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fix the issue of representation.from_string
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@qzhu2017
qzhu2017 committed Mar 2, 2024
1 parent e489ebb commit acf2c65
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Showing 3 changed files with 59 additions and 51 deletions.
48 changes: 24 additions & 24 deletions pyxtal/interface/dftb.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -73,17 +73,17 @@ def make_Hamiltonian(skf_dir, atom_types, disp, kpts, write_band=False, use_omp=
'Analysis_MullikenAnalysis': 'No',
'Analysis_CalculateForces': 'Yes',
}
if write_band:
if write_band:
kwargs['Analysis_WriteBandOut'] = 'Yes'
if use_omp:
kwargs['Parallel_'] = ''
kwargs['Parallel_UseOmpThreads'] = 'Yes'
if dispersion is not None:
kwargs['Hamiltonian_Dispersion'] = dispersion

if skf_dir.find('3ob') > 0:
if skf_dir.find('3ob') > 0:
calc_type = '3ob'
elif skf_dir.find('mio') > 0:
elif skf_dir.find('mio') > 0:
calc_type = 'mio'
elif skf_dir.find('pbc') > 0:
calc_type = 'pbc'
Expand All @@ -97,16 +97,16 @@ def make_Hamiltonian(skf_dir, atom_types, disp, kpts, write_band=False, use_omp=
HD = {"Br": -0.0573,
"C": -0.1492,
"N": -0.1535,
"Ca": -0.0340,
"Ca": -0.0340,
"Na": -0.0454,
"Cl": -0.0697,
"Cl": -0.0697,
"Zn": -0.03,
"O": -0.1575,
"F": -0.1623,
"P": -0.14,
"H": -0.1857,
"H": -0.1857,
"S": -0.11,
"I": -0.0433,
"I": -0.0433,
"K": -0.0339,
}
strs = '{'
Expand Down Expand Up @@ -144,7 +144,7 @@ def make_Hamiltonian(skf_dir, atom_types, disp, kpts, write_band=False, use_omp=
kwargs['Hamiltonian_MaxAngularMomentum_'+ele]='d'
else:
raise RuntimeError(calc_type, "doesnot support", ele)

#DFTB2

#pbc-0-3
Expand Down Expand Up @@ -183,7 +183,7 @@ def DFTB_relax(struc, skf_dir, opt_cell=False, step=500, \
struc.set_calculator(calc)

# impose symmetry
if symmetrize: struc.set_constraint(FixSymmetry(struc))
if symmetrize: struc.set_constraint(FixSymmetry(struc))

# impose cell constraints
if opt_cell:
Expand All @@ -210,8 +210,8 @@ def DFTB_SCF(struc, skf_dir, kresol=0.10, folder='tmp', disp=None, filename=None
Args:
struc: ase atoms object
skf_dir:
kresol:
skf_dir:
kresol:
filename: band structure output
"""
if not os.path.exists(folder):
Expand Down Expand Up @@ -257,10 +257,10 @@ class DFTB():
use_omp: True/False
"""

def __init__(self, struc, skf_dir,
disp = 'D3',
kresol = 0.10,
folder = 'tmp',
def __init__(self, struc, skf_dir,
disp = 'D3',
kresol = 0.10,
folder = 'tmp',
label = 'test',
prefix = 'geo_final',
use_omp = False,
Expand All @@ -276,7 +276,7 @@ def __init__(self, struc, skf_dir,
self.prefix = prefix
self.use_omp = use_omp
if not os.path.exists(self.folder):
os.makedirs(self.folder)
os.makedirs(self.folder)

def get_calculator(self, mode, step=500, ftol=1e-3, FixAngles=False, eVperA=True, md_params={}):
"""
Expand All @@ -295,7 +295,7 @@ def get_calculator(self, mode, step=500, ftol=1e-3, FixAngles=False, eVperA=True
if eVperA: ftol *= 0.194469064593167E-01
atom_types = set(self.struc.get_chemical_symbols())
kwargs = make_Hamiltonian(self.skf_dir, atom_types, self.disp, self.kpts, use_omp=self.use_omp)

