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Merged
amcadmus merged 2 commits into from
Apr 16, 2020
Merged

Devel #97

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a8c34fd
add a unittest to lammps dump shift origin
felix5572 Apr 16, 2020
2310a54
fix bug #74
felix5572 Apr 16, 2020
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3 changes: 2 additions & 1 deletion dpdata/xyz/quip_gap_xyz.py
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Expand Up @@ -127,6 +127,7 @@ def handle_single_xyz_frame(lines):
info_dict['coords'] = np.array([coords_array]).astype('float32')
info_dict['energies'] = np.array([field_dict['energy']]).astype('float32')
info_dict['forces'] = np.array([force_array]).astype('float32')
info_dict['virials'] = virials
if virials is not None:
info_dict['virials'] = virials
info_dict['orig'] = [0,0,0]
return info_dict
3 changes: 2 additions & 1 deletion setup.py
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Expand Up @@ -36,7 +36,8 @@
'dpdata/xyz',
'dpdata/pwmat',
'dpdata/amber',
'dpdata/fhi_aims'],
'dpdata/fhi_aims',
'dpdata/gromacs'],
package_data={'dpdata':['*.json']},
classifiers=[
"Programming Language :: Python :: 3.6",
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17 changes: 17 additions & 0 deletions tests/POSCAR
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H6 O3
1.0
7.8228387655643719e+00 0.0000000000000000e+00 1.0000000000000000e+00
2.0000000000000000e+00 7.3535726471820508e+00 3.0000000000000000e+00
4.0000000000000000e+00 5.0000000000000000e+00 9.0365185154237526e+00
H O
6 3
Cartesian
1.7700000000 1.4900000000 2.6200000000
0.4600000000 1.4900000000 3.3900000000
5.6700000000 4.8100000000 0.3500000000
5.6800000000 4.8100000000 1.8600000000
6.5300000000 6.3400000000 3.3600000000
7.4300000000 5.1200000000 3.3600000000
1.3500000000 1.8300000000 3.4100000000
5.2000000000 4.4700000000 1.1100000000
6.5100000000 5.3900000000 3.3500000000
26 changes: 26 additions & 0 deletions tests/poscars/shift_origin.dump
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@@ -0,0 +1,26 @@
ITEM: TIMESTEP
0
ITEM: NUMBER OF ATOMS
4
ITEM: BOX BOUNDS xy xz yz pp pp pp
-2 6 0
0 5 0
0 3 0
ITEM: ATOMS id type xs ys zs fx fy fz
1 1 0 0 0 -1.04083e-17 2.76472e-17 1.83013e-16
2 1 0.5 0.5 0.5 1.21431e-17 5.04493e-17 -9.96382e-17
3 1 0.5 0 0.75 1.21431e-17 1.39964e-17 -3.65837e-16
4 1 0 0.5 0.25 -2.77556e-17 -9.16896e-17 2.23779e-16
ITEM: TIMESTEP
100
ITEM: NUMBER OF ATOMS
4
ITEM: BOX BOUNDS xy xz yz pp pp pp
1 9 0
0 5 0
0 3 0
ITEM: ATOMS id type xs ys zs fx fy fz
1 1 0 0 0 -1.04083e-17 2.76472e-17 1.83013e-16
2 1 0.5 0.5 0.5 1.21431e-17 5.04493e-17 -9.96382e-17
3 1 0.5 0 0.75 1.21431e-17 1.39964e-17 -3.65837e-16
4 1 0 0.5 0.25 -2.77556e-17 -9.16896e-17 2.23779e-16
14 changes: 14 additions & 0 deletions tests/test_lammps_dump_shift_origin.py
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@@ -0,0 +1,14 @@
import os
import numpy as np
import unittest
from context import dpdata
from comp_sys import CompSys, IsPBC

class TestLammpsDumpShiftOrigin(unittest.TestCase, CompSys, IsPBC):
def setUp (self):
self.system_1 = dpdata.System('poscars/shift_origin.dump', fmt = 'lammps/dump')[0]
self.system_2 = dpdata.System('poscars/shift_origin.dump', fmt = 'lammps/dump')[1]
self.places = 6

if __name__ == '__main__':
unittest.main()
11 changes: 11 additions & 0 deletions tests/test_quip_gap_xyz.py
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Expand Up @@ -75,6 +75,17 @@ def setUp (self) :
self.f_places = 6
self.v_places = 4

class TestQuipGapxyzNoVirials(unittest.TestCase, CompLabeledSys, IsPBC):
def setUp(self):
self.multi_systems_1 = dpdata.MultiSystems.from_file('xyz/xyz_B5C7_novirials.xyz', fmt='quip/gap/xyz')
self.system_1 = self.multi_systems_1.systems['B5C7']
self.system_1.sort_atom_types()
self.system_2 = dpdata.LabeledSystem('xyz/B5C7_novirials', fmt='deepmd/raw')
self.places = 6
self.e_places = 6
self.f_places = 6



if __name__ == '__main__':
unittest.main()
1 change: 1 addition & 0 deletions tests/xyz/B5C7_novirials/box.raw
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2.405388593673706055e+00 0.000000000000000000e+00 0.000000000000000000e+00 6.669999947916949168e-07 8.830761909484863281e+00 0.000000000000000000e+00 2.145883798599243164e+00 6.300000165992969414e-08 2.066179037094116211e+00
1 change: 1 addition & 0 deletions tests/xyz/B5C7_novirials/coord.raw
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3.195669889450073242e+00 9.796500205993652344e-01 1.522500038146972656e+00 1.355610013008117676e+00 9.796500205993652344e-01 5.436800122261047363e-01 1.355610013008117676e+00 7.851109981536865234e+00 5.436800122261047363e-01 3.195669889450073242e+00 7.851109981536865234e+00 1.522500038146972656e+00 2.275640010833740234e+00 4.415380001068115234e+00 1.033089995384216309e+00 1.959050059318542480e+00 6.235050201416015625e+00 1.539360046386718750e+00 2.592220067977905273e+00 6.235050201416015625e+00 5.268200039863586426e-01 2.592220067977905273e+00 2.595710039138793945e+00 5.268200039863586426e-01 1.959050059318542480e+00 2.595710039138793945e+00 1.539360046386718750e+00 2.275640010833740234e+00 1.560019969940185547e+00 1.033089995384216309e+00 2.275640010833740234e+00 7.270740032196044922e+00 1.033089995384216309e+00 2.275640010833740234e+00 0.000000000000000000e+00 1.033089995384216309e+00
1 change: 1 addition & 0 deletions tests/xyz/B5C7_novirials/energy.raw
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2.397022962570190430e+00
1 change: 1 addition & 0 deletions tests/xyz/B5C7_novirials/force.raw
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-7.255659103393554688e+00 -8.829194068908691406e+00 4.687431812286376953e+00 7.255657196044921875e+00 -8.829194068908691406e+00 -4.687431812286376953e+00 7.255659103393554688e+00 8.829194068908691406e+00 -4.687431812286376953e+00 -7.255657196044921875e+00 8.829194068908691406e+00 4.687431812286376953e+00 -0.000000000000000000e+00 -0.000000000000000000e+00 0.000000000000000000e+00 -1.439490795135498047e+01 -1.912936592102050781e+01 -4.678572177886962891e+00 1.439490509033203125e+01 -1.912936592102050781e+01 4.678572177886962891e+00 1.439490795135498047e+01 1.912936592102050781e+01 4.678572177886962891e+00 -1.439490509033203125e+01 1.912936592102050781e+01 -4.678572177886962891e+00 -0.000000000000000000e+00 -4.519358158111572266e+00 0.000000000000000000e+00 0.000000000000000000e+00 4.519358158111572266e+00 0.000000000000000000e+00 -0.000000000000000000e+00 -0.000000000000000000e+00 0.000000000000000000e+00
12 changes: 12 additions & 0 deletions tests/xyz/B5C7_novirials/type.raw
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0
0
0
0
0
1
1
1
1
1
1
1
2 changes: 2 additions & 0 deletions tests/xyz/B5C7_novirials/type_map.raw
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B
C
14 changes: 14 additions & 0 deletions tests/xyz/xyz_B5C7_novirials.xyz
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energy=2.397023 Lattice="2.405388711 0.0 0.0 6.67e-07 8.830761667 0.0 2.145883783 6.3e-08 2.066179013" Properties=species:S:1:pos:R:3:Z:I:1:force:R:3
B 3.19567000000 0.97965000000 1.52250000000 5 -7.25565900000 -8.82919400000 4.68743200000
B 1.35561000000 0.97965000000 0.54368000000 5 7.25565700000 -8.82919400000 -4.68743200000
B 1.35561000000 7.85111000000 0.54368000000 5 7.25565900000 8.82919400000 -4.68743200000
B 3.19567000000 7.85111000000 1.52250000000 5 -7.25565700000 8.82919400000 4.68743200000
B 2.27564000000 4.41538000000 1.03309000000 5 -0.00000000000 -0.00000000000 0.00000000000
C 1.95905000000 6.23505000000 1.53936000000 6 -14.39490800000 -19.12936600000 -4.67857200000
C 2.59222000000 6.23505000000 0.52682000000 6 14.39490500000 -19.12936600000 4.67857200000
C 2.59222000000 2.59571000000 0.52682000000 6 14.39490800000 19.12936600000 4.67857200000
C 1.95905000000 2.59571000000 1.53936000000 6 -14.39490500000 19.12936600000 -4.67857200000
C 2.27564000000 1.56002000000 1.03309000000 6 -0.00000000000 -4.51935800000 0.00000000000
C 2.27564000000 7.27074000000 1.03309000000 6 0.00000000000 4.51935800000 0.00000000000
C 2.27564000000 0.00000000000 1.03309000000 6 -0.00000000000 -0.00000000000 0.00000000000