From 43954fc74e47f0a891d729e6e2fedcb2448183a0 Mon Sep 17 00:00:00 2001
From: Lauri Himanen <lauri.himanen@aalto.fi>
Date: Wed, 20 Jul 2016 19:35:19 +0300
Subject: [PATCH] Fixed issue that created only one section_system in geo_opt.
---
.../cpmdparser/versions/cpmd41/commonparser.py | 12 +++++++-----
.../cpmdparser/versions/cpmd41/geooptparser.py | 9 +++++++--
.../cpmdparser/versions/cpmd41/singlepointparser.py | 3 +++
test/unittests/cpmd_4.1/run_tests.py | 2 +-
4 files changed, 18 insertions(+), 8 deletions(-)
diff --git a/parser/parser-cpmd/cpmdparser/versions/cpmd41/commonparser.py b/parser/parser-cpmd/cpmdparser/versions/cpmd41/commonparser.py
index 46a9221..154ecf8 100644
--- a/parser/parser-cpmd/cpmdparser/versions/cpmd41/commonparser.py
+++ b/parser/parser-cpmd/cpmdparser/versions/cpmd41/commonparser.py
@@ -21,7 +21,10 @@ class CPMDCommonParser(CommonParser):
#=======================================================================
# Globally cached values
- self.cache_service.add("initial_positions")
+ self.cache_service.add("initial_positions", single=False, update=False)
+ self.cache_service.add("atom_labels", single=False, update=False)
+ self.cache_service.add("number_of_atoms", single=False, update=False)
+ self.cache_service.add("simulation_cell", single=False, update=False)
#===========================================================================
# Common SimpleMatchers
@@ -235,7 +238,7 @@ class CPMDCommonParser(CommonParser):
A2_array = self.vector_from_string(A2)
A3_array = self.vector_from_string(A3)
cell = np.vstack((A1_array, A2_array, A3_array))
- backend.addArrayValues("simulation_cell", cell, unit="bohr")
+ self.cache_service["simulation_cell"] = cell
# Plane wave basis
cutoff = section.get_latest_value("x_cpmd_wave_function_cutoff")
@@ -291,9 +294,8 @@ class CPMDCommonParser(CommonParser):
# If anything found, push the results to the correct section
if len(coordinates) != 0:
self.cache_service["initial_positions"] = coordinates
- # parser.backend.addArrayValues("atom_positions", coordinates, unit="bohr")
- parser.backend.addArrayValues("atom_labels", labels)
- parser.backend.addValue("number_of_atoms", coordinates.shape[0])
+ self.cache_service["atom_labels"] = labels
+ self.cache_service["number_of_atoms"] = coordinates.shape[0]
return wrapper
diff --git a/parser/parser-cpmd/cpmdparser/versions/cpmd41/geooptparser.py b/parser/parser-cpmd/cpmdparser/versions/cpmd41/geooptparser.py
index 75b7d0f..546e4fa 100644
--- a/parser/parser-cpmd/cpmdparser/versions/cpmd41/geooptparser.py
+++ b/parser/parser-cpmd/cpmdparser/versions/cpmd41/geooptparser.py
@@ -35,7 +35,7 @@ class CPMDGeoOptParser(MainHierarchicalParser):
# Main structure
self.root_matcher = SM("",
forwardMatch=True,
- sections=['section_run', "section_frame_sequence", "section_sampling_method", "section_system", "section_method"],
+ sections=['section_run', "section_frame_sequence", "section_sampling_method", "section_method"],
subMatchers=[
self.cm.header(),
self.cm.method(),
@@ -65,7 +65,7 @@ class CPMDGeoOptParser(MainHierarchicalParser):
forwardMatch=True,
endReStr=re.escape(" *** CNSTR="),
repeats=True,
- sections=["section_single_configuration_calculation", "x_cpmd_section_geo_opt_step"],
+ sections=["section_single_configuration_calculation", "section_system", "x_cpmd_section_geo_opt_step"],
subMatchers=[
SM( "\s+(?P<x_cpmd_geo_opt_scf_nfi>{0})\s+(?P<x_cpmd_geo_opt_scf_gemax>{1})\s+(?P<x_cpmd_geo_opt_scf_cnorm>{1})\s+(?P<x_cpmd_geo_opt_scf_etot__hartree>{1})\s+(?P<x_cpmd_geo_opt_scf_detot__hartree>{1})\s+(?P<x_cpmd_geo_opt_scf_tcpu__s>{1})".format(self.regexs.int, self.regexs.float),
sections=["x_cpmd_section_geo_opt_scf_iteration"],
@@ -129,5 +129,10 @@ class CPMDGeoOptParser(MainHierarchicalParser):
self.sampling_method_gid = gIndex
backend.addValue("sampling_method", "geometry_optimization")
+ def onClose_section_system(self, backend, gIndex, section):
+ self.cache_service.addArrayValues("atom_labels")
+ self.cache_service.addArrayValues("simulation_cell", unit="bohr")
+ self.cache_service.addValue("number_of_atoms")
+
#=======================================================================
# adHoc
diff --git a/parser/parser-cpmd/cpmdparser/versions/cpmd41/singlepointparser.py b/parser/parser-cpmd/cpmdparser/versions/cpmd41/singlepointparser.py
index 829f6f3..f8b007d 100644
--- a/parser/parser-cpmd/cpmdparser/versions/cpmd41/singlepointparser.py
+++ b/parser/parser-cpmd/cpmdparser/versions/cpmd41/singlepointparser.py
@@ -84,6 +84,9 @@ class CPMDSinglePointParser(MainHierarchicalParser):
def onClose_section_system(self, backend, gIndex, section):
self.cache_service.addArrayValues("atom_positions", "initial_positions", unit="bohr")
+ self.cache_service.addArrayValues("atom_labels")
+ self.cache_service.addArrayValues("simulation_cell", unit="bohr")
+ self.cache_service.addValue("number_of_atoms")
#=======================================================================
# adHoc
diff --git a/test/unittests/cpmd_4.1/run_tests.py b/test/unittests/cpmd_4.1/run_tests.py
index 0c1d1fe..da888cf 100644
--- a/test/unittests/cpmd_4.1/run_tests.py
+++ b/test/unittests/cpmd_4.1/run_tests.py
@@ -73,7 +73,7 @@ class TestInputParser(unittest.TestCase):
self.assertEqual(result, "*H_MT_LDA.psp\nLMAX=S\n2\n4.371 4.000 4.000\n3.629 4.000 4.000")
def test_x_cpmd_input_optimize_wavefunction(self):
- result = self.results["x_cpmd_section_input_CPMD.OPTIMIZE_WAVEFUNCTION"]
+ self.results["x_cpmd_section_input_CPMD.OPTIMIZE_WAVEFUNCTION"]
#===============================================================================
--
GitLab