if mode in ['relax', 'vc-relax']:
#kwargs['Driver_'] = 'ConjugateGradient'
kwargs['Driver_'] = 'GeometryOptimization'
Expand All @@ -305,7 +305,7 @@ def get_calculator(self, mode, step=500, ftol=1e-3, FixAngles=False, eVperA=True
kwargs['Driver_OutputPrefix'] = self.prefix
kwargs['Driver_Convergence_'] = ''
kwargs['Driver_Convergence_GradElem'] = ftol

if mode == 'vc-relax':
kwargs['Driver_MovedAtoms'] = "1:-1"
kwargs['Driver_LatticeOpt'] = "Yes"
Expand Down Expand Up @@ -343,7 +343,7 @@ def get_calculator(self, mode, step=500, ftol=1e-3, FixAngles=False, eVperA=True
kwargs['Driver_Barostat_Pressure [Pa]'] = dicts['pressure']
kwargs['Driver_Barostat_Timescale [ps]'] = 0.1


calc = Dftb(label=self.label,
#run_manyDftb_steps=True,
atoms=self.struc,
Expand Down Expand Up @@ -383,10 +383,10 @@ def run(self, mode, step=500, ftol=1e-3, FixAngles=False, md_params={}):

class Dftb(FileIOCalculator):
""" This module defines a FileIOCalculator for DFTB+
http://www.dftbplus.org/
http://www.dftb.org/
Initial development: [email protected]
Modified by QZ to avoid the I/O load
"""
Expand Down Expand Up @@ -654,7 +654,7 @@ def read_forces(self):
# reaches outside of the for loop
index_force_begin = -1
index_force_end = -1

# Force line indexes
fstring = 'forces '
for iline, line in enumerate(self.lines):
Expand All @@ -670,8 +670,8 @@ def read_forces(self):
gradients.append([float(word[k]) for k in range(0, 3)])
gradients = np.array(gradients)* Hartree / Bohr

return gradients
return gradients

def read_eigenvalues(self):
""" Read Eigenvalues from dftb output file (results.tag).
Unfortunately, the order seems to be scrambled. """
Expand Down
32 changes: 16 additions & 16 deletions pyxtal/interface/lammpslib.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -32,7 +32,7 @@ def opt_lammpslib(struc, lmp, parameters=None, mask=None, logfile='-',

#check_symmetry(si, 1.0e-6, verbose=True)
struc.set_calculator(lammps)
struc.set_constraint(FixSymmetry(struc))
struc.set_constraint(FixSymmetry(struc))
if opt_cell:
ecf = ExpCellFilter(struc, mask)
if method == 'FIRE':
Expand Down Expand Up @@ -84,17 +84,17 @@ def run_lammpslib(struc, lmp, parameters=None, path='tmp', \
f"min_style {min_style}",
f"minimize 1e-15 1e-15 {steps} {steps}",
]

else:
parameter0 += ['run 0']

lammps = LAMMPSlib(lmp=lmp, lmpcmds=parameter0, molecule=molecule, \
lmp_file=lmp_file, log_file='lammps.log', path=path)

struc.set_calculator(lammps)

Eng = struc.get_potential_energy()

return struc, Eng


Expand Down Expand Up @@ -159,7 +159,7 @@ def __init__(self, lmp, lmpcmds=None, path='tmp', molecule=False,
if not self.molecule and para.find('pair_coeff') >= 0:
tmp = para.split()
filename = tmp[3]
filename1 = self.ffpath + '/' + filename
filename1 = self.ffpath + '/' + filename
para = para.replace(filename, filename1)
self.paras.append(para)

Expand All @@ -172,7 +172,7 @@ def calculate(self, atoms):
boundary = ''
for i in range(3):
if atoms.pbc[i]:
boundary += 'p '
boundary += 'p '
else:
boundary += 'f '
if boundary in ['f f p ', 'p p f ']: #needs some work later
Expand Down Expand Up @@ -203,8 +203,8 @@ def calculate(self, atoms):

pos = np.array(
[x for x in self.lmp.gather_atoms("x", 1, 3)]).reshape(-1, 3)
self.energy = self.lmp.extract_variable('pe', None, 0)

self.energy = self.lmp.extract_variable('pe', None, 0)
#print('update lammps energy')

xlo = self.lmp.extract_global("boxxlo", 1)
Expand Down Expand Up @@ -274,7 +274,7 @@ def write_lammps_in(self):
fh.write('boundary p p s\n')
else:
fh.write('boundary {:s}\n'.format(self.boundary))
fh.write('atom_modify sort 0 0.0\n')
fh.write('atom_modify sort 0 0.0\n')
if not self.molecule:
fh.write('read_data {:s}\n'.format(self.lammps_data))
fh.write('\n### interactions\n')
Expand All @@ -297,7 +297,7 @@ def write_lammps_in(self):
tmp += LAMMPS_collections().dict['GB_opt']
for i in tmp:
fh.write(i)

if self.calc_type.find('GB') >= 0:
fh.write('thermo_style custom pe pxx pyy pzz pyz pxz pxy c_eatoms\n')
else:
Expand All @@ -306,7 +306,7 @@ def write_lammps_in(self):
fh.write('thermo 1\n')
fh.write('run 1\n')

#fh.write('print "__end_of_ase_invoked_calculation__"\n')
#fh.write('print "__end_of_ase_invoked_calculation__"\n')

def write_lammps_data(self, atoms):
atom_types = np.array(atoms.get_tags()) #[1]*len(atoms)
Expand Down Expand Up @@ -399,11 +399,11 @@ def write_lammps_data_water(self, atoms):
for i in range(N_mol):
fh.write('{:4d} {:4d} {:4d} {:4d}\n'.format(i*2+1,1,i*3+1,i*3+2))
fh.write('{:4d} {:4d} {:4d} {:4d}\n'.format(i*2+2,1,i*3+1,i*3+3))

fh.write('\nAngles \n\n')
for i in range(N_angle):
fh.write('{:4d} {:4d} {:4d} {:4d} {:4d}\n'.format(i+1,1,i*3+2,i*3+1,i*3+3))


def update(self, atoms):
if not hasattr(self, 'atoms') or self.atoms != atoms:
Expand Down Expand Up @@ -458,7 +458,7 @@ def __init__(self, temp=500):
"unfix f1\n",
"unfix f2\n",
]

self.dict['GB_md'] = [
"# ---------- Run GB MD ---------\n",
"thermo 100\n",
Expand Down
30 changes: 19 additions & 11 deletions pyxtal/representation.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -243,7 +243,7 @@ def from_string(cls, inputs, smiles, composition=None):
msg = "Composition is inconsistent: {:d}/{:d}\n".format(sum(composition), n_site)
msg += str(inputs)
raise ValueError(msg)
n_cell += 1
#n_cell += 1

for i, smile in enumerate(smiles):
if smile.endswith('.smi'):
Expand All @@ -253,16 +253,20 @@ def from_string(cls, inputs, smiles, composition=None):
n_mol = 4
else:
n_torsion = len(find_rotor_from_smile(smile))
n_mol = 7 + n_torsion
n_mol = 8 + n_torsion # (wp_id, x, y, z, ori_x, ori_y, ori_z, inv) + torsion
#inversion
inputs[n_cell+n_mol-2] = int(inputs[n_cell+n_mol-2])
x.append(inputs[n_cell-1:n_cell+n_mol-1])
#print(n_mol, n_cell, len(inputs))
inputs[n_cell] = int(inputs[n_cell])
inputs[n_cell+n_mol-1] = int(inputs[n_cell+n_mol-1])
x.append(inputs[n_cell:n_cell+n_mol])#; print('string', x[-1])
n_cell += n_mol
assert(n_cell == len(inputs))
return cls(x, smiles)

