From f89ecb62c8d007b2171a17f39b9c8ace955b9af5 Mon Sep 17 00:00:00 2001 From: Aliaksandr Yakutovich Date: Thu, 9 Jul 2020 13:49:01 +0000 Subject: [PATCH] Remove parsing of coordinates and atomic numbers --- aiida_quantumespresso/parsers/pp.py | 12 ++---------- 1 file changed, 2 insertions(+), 10 deletions(-) diff --git a/aiida_quantumespresso/parsers/pp.py b/aiida_quantumespresso/parsers/pp.py index b98d76284..a2dd0732c 100644 --- a/aiida_quantumespresso/parsers/pp.py +++ b/aiida_quantumespresso/parsers/pp.py @@ -213,9 +213,9 @@ def detect_important_message(logs, line): # Parse useful data from stdout for line in stdout_lines: - if 'Check:' in line: + if 'Check:' in line: # QE < 6.5 split_line = line.split('=') - if 'negative/imaginary' in line: # QE6.1 + if 'negative/imaginary' in line: # QE6.1-6.3 output_dict['negative_core_charge'] = float(split_line[-1].split()[0]) output_dict['imaginary_core_charge'] = float(split_line[-1].split()[-1]) else: # QE6.4 @@ -354,12 +354,6 @@ def parse_gaussian(self, data_file_str): voxel_array = np.array([[x_line[1], x_line[2], x_line[3]], [y_line[1], y_line[2], y_line[3]], [z_line[1], z_line[2], z_line[3]]], dtype=np.float64) - atomic_numbers = np.empty(natoms, int) - coordinates = np.empty((natoms, 3)) - for i in range(natoms): - line = header[6 + i].split() - atomic_numbers[i] = int(line[0]) - coordinates[i] = [float(s) for s in line[2:]] # Get the volumetric data data_array = np.empty(xdim * ydim * zdim, dtype=float) @@ -378,7 +372,5 @@ def parse_gaussian(self, data_file_str): arraydata.set_array('data', data_array) arraydata.set_array('data_units', np.array(data_units)) arraydata.set_array('coordinates_units', np.array(coordinates_units)) - arraydata.set_array('coordinates', coordinates) - arraydata.set_array('atomic_numbers', atomic_numbers) return arraydata