Skip to content
GitLab
Commit bf92ab97 authored by Lauri Himanen's avatar Lauri Himanen
Browse files

Started working on MD parsing, imporoved the CSV tool.

parent fe625fdc
Expand all Hide whitespace changes
Inline Side-by-side
parser/parser-cp2k/cp2kparser/generic/csvparsing.py
View file @ bf92ab97
......@@ -34,7 +34,7 @@ def iread(filepath, columns, delimiter=r"\s+", comments=r"#", start=None, end=No
if line:
return compiled_delimiter.split(line)
else:
return []
return None
def is_end(line):
"""Check if the given line matches the separator pattern.
......@@ -69,22 +69,11 @@ def iread(filepath, columns, delimiter=r"\s+", comments=r"#", start=None, end=No
# Start iterating
configuration = []
started = False
with open(filepath, "r") as f:
for line in f: # This actually reads line by line and only keeps the current line in memory
# If a start regex is provided, use it to detect the start of a configuration
if is_start(line):
started = True
continue
# If separator encountered, yield the stored configuration
if is_end(line):
started = False
if configuration:
yield np.array(configuration)
configuration = []
elif start is not None and started:
# If no starting and ending condition are provided, read configuration by line
if start is None and end is None:
with open(filepath, "r") as f:
for line in f: # This actually reads line by line and only keeps the current line in memory
# Ignore comments, separate by delimiter
vals = split_line(line)
line_forces = []
......@@ -102,9 +91,48 @@ def iread(filepath, columns, delimiter=r"\s+", comments=r"#", start=None, end=No
return
else:
line_forces.append(value)
configuration.append(line_forces)
yield np.array(line_forces)
# If starting and ending condition are provided, after starting condition
# is detected, add the values from lines to a new array that is returned
# when the end condition is met
elif start is not None and end is not None:
with open(filepath, "r") as f:
for line in f: # This actually reads line by line and only keeps the current line in memory
# If a start regex is provided, use it to detect the start of a configuration
if is_start(line):
started = True
continue
# If separator encountered, yield the stored configuration
if is_end(line):
started = False
if configuration:
yield np.array(configuration)
configuration = []
elif start is not None and started:
# Ignore comments, separate by delimiter
vals = split_line(line)
line_forces = []
if vals:
for column in columns:
try:
value = vals[column]
except IndexError:
logger.warning("The given index '{}' could not be found on the line '{}'. The given delimiter or index could be wrong.".format(column, line))
return
try:
value = float(value)
except ValueError:
logger.warning("Could not cast value '{}' to float. Currently only floating point values are accepted".format(value))
return
else:
line_forces.append(value)
configuration.append(line_forces)
# The last configuration is yielded even if separator is not present at
# the end of file or is not given at all
if configuration:
yield np.array(configuration)
# The last configuration is yielded even if separator is not present at
# the end of file or is not given at all
if configuration:
yield np.array(configuration)
src/main/scala/eu/nomad_lab/parsers/Cp2kParser.scala
View file @ bf92ab97
......@@ -47,6 +47,7 @@ object Cp2kParser extends SimpleExternalParserGenerator(
"parser-cp2k/cp2kparser/versions/cp2k262/__init__.py",
"parser-cp2k/cp2kparser/versions/cp2k262/singlepointparser.py",
"parser-cp2k/cp2kparser/versions/cp2k262/geooptparser.py",
"parser-cp2k/cp2kparser/versions/cp2k262/mdparser.py",
"parser-cp2k/cp2kparser/versions/cp2k262/singlepointforceparser.py",
"parser-cp2k/cp2kparser/versions/cp2k262/inputparser.py",
"parser-cp2k/cp2kparser/versions/cp2k262/commonmatcher.py",
......