def to_standard_setting(self):
xtal = self.to_pyxtal()
rep0 = representation.from_pyxtal(xtal, standard=True)
xtal.optimize_lattice(standard=True)
rep0 = representation.from_pyxtal(xtal)
self.x = rep0.x

def to_pyxtal(self, smiles=None, composition=None):
Expand Down Expand Up @@ -335,7 +339,7 @@ def to_pyxtal(self, smiles=None, composition=None):
dicts['center'] = v[1:4]
if smile not in ["Cl-"]:
dicts['orientation'] = np.array(v[4:7])
dicts['rotor'] = v[7:-1]
dicts['rotor'] = v[7:-1]#; print('ro', dicts['rotor'])
dicts['reflect'] = int(v[-1])
site = mol_site.from_1D_dicts(dicts)

Expand Down Expand Up @@ -389,7 +393,7 @@ def to_string(self, time=None, eng=None, tag=None):
strs += "{:5.1f} ".format(c)

# data for molecule
strs += "{:d} ".format(len(x)-1)
strs += "{:d} ".format(len(x)-1)#; print(x[1])
for i in range(1, len(x)):
strs += "{:d} ".format(x[i][0])
for v in x[i][1:4]:
Expand Down Expand Up @@ -472,7 +476,7 @@ def get_dist(self, rep):

#aspirin
smiles = ['CC(=O)OC1=CC=CC=C1C(=O)O']
x = [[81,11.43,6.49,11.19,83.31],[0.77,0.57,0.53,48.55,24.31,145.94,-77.85,-4.40,170.86,False]]
x = [[81,11.43,6.49,11.19,83.31],[0, 0.77,0.57,0.53,48.55,24.31,145.94,-77.85,-4.40,170.86,False]]
#rep0 = representation(x, smiles)
#print(rep0.to_string())
rep1 = representation(x, smiles)
Expand All @@ -481,16 +485,20 @@ def get_dist(self, rep):
rep2 = representation.from_pyxtal(xtal)
print(rep2.to_pyxtal())
print(rep2.to_string())
string = "82 11.43 6.49 11.19 83.31 1 0.77 0.57 0.53 48.55 24.31 145.9 -77.85 -4.40 170.9 0"

print('Test read from string')
string = "82 11.43 6.49 11.19 83.31 1 0 0.77 0.57 0.53 48.55 24.31 145.9 -77.85 -4.40 170.9 0"
rep3 = representation.from_string(string, smiles)
print(rep3.to_string())
print(rep3.to_pyxtal())
#x = rep3.to_pyxtal(); x.optimize_lattice(standard=True); print(x)
rep3.to_standard_setting()
print(rep3.to_pyxtal())
print(rep3.to_string())

string1 = "81 14.08 6.36 25.31 83.9 1 0.83 0.40 0.63 136.6 -21.6 -151.1 -101.1 -131.2 154.7 -176.4 -147.8 178.2 -179.1 -53.3 0"
string2 = "81 14.08 6.36 25.31 83.9 1 0.03 0.84 0.89 149.1 -8.0 -37.8 -39.9 -104.2 176.2 -179.6 137.8 -178.5 -173.3 -103.6 0"
print("Test other cases")
string1 = "81 14.08 6.36 25.31 83.9 1 0 0.83 0.40 0.63 136.6 -21.6 -151.1 -101.1 -131.2 154.7 -176.4 -147.8 178.2 -179.1 -53.3 0"
string2 = "81 14.08 6.36 25.31 83.9 1 0 0.03 0.84 0.89 149.1 -8.0 -37.8 -39.9 -104.2 176.2 -179.6 137.8 -178.5 -173.3 -103.6 0"
smiles = ['CC1=CC=C(C=C1)S(=O)(=O)C2=C(N=C(S2)C3=CC=C(C=C3)NC(=O)OCC4=CC=CC=C4)C']
rep4 = representation.from_string(string1, smiles)
rep5 = representation.from_string(string2, smiles)
Expand Down

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