diff --git a/.gitignore b/.gitignore
index 6f8ec4578462901c710bad08f338d6e62ab6187f..89fab064ccd7d05bccee889818d8ef84ffb65fb8 100644
--- a/.gitignore
+++ b/.gitignore
@@ -53,4 +53,5 @@ TAGS
lib/
env/
-# CP2K files
+# CPMD files
+parser/parser-cpmd/cpmdparser.egg-info/
diff --git a/parser/parser-cpmd/cpmdparser/parser.py b/parser/parser-cpmd/cpmdparser/parser.py
index f3f0fae1b4f899b00286abec300e2f7912aa5da1..8f6ecd9ffa1e538d757c33594f526191a701cdc1 100644
--- a/parser/parser-cpmd/cpmdparser/parser.py
+++ b/parser/parser-cpmd/cpmdparser/parser.py
@@ -3,8 +3,8 @@ from builtins import range
import os
import re
import logging
+import importlib
from nomadcore.baseclasses import ParserInterface
-from cpmdparser.versions.versionsetup import get_main_parser
logger = logging.getLogger("nomad")
@@ -27,28 +27,19 @@ class CPMDParser(ParserInterface):
# Search for the CP2K version specification and the RUN_TYPE for the
# calculation. The correct and optimized parser is initialized based on
# this information.
- regex_version = re.compile(r" CP2K\| version string:\s+CP2K version ([\d\.]+)")
- regex_run_type = re.compile(r"\s+GLOBAL\| Run type\s+(.+)")
+ regex_version = re.compile("\s+VERSION ([\d\.]+)")
n_lines = 50
version_id = None
- run_type = None
with open(self.parser_context.main_file, 'r') as outputfile:
for i_line in range(n_lines):
line = next(outputfile)
result_version = regex_version.match(line)
- result_run_type = regex_run_type.match(line)
if result_version:
version_id = result_version.group(1).replace('.', '')
- if result_run_type:
- run_type = result_run_type.group(1)
if version_id is None:
msg = "Could not find a version specification from the given main file."
logger.exception(msg)
raise RuntimeError(msg)
- if run_type is None:
- msg = "Could not find a version specification from the given main file."
- logger.exception(msg)
- raise RuntimeError(msg)
# Setup the root folder to the fileservice that is used to access files
dirpath, filename = os.path.split(self.parser_context.main_file)
@@ -58,10 +49,33 @@ class CPMDParser(ParserInterface):
# Setup the correct main parser based on the version id. If no match
# for the version is found, use the main parser for CP2K 2.6.2
- self.main_parser = get_main_parser(version_id, run_type)(self.parser_context.main_file, self.parser_context)
+ self.setup_main_parser(version_id)
def get_metainfo_filename(self):
return "cpmd.nomadmetainfo.json"
def get_parser_info(self):
return {'name': 'cpmd-parser', 'version': '1.0'}
+
+ def setup_main_parser(self, version_id):
+ # Currently the version id is a pure integer, so it can directly be mapped
+ # into a package name.
+ base = "cpmdparser.versions.cpmd{}.mainparser".format(version_id)
+ parser_module = None
+ parser_class = None
+ try:
+ parser_module = importlib.import_module(base)
+ except ImportError:
+ logger.warning("Could not find a parser for version '{}'. Trying to default to the base implementation for CPMD 4.1".format(version_id))
+ base = "cpmdparser.versions.cp2k41.mainparser"
+ try:
+ parser_module = importlib.import_module(base)
+ except ImportError:
+ logger.exception("Tried to default to the CPMD 4.1 implementation but could not find the correct module.")
