How to use the cclib.io.ccio.ccread function in cclib

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github cclib / cclib / test / io / testccio.py View on Github external
def setUp(self):
        self.ccread = cclib.io.ccio.ccread
github CCQC / PES-Learn / peslearn / datagen / outputfile.py View on Github external
def extract_energy_with_cclib(self, cclib_attribute, energy_index=-1):
        """
        Attempts to extract energies with cclib 
        Parameters
        ---------
        cclib_attribute : str
            The cclib target attribute. Valid options can be found in cclib documentation.
            Examples include "ccenergies", "scfenergies", or "mpenergies"
        energy_index : int
            Which energy to grab from the output file which matches the cclib_attribute. 
            Default is -1, the last energy printed in the output file which matches the cclib_attribute. 
        """
        try:
            cclib_outputobj = ccio.ccread(self.output_path) 
        except:
            e = None 
            return e
        e = None 
        # for whatever reason, sometimes each energy is a single element list, so we have to code around that 
        # also, cclib does not handle things well if something fails to parse, needtry/except pairs 
        if cclib_attribute == "scfenergies":
            try:
                e = cclib_outputobj.scfenergies[-1] 
                if isinstance(e, list):
                    e = e[0]
            except:
                e = None 
        if cclib_attribute == "mpenergies":
            try:
                e = cclib_outputobj.mpenergies[-1]
github CCQC / PES-Learn / peslearn / outputfile.py View on Github external
def extract_cartesian_gradient_with_cclib(self, grad_index=-1):
        """
        Attempts to extract the cartesian gradient with cclib 
        Parameters
        ---------
        grad_index : int
            Which gradient to grab from the output file. 
            Default is -1, the last gradient printed in the output file which matches the cclib_attribute. 
        """
        # warning: cartesian reorientation by quantum chemistry software may mess this up
        cclib_outputobj = ccio.ccread(self.output_path) 
        if hasattr(cclib_outputobj, 'grads'):
            return cclib_outputobj.grads[-1]
        else:
            return None
github CCQC / PES-Learn / peslearn / outputfile.py View on Github external
def extract_energy_with_cclib(self, cclib_attribute, energy_index=-1):
        """
        Attempts to extract energies with cclib 
        Parameters
        ---------
        cclib_attribute : str
            The cclib target attribute. Valid options can be found in cclib documentation.
            Examples include "ccenergies", "scfenergies", or "mpenergies"
        energy_index : int
            Which energy to grab from the output file which matches the cclib_attribute. 
            Default is -1, the last energy printed in the output file which matches the cclib_attribute. 
        """
        try:
            cclib_outputobj = ccio.ccread(self.output_path) 
        except:
            e = None 
            return e
        e = None 
        # for whatever reason, sometimes each energy is a single element list, so we have to code around that 
        # also, cclib does not handle things well if something fails to parse, needtry/except pairs 
        if cclib_attribute == "scfenergies":
            try:
                e = cclib_outputobj.scfenergies[-1] 
                if isinstance(e, list):
                    e = e[0]
            except:
                e = None 
        if cclib_attribute == "mpenergies":
            try:
                e = cclib_outputobj.mpenergies[-1]
github CCQC / PES-Learn / peslearn / datagen / outputfile.py View on Github external
def extract_cartesian_gradient_with_cclib(self, grad_index=-1):
        """
        Attempts to extract the cartesian gradient with cclib 
        Parameters
        ---------
        grad_index : int
            Which gradient to grab from the output file. 
            Default is -1, the last gradient printed in the output file which matches the cclib_attribute. 
        """
        # warning: cartesian reorientation by quantum chemistry software may mess this up
        cclib_outputobj = ccio.ccread(self.output_path) 
        if hasattr(cclib_outputobj, 'grads'):
            return cclib_outputobj.grads[-1]
        else:
            return None
github CCQC / PES-Learn / MLChem / outputfile.py View on Github external
def extract_cartesian_gradient_with_cclib(self, grad_index=-1):
        """
        Attempts to extract the cartesian gradient with cclib 
        Parameters
        ---------
        grad_index : int
            Which gradient to grab from the output file. 
            Default is -1, the last gradient printed in the output file which matches the cclib_attribute. 
        """
        # warning: cartesian reorientation by quantum chemistry software may mess this up
        cclib_outputobj = ccio.ccread(self.output_path) 
        if hasattr(cclib_outputobj, 'grads'):
            return cclib_outputobj.grads[-1]
        else:
            return None
github CCQC / PES-Learn / MLChem / outputfile.py View on Github external
def extract_energy_with_cclib(self, cclib_attribute, energy_index=-1):
        """
        Attempts to extract energies with cclib 
        Parameters
        ---------
        cclib_attribute : str
            The cclib target attribute. Valid options can be found in cclib documentation.
            Examples include "ccenergies", "scfenergies", or "mpenergies"
        energy_index : int
            Which energy to grab from the output file which matches the cclib_attribute. 
            Default is -1, the last energy printed in the output file which matches the cclib_attribute. 
        """
        cclib_outputobj = ccio.ccread(self.output_path) 
        e = None 
        # for whatever reason, sometimes each energy is a single element list, so we have to code around that 
        # also, cclib does not handle things well if something fails to parse, needtry/except pairs 
        if cclib_attribute == "scfenergies":
            try:
                e = cclib_outputobj.scfenergies[-1] 
                if isinstance(e, list):
                    e = e[0]
            except:
                e = None 
        if cclib_attribute == "mpenergies":
            try:
                e = cclib_outputobj.mpenergies[-1] 
                if isinstance(e, list):
                    e = e[0]
            except: