def Al1st(qminp, runjob=False, ref_dir='restart_path', **setting):
#assert os.path.exists(ref_dir)
if 'ref_dir' in setting:
ref_dir = setting['ref_dir']
setting['ref_dir'] = os.path.abspath(ref_dir)
if 'runjob' not in setting:
setting['runjob'] = False
qminp = copy.deepcopy(univ.toInp(qminp, **setting))
if hasattr(qminp.setting, 'save_restart'):
qminp.setting['save_restart'] = False
name = qminp.molecule.name
if 'out_dir' in setting:
name = setting['out_dir']
del setting['out_dir']
qminp.molecule.name = name
qminp.setting['root_dir'] = name
if qminp.setting['program'] == 'cpmd':
setting['restart'] = True
setting['scf_step'] = 1
rst = os.path.join(setting['ref_dir'], 'RESTART')
assert os.path.exists(rst)
rst = os.path.abspath(rst)
if 'dependent_files' in setting:
setting['dependent_files'].append(rst)
else:
setting['dependent_files'] = [rst]
elif qminp.setting['program'] == 'abinit':
setting['restart'] = True
setting['scf_step'] = 0
rstList = sorted(glob.glob(os.path.join(setting['ref_dir'], '*o_*WFK')))
assert len(rstList) > 0
rstSrc = rstList[-1]
if 'dependent_file' in setting:
setting['dependent_files'].append([rstSrc, name+'i_WFK'])
else:
setting['dependent_files'] = [[rstSrc, name+'i_WFK']]
denList = sorted(glob.glob(os.path.join(setting['ref_dir'], '*o_*DEN')))
if len(denList) > 0:
setting['restart_density'] = True
denSrc = denList[-1]
setting['dependent_files'].append([denSrc, name+'i_DEN'])
elif qminp.setting['program'] == 'espresso':
wfn = glob.glob(setting['ref_dir'] + '/*.wfc[0-9]*')
if 'threads' not in setting or setting['threads'] != len(wfn):
qtk.warning('threads must be the same as ref_dir, reset to %d'\
% len(wfn))
setting['threads'] = len(wfn)
setting['restart'] = True
setting['scf_step'] = 1
rst = glob.glob(setting['ref_dir'] + '/*.restart*')
save = glob.glob(setting['ref_dir'] + '/*.save')
if 'dependent_files' in setting:
for lst in [wfn, rst, save]:
setting['dependent_files'].extend(lst)
else:
setting['dependent_files'] = wfn
for lst in [rst, save]:
setting['dependent_files'].extend(lst)
elif qminp.setting['program'] == 'vasp':
setting['restart'] = True
setting['scf_step'] = 1
wfn_list = sorted(glob.glob(setting['ref_dir'] + '/WAVECAR'))
assert len(wfn_list) == 1
wfn = wfn_list[0]
if 'dependent_files' in setting:
setting['dependent_files'].append(wfn)
else:
setting['dependent_files'] = [wfn]
elif qminp.setting['program'] == 'bigdft':
pass
elif qminp.setting['program'] == 'nwchem':
pass
if setting['runjob']:
qmout = qminp.run(name, **setting)
return qmout
else:
qminp.molecule.name = name
qminp.setting.update(setting)
new_inp = qtk.QMInp(qminp.molecule, **qminp.setting)
return new_inp
def __init__(self, ref, tar, **kwargs):
self.setting = kwargs
if 'pp_string' not in kwargs:
self.setting['pp_string'] = 'pbe'
self.ref = univ.toInp(ref, **self.setting)
self.tar = univ.toInp(tar, **self.setting)
self.name = self.ref.molecule.name + '_' + self.tar.molecule.name
self.mutation = {}
qm_setting = {}
if 'qm_setting' in self.setting:
qm_setting.update(kwargs['qm_setting'])
if 'qm_setting' in kwargs:
qm_setting.update(kwargs['qm_setting'])
if 'program' not in qm_setting:
qm_setting['program'] = self.ref.setting['program']
