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nomad-lab
parser-cp2k
Commits
30b1c39e
Commit
30b1c39e
authored
Mar 11, 2016
by
Lauri Himanen
Browse files
Changes in tests.
parent
a1a611bf
Changes
3
Hide whitespace changes
Inline
Side-by-side
parser/parser-cp2k/cp2kparser/utils/baseclasses.py
View file @
30b1c39e
...
...
@@ -312,6 +312,7 @@ class FileParser(object):
self
.
default_data_caching_level
=
CachingLevel
.
ForwardAndCache
self
.
default_section_caching_level
=
CachingLevel
.
Forward
self
.
onClose
=
{}
self
.
caching_backend
=
None
def
parse
(
self
):
"""Parser the information from the given file(s). By default uses the
...
...
@@ -342,7 +343,7 @@ class FileParser(object):
onClose
[
attr
]
=
[
callback
]
# Setup the backend that caches ond handles triggers
active
_backend
=
ActiveBackend
.
activeBackend
(
self
.
caching
_backend
=
ActiveBackend
.
activeBackend
(
metaInfoEnv
=
self
.
backend
.
metaInfoEnv
(),
cachingLevelForMetaName
=
self
.
caching_level_for_metaname
,
defaultDataCachingLevel
=
self
.
default_data_caching_level
,
...
...
@@ -357,11 +358,11 @@ class FileParser(object):
self
.
backend
.
fileOut
.
write
(
"["
)
uri
=
"file://"
+
fileToParse
parserInfo
=
{
'name'
:
'cp2k-parser'
,
'version'
:
'1.0'
}
active
_backend
.
startedParsingSession
(
uri
,
parserInfo
)
self
.
caching
_backend
.
startedParsingSession
(
uri
,
parserInfo
)
with
open
(
fileToParse
,
"r"
)
as
fIn
:
parser
=
parserBuilder
.
buildParser
(
PushbackLineFile
(
fIn
),
active
_backend
,
superContext
=
self
)
parser
=
parserBuilder
.
buildParser
(
PushbackLineFile
(
fIn
),
self
.
caching
_backend
,
superContext
=
self
)
parser
.
parse
()
active
_backend
.
finishedParsingSession
(
"ParseSuccess"
,
None
)
self
.
caching
_backend
.
finishedParsingSession
(
"ParseSuccess"
,
None
)
self
.
backend
.
fileOut
.
write
(
"]
\n
"
)
def
get_metainfos
(
self
):
...
...
test/unittests/cp2k_2.6.2/run_tests.py
View file @
30b1c39e
...
...
@@ -35,7 +35,7 @@ def get_results(folder, metainfo_to_keep=None):
def
get_result
(
folder
,
metaname
):
results
=
get_results
(
folder
,
metaname
)
result
=
results
[
metaname
]
return
result
.
value
return
result
#===============================================================================
...
...
@@ -61,20 +61,21 @@ class TestXCFunctional(unittest.TestCase):
#===============================================================================
class
TestSectionSingleConfigurationCalculation
(
unittest
.
TestCase
):
results
=
get_results
(
"section_single_configuration_calculation"
,
"section_single_configuration_calculation"
)
def
setUp
(
self
):
self
.
results
=
get_results
(
"section_single_configuration_calculation"
,
"section_single_configuration_calculation"
)
def
test_energy_total_scf_iteration
(
self
):
energy_total
=
self
.
results
[
"energy_total_scf_iteration"
]
.
value
energy_total
=
self
.
results
[
"energy_total_scf_iteration"
]
expected_result
=
convert_unit
(
np
.
array
(
-
32.2320848878
),
"hartree"
)
self
.
assertTrue
(
np
.
array_equal
(
energy_total
[
0
],
expected_result
))
def
test_energy_total
(
self
):
energy_total
=
self
.
results
[
"energy_total"
]
.
value
energy_total
=
self
.
results
[
"energy_total"
]
expected_result
=
convert_unit
(
np
.
array
(
-
31.297885372811063
),
"hartree"
)
self
.
assertTrue
(
np
.
array_equal
(
energy_total
,
expected_result
))
def
test_atom_forces
(
self
):
atomic_forces
=
self
.
results
[
"atom_forces"
]
.
value
atomic_forces
=
self
.
results
[
"atom_forces"
]
expected_result
=
convert_unit
(
np
.
array
([
[
0.00000000
,
0.00000000
,
0.00000000
],
...
...
@@ -94,15 +95,16 @@ class TestSectionSingleConfigurationCalculation(unittest.TestCase):
#===============================================================================
class
TestSectionSystemDescription
(
unittest
.
