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fix double count bug #107

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Merged
amcadmus merged 1 commit into from
Aug 2, 2020
Merged

fix double count bug #107

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25 changes: 13 additions & 12 deletions dpdata/cp2k/output.py
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Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@

class Cp2kSystems(object):
"""
deal with cp2k outputfile
deal with cp2k outputfile
"""
def __init__(self, log_file_name, xyz_file_name):
self.log_file_object = open(log_file_name, 'r')
Expand Down Expand Up @@ -69,7 +69,7 @@ def get_log_block_generator(self):
break
if delimiter_flag is True:
raise RuntimeError('This file lacks some content, please check')

def get_xyz_block_generator(self):
p3 = re.compile(r'^\s*(\d+)\s*')
while True:
Expand Down Expand Up @@ -116,7 +116,7 @@ def handle_single_log_frame(self, lines):
if cell_length_pattern.match(line):
cell_A = float(cell_length_pattern.match(line).groupdict()['A']) * AU_TO_ANG
cell_B = float(cell_length_pattern.match(line).groupdict()['B']) * AU_TO_ANG
cell_C = float(cell_length_pattern.match(line).groupdict()['C']) * AU_TO_ANG
cell_C = float(cell_length_pattern.match(line).groupdict()['C']) * AU_TO_ANG
cell_flag+=1
if cell_angle_pattern.match(line):
cell_alpha = np.deg2rad(float(cell_angle_pattern.match(line).groupdict()['alpha']))
Expand Down Expand Up @@ -148,10 +148,10 @@ def handle_single_log_frame(self, lines):
element_index +=1
element_dict[line_list[2]]=[element_index,1]
atom_types_list.append(element_dict[line_list[2]][0])
forces_list.append([float(line_list[3])*AU_TO_EV_EVERY_ANG,
float(line_list[4])*AU_TO_EV_EVERY_ANG,
forces_list.append([float(line_list[3])*AU_TO_EV_EVERY_ANG,
float(line_list[4])*AU_TO_EV_EVERY_ANG,
float(line_list[5])*AU_TO_EV_EVERY_ANG])

atom_names=list(element_dict.keys())
atom_numbs=[]
for ii in atom_names:
Expand Down Expand Up @@ -190,8 +190,8 @@ def handle_single_xyz_frame(self, lines):
element_index +=1
element_dict[line_list[0]]=[element_index,1]
atom_types_list.append(element_dict[line_list[0]][0])
coords_list.append([float(line_list[1])*AU_TO_ANG,
float(line_list[2])*AU_TO_ANG,
coords_list.append([float(line_list[1])*AU_TO_ANG,
float(line_list[2])*AU_TO_ANG,
float(line_list[3])*AU_TO_ANG])
atom_names=list(element_dict.keys())
atom_numbs=[]
Expand All @@ -203,29 +203,30 @@ def handle_single_xyz_frame(self, lines):
info_dict['coords'] = np.asarray([coords_list]).astype('float32')
info_dict['energies'] = np.array([energy]).astype('float32')
info_dict['orig']=[0,0,0]
return info_dict
return info_dict

#%%

def get_frames (fname) :
coord_flag = False
force_flag = False
eV = 2.72113838565563E+01 # hatree to eV
angstrom = 5.29177208590000E-01 # Bohrto Angstrom
angstrom = 5.29177208590000E-01 # Bohrto Angstrom
fp = open(fname)
atom_symbol_list = []
cell = []
coord = []
force = []

coord_count = 0
for idx, ii in enumerate(fp) :
if 'CELL| Vector' in ii :
cell.append(ii.split()[4:7])
if 'Atom Kind Element' in ii :
coord_flag = True
coord_idx = idx
coord_count += 1
# get the coord block info
if coord_flag :
if coord_flag and (coord_count == 1):
if (idx > coord_idx + 1) :
if (ii == '\n') :
coord_flag = False
Expand Down
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