self.qm_setting = qm_setting
# !!!!!!!!!!!!!!!!!!!!!!!
# construct mutation list
# tar_list: list of matching location
ref = self.ref.molecule
tar = self.tar.molecule
tar_list = [True for i in range(tar.N)]
to_void = True
ref_ind = []
tar_ind = []
mutation_fix = []
mutation_ind = ref_ind
mutation_ref = []
mutation_tar = []
mutation_crd = []
mutation_string = []
# loop through every atom in reference system
for i in range(ref.N):
Zi = ref.type_list[i]
Ri = copy.deepcopy(ref.R[i])
# loop through every atom in target system
for j in range(tar.N):
# every atom-pair distance
Rj = copy.deepcopy(tar.R[j])
diff = np.linalg.norm(Ri-Rj)
# search for atoms at same location
if diff < 10E-6:
to_void = False
tar_list[j] = False
Zj = tar.type_list[j]
if Zi != Zj:
ref_ind.append(i)
mutation_ref.append(Zi)
mutation_tar.append(Zj)
mutation_crd.append(Ri)
else:
mutation_fix.append(i)
# when no distance matched, set atom target to void
if to_void:
ref_ind.append(i)
mutation_ref.append(Zi)
mutation_tar.append('VOID')
mutation_crd.append(Ri)
# loop through every target atom for non-matching atoms
N = ref.N
for j in range(tar.N):
if tar_list[j]:
ref_ind.append(j)
mutation_ref.append('VOID')
mutation_tar.append(tar.type_list[j])
mutation_crd.append(tar.R[j])
for k in range(len(mutation_ref)):
string = mutation_ref[k] + '2' + mutation_tar[k]
if self.setting['pp_string']:
string = string + '_' + self.setting['pp_string']
mutation_string.append(string)
self.mutation ={
'ind': mutation_ind,
'ref': mutation_ref,
'tar': mutation_tar,
'crd': mutation_crd,
'fix': mutation_fix,
'string': mutation_string,
}
def Al1st(qminp, **setting):
assert 'ref_dir' in setting
assert os.path.exists(setting['ref_dir'])
if 'runjob' not in setting:
setting['runjob'] = True
qminp = copy.deepcopy(univ.toInp(qminp, **setting))
name = qminp.molecule.name
if 'out_dir' in setting:
name = setting['out_dir']
del setting['out_dir']
qminp.molecule.name = name
qminp.setting['root_dir'] = name
if qminp.setting['program'] == 'cpmd':
setting['restart'] = True
setting['scf_step'] = 1
rst = os.path.join(setting['ref_dir'], 'RESTART')
assert os.path.exists(rst)
rst = os.path.abspath(rst)
if 'dependent_files' in setting:
setting['dependent_files'].append(rst)
else:
setting['dependent_files'] = [rst]
elif qminp.setting['program'] == 'abinit':
setting['restart'] = True
setting['scf_step'] = 0
rstList = glob.glob(os.path.join(setting['ref_dir'], '*o_WFK'))
assert len(rstList) > 0
rstSrc = rstList[-1]
rstTar = rstSrc.replace('o_WFK', 'i_WFK')
rstTar = os.path.split(rstTar)[-1]
if 'dependent_file' in setting:
setting['dependent_files'].append([rstSrc, name+'i_WFK'])
else:
setting['dependent_files'] = [[rstSrc, name+'i_WFK']]
elif qminp.setting['program'] == 'espresso':
wfn = glob.glob(setting['ref_dir'] + '/*.wfc[0-9]*')
if 'threads' not in setting or setting['threads'] != len(wfn):
qtk.warning('threads must be the same as ref_dir, reset to %d'\
% len(wfn))
setting['threads'] = len(wfn)
setting['restart'] = True
setting['scf_step'] = 1
rst = glob.glob(setting['ref_dir'] + '/*.restart*')
save = glob.glob(setting['ref_dir'] + '/*.save')
if 'dependent_files' in setting:
for lst in [wfn, rst, save]:
setting['dependent_files'].extend(lst)
else:
setting['dependent_files'] = wfn
for lst in [rst, save]:
setting['dependent_files'].extend(lst)
elif qminp.setting['program'] == 'vasp':
setting['restart'] = True
setting['scf_step'] = 1
wfn_list = glob.glob(setting['ref_dir'] + '/WAVECAR')
assert len(wfn_list) == 1
wfn = wfn_list[0]
if 'dependent_files' in setting:
setting['dependent_files'].append(wfn)
else:
setting['dependent_files'] = [wfn]
elif qminp.setting['program'] == 'bigdft':
pass
elif qminp.setting['program'] == 'nwchem':
pass
if setting['runjob']:
qmout = qminp.run(name, **setting)
return qmout
else:
qminp.molecule.name = name
qminp.setting.update(setting)
new_inp = qtk.QMInp(qminp.molecule, **qminp.setting)
return new_inp
def __init__(self, ref, tar, **kwargs):
self.setting = kwargs
if 'pp_string' not in kwargs:
self.setting['pp_string'] = 'pbe'
self.ref = univ.toInp(ref, **self.setting)
self.tar = univ.toInp(tar, **self.setting)
self.name = self.ref.molecule.name + '_' + self.tar.molecule.name
self.mutation = {}
qm_setting = {}
if 'qm_setting' in self.setting:
qm_setting.update(kwargs['qm_setting'])
if 'qm_setting' in kwargs:
qm_setting.update(kwargs['qm_setting'])
if 'program' not in qm_setting:
qm_setting['program'] = self.ref.setting['program']
self.qm_setting = qm_setting
# !!!!!!!!!!!!!!!!!!!!!!!
# construct mutation list
# tar_list: list of matching location
ref = self.ref.molecule
tar = self.tar.molecule
tar_list = [True for i in range(tar.N)]
to_void = True
ref_ind = []
tar_ind = []
mutation_fix = []
mutation_ind = ref_ind
mutation_ref = []
mutation_tar = []
mutation_crd = []
mutation_string = []
# loop through every atom in reference system
for i in range(ref.N):
Zi = ref.type_list[i]
Ri = copy.deepcopy(ref.R[i])
# loop through every atom in target system
for j in range(tar.N):
# every atom-pair distance
Rj = copy.deepcopy(tar.R[j])
diff = np.linalg.norm(Ri - Rj)
# search for atoms at same location
if diff < 10E-6:
to_void = False
tar_list[j] = False
Zj = tar.type_list[j]
if Zi != Zj:
ref_ind.append(i)
mutation_ref.append(Zi)
mutation_tar.append(Zj)
mutation_crd.append(Ri)
else:
mutation_fix.append(i)
# when no distance matched, set atom target to void
if to_void:
ref_ind.append(i)
mutation_ref.append(Zi)
mutation_tar.append('VOID')
mutation_crd.append(Ri)
# loop through every target atom for non-matching atoms
N = ref.N
for j in range(tar.N):
if tar_list[j]:
ref_ind.append(j)
mutation_ref.append('VOID')
mutation_tar.append(tar.type_list[j])
mutation_crd.append(tar.R[j])
for k in range(len(mutation_ref)):
string = mutation_ref[k] + '2' + mutation_tar[k]
if self.setting['pp_string']:
string = string + '_' + self.setting['pp_string']
mutation_string.append(string)
self.mutation = {
'ind': mutation_ind,
'ref': mutation_ref,
'tar': mutation_tar,
'crd': mutation_crd,
'fix': mutation_fix,
'string': mutation_string,
}