TestCase
):
results
=
get_results
(
"section_system_description"
,
"section_system_description"
)
def
setUp
(
self
):
self
.
results
=
get_results
(
"section_system_description"
,
"section_system_description"
)
def
test_atom_label
(
self
):
atom_labels
=
self
.
results
[
"atom_label"
]
.
value
atom_labels
=
self
.
results
[
"atom_label"
]
expected_labels
=
np
.
array
(
8
*
[
"Si"
])
self
.
assertTrue
(
np
.
array_equal
(
atom_labels
,
expected_labels
))
def
test_simulation_cell
(
self
):
cell
=
self
.
results
[
"simulation_cell"
]
.
value
cell
=
self
.
results
[
"simulation_cell"
]
n_vectors
=
cell
.
shape
[
0
]
n_dim
=
cell
.
shape
[
1
]
self
.
assertEqual
(
n_vectors
,
3
)
...
...
@@ -111,17 +113,18 @@ class TestSectionSystemDescription(unittest.TestCase):
self
.
assertTrue
(
np
.
array_equal
(
cell
,
expected_cell
))
def
test_number_of_atoms
(
self
):
n_atoms
=
self
.
results
[
"number_of_atoms"
]
.
value
n_atoms
=
self
.
results
[
"number_of_atoms"
]
self
.
assertEqual
(
n_atoms
,
8
)
def
test_atom_position
(
self
):
atom_position
=
self
.
results
[
"atom_position"
]
.
value
atom_position
=
self
.
results
[
"atom_position"
]
expected_position
=
convert_unit
(
np
.
array
([
4.073023
,
4.073023
,
1.357674
]),
"angstrom"
)
self
.
assertTrue
(
np
.
array_equal
(
atom_position
[
-
1
,
:],
expected_position
))
#===============================================================================
if
__name__
==
'__main__'
:
pass
logger
=
logging
.
getLogger
(
"cp2kparser"
)
logger
.
setLevel
(
logging
.
ERROR
)
...
...
test/unittests/cp2k_2.6.2/section_single_configuration_calculation/si_bulk8.out
View file @
30b1c39e
...
...
@@ -9,10 +9,10 @@
DBCSR| Communication thread load 87
**** **** ****** ** PROGRAM STARTED AT 2016-0
2-22 21:55:14.59
4
**** **** ****** ** PROGRAM STARTED AT 2016-0
3-10 22:35:13.17
4
***** ** *** *** ** PROGRAM STARTED ON lauri-Lenovo-Z50-70
** **** ****** PROGRAM STARTED BY lauri
***** ** ** ** ** PROGRAM PROCESS ID
5052
***** ** ** ** ** PROGRAM PROCESS ID
7335
**** ** ******* ** PROGRAM STARTED IN /home/lauri/Dropbox/nomad-dev/nomad-l
ab-base/parsers/cp2k/test/unittests/c
p2k_2.6.2/section_single_configuratio
...
...
@@ -46,13 +46,13 @@
MEMORY| system memory details [Kb]
MEMORY| rank 0 min max average
MEMORY| MemTotal 807038
4
807038
4
807038
4
807038
4
MEMORY| MemFree
3544704 3544704 3544704 3544704
MEMORY| Buffers
267372
267372
267372
267372
MEMORY| Cached 2
047768
2
047768
2
047768
2
047768
MEMORY| Slab
2
984
72
2
984
72
2
984
72
2
984
72
MEMORY| SReclaimable
254424
254424
254424
254424
MEMORY| MemLikelyFree 6
114268
6
114268
6
114268
6
114268
MEMORY| MemTotal 807038
8
807038
8
807038
8
807038
8
MEMORY| MemFree
2886880 2886880 2886880 2886880
MEMORY| Buffers
859068
859068
859068
859068
MEMORY| Cached 2
349220
2
349220
2
349220
2
349220
MEMORY| Slab
456
984
456
984
456
984
456
984
MEMORY| SReclaimable
417916
417916
417916
417916
MEMORY| MemLikelyFree 6
513084
6
513084
6
513084
6
513084
*** Fundamental physical constants (SI units) ***
...
...
@@ -479,7 +479,7 @@
Total charge density on r-space grids: -0.0000000043
Total charge density g-space grids: -0.0000000043
1 NoMix/Diag. 0.40E+00 0.
8
0.75558724 -32.2320848878 -3.22E+01
1 NoMix/Diag. 0.40E+00 0.
9
0.75558724 -32.2320848878 -3.22E+01
Trace(PS): 32.0000000000
Electronic density on regular grids: -31.9999999956 0.0000000044
...
...
@@ -487,7 +487,7 @@
Total charge density on r-space grids: -0.0000000017
Total charge density g-space grids: -0.0000000017
2 Broy./Diag. 0.40E+00 1.
4
0.05667976 -31.1418135481 1.09E+00
2 Broy./Diag. 0.40E+00 1.
3
0.05667976 -31.1418135481 1.09E+00
Trace(PS): 32.0000000000
Electronic density on regular grids: -31.9999999907 0.0000000093
...
...
@@ -654,13 +654,13 @@
ROUTINE CALLS TOT TIME [s] AVE VOLUME [Bytes] PERFORMANCE [MB/s]
MP_Group 5 0.000
MP_Bcast 12 0.0
0
0 5. 0.
25
MP_Allreduce 171 0.000 42. 3
8.42
MP_Bcast 12 0.0
1
0 5. 0.
01
MP_Allreduce 171 0.000 42. 3
1.37
MP_Sync 4 0.000
MP_Alltoall 183 0.000 15743. 1
2047.92
MP_Alltoall 183 0.000 15743. 1
1176.59
MP_Wait 264 0.000
MP_ISend 88 0.001 13472. 1
836.51
MP_IRecv 88 0.000 13472. 13
441.60
MP_ISend 88 0.001 13472. 1
589.34
MP_IRecv 88 0.000 13472. 13
580.33
MP_Memory 264 0.000
-------------------------------------------------------------------------------
...
...
@@ -732,32 +732,33 @@
-------------------------------------------------------------------------------
SUBROUTINE CALLS ASD SELF TIME TOTAL TIME
MAXIMUM AVERAGE MAXIMUM AVERAGE MAXIMUM
CP2K 1 1.0 0.003 0.003 16.479 16.479
qs_forces 1 2.0 0.000 0.000 16.388 16.388
qs_energies_scf 1 3.0 0.000 0.000 14.665 14.665
scf_env_do_scf 1 4.0 0.000 0.000 13.723 13.723
scf_env_do_scf_inner_loop 10 5.0 0.001 0.001 13.723 13.723
rebuild_ks_matrix 11 6.7 0.000 0.000 9.054 9.054
qs_ks_build_kohn_sham_matrix 11 7.7 0.001 0.001 9.054 9.054
sum_up_and_integrate 11 8.7 0.004 0.004 8.756 8.756
integrate_v_rspace 11 9.7 8.630 8.630 8.752 8.752
qs_ks_update_qs_env 10 6.0 0.000 0.000 8.002 8.002
qs_rho_update_rho 11 6.0 0.000 0.000 5.971 5.971
calculate_rho_elec 11 7.0 5.718 5.718 5.971 5.971
qs_ks_update_qs_env_forces 1 3.0 0.000 0.000 1.052 1.052
build_core_hamiltonian_matrix_ 1 3.0 0.000 0.000 0.671 0.671
init_scf_run 1 4.0 0.000 0.000 0.601 0.601
scf_env_initial_rho_setup 1 5.0 0.000 0.000 0.601 0.601
fft_wrap_pw1pw2 120 9.8 0.001 0.001 0.553 0.553
fft_wrap_pw1pw2_150 54 10.1 0.029 0.029 0.502 0.502
fft3d_s 121 11.7 0.353 0.353 0.366 0.366
build_core_ppnl_forces 1 4.0 0.345 0.345 0.345 0.345
CP2K 1 1.0 0.031 0.031 17.001 17.001
qs_forces 1 2.0 0.001 0.001 16.583 16.583
qs_energies_scf 1 3.0 0.035 0.035 14.881 14.881
scf_env_do_scf 1 4.0 0.000 0.000 13.705 13.705
scf_env_do_scf_inner_loop 10 5.0 0.038 0.038 13.705 13.705
rebuild_ks_matrix 11 6.7 0.000 0.000 8.992 8.992
qs_ks_build_kohn_sham_matrix 11 7.7 0.003 0.003 8.992 8.992
sum_up_and_integrate 11 8.7 0.004 0.004 8.699 8.699
integrate_v_rspace 11 9.7 8.574 8.574 8.696 8.696
qs_ks_update_qs_env 10 6.0 0.000 0.000 7.928 7.928
qs_rho_update_rho 11 6.0 0.000 0.000 5.952 5.952
calculate_rho_elec 11 7.0 5.705 5.705 5.952 5.952
qs_ks_update_qs_env_forces 1 3.0 0.000 0.000 1.064 1.064
init_scf_run 1 4.0 0.007 0.007 0.735 0.735
scf_env_initial_rho_setup 1 5.0 0.001 0.001 0.666 0.666
build_core_hamiltonian_matrix_ 1 3.0 0.000 0.000 0.637 0.637
fft_wrap_pw1pw2 120 9.8 0.001 0.001 0.562 0.562
fft_wrap_pw1pw2_150 54 10.1 0.028 0.028 0.515 0.515
fft3d_s 121 11.7 0.363 0.363 0.430 0.430
qs_energies_init_hamiltonians 1 4.0 0.001 0.001 0.349 0.349
build_core_ppnl_forces 1 4.0 0.340 0.340 0.340 0.340
-------------------------------------------------------------------------------
**** **** ****** ** PROGRAM ENDED AT 2016-0
2-22 21:55:31.153
**** **** ****** ** PROGRAM ENDED AT 2016-0
3-10 22:35:30.794
***** ** *** *** ** PROGRAM RAN ON lauri-Lenovo-Z50-70
** **** ****** PROGRAM RAN BY lauri
***** ** ** ** ** PROGRAM PROCESS ID
5052
***** ** ** ** ** PROGRAM PROCESS ID
7335
**** ** ******* ** PROGRAM STOPPED IN /home/lauri/Dropbox/nomad-dev/nomad-l
ab-base/parsers/cp2k/test/unittests/c
p2k_2.6.2/section_single_configuratio
...
...
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