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Select frames which are convergent in SC-calculatio of VASP #7

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Jul 1, 2019
Merged

Select frames which are convergent in SC-calculatio of VASP #7

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f9c157b
Select frames which are convergent in SC-calculatio of VASP
AnguseZhang Jun 30, 2019
74be653
add unit test for unconverged OUTCAR
AnguseZhang Jun 30, 2019
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41 changes: 25 additions & 16 deletions dpdata/vasp/outcar.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,17 +3,21 @@
def system_info (lines, type_idx_zero = False) :
atom_names = []
atom_numbs = None
nelm = None
for ii in lines:
if 'TITEL =' in ii :
# get atom names from POTCAR info, tested only for PAW_PBE ...
atom_names.append(ii.split()[3])
elif 'NELM' in ii :
nelm = int(ii.split()[2][:-1])
break;
elif 'ions per type' in ii :
atom_numbs_ = [int(s) for s in ii.split()[4:]]
if atom_numbs is None :
atom_numbs = atom_numbs_
else :
assert (atom_numbs == atom_numbs_), "in consistent numb atoms in OUTCAR"
break
assert(nelm is not None), "cannot find maximum steps for each SC iteration"
assert(atom_numbs is not None), "cannot find ion type info in OUTCAR"
atom_names = atom_names[:len(atom_numbs)]
atom_types = []
Expand All @@ -23,7 +27,7 @@ def system_info (lines, type_idx_zero = False) :
atom_types.append(idx)
else :
atom_types.append(idx+1)
return atom_names, atom_numbs, np.array(atom_types, dtype = int)
return atom_names, atom_numbs, np.array(atom_types, dtype = int), nelm


def get_outcar_block(fp) :
Expand All @@ -41,7 +45,7 @@ def get_frames (fname, begin = 0, step = 1) :
fp = open(fname)
blk = get_outcar_block(fp)

atom_names, atom_numbs, atom_types = system_info(blk, type_idx_zero = True)
atom_names, atom_numbs, atom_types, nelm = system_info(blk, type_idx_zero = True)
ntot = sum(atom_numbs)

all_coords = []
Expand All @@ -53,31 +57,36 @@ def get_frames (fname, begin = 0, step = 1) :
cc = 0
while len(blk) > 0 :
if cc >= begin and (cc - begin) % step == 0 :
coord, cell, energy, force, virial = analyze_block(blk, ntot)
if len(coord) == 0:
break
all_coords.append(coord)
all_cells.append(cell)
all_energies.append(energy)
all_forces.append(force)
if virial is not None :
all_virials.append(virial)
coord, cell, energy, force, virial, is_converge = analyze_block(blk, ntot, nelm)
if is_converge :
if len(coord) == 0:
break
all_coords.append(coord)
all_cells.append(cell)
all_energies.append(energy)
all_forces.append(force)
if virial is not None :
all_virials.append(virial)
blk = get_outcar_block(fp)
cc += 1

fp.close()
return atom_names, atom_numbs, atom_types, np.array(all_cells), np.array(all_coords), np.array(all_energies), np.array(all_forces), np.array(all_virials)


def analyze_block(lines, ntot) :
def analyze_block(lines, ntot, nelm) :
coord = []
cell = []
energy = None
force = []
virial = None
is_converge = True
sc_index = 0
for idx,ii in enumerate(lines) :
if 'Iteration' in ii:
pass
sc_index = int(ii.split()[3][:-1])
if sc_index >= nelm:
is_converge = False
elif 'free energy TOTEN' in ii:
energy = float(ii.split()[4])
assert((force is not None) and len(coord) > 0 and len(cell) > 0)
Expand All @@ -87,7 +96,7 @@ def analyze_block(lines, ntot) :
# all_forces.append(force)
# if virial is not None :
# all_virials.append(virial)
return coord, cell, energy, force, virial
return coord, cell, energy, force, virial, is_converge
elif 'VOLUME and BASIS' in ii:
for dd in range(3) :
tmp_l = lines[idx+5+dd]
Expand All @@ -111,4 +120,4 @@ def analyze_block(lines, ntot) :
info = [float(ss) for ss in tmp_l.split()]
coord.append(info[:3])
force.append(info[3:])
return coord, cell, energy, force, virial
return coord, cell, energy, force, virial, is_converge
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