src/test/scala/eu/nomad_lab/parsers/Cp2kParserSpec.scala
View file @ bf92ab97
......@@ -15,4 +15,7 @@ object Cp2kParserSpec extends Specification {
"test geo_opt with json" >> {
ParserRun.parse(Cp2kParser, "parsers/cp2k/test/examples/geo_opt/H2O.out", "json") must_== ParseResult.ParseSuccess
}
"test md with json" >> {
ParserRun.parse(Cp2kParser, "parsers/cp2k/test/examples/md/H2O-32.out", "json") must_== ParseResult.ParseSuccess
}
}
test/examples/md/H2O-32-1.ener 0 → 100644
View file @ bf92ab97
# Step Nr. Time[fs] Kin.[a.u.] Temp[K] Pot.[a.u.] Cons Qty[a.u.] UsedTime[s]
0 0.000000 0.007125335 300.000000000 -34.330396471 -34.323271136 0.000000000
1 0.500000 0.006533348 275.075405378 -34.329778993 -34.323245645 5.596860174
2 1.000000 0.005583688 235.091633019 -34.328790653 -34.323206964 2.152504481
3 1.500000 0.004815598 202.752506973 -34.327998978 -34.323183380 2.176433628
4 2.000000 0.004566544 192.266488819 -34.327754290 -34.323187747 2.145689724
5 2.500000 0.004788928 201.629598676 -34.327997890 -34.323208962 2.183614561
6 3.000000 0.005184860 218.299664775 -34.328412394 -34.323227533 2.156728805
7 3.500000 0.005470470 230.324748558 -34.328704052 -34.323233583 1.372403022
8 4.000000 0.005526692 232.691881533 -34.328757407 -34.323230715 2.158405874
9 4.500000 0.005371243 226.146979313 -34.328598255 -34.323227013 2.157126734
10 5.000000 0.005062914 213.165337396 -34.328287038 -34.323224123 2.141358878
test/examples/md/H2O-32-pos-1.xyz 0 → 100644
View file @ bf92ab97
6
i = 0, time = 0.000, E = -34.3303964710
O 2.2803980000 9.1465390000 5.0886960000
O 1.2517030000 2.4062610000 7.7699080000
H 1.7620190000 9.8204290000 5.5284540000
H 3.0959870000 9.1070880000 5.5881860000
H 0.5541290000 2.9826340000 8.0820240000
H 1.7712570000 2.9547790000 7.1821810000
6
i = 1, time = 0.500, E = -34.3297789925
O 2.2807055575 9.1465838595 5.0883919888
O 1.2498929917 2.4074289284 7.7692382491
H 1.7550641677 9.8178358845 5.5212255966
H 3.1112981302 9.0969170746 5.5956143531
H 0.5663993495 2.9792400173 8.0854791515
H 1.7745194198 2.9517247311 7.1939396477
6
i = 2, time = 1.000, E = -34.3287906528
O 2.2810938851 9.1465143736 5.0880057320
O 1.2481430886 2.4083371258 7.7685912598
H 1.7468317341 9.8169710643 5.5154127828
H 3.1265398790 9.0869161313 5.6032028662
H 0.5758344344 2.9781042647 8.0902773264
H 1.7797622574 2.9504835298 7.2036786282
6
i = 3, time = 1.500, E = -34.3279989781
O 2.2816569948 9.1463220223 5.0875919643
O 1.2464808250 2.4089259514 7.7679581102
H 1.7376017910 9.8176768475 5.5110703534
H 3.1398366791 9.0773366634 5.6100676793
H 0.5816795339 2.9798971014 8.0968435085
H 1.7872918494 2.9513202206 7.2111353246
6
i = 4, time = 2.000, E = -34.3277542904
O 2.2824536844 9.1460139717 5.0872014341
O 1.2449189507 2.4091830380 7.7673245034
H 1.7278297775 9.8195589149 5.5080907122
H 3.1497224743 9.0684159063 5.6155281103
