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@@ -177,9 +177,9 @@
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    """ Allows command line options such as "yes" and "True" to be converted into Booleans. """
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    if isinstance(v, bool):
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        return v
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    if v.lower() in ('yes', 'true', 't', 'y', '1'):
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    if v.lower() in ('yes', 'on', 'true', 't', 'y', '1'):
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        return True
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    elif v.lower() in ('no', 'false', 'f', 'n', '0'):
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    elif v.lower() in ('no', 'off', 'false', 'f', 'n', '0'):
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        return False
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    else:
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        raise argparse.ArgumentTypeError('Boolean value expected.')
@@ -249,6 +249,10 @@
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    grp_jobtype.add_argument('--meci', type=str, help='Provide second input file and search for minimum-energy conical\n '
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                             'intersection or crossing point between two SCF solutions (TeraChem and Q-Chem supported).\n'
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                             'Or, provide "engine" if the engine directly provides the MECI objective function and gradient.')
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    grp_jobtype.add_argument('--meci_sigma', type=float, help='Sigma parameter for MECI penalty function (default 3.5).\n'
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                            'Not used if the engine computes the MECI objective function directly.\n ')
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    grp_jobtype.add_argument('--meci_alpha', type=float, help='Alpha parameter for MECI penalty function (default 0.025).\n'
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                             'Not used if the engine computes the MECI objective function directly.')
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    grp_hessian = parser.add_argument_group('hessian', 'Control the calculation of Hessian (force constant) matrices and derived quantities')
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    grp_hessian.add_argument('--hessian', type=str, help='Specify when to calculate Cartesian Hessian using finite difference of gradient.\n'
@@ -259,12 +263,12 @@
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                             '"each" : Calculate for each step in the optimization (costly).\n'
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                             '"stop" : Calculate Hessian for initial structure, then exit.\n'
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                             'file:<path> : Read initial Hessian data in NumPy format from path, e.g. file:folder/hessian.txt\n ')
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    grp_hessian.add_argument('--port', type=int, help='Work Queue port used to distribute Hessian calculations. Workers must be started separately.')
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    grp_hessian.add_argument('--frequency', type=str2bool, help='Perform frequency analysis whenever Hessian is calculated, default is yes/true.\n ')
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    grp_hessian.add_argument('--thermo', type=float, nargs=2, help='Temperature (K) and pressure (bar) for harmonic free energy\n'
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                             'following frequency analysis, default is 300 K and 1.0 bar.\n ')
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    grp_hessian.add_argument('--wigner', type=int, help='Number of desired samples from Wigner distribution after frequency analysis.\n'
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                             'Provide negative number to overwrite any existing samples.\n ')
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    grp_hessian.add_argument('--port', type=int, help='Work Queue port used to distribute Hessian calculations. Workers must be started separately.')
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    grp_optparam = parser.add_argument_group('optparam', 'Control various aspects of the optimization algorithm')
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    grp_optparam.add_argument('--maxiter', type=int, help='Maximum number of optimization steps, default 300.\n ')
@@ -297,13 +301,7 @@
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    grp_output.add_argument('--qdata', type=str2bool, help='Provide "yes" to write qdata.txt containing coordinates, energies, gradients for each structure.\n ')
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    grp_output.add_argument('--logINI',  type=str, dest='logIni', help='.ini file for customizing logging output.\n ')
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    grp_output.add_argument('--write_cart_hess', type=str, help='Write approximate cartesian Hessian at optimized geometry to specified file.')
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    grp_meci = parser.add_argument_group('meci', 'Relevant for conical intersection optimization')
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    grp_meci.add_argument('--meci_sigma', type=float, help='Sigma parameter for MECI penalty function (default 3.5).\n'
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                        'Not used if the engine computes the MECI objective function directly.\n ')
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    grp_meci.add_argument('--meci_alpha', type=float, help='Alpha parameter for MECI penalty function (default 0.025).\n'
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                        'Not used if the engine computes the MECI objective function directly.')
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    grp_software = parser.add_argument_group('molpro', 'Options specific for certain software packages')
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    grp_software.add_argument('--molproexe', type=str, help='Specify absolute path of Molpro executable.\n ')
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    grp_software.add_argument('--molcnv', type=str2bool, help='Provide "yes" to use Molpro style convergence criteria instead of the default.\n ')
Files Coverage
geometric 69.90%
Project Totals (15 files) 69.90%
554.2
TRAVIS_PYTHON_VERSION=3.5
TRAVIS_OS_NAME=linux
554.1
TRAVIS_PYTHON_VERSION=2.7
TRAVIS_OS_NAME=linux
554.4
TRAVIS_PYTHON_VERSION=3.7
TRAVIS_OS_NAME=linux
554.3
TRAVIS_PYTHON_VERSION=3.6
TRAVIS_OS_NAME=linux
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coverage:
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  ignore:
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    - geometric/tests/.*
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    - geometric/PDB.py
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    - geometric/_version.py
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    - docs/*
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    - setup.py
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  status:
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    patch: false
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comment:
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  layout: "header"
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  require_changes: false
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  branches: null
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  behavior: default
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  flags: null
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  paths: null
Sunburst
The inner-most circle is the entire project, moving away from the center are folders then, finally, a single file. The size and color of each slice is representing the number of statements and the coverage, respectively.
Icicle
The top section represents the entire project. Proceeding with folders and finally individual files. The size and color of each slice is representing the number of statements and the coverage, respectively.
Grid
Each block represents a single file in the project. The size and color of each block is represented by the number of statements and the coverage, respectively.
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