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fix the bug of energy file with comments, warning when ibrav is nor supported #76

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Merged
amcadmus merged 1 commit into from
Jan 12, 2020
Merged

fix the bug of energy file with comments, warning when ibrav is nor supported #76

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20 changes: 12 additions & 8 deletions dpdata/qe/traj.py
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
#!/usr/bin/python3

import numpy as np
import dpdata
import dpdata,warnings

ry2ev = 13.605693009
hartree2ev = 27.211386018
Expand Down Expand Up @@ -36,8 +36,10 @@ def convert_celldm(ibrav, celldm) :
return celldm[0] * 0.5 * np.array([[1,1,1], [-1,1,1], [-1,-1,1]])
elif ibrav == -3 :
return celldm[0] * 0.5 * np.array([[-1,1,1], [1,-1,1], [1,1,-1]])
else :
raise RuntimeError('unsupported ibrav ' + str(ibrav))
else :
warnings.warn('unsupported ibrav ' + str(ibrav) + ' if no .cel file, the cell convertion may be wrong. ')
return np.eye(3)
#raise RuntimeError('unsupported ibrav ' + str(ibrav))

def load_cell_parameters(lines) :
blk = load_block(lines, 'CELL_PARAMETERS', 3)
Expand Down Expand Up @@ -152,11 +154,13 @@ def load_energy(fname, begin = 0, step = 1) :
for ii in data[begin::step,0]:
steps.append('%d'%ii)
with open(fname) as fp:
line = fp.readline()
if line :
nw = len(line.split())
else :
return None
while True:
line = fp.readline()
if not line :
return None
if line.split()[0][0] != '#':
nw = len(line.split())
break
data = np.reshape(data, [-1, nw])
return energy_convert * data[begin::step,5], steps

Expand Down
1 change: 1 addition & 0 deletions tests/qe.traj/traj6.evp
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Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
# comments here
195 9.433649E-03 1.290500E-05 0.000000E+00 1.057182E-02 -1100.03076389 -1100.03076389 -1100.03075434 -1100.03073209 1.300606E+04 -3.31610
200 9.675537E-03 7.090171E-05 0.000000E+00 1.257319E+00 -1100.03189493 -1100.03189493 -1100.03076015 -1100.03068120 1.300606E+04 -3.31683
201 9.675537E-03 7.090171E-05 0.000000E+00 2.257319E+00 -1100.03189493 -1100.03189493 -1100.03076015 -1100.03068120 1.300606E+04 -3.31683
Expand Down
13 changes: 10 additions & 3 deletions tests/test_qe_cp_traj.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
from context import dpdata


class TestPWSCFProps :
class TestCPTRAJProps :
def test_atom_names(self) :
self.assertEqual(self.system.data['atom_names'], ['O','H'])

Expand Down Expand Up @@ -44,18 +44,25 @@ def test_coord(self) :
self.assertAlmostEqual(self.system['coords'][-1][ii][jj], coords[ii][jj])


class TestPWSCFTraj(unittest.TestCase, TestPWSCFProps):
class TestCPTRAJTraj(unittest.TestCase, TestCPTRAJProps):

def setUp(self):
self.system = dpdata.System('qe.traj/oh-md', fmt = 'qe/cp/traj')


class TestPWSCFLabeledTraj(unittest.TestCase, TestPWSCFProps):
class TestCPTRAJLabeledTraj(unittest.TestCase, TestCPTRAJProps):

def setUp(self):
self.system = dpdata.LabeledSystem('qe.traj/oh-md', fmt = 'qe/cp/traj')


class TestConverCellDim(unittest.TestCase):
def test_case_null(self):
cell = dpdata.qe.traj.convert_celldm(8, [1, 1, 1])
ref = np.eye(3)
for ii in range(3):
for jj in range(3):
self.assertAlmostEqual(cell[ii][jj], ref[ii][jj])


if __name__ == '__main__':
Expand Down