H 0.5837476503 2.9848496112 8.1053394370
H 1.7970573968 2.9542015292 7.2164224211
6
i = 5, time = 2.500, E = -34.3279978897
O 2.2835075421 9.1456102023 5.0868767781
O 1.2434524580 2.4091462088 7.7666758161
H 1.7181028654 9.8220570351 5.5062468114
H 3.1552105753 9.0603654046 5.6191356782
H 0.5824842170 2.9926888277 8.1156135109
H 1.8086404408 2.9588109314 7.2199843450
6
i = 6, time = 3.000, E = -34.3284123938
O 2.2848116168 9.1451387997 5.0866494510
O 1.2420611951 2.4088940254 7.7660011551
H 1.7090732160 9.8245375564 5.5052476019
H 3.1557721856 9.0533599447 5.6206772705
H 0.5788535575 3.0026992793 8.1272265032
H 1.8213326965 2.9646247282 7.2224917951
6
i = 7, time = 3.500, E = -34.3287040522
O 2.2863340532 9.1446310518 5.0865370925
O 1.2407164792 2.4085282817 7.7652951031
H 1.7013784598 9.8263832260 5.5047906840
H 3.1513029381 9.0475240318 5.6201716574
H 0.5741065883 3.0138823014 8.1395347678
H 1.8342810097 2.9710164962 7.2247109095
6
i = 8, time = 4.000, E = -34.3287574070
O 2.2880225370 9.1441174852 5.0865411149
O 1.2393883154 2.4081553744 7.7645574288
H 1.6955650581 9.8270646411 5.5046034983
H 3.1421140712 9.0429166182 5.6178695663
H 0.5695320041 3.0251531775 8.1517995491
H 1.8466448643 2.9773546982 7.2273850117
6
i = 9, time = 4.500, E = -34.3285982555
O 2.2898069785 9.1436252146 5.0866444773
O 1.2380505706 2.4078718032 7.7637918013
H 1.6920290647 9.8261894866 5.5044715741
H 3.1289538455 9.0395163855 5.6142598682
H 0.5662695747 3.0355160242 8.1632992842
H 1.8577079508 2.9830741256 7.2311516146
6
i = 10, time = 5.000, E = -34.3282870379
O 2.2916014875 9.1431763260 5.0868100688
O 1.2366834078 2.4077552776 7.7630044423
H 1.6909790671 9.8235337924 5.5042564094
H 3.1130341664 9.0372111810 5.6100739746
H 0.5652070478 3.0441761067 8.1734257299
H 1.8669280879 2.9877213524 7.2364955946
test/examples/md/H2O-32.inp 0 → 100644
View file @ bf92ab97
&FORCE_EVAL
METHOD QS
&DFT
BASIS_SET_FILE_NAME ../../BASIS_SET
POTENTIAL_FILE_NAME ../../GTH_POTENTIALS
&MGRID
CUTOFF 200
REL_CUTOFF 30
&END MGRID
&QS
EPS_DEFAULT 1.0E-12
WF_INTERPOLATION PS
EXTRAPOLATION_ORDER 3
&END QS
&SCF
SCF_GUESS ATOMIC
&PRINT
&RESTART OFF
&END
&END
&END SCF
&XC
&XC_FUNCTIONAL Pade
&END XC_FUNCTIONAL
&END XC
&END DFT
&SUBSYS
&CELL
ABC 9.8528 9.8528 9.8528
&END CELL
&COORD
O 2.280398 9.146539 5.088696
O 1.251703 2.406261 7.769908
H 1.762019 9.820429 5.528454
H 3.095987 9.107088 5.588186
H 0.554129 2.982634 8.082024
H 1.771257 2.954779 7.182181
&END COORD
&KIND H
BASIS_SET DZVP-GTH-PADE
POTENTIAL GTH-PADE-q1
&END KIND
&KIND O
BASIS_SET DZVP-GTH-PADE
POTENTIAL GTH-PADE-q6
&END KIND
&END SUBSYS
&END FORCE_EVAL
&GLOBAL
PROJECT H2O-32
RUN_TYPE MD
PRINT_LEVEL MEDIUM
&END GLOBAL
&MOTION
&MD
ENSEMBLE NVE
STEPS 10
TIMESTEP 0.5
TEMPERATURE 300.0
&END MD
&END MOTION
test/examples/md/H2O-32.out 0 → 100644
View file @ bf92ab97
This diff is collapsed.