+ raise
+ try:
+ parser_class = getattr(parser_module, "CPMDMainParser")
+ except AttributeError:
+ logger.exception("A parser class 'CPMDMainParser' could not be found in the module '[]'.".format(parser_module))
+ raise
+ self.main_parser = parser_class(self.parser_context.main_file, self.parser_context)
diff --git a/parser/parser-cpmd/cpmdparser/versions/cpmd41/commonmatcher.py b/parser/parser-cpmd/cpmdparser/versions/cpmd41/commonmatcher.py
new file mode 100644
index 0000000000000000000000000000000000000000..9ea4ee49fa11ca52432e93921666a31613406c3c
--- /dev/null
+++ b/parser/parser-cpmd/cpmdparser/versions/cpmd41/commonmatcher.py
@@ -0,0 +1,18 @@
+from nomadcore.baseclasses import CommonMatcher
+
+
+#===============================================================================
+class CPMDCommonMatcher(CommonMatcher):
+ """
+ This class is used to store and instantiate common parts of the
+ hierarchical SimpleMatcher structure used in the parsing of a CPMD
+ calculation.
+ """
+ def __init__(self, parser_context):
+ super(CPMDCommonMatcher, self).__init__(parser_context)
+
+ #===========================================================================
+ # onClose triggers
+ def onClose_section_run(self, backend, gIndex, section):
+ backend.addValue("program_name", "CPMD")
+ backend.addValue("program_basis_set_type", "plane waves")
diff --git a/parser/parser-cpmd/cpmdparser/versions/cpmd41/inputparser.py b/parser/parser-cpmd/cpmdparser/versions/cpmd41/inputparser.py
new file mode 100644
index 0000000000000000000000000000000000000000..1e9b3b7fb1c7b84d1638fb2bc35c9b0923d8254d
--- /dev/null
+++ b/parser/parser-cpmd/cpmdparser/versions/cpmd41/inputparser.py
@@ -0,0 +1,43 @@
+from __future__ import absolute_import
+from nomadcore.simple_parser import SimpleMatcher as SM
+from nomadcore.baseclasses import MainHierarchicalParser
+from nomadcore.caching_backend import CachingLevel
+from .commonmatcher import CommonMatcher
+import logging
+logger = logging.getLogger("nomad")
+
+
+#===============================================================================
+class CPMDSinglePointParser(MainHierarchicalParser):
+ """The main parser class. Used to parse the CP2K calculation with run types:
+ -ENERGY
+ -ENERGY_FORCE
+ """
+ def __init__(self, file_path, parser_context):
+ """
+ """
+ super(CPMDSinglePointParser, self).__init__(file_path, parser_context)
+ self.setup_common_matcher(CommonMatcher(parser_context))
+
+ #=======================================================================
+ # Cache levels
+ self.caching_level_for_metaname.update({
+ 'x_cp2k_energy_total_scf_iteration': CachingLevel.ForwardAndCache,
+ 'x_cp2k_energy_XC_scf_iteration': CachingLevel.ForwardAndCache,
+ 'x_cp2k_energy_change_scf_iteration': CachingLevel.ForwardAndCache,
+ 'x_cp2k_stress_tensor': CachingLevel.ForwardAndCache,
+ 'x_cp2k_section_stress_tensor': CachingLevel.ForwardAndCache,
+ })
+
+ #=======================================================================
+ # SimpleMatchers
+ self.root_matcher = SM("",
+ forwardMatch=True,
+ sections=['section_run', "section_single_configuration_calculation", "section_system", "section_method"],
+ otherMetaInfo=["atom_forces"],
+ subMatchers=[
+ self.cm.header(),
+ self.cm.quickstep_header(),
+ self.cm.quickstep_calculation(),
+ ]
+ )
diff --git a/parser/parser-cpmd/cpmdparser/versions/cpmd41/mainparser.py b/parser/parser-cpmd/cpmdparser/versions/cpmd41/mainparser.py
new file mode 100644
index 0000000000000000000000000000000000000000..39de580e9f4d5849ec6726471c34a9453521998b
--- /dev/null
+++ b/parser/parser-cpmd/cpmdparser/versions/cpmd41/mainparser.py
@@ -0,0 +1,67 @@
+from __future__ import absolute_import
+from nomadcore.simple_parser import SimpleMatcher as SM
+from nomadcore.baseclasses import MainHierarchicalParser
+from nomadcore.caching_backend import CachingLevel
+from .commonmatcher import CPMDCommonMatcher
+import re
+import logging
+import datetime
+logger = logging.getLogger("nomad")
+
+
+#===============================================================================
+class CPMDMainParser(MainHierarchicalParser):
+ """The main parser class that is called for all run types. Parses the CPMD
+ output file.
+ """
+ def __init__(self, file_path, parser_context):
+ """
+ """
+ super(CPMDMainParser, self).__init__(file_path, parser_context)
+ self.setup_common_matcher(CPMDCommonMatcher(parser_context))
+
+ #=======================================================================
+ # Cache levels
+ # self.caching_levels.update({
+ # 'section_run': CachingLevel.ForwardAndCache,
+ # })
+
+ #=======================================================================
+ # SimpleMatchers
+ self.root_matcher = SM("",
+ forwardMatch=True,
+ sections=['section_run', "section_single_configuration_calculation", "section_system", "section_method"],
+ subMatchers=[
+ SM( " PROGRAM CPMD STARTED AT: (?P<x_cpmd_start_datetime>{})".format(self.regexs.regex_eol)),
+ SM( "\s+VERSION (?P<program_version>\d+\.\d+)"),
+ SM( " THE INPUT FILE IS:\s+(?P<x_cpmd_input_file>{})".format(self.regexs.regex_eol)),
+ SM( " THIS JOB RUNS ON:\s+(?P<x_cpmd_run_host_name>{})".format(self.regexs.regex_eol)),
+ SM( " THE JOB WAS SUBMITTED BY:\s+(?P<x_cpmd_run_user_name>{})".format(self.regexs.regex_eol)),
+ ]
+ )
+
+ #=======================================================================
+ # onClose triggers
+ def onClose_section_run(self, backend, gIndex, section):
+ start_datetime = section.get_latest_value("x_cpmd_start_datetime")
+ start_date_stamp, start_wall_time = self.timestamp_from_string(start_datetime)
+ backend.addValue("time_run_date_start", start_date_stamp)
+ backend.addValue("time_run_wall_start", start_wall_time)
+
+ #=======================================================================
+ # misc. functions
+ def timestamp_from_string(self, timestring):
+ timestring = timestring.strip()
+ date, time = timestring.split()
+ year, month, day = [int(x) for x in date.split("-")]
+ hour, minute, second, msec = [float(x) for x in re.split("[:.]", time)]
+ date_stamp = datetime.datetime(year, month, day).timestamp()
+ wall_time = hour*3600+minute*60+second+0.001*msec
+ return date_stamp, wall_time
+
+ #=======================================================================
+ # adHoc
+ def debug(self):
+ def wrapper(parser):
+ print("DEBUG")
+ return wrapper
diff --git a/parser/parser-cpmd/cpmdparser/versions/versionsetup.py b/parser/parser-cpmd/cpmdparser/versions/versionsetup.py
deleted file mode 100644
index e4f917686feff161e52adc8160f1fceecc44c56a..0000000000000000000000000000000000000000
--- a/parser/parser-cpmd/cpmdparser/versions/versionsetup.py
+++ /dev/null
@@ -1,62 +0,0 @@
-import importlib
-import logging
-logger = logging.getLogger("nomad")
-
-
-#===============================================================================
-def get_main_parser(version_id, run_type):
- """
- Setups a main parser class for this calculation. The main class can be
- different for each version and run type.
-
- Args:
- version_id: An integer representing the CP2K version. The version
- number is originally a string the form '2.6.2', but here the numbers
- are just concatenated into a single integer number 262.
- run_type: A string that identifies the RUN_TYPE for the calculation.
- All the possible run types can be found in the CP2K reference manual.
-
- Returns:
- A python class that should be instantiated later with the correct
- parameters.
- """
-
- # Search for a RUN_TYPE specific parser
- parser_map = {
- "ENERGY": "SinglePointParser",
- "ENERGY_FORCE": "SinglePointParser",
- "WAVEFUNCTION_OPTIMIZATION": "SinglePointParser",
- "WFN_OPT": "SinglePointParser",
- "GEO_OPT": "GeoOptParser",
- "GEOMETRY_OPTIMIZATION": "GeoOptParser",
- "MD": "MDParser",
- "MOLECULAR_DYNAMICS": "MDParser",
- }
- try:
- parser = parser_map[run_type]
- except KeyError:
- logger.exception("A parser corresponding to the run_type '{}' could not be found.".format(run_type))
- raise
-
- # Currently the version id is a pure integer, so it can directly be mapped
- # into a package name.
- base = "cpmdparser.versions.cp2k{}.{}".format(version_id, parser.lower())
- parser_module = None
- parser_class = None
- try:
- parser_module = importlib.import_module(base)
- except ImportError:
- logger.warning("Could not find a parser for version '{}' and run type '{}'. Trying to default to the base implementation for CP2K 2.6.2".format(version_id, run_type))
- base = "cp2kparser.versions.cp2k262.{}".format(parser.lower())
- try:
- parser_module = importlib.import_module(base)
- except ImportError:
- logger.exception("Tried to default to the CP2K 2.6.2 implementation but could not find the correct modules for run_type '{}'.".format(run_type))
- raise
- try:
- parser_class = getattr(parser_module, "CP2K{}".format(parser))
- except AttributeError:
- logger.exception("A parser class '{}' could not be found in the module '[]'.".format(parser_class, parser_module))
- raise
-
- return parser_class
diff --git a/setup.py b/setup.py
index fc623cc72744fdc9f2fb061fa484d904991bd93d..ff76355dc746f1088aab71f87c0aedd60688fc03 100644
--- a/setup.py
+++ b/setup.py
@@ -11,20 +11,15 @@ def main():
setup(
name="cpmdparser",
version="0.1",
- # package_data={
- # 'cp2kparser.versions.cp2k262': ['input_data/cp2k_input_tree.pickle'],
- # },
description="NoMaD parser implementation for CPMD.",
author="Lauri Himanen",
author_email="lauri.himanen@aalto.fi",
license="GPL3",
- # package_dir={'': 'parser/parser-cp2k'},
+ package_dir={'': 'parser/parser-cpmd'},
packages=find_packages(),
install_requires=[
'pint',
'numpy',
- # 'mdtraj',
- # 'ase'
],
)
diff --git a/src/main/scala/eu/nomad_lab/parsers/CpmdParser.scala b/src/main/scala/eu/nomad_lab/parsers/CpmdParser.scala
index c0305e7da182389759d3f4e14895f80394a48c9b..8e2c8f1d89ee9ef447907afecd16733471e41be8 100644
--- a/src/main/scala/eu/nomad_lab/parsers/CpmdParser.scala
+++ b/src/main/scala/eu/nomad_lab/parsers/CpmdParser.scala
@@ -5,11 +5,11 @@ import eu.nomad_lab.DefaultPythonInterpreter
import org.{ json4s => jn }
import scala.collection.breakOut
-object Cp2kParser extends SimpleExternalParserGenerator(
- name = "Cp2kParser",
+object CpmdParser extends SimpleExternalParserGenerator(
+ name = "CpmdParser",
parserInfo = jn.JObject(
("name" -> jn.JString("CpmdParser")) ::
- ("parserId" -> jn.JString("CpmdParser" + lab.Cp2kVersionInfo.version)) ::
+ ("parserId" -> jn.JString("CpmdParser" + lab.CpmdVersionInfo.version)) ::
("versionInfo" -> jn.JObject(
("nomadCoreVersion" -> jn.JