How to use the result.GamessResult function in result

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github gc3pie / gc3pie / markstools / markstools / calculators / gamess / calculator.py View on Github external
def parse(self, a_job, force_a_reparse=False):
        """Rather than running GAMESS, we just read
        and parse the results already in the database."""
        from markstools.io.gamess import ReadGamessInp
        parser = None
        print a_job.parsed
        if not force_a_reparse:            
            parser = a_job.parser 
            if parser != self.__class__.__name__:
                raise MyTypeError('Can not reparse, parsed results are from %s, expecting %s'%(parser, self.__class__.__name_))
            a_result = a_job.parsed
            if a_result:
                if not isinstance(a_result, GamessResult):
                    raise MyTypeError('Unpickled parse results are of type %s, expecting %s'%(type(a_result)), GamessResult)
                markstools.log.info('Using previously parsed results for Job %s'%(a_job.id))
        if a_result is None:
            markstools.log.info('Starting to parse Job %s results'%(a_job.id))
            markstools.log.debug('Starting to parse Run %s results'%(a_job.run.id))
            f_inp = a_job.get_attachment('inp')
            if f_inp is None:
                raise DocumentError('Run %s does not contain a .inp file'%(a_job.run.id))
            reader = ReadGamessInp(f_inp)
            f_inp.close()
            f_dat = a_job.get_attachment('dat')
            if f_dat is None:
                raise DocumentError('Run %s does not contain a .dat file'%(a_job.run.id))
            self.parsed_dat.parse_file(f_dat)
            f_dat.close()
            f_stdout = a_job.get_attachment('stdout')
github gc3pie / gc3pie / markstools / markstools / calculators / gamess / calculator.py View on Github external
def parse(self, a_job, force_a_reparse=False):
        """Rather than running GAMESS, we just read
        and parse the results already in the database."""
        from markstools.io.gamess import ReadGamessInp
        parser = None
        print a_job.parsed
        if not force_a_reparse:            
            parser = a_job.parser 
            if parser != self.__class__.__name__:
                raise MyTypeError('Can not reparse, parsed results are from %s, expecting %s'%(parser, self.__class__.__name_))
            a_result = a_job.parsed
            if a_result:
                if not isinstance(a_result, GamessResult):
                    raise MyTypeError('Unpickled parse results are of type %s, expecting %s'%(type(a_result)), GamessResult)
                markstools.log.info('Using previously parsed results for Job %s'%(a_job.id))
        if a_result is None:
            markstools.log.info('Starting to parse Job %s results'%(a_job.id))
            markstools.log.debug('Starting to parse Run %s results'%(a_job.run.id))
            f_inp = a_job.get_attachment('inp')
            if f_inp is None:
                raise DocumentError('Run %s does not contain a .inp file'%(a_job.run.id))
            reader = ReadGamessInp(f_inp)
            f_inp.close()
            f_dat = a_job.get_attachment('dat')
            if f_dat is None:
                raise DocumentError('Run %s does not contain a .dat file'%(a_job.run.id))
            self.parsed_dat.parse_file(f_dat)
            f_dat.close()
            f_stdout = a_job.get_attachment('stdout')
            if f_stdout is None:
github gc3pie / gc3pie / markstools / markstools / calculators / gamess / calculator.py View on Github external
f_inp = a_job.get_attachment('inp')
            if f_inp is None:
                raise DocumentError('Run %s does not contain a .inp file'%(a_job.run.id))
            reader = ReadGamessInp(f_inp)
            f_inp.close()
            f_dat = a_job.get_attachment('dat')
            if f_dat is None:
                raise DocumentError('Run %s does not contain a .dat file'%(a_job.run.id))
            self.parsed_dat.parse_file(f_dat)
            f_dat.close()
            f_stdout = a_job.get_attachment('stdout')
            if f_stdout is None:
                raise DocumentError('Run %s does not contain a .stdout file'%(a_job.run.id))
            self.parsed_out.parse_file(f_stdout)
            f_stdout.close()
            a_result = GamessResult(reader.atoms, reader.params, self.parsed_dat.group, self.parsed_out.group)
            self._save_parsed_result(a_job, a_result)
        return a_result
github gc3pie / gc3pie / markstools / markstools / calculators / gamess / calculator.py View on Github external
def preexisting_result(self, f_name):
        """Rather than running GAMESS, we just read
        and parse the results already on the file system."""
        from markstools.io.gamess import ReadGamessInp
        f_dict = self.get_files(f_name)
        new_reader = ReadGamessInp(f_dict['inp'])
        result = GamessResult(new_reader.atoms, new_reader.params, self)        
        result.a_job = f_name
        return result
github gc3pie / gc3pie / markstools / markstools / calculators / gamess / calculator.py View on Github external
def calculate(self, f_name):
        import os
        from markstools.io.gamess import WriteGamessInp
        result = GamessResult(atoms, params, self)
        cmd = 'cd %s; %s %s.%s 1> %s.%s 2> %s.%s'%(self.f_dir, self.CMD_GAMESS, 
                                          f_name, self.EXT_INPUT_FILE, f_name, self.EXT_STDOUT_FILE, 
                                          f_name, self.EXT_STDERR_FILE)
        return_code = os.system(cmd)
        assert return_code == 0, 'Error runing GAMESS. Check %s/%s.%s'%(self.f_dir, f_name, self.EXT_STDOUT_FILE)
        result.a_job = f_name
        return result