test/unittests/cp2k_2.6.2/run_tests.py
View file @ bf92ab97
......@@ -687,12 +687,79 @@ class TestMD(unittest.TestCase):
cls.results = get_results("md/nve", "section_run")
def test_ensemble_type(self):
result = self.results["x_cp2k_md_ensemble_type"]
result = self.results["ensemble_type"]
self.assertEqual(result, "NVE")
# md = self.results["x_cp2k_section_md"][0]
# for key, value in md.simpleValues.iteritems():
# print "{}: {}".format(key, value)
def test_sampling_method(self):
result = self.results["sampling_method"]
self.assertEqual(result, "molecular_dynamics")
def test_atom_positions(self):
result = self.results["atom_positions"]
expected_start = convert_unit(
np.array([
[2.2803980000, 9.1465390000, 5.0886960000],
[1.2517030000, 2.4062610000, 7.7699080000],
[1.7620190000, 9.8204290000, 5.5284540000],
[3.0959870000, 9.1070880000, 5.5881860000],
[0.5541290000, 2.9826340000, 8.0820240000],
[1.7712570000, 2.9547790000, 7.1821810000],
]),
"angstrom"
)
expected_end = convert_unit(
np.array([
[2.2916014875, 9.1431763260, 5.0868100688],
[1.2366834078, 2.4077552776, 7.7630044423],
[1.6909790671, 9.8235337924, 5.5042564094],
[3.1130341664, 9.0372111810, 5.6100739746],
[0.5652070478, 3.0441761067, 8.1734257299],
[1.8669280879, 2.9877213524, 7.2364955946],
]),
"angstrom"
)
self.assertTrue(np.array_equal(result[0,:], expected_start))
self.assertTrue(np.array_equal(result[-1,:], expected_end))
def test_frame_sequence_potential_energy(self):
result = self.results["frame_sequence_potential_energy"]
expected_result = convert_unit(
np.array([
-34.330396471,
-34.329778993,
-34.328790653,
-34.327998978,
-34.327754290,
-34.327997890,
-34.328412394,
-34.328704052,
-34.328757407,
-34.328598255,
-34.328287038,
]),
"hartree"
)
self.assertTrue(np.array_equal(result, expected_result))
def test_frame_sequence_kinetic_energy(self):
result = self.results["frame_sequence_kinetic_energy"]
expected_result = convert_unit(
np.array([
0.007125335,
0.006533348,
0.005583688,
0.004815598,
0.004566544,
0.004788928,
0.005184860,
0.005470470,
0.005526692,
0.005371243,
0.005062914,
]),
"hartree"
)
self.assertTrue(np.array_equal(result, expected_result))
#===============================================================================
......@@ -701,19 +768,19 @@ if __name__ == '__main__':
logger.setLevel(logging.ERROR)
suites = []
# suites.append(unittest.TestLoader().loadTestsFromTestCase(TestErrors))
# suites.append(unittest.TestLoader().loadTestsFromTestCase(TestXCFunctional))
# suites.append(unittest.TestLoader().loadTestsFromTestCase(TestEnergyForce))
# suites.append(unittest.TestLoader().loadTestsFromTestCase(TestStressTensorMethods))
# suites.append(unittest.TestLoader().loadTestsFromTestCase(TestSelfInteractionCorrectionMethod))
# suites.append(unittest.TestLoader().loadTestsFromTestCase(TestConfigurationPeriodicDimensions))
# suites.append(unittest.TestLoader().loadTestsFromTestCase(TestSCFConvergence))
# suites.append(unittest.TestLoader().loadTestsFromTestCase(TestForceFiles))
# suites.append(unittest.TestLoader().loadTestsFromTestCase(TestPreprocessor))
# suites.append(unittest.TestLoader().loadTestsFromTestCase(TestGeoOpt))
# suites.append(unittest.TestLoader().loadTestsFromTestCase(TestGeoOptTrajFormats))
# suites.append(unittest.TestLoader().loadTestsFromTestCase(TestGeoOptOptimizers))
# suites.append(unittest.TestLoader().loadTestsFromTestCase(TestGeoOptTrajectory))
suites.append(unittest.TestLoader().loadTestsFromTestCase(TestErrors))
suites.append(unittest.TestLoader().loadTestsFromTestCase(TestXCFunctional))
suites.append(unittest.TestLoader().loadTestsFromTestCase(TestEnergyForce))
suites.append(unittest.TestLoader().loadTestsFromTestCase(TestStressTensorMethods))
suites.append(unittest.TestLoader().loadTestsFromTestCase(TestSelfInteractionCorrectionMethod))
suites.append(unittest.TestLoader().loadTestsFromTestCase(TestConfigurationPeriodicDimensions))
suites.append(unittest.TestLoader().loadTestsFromTestCase(TestSCFConvergence))
suites.append(unittest.TestLoader().loadTestsFromTestCase(TestForceFiles))
suites.append(unittest.TestLoader().loadTestsFromTestCase(TestPreprocessor))
suites.append(unittest.TestLoader().loadTestsFromTestCase(TestGeoOpt))
suites.append(unittest.TestLoader().loadTestsFromTestCase(TestGeoOptTrajFormats))
suites.append(unittest.TestLoader().loadTestsFromTestCase(TestGeoOptOptimizers))
suites.append(unittest.TestLoader().loadTestsFromTestCase(TestGeoOptTrajectory))
suites.append(unittest.TestLoader().loadTestsFromTestCase(TestMD))
alltests = unittest.TestSuite(suites)
unittest.TextTestRunner(verbosity=0).run(alltests)
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment