diff --git a/Framework/PythonInterface/plugins/algorithms/Abins.py b/Framework/PythonInterface/plugins/algorithms/Abins.py
index ce744ec8e744ec858f0d3ff95ae285b66ba2b7c7..39a7ea5570040eb9233f2e06c49eb981a8d44df8 100644
--- a/Framework/PythonInterface/plugins/algorithms/Abins.py
+++ b/Framework/PythonInterface/plugins/algorithms/Abins.py
@@ -14,7 +14,7 @@ from mantid.api import WorkspaceFactory, AnalysisDataService
# noinspection PyProtectedMember
from mantid.api._api import WorkspaceGroup
-from mantid.simpleapi import CloneWorkspace, GroupWorkspaces, SaveAscii, Load
+from mantid.simpleapi import CloneWorkspace, GroupWorkspaces, SaveAscii, Load, Scale
from mantid.kernel import logger, StringListValidator, Direction, StringArrayProperty, Atom
import AbinsModules
@@ -26,6 +26,7 @@ class Abins(PythonAlgorithm):
_phonon_file = None
_experimental_file = None
_temperature = None
+ _bin_width = None
_scale = None
_sample_form = None
_instrument_name = None
@@ -67,11 +68,13 @@ class Abins(PythonAlgorithm):
extensions=["raw", "dat"]),
doc="File with the experimental inelastic spectrum to compare.")
- self.declareProperty(name="Temperature",
+ self.declareProperty(name="TemperatureInKelvin",
direction=Direction.Input,
defaultValue=10.0,
doc="Temperature in K for which dynamical structure factor S should be calculated.")
+ self.declareProperty(name="BinWidthInWavenumber", defaultValue=1.0, doc="Width of bins used during rebining.")
+
self.declareProperty(name="Scale", defaultValue=1.0,
doc='Scale the intensity by the given factor. Default is no scaling.')
@@ -122,14 +125,18 @@ class Abins(PythonAlgorithm):
issues = dict()
- temperature = self.getProperty("Temperature").value
+ temperature = self.getProperty("TemperatureInKelvin").value
if temperature < 0:
- issues["Temperature"] = "Temperature must be positive."
+ issues["TemperatureInKelvin"] = "Temperature must be positive."
scale = self.getProperty("Scale").value
if scale < 0:
issues["Scale"] = "Scale must be positive."
+ bin_width = self.getProperty("BinWidthInWavenumber").value
+ if not (isinstance(bin_width, float) and 1.0 <= bin_width <= 10.0):
+ issues["BinWidthInWavenumber"] = ["Invalid bin width. Valid range is [1.0, 10.0] cm^-1"]
+
dft_program = self.getProperty("DFTprogram").value
phonon_filename = self.getProperty("PhononFile").value
output = input_file_validators[dft_program](filename_full_path=phonon_filename)
@@ -177,7 +184,8 @@ class Abins(PythonAlgorithm):
s_calculator = AbinsModules.CalculateS.init(filename=self._phonon_file, temperature=self._temperature,
sample_form=self._sample_form, abins_data=dft_data,
instrument=self._instrument,
- quantum_order_num=self._num_quantum_order_events)
+ quantum_order_num=self._num_quantum_order_events,
+ bin_width=self._bin_width)
s_data = s_calculator.get_formatted_data()
prog_reporter.report("Dynamical structure factors have been determined.")
@@ -227,7 +235,8 @@ class Abins(PythonAlgorithm):
num_workspaces = mtd[self._out_ws_name].getNumberOfEntries()
for wrk_num in range(num_workspaces):
wrk = mtd[self._out_ws_name].getItem(wrk_num)
- SaveAscii(InputWorkspace=wrk, Filename=wrk.name() + ".dat", Separator="Space", WriteSpectrumID=False)
+ SaveAscii(InputWorkspace=Scale(wrk, 1.0/self._bin_width, "Multiply"),
+ Filename=wrk.name() + ".dat", Separator="Space", WriteSpectrumID=False)
prog_reporter.report("All workspaces have been saved to ASCII files.")
# 9) set OutputWorkspace
@@ -544,11 +553,6 @@ class Abins(PythonAlgorithm):
if not (isinstance(pkt_per_peak, six.integer_types) and 1 <= pkt_per_peak <= 1000):
raise RuntimeError("Invalid value of pkt_per_peak" + message_end)
- # bin width is expressed in cm^-1
- bin_width = AbinsModules.AbinsParameters.bin_width
- if not (isinstance(bin_width, float) and 1.0 <= bin_width <= 10.0):
- raise RuntimeError("Invalid value of bin_width" + message_end)
-
min_wavenumber = AbinsModules.AbinsParameters.min_wavenumber
if not (isinstance(min_wavenumber, float) and min_wavenumber >= 0.0):
raise RuntimeError("Invalid value of min_wavenumber" + message_end)
@@ -723,7 +727,8 @@ class Abins(PythonAlgorithm):
self._dft_program = self.getProperty("DFTprogram").value
self._phonon_file = self.getProperty("PhononFile").value
self._experimental_file = self.getProperty("ExperimentalFile").value
- self._temperature = self.getProperty("Temperature").value
+ self._temperature = self.getProperty("TemperatureInKelvin").value
+ self._bin_width = self.getProperty("BinWidthInWavenumber").value
self._scale = self.getProperty("Scale").value
self._sample_form = self.getProperty("SampleForm").value
@@ -749,7 +754,7 @@ class Abins(PythonAlgorithm):
# AbinsModules.AbinsParameters.min_wavenumber
# AbinsModules.AbinsParameters.max_wavenumber
# with bin width AbinsModules.AbinsParameters.bin_width
- step = AbinsModules.AbinsParameters.bin_width
+ step = self._bin_width
start = AbinsModules.AbinsParameters.min_wavenumber + step / 2.0
stop = AbinsModules.AbinsParameters.max_wavenumber + step / 2.0
self._bins = np.arange(start=start, stop=stop, step=step, dtype=AbinsModules.AbinsConstants.FLOAT_TYPE)
diff --git a/Framework/PythonInterface/test/python/plugins/algorithms/AbinsAdvancedParametersTest.py b/Framework/PythonInterface/test/python/plugins/algorithms/AbinsAdvancedParametersTest.py
index 34f994fa9a98b60d65ca4ea190379fd80f7123ab..eb2bb4ede7c3ff1a19a0252bf566fe572e47b8b5 100644
--- a/Framework/PythonInterface/test/python/plugins/algorithms/AbinsAdvancedParametersTest.py
+++ b/Framework/PythonInterface/test/python/plugins/algorithms/AbinsAdvancedParametersTest.py
@@ -159,25 +159,6 @@ class AbinsAdvancedParametersTest(unittest.TestCase):
AbinsParameters.powder_data_group = "NiceName"
self.assertRaises(RuntimeError, Abins, PhononFile=self._Si2 + ".phonon", OutputWorkspace=self._wrk_name)
- # Test for rebinning parameters
- def test_wrong_bin_width(self):
-
- # width cannot be 0
- AbinsParameters.bin_width = 0.0
- self.assertRaises(RuntimeError, Abins, PhononFile=self._Si2 + ".phonon", OutputWorkspace=self._wrk_name)
-
- # width must be float
- AbinsParameters.bin_width = 5
- self.assertRaises(RuntimeError, Abins, PhononFile=self._Si2 + ".phonon", OutputWorkspace=self._wrk_name)
-
- # width must be positive
- AbinsParameters.bin_width = -1.0
- self.assertRaises(RuntimeError, Abins, PhononFile=self._Si2 + ".phonon", OutputWorkspace=self._wrk_name)
-
- # width should be smaller than 10 cm^-1
- AbinsParameters.bin_width = 20.0
- self.assertRaises(RuntimeError, Abins, PhononFile=self._Si2 + ".phonon", OutputWorkspace=self._wrk_name)
-
def test_wrong_min_wavenumber(self):
# minimum wavenumber cannot be negative
diff --git a/Framework/PythonInterface/test/python/plugins/algorithms/AbinsBasicTest.py b/Framework/PythonInterface/test/python/plugins/algorithms/AbinsBasicTest.py
index 76263f6c84848fdf97272df54f924251f32d783b..b0ca8bb78c4ce7279d6a30d7a5ec9eb5a365d849 100644
--- a/Framework/PythonInterface/test/python/plugins/algorithms/AbinsBasicTest.py
+++ b/Framework/PythonInterface/test/python/plugins/algorithms/AbinsBasicTest.py
@@ -49,14 +49,14 @@ class AbinsBasicTest(unittest.TestCase):
AllKpointsGiven=False, OutputWorkspace=self._workspace_name)
# no name for workspace
- self.assertRaises(RuntimeError, Abins, PhononFile=self._si2 + ".phonon", Temperature=self._temperature)
