#ECP
bs_str = bs_str.replace(
"ECP", "ecp \"" + element_str + "_" + bas_name + "\"")
output_file.write(bs_str)
#
print(bas_name + " " + element_str)
return