+ self.assertRaises(RuntimeError, Abins, PhononFile=self._si2 + ".phonon", TemperatureInKelvin=self._temperature)
# keyword total in the name of the workspace
- self.assertRaises(RuntimeError, Abins, PhononFile=self._si2 + ".phonon", Temperature=self._temperature,
+ self.assertRaises(RuntimeError, Abins, PhononFile=self._si2 + ".phonon", TemperatureInKelvin=self._temperature,
OutputWorkspace=self._workspace_name + "total")
# negative temperature in K
- self.assertRaises(RuntimeError, Abins, PhononFile=self._si2 + ".phonon", Temperature=-1.0,
+ self.assertRaises(RuntimeError, Abins, PhononFile=self._si2 + ".phonon", TemperatureInKelvin=-1.0,
OutputWorkspace=self._workspace_name)
# negative scale
@@ -86,7 +86,7 @@ class AbinsBasicTest(unittest.TestCase):
"""
wrk_ref = Abins(DFTprogram=self._dft_program,
PhononFile=self._squaricn + ".phonon",
- Temperature=self._temperature,
+ TemperatureInKelvin=self._temperature,
SampleForm=self._sample_form,
Instrument=self._instrument_name,
Atoms=self._atoms,
@@ -98,7 +98,7 @@ class AbinsBasicTest(unittest.TestCase):
wrk = Abins(DFTprogram=self._dft_program,
PhononFile=self._squaricn + ".phonon",
- Temperature=self._temperature,
+ TemperatureInKelvin=self._temperature,
SampleForm=self._sample_form,
Instrument=self._instrument_name,
Atoms=self._atoms,
@@ -121,7 +121,7 @@ class AbinsBasicTest(unittest.TestCase):
Abins(DFTprogram=self._dft_program,
PhononFile="benzene_Abins.phonon",
ExperimentalFile="benzene_Abins.dat",
- Temperature=self._temperature,
+ TemperatureInKelvin=self._temperature,
SampleForm=self._sample_form,
Instrument=self._instrument_name,
Atoms=self._atoms,
@@ -148,7 +148,7 @@ class AbinsBasicTest(unittest.TestCase):
wrk_ref = Abins(DFTprogram=self._dft_program,
PhononFile=self._squaricn + ".phonon",
ExperimentalFile=experimental_file,
- Temperature=self._temperature,
+ TemperatureInKelvin=self._temperature,
SampleForm=self._sample_form,
Instrument=self._instrument_name,
Atoms=self._atoms,
diff --git a/Testing/Data/SystemTest/BenzeneBinWidthCASTEP.nxs.md5 b/Testing/Data/SystemTest/BenzeneBinWidthCASTEP.nxs.md5
new file mode 100644
index 0000000000000000000000000000000000000000..949f9d5f2af3e83b1e89d822ef2eb3a0df69e725
--- /dev/null
+++ b/Testing/Data/SystemTest/BenzeneBinWidthCASTEP.nxs.md5
@@ -0,0 +1 @@
+9f52c317a2ed01f26514b539139df5e6
diff --git a/Testing/Data/SystemTest/BenzeneBinWidthCASTEP.phonon.md5 b/Testing/Data/SystemTest/BenzeneBinWidthCASTEP.phonon.md5
new file mode 100644
index 0000000000000000000000000000000000000000..39fee330d857b5fae54c6c887f8608bf181f3546
--- /dev/null
+++ b/Testing/Data/SystemTest/BenzeneBinWidthCASTEP.phonon.md5
@@ -0,0 +1 @@
+ec53aa8ff74b7cd257d7a82c3d6547fd
diff --git a/Testing/Data/UnitTest/BENZENE4_g03_win_LoadGAUSSIAN_data.txt.md5 b/Testing/Data/UnitTest/BENZENE4_g03_win_LoadGAUSSIAN_data.txt.md5
index e3eeb3cd4596e1fd2fa72bdf04feb117f15c34cc..7b52d96e871aaa6383c00f35ea3877048da88efa 100644
--- a/Testing/Data/UnitTest/BENZENE4_g03_win_LoadGAUSSIAN_data.txt.md5
+++ b/Testing/Data/UnitTest/BENZENE4_g03_win_LoadGAUSSIAN_data.txt.md5
@@ -1 +1 @@
-2032778ae20e60af1de825be6248aff3
+6b5197fbef6bee2cf77af67b69a2b7c7
diff --git a/Testing/Data/UnitTest/BENZENE4_g09_win_LoadGAUSSIAN_data.txt.md5 b/Testing/Data/UnitTest/BENZENE4_g09_win_LoadGAUSSIAN_data.txt.md5
index 3431a1585dad567535f79707561b88c73e622d7d..2bff40fa76f5352e176ac45c8c028f5fdbe0f348 100644
--- a/Testing/Data/UnitTest/BENZENE4_g09_win_LoadGAUSSIAN_data.txt.md5
+++ b/Testing/Data/UnitTest/BENZENE4_g09_win_LoadGAUSSIAN_data.txt.md5
@@ -1 +1 @@
-ee3349c525b6601afc84643acc49fdc8
+cf3e550f13a672eb6a96cf01c94a5bb7
diff --git a/Testing/Data/UnitTest/C6H5Cl_LoadGAUSSIAN_data.txt.md5 b/Testing/Data/UnitTest/C6H5Cl_LoadGAUSSIAN_data.txt.md5
index a2625c0bac4525f992391369ed53f36958744a75..842e130c16ae2086b418006808b1087a96091e6b 100644
--- a/Testing/Data/UnitTest/C6H5Cl_LoadGAUSSIAN_data.txt.md5
+++ b/Testing/Data/UnitTest/C6H5Cl_LoadGAUSSIAN_data.txt.md5
@@ -1 +1 @@
-26850832776754a46affe765b25ca483
+dff2c2d024be9dd9eca8c13f05bfc53f
diff --git a/Testing/Data/UnitTest/LTA_40_O2_LoadDMOL3_data.txt.md5 b/Testing/Data/UnitTest/LTA_40_O2_LoadDMOL3_data.txt.md5
index 6485be690a605f2f07445a2ca93c3450708ba668..b62f96a44867eca8b10e70df82d8206223943bdb 100644
--- a/Testing/Data/UnitTest/LTA_40_O2_LoadDMOL3_data.txt.md5
+++ b/Testing/Data/UnitTest/LTA_40_O2_LoadDMOL3_data.txt.md5
@@ -1 +1 @@
-d49a0a0f8dc9181978afe3405e0eea87
+c520c602a74b93695bbe1a89691678d3
diff --git a/Testing/Data/UnitTest/MgO-222-DISP_LoadCRYSTAL_data.txt.md5 b/Testing/Data/UnitTest/MgO-222-DISP_LoadCRYSTAL_data.txt.md5
index 1bee96dafaa649c6111045b90c5da0cbb1a036b9..c963b21e0444242d97d6d86de51810c0f8483761 100644
--- a/Testing/Data/UnitTest/MgO-222-DISP_LoadCRYSTAL_data.txt.md5
+++ b/Testing/Data/UnitTest/MgO-222-DISP_LoadCRYSTAL_data.txt.md5
@@ -1 +1 @@
-e3da9633a53d6b455c1ee0ad29165fa6
+577a6eec372861923277b3b1c3faaafb
diff --git a/Testing/Data/UnitTest/Na2SiF6_LoadDMOL3_data.txt.md5 b/Testing/Data/UnitTest/Na2SiF6_LoadDMOL3_data.txt.md5
index 815fca680ac2de053e1056d05b93d3033ead8ee8..e5cec5364fcf673405749b5e88e2afa06c8de671 100644
--- a/Testing/Data/UnitTest/Na2SiF6_LoadDMOL3_data.txt.md5
+++ b/Testing/Data/UnitTest/Na2SiF6_LoadDMOL3_data.txt.md5
@@ -1 +1 @@
-90c877eb6b8135167b9b3a20b30983d6
+65f9da379be14b6ca29dbf0bf13cbba3
diff --git a/Testing/Data/UnitTest/Si2-phonon_LoadCASTEP_data.txt.md5 b/Testing/Data/UnitTest/Si2-phonon_LoadCASTEP_data.txt.md5
index 823a708ee7ada2d9f9bb378ed62e30277e3906bb..c234c4a8620c77cf44edfdd1424174eded29a612 100644
--- a/Testing/Data/UnitTest/Si2-phonon_LoadCASTEP_data.txt.md5
+++ b/Testing/Data/UnitTest/Si2-phonon_LoadCASTEP_data.txt.md5
@@ -1 +1 @@
-123cb44bf4f85a910c76f09707a7269a
+80e89da494a27217a5f7bb6076dd3acc
diff --git a/Testing/Data/UnitTest/Si2-sc_LoadCASTEP_data.txt.md5 b/Testing/Data/UnitTest/Si2-sc_LoadCASTEP_data.txt.md5
index d991e12a019dbe23957a2de75d74f08a688440e9..a1005479e0bda7dd781ce4a51805aec60b29f7d8 100644
--- a/Testing/Data/UnitTest/Si2-sc_LoadCASTEP_data.txt.md5
+++ b/Testing/Data/UnitTest/Si2-sc_LoadCASTEP_data.txt.md5
@@ -1 +1 @@
-5170df22d172e8c3119822ec737f63ac
+f4ea42523fbc06af7483c3d83fb3b840
diff --git a/Testing/Data/UnitTest/crystalB3LYP_LoadCRYSTAL_data.txt.md5 b/Testing/Data/UnitTest/crystalB3LYP_LoadCRYSTAL_data.txt.md5
index ae6e02b501f01588953727435650a5db71fd83f8..8cd88ad2b04aefd2ff24860bf3781077a7c6cc9b 100644
--- a/Testing/Data/UnitTest/crystalB3LYP_LoadCRYSTAL_data.txt.md5
+++ b/Testing/Data/UnitTest/crystalB3LYP_LoadCRYSTAL_data.txt.md5
@@ -1 +1 @@
-1ac7f6365ed8e892792282e6e90c2105
+b8f79f3908691d510118b488022bb8ac
diff --git a/Testing/Data/UnitTest/crystal_set_key_LoadCRYSTAL_data.txt.md5 b/Testing/Data/UnitTest/crystal_set_key_LoadCRYSTAL_data.txt.md5
index 405e268a1b1254ef600b9951a18285e1b70e6801..3779aea147e516400b2af749977bf610e9bc8b74 100644
--- a/Testing/Data/UnitTest/crystal_set_key_LoadCRYSTAL_data.txt.md5
+++ b/Testing/Data/UnitTest/crystal_set_key_LoadCRYSTAL_data.txt.md5
@@ -1 +1 @@
-9d387ae304bce294e0a519faf78e3eec
+8b770a47fda2ebfef83d629f249afbb7
diff --git a/Testing/Data/UnitTest/mgo-GX_LoadCRYSTAL_data.txt.md5 b/Testing/Data/UnitTest/mgo-GX_LoadCRYSTAL_data.txt.md5
index efd214fe9f325f56d9afd99a2585b210f494c537..5654e4c8cd98709e45f68d76067e021d524c6c76 100644
--- a/Testing/Data/UnitTest/mgo-GX_LoadCRYSTAL_data.txt.md5
+++ b/Testing/Data/UnitTest/mgo-GX_LoadCRYSTAL_data.txt.md5
@@ -1 +1 @@
-3506d19561fc285fac73b60fa3035f8a
+2692a6473cb7a15fc08374edefbea78d
diff --git a/Testing/Data/UnitTest/squaricn_no_sum_LoadCASTEP_data.txt.md5 b/Testing/Data/UnitTest/squaricn_no_sum_LoadCASTEP_data.txt.md5
index 6129cb61d1c2f36d8a9feebe3a987c9e13c26e26..e662c8c63dca8c899ebe8968f27d95149a52e43d 100644
--- a/Testing/Data/UnitTest/squaricn_no_sum_LoadCASTEP_data.txt.md5
+++ b/Testing/Data/UnitTest/squaricn_no_sum_LoadCASTEP_data.txt.md5
@@ -1 +1 @@
-98c2ca72a9e327319d8ca57cdd97b5d2
+d3e5e26e8ba40e6a56bb8a784c5bd3bd
diff --git a/Testing/Data/UnitTest/squaricn_sum_LoadCASTEP_data.txt.md5 b/Testing/Data/UnitTest/squaricn_sum_LoadCASTEP_data.txt.md5
index fa3dfc0b25fe56822c9c1736e89a1cb0afcddeea..60ae627f2cb3c45ae46b482ed312d0da4196e6a7 100644
--- a/Testing/Data/UnitTest/squaricn_sum_LoadCASTEP_data.txt.md5
+++ b/Testing/Data/UnitTest/squaricn_sum_LoadCASTEP_data.txt.md5
@@ -1 +1 @@
-fd1c5797c11dd7d457f0d6c5bb4adefe
+0e70113b983001d0b3b01e12d5e8fce4
diff --git a/Testing/Data/UnitTest/toluene_molecule_LoadCRYSTAL_data.txt.md5 b/Testing/Data/UnitTest/toluene_molecule_LoadCRYSTAL_data.txt.md5
index 073be69b37b4d53521e4e0e1e8140356347bd9b8..3eddc1fa45e6ebf91b8550a34149d0c94dfd4a62 100644
--- a/Testing/Data/UnitTest/toluene_molecule_LoadCRYSTAL_data.txt.md5
+++ b/Testing/Data/UnitTest/toluene_molecule_LoadCRYSTAL_data.txt.md5
@@ -1 +1 @@
-0841e8243fd2c4d3bdbc5b3e6c791f6c
+987fbda90cd24c1caa6f5b3b1fa099dd
diff --git a/Testing/SystemTests/tests/analysis/AbinsTest.py b/Testing/SystemTests/tests/analysis/AbinsTest.py
index 8c345d86a8ee0b2560b0035608f844e36e21009e..e5d4cb8e1e43354cf2d1d04ca96f188ee8760bf4 100644
--- a/Testing/SystemTests/tests/analysis/AbinsTest.py
+++ b/Testing/SystemTests/tests/analysis/AbinsTest.py
@@ -17,11 +17,17 @@ class HelperTestingClass(object):
self._output_name = "output_workspace"
self._ref = "reference_workspace"
self._scale = 1.0
+ self._bin_width = 1.0
self._dft_program = None
self._quantum_order_event = None
self._system_name = None
+ def set_bin_width(self, width):
+ if not (isinstance(width, float) and 1.0 <= width <= 10.0):
+ raise ValueError("Invalid bin width: {}. ".format(width) + "Valid range is [1.0, 10.0] cm^-1")
+ self._bin_width = width
+
def set_instrument_name(self, instrument_name=None):
if instrument_name in AbinsConstants.ALL_INSTRUMENTS:
@@ -70,7 +76,8 @@ class HelperTestingClass(object):
User performs calculation from scratch (not loaded from hdf file). All data is calculated.
"""
Abins(DFTprogram=self._dft_program, PhononFile=self._system_name + self._extension[self._dft_program],
- Temperature=self._temperature, SampleForm=self._sample_form, Instrument=self._instrument_name,
+ TemperatureInKelvin=self._temperature, SampleForm=self._sample_form, Instrument=self._instrument_name,
+ BinWidthInWavenumber=self._bin_width,
Atoms=self._atoms, SumContributions=self._sum_contributions,
QuantumOrderEventsNumber=str(self._quantum_order_event), Scale=self._scale,
ScaleByCrossSection=self._cross_section_factor, OutputWorkspace=self._output_name)
@@ -88,21 +95,24 @@ class HelperTestingClass(object):
# T = 10 K
Abins(DFTprogram=self._dft_program, PhononFile=self._system_name + self._extension[self._dft_program],
- Temperature=self._temperature, SampleForm=self._sample_form, Instrument=self._instrument_name,
+ TemperatureInKelvin=self._temperature, SampleForm=self._sample_form, Instrument=self._instrument_name,
+ BinWidthInWavenumber=self._bin_width,
Atoms=self._atoms, SumContributions=self._sum_contributions, Scale=self._scale,
QuantumOrderEventsNumber=str(self._quantum_order_event), ScaleByCrossSection=self._cross_section_factor,
OutputWorkspace=wrk_name + "init")
# T = 20 K
Abins(DFTprogram=self._dft_program, PhononFile=self._system_name + self._extension[self._dft_program],
- Temperature=temperature_for_test, SampleForm=self._sample_form, Instrument=self._instrument_name,
+ TemperatureInKelvin=temperature_for_test, SampleForm=self._sample_form, Instrument=self._instrument_name,
+ BinWidthInWavenumber=self._bin_width,
Atoms=self._atoms, SumContributions=self._sum_contributions, Scale=self._scale,
QuantumOrderEventsNumber=str(self._quantum_order_event), ScaleByCrossSection=self._cross_section_factor,
OutputWorkspace=wrk_name + "_mod")
# T = 10 K
Abins(DFTprogram=self._dft_program, PhononFile=self._system_name + self._extension[self._dft_program],
- Temperature=self._temperature, SampleForm=self._sample_form, Instrument=self._instrument_name,
+ TemperatureInKelvin=self._temperature, SampleForm=self._sample_form, Instrument=self._instrument_name,
+ BinWidthInWavenumber=self._bin_width,
Atoms=self._atoms, SumContributions=self._sum_contributions, Scale=self._scale,
QuantumOrderEventsNumber=str(self._quantum_order_event),
ScaleByCrossSection=self._cross_section_factor, OutputWorkspace=self._output_name)
@@ -117,7 +127,8 @@ class HelperTestingClass(object):
self.case_from_scratch()
DeleteWorkspace(self._output_name)
Abins(DFTprogram=self._dft_program, PhononFile=self._system_name + self._extension[self._dft_program],
- Temperature=self._temperature, SampleForm=self._sample_form, Instrument=self._instrument_name,
+ TemperatureInKelvin=self._temperature, SampleForm=self._sample_form, Instrument=self._instrument_name,
+ BinWidthInWavenumber=self._bin_width,
Atoms=self._atoms, SumContributions=self._sum_contributions, Scale=self._scale,
QuantumOrderEventsNumber=str(order), ScaleByCrossSection=self._cross_section_factor,
OutputWorkspace=self._output_name)
@@ -414,3 +425,28 @@ class AbinsGAUSSIANestScratch(stresstesting.MantidStressTest, HelperTestingClass
def validate(self):
self.tolerance = 1e-2
return self._output_name, self.ref_result
+
+
+class AbinsBinWidth(stresstesting.MantidStressTest, HelperTestingClass):
+ """
+ In this benchmark it is tested if calculation with bin width different than the default value is correct.
+ Calculation performed for crystalline benzene for 1st and 2nd quantum event for output from CASTEP and bin width
+ 3 cm^-1. This system test should be fast so no need for excludeInPullRequests flag.
+ """
+ tolerance = None
+ ref_result = None
+
+ def runTest(self):
+ HelperTestingClass.__init__(self)
+ name = "BenzeneBinWidthCASTEP"
+ self.ref_result = name + ".nxs"
+ self.set_dft_program("CASTEP")
+ self.set_name(name)
+ self.set_order(AbinsConstants.QUANTUM_ORDER_TWO)
+ self.set_cross_section(cross_section="Incoherent")
+ self.set_bin_width(width=3.0)
+ self.case_from_scratch()
+
+ def validate(self):
+ self.tolerance = 1e-2
+ return self._output_name, self.ref_result
diff --git a/docs/source/algorithms/Abins-v1.rst b/docs/source/algorithms/Abins-v1.rst
index afdba918ec56bd69ab5d63724c754082a71db4a5..d3fbd678a1adc17d851b7e390b1b7ec83377c031 100644
--- a/docs/source/algorithms/Abins-v1.rst
+++ b/docs/source/algorithms/Abins-v1.rst
@@ -93,8 +93,9 @@ Output:
.. testcode:: AbinsexplicitParameters
wrk_verbose=Abins(DFTprogram="CASTEP", PhononFile="benzene.phonon", ExperimentalFile="benzene_experimental.dat",
- Temperature=10, SampleForm="Powder", Instrument="TOSCA", Atoms="H", SumContributions=True,
- QuantumOrderEventsNumber="1", ScaleByCrossSection="Incoherent")
+ TemperatureInKelvin=10, BinWidthInWavenumber=1.0, SampleForm="Powder", Instrument="TOSCA",
+ Atoms="H", SumContributions=True,
+ QuantumOrderEventsNumber="1", ScaleByCrossSection="Incoherent")
for name in wrk_verbose.getNames():
print(name)
diff --git a/scripts/AbinsModules/AbinsParameters.py b/scripts/AbinsModules/AbinsParameters.py
index 32cd5add0905d7a2e727d4ddea69109f468da6f2..25d596e39aa8d355ebab24a5adce692f957b68e6 100644
--- a/scripts/AbinsModules/AbinsParameters.py
+++ b/scripts/AbinsModules/AbinsParameters.py
@@ -39,7 +39,6 @@ crystal_data_group = "SingleCrystal" # name of the group where SingleCrystalDat
s_data_group = "S" # name of the group where dynamical factor is stored
pkt_per_peak = 50 # number of points for each peak broadened by the experimental resolution
-bin_width = 1.0 # defines width of bins used in rebinning of S
max_wavenumber = 4100.0 # maximum wavenumber in cm^-1 taken into account while creating workspaces (exclusive)
min_wavenumber = 0.0 # minimal wavenumber in cm^-1 taken into account while creating workspaces (exclusive)
acoustic_phonon_threshold = 0.0 # frequencies below this value are treated as acoustic and neglected.
diff --git a/scripts/AbinsModules/CalculateS.py b/scripts/AbinsModules/CalculateS.py
index 4bc0cfaf60cc0e3a5466d5ed27c2b30d1d440cdf..35cb2925cff554074bc4fb7c1c1a4edf63004a51 100644
--- a/scripts/AbinsModules/CalculateS.py
+++ b/scripts/AbinsModules/CalculateS.py
@@ -12,7 +12,7 @@ class CalculateS(object):
@staticmethod
def init(filename=None, temperature=None, sample_form=None, abins_data=None, instrument=None,
- quantum_order_num=None):
+ quantum_order_num=None, bin_width=1.0):
"""
:param filename: name of input DFT file (CASTEP: foo.phonon)
:param temperature: temperature in K for which calculation of S should be done
@@ -20,13 +20,15 @@ class CalculateS(object):
:param abins_data: object of type AbinsData with data from phonon file
:param instrument: object of type Instrument for which simulation should be performed
:param quantum_order_num: number of quantum order events taken into account during the simulation
+ :param bin_width: width of bins in wavenumber
"""
if sample_form in AbinsModules.AbinsConstants.ALL_SAMPLE_FORMS:
if sample_form == "Powder":
return AbinsModules.SPowderSemiEmpiricalCalculator(filename=filename, temperature=temperature,
abins_data=abins_data, instrument=instrument,
- quantum_order_num=quantum_order_num)
+ quantum_order_num=quantum_order_num,
+ bin_width=bin_width)
# TODO: implement numerical powder averaging
# elif sample == "SingleCrystal": #TODO implement single crystal scenario
diff --git a/scripts/AbinsModules/SData.py b/scripts/AbinsModules/SData.py
index 7660cce9635f519aec5f38c14ff5f0aa6fdb81ff..fa02e8f0b02dd34bbfd2cf2672cde1dbd5af4c7d 100644
--- a/scripts/AbinsModules/SData.py
+++ b/scripts/AbinsModules/SData.py
@@ -21,6 +21,10 @@ class SData(AbinsModules.GeneralData):
raise ValueError("Invalid sample form %s" % sample_form)
self._data = None # dictionary which stores dynamical structure factor for all atoms
+ self._bin_width = None
+
+ def set_bin_width(self, width=None):
+ self._bin_width = width
def set(self, items=None):
"""
@@ -44,7 +48,7 @@ class SData(AbinsModules.GeneralData):
elif "frequencies" == item:
- step = AbinsModules.AbinsParameters.bin_width
+ step = self._bin_width
bins = np.arange(start=AbinsModules.AbinsParameters.min_wavenumber,
stop=AbinsModules.AbinsParameters.max_wavenumber + step,
step=step,
diff --git a/scripts/AbinsModules/SPowderSemiEmpiricalCalculator.py b/scripts/AbinsModules/SPowderSemiEmpiricalCalculator.py
index fd58b3bb10405589b8eeae60431d8bbc5a6c66a8..a7f050950de2d0b0eac270b4f2c5fedf95d0cc2f 100644
--- a/scripts/AbinsModules/SPowderSemiEmpiricalCalculator.py
+++ b/scripts/AbinsModules/SPowderSemiEmpiricalCalculator.py
@@ -34,7 +34,8 @@ class SPowderSemiEmpiricalCalculator(object):
Class for calculating S(Q, omega)
"""
- def __init__(self, filename=None, temperature=None, abins_data=None, instrument=None, quantum_order_num=None):
+ def __init__(self, filename=None, temperature=None, abins_data=None, instrument=None, quantum_order_num=None,
+ bin_width=1.0):
"""
:param filename: name of input DFT file (CASTEP: foo.phonon)
:param temperature: temperature in K for which calculation of S should be done
@@ -42,6 +43,7 @@ class SPowderSemiEmpiricalCalculator(object):
:param abins_data: object of type AbinsData with data from phonon file
:param instrument: name of instrument (str)
:param quantum_order_num: number of quantum order events taken into account during the simulation
+ :param bin_width: bin width used in rebining in wavenumber
"""
if not isinstance(temperature, (int, float)):
raise ValueError("Invalid value of the temperature. Number was expected.")
@@ -96,7 +98,8 @@ class SPowderSemiEmpiricalCalculator(object):
AbinsModules.AbinsConstants.QUANTUM_ORDER_THREE: self._calculate_order_three,
AbinsModules.AbinsConstants.QUANTUM_ORDER_FOUR: self._calculate_order_four}
- step = AbinsModules.AbinsParameters.bin_width
+ step = bin_width
+ self._bin_width = bin_width
start = AbinsModules.AbinsParameters.min_wavenumber + step
stop = AbinsModules.AbinsParameters.max_wavenumber + step
self._bins = np.arange(start=start, stop=stop, step=step, dtype=AbinsModules.AbinsConstants.FLOAT_TYPE)
@@ -281,6 +284,7 @@ class SPowderSemiEmpiricalCalculator(object):
# put data to SData object
s_data = AbinsModules.SData(temperature=self._temperature, sample_form=self._sample_form)
+ s_data.set_bin_width(width=self._bin_width)
s_data.set(items=data)
return s_data
@@ -505,7 +509,8 @@ class SPowderSemiEmpiricalCalculator(object):
rebined_broad_spectrum = self._fix_empty_array()
# multiply by k-point weight and scaling constant
- factor = self._weight / AbinsModules.AbinsParameters.bin_width
+ # factor = self._weight / self._bin_width
+ factor = self._weight
rebined_broad_spectrum = rebined_broad_spectrum * factor
return local_freq, local_coeff, rebined_broad_spectrum
@@ -655,9 +660,8 @@ class SPowderSemiEmpiricalCalculator(object):
else:
inds = np.digitize(x=array_x, bins=self._bins) - AbinsModules.AbinsConstants.PYTHON_INDEX_SHIFT
output_array_x = self._frequencies
- output_array_y = np.asarray(
- a=[array_y[inds == i].sum() for i in range(self._freq_size)],
- dtype=AbinsModules.AbinsConstants.FLOAT_TYPE) / AbinsModules.AbinsParameters.bin_width
+ output_array_y = np.asarray(a=[array_y[inds == i].sum() for i in range(self._freq_size)],
+ dtype=AbinsModules.AbinsConstants.FLOAT_TYPE)
return output_array_x, output_array_y
@@ -725,6 +729,7 @@ class SPowderSemiEmpiricalCalculator(object):
data["datasets"]["data"] = temp_data
s_data = AbinsModules.SData(temperature=self._temperature, sample_form=self._sample_form)
+ s_data.set_bin_width(width=self._bin_width)
s_data.set(items=data["datasets"]["data"])
return s_data
diff --git a/scripts/test/AbinsCalculateSPowderTest.py b/scripts/test/AbinsCalculateSPowderTest.py
index 5d8e58a61a52f274ce53b035c02e428d7537387a..730af9dbc9c3ee67dabc49e78f78dd1ae58dd808 100644
--- a/scripts/test/AbinsCalculateSPowderTest.py
+++ b/scripts/test/AbinsCalculateSPowderTest.py
@@ -32,28 +32,24 @@ class AbinsCalculateSPowderTest(unittest.TestCase):
# wrong filename
with self.assertRaises(ValueError):
-
AbinsModules.CalculateS.init(filename=1, temperature=self._temperature, sample_form=self._sample_form,
abins_data=good_data, instrument=self._instrument,
quantum_order_num=self._order_event)
# wrong temperature
with self.assertRaises(ValueError):
-
AbinsModules.CalculateS.init(filename=full_path_filename, temperature=-1, sample_form=self._sample_form,
abins_data=good_data, instrument=self._instrument,
quantum_order_num=self._order_event)
# wrong sample
with self.assertRaises(ValueError):
-
- AbinsModules.CalculateS.init(filename=full_path_filename, temperature=self._temperature, sample_form="SOLID",
- abins_data=good_data, instrument=self._instrument,
+ AbinsModules.CalculateS.init(filename=full_path_filename, temperature=self._temperature,
+ sample_form="SOLID", abins_data=good_data, instrument=self._instrument,
quantum_order_num=self._order_event)
# wrong abins data: content of abins data instead of object abins_data
with self.assertRaises(ValueError):
-
AbinsModules.CalculateS.init(filename=full_path_filename, temperature=self._temperature,
sample_form=self._sample_form, abins_data=good_data.extract(),
instrument=self._instrument, quantum_order_num=self._order_event)
@@ -75,18 +71,18 @@ class AbinsCalculateSPowderTest(unittest.TestCase):
# calculation of powder data
good_data = self._get_good_data(filename=name)
good_tester = AbinsModules.CalculateS.init(
- filename=AbinsModules.AbinsTestHelpers.find_file(filename=name + ".phonon"),
- temperature=self._temperature, sample_form=self._sample_form, abins_data=good_data["DFT"],
- instrument=self._instrument, quantum_order_num=self._order_event)
+ filename=AbinsModules.AbinsTestHelpers.find_file(filename=name + ".phonon"), temperature=self._temperature,
+ sample_form=self._sample_form, abins_data=good_data["DFT"], instrument=self._instrument,
+ quantum_order_num=self._order_event)
calculated_data = good_tester.get_formatted_data()
self._check_data(good_data=good_data["S"], data=calculated_data.extract())
# check if loading powder data is correct
- new_tester = AbinsModules.CalculateS.init(filename=AbinsModules.AbinsTestHelpers.find_file(filename=name + ".phonon"),
- temperature=self._temperature, sample_form=self._sample_form,
- abins_data=good_data["DFT"], instrument=self._instrument,
- quantum_order_num=self._order_event)
+ new_tester = AbinsModules.CalculateS.init(
+ filename=AbinsModules.AbinsTestHelpers.find_file(filename=name + ".phonon"), temperature=self._temperature,
+ sample_form=self._sample_form, abins_data=good_data["DFT"], instrument=self._instrument,
+ quantum_order_num=self._order_event)
loaded_data = new_tester.load_formatted_data()
self._check_data(good_data=good_data["S"], data=loaded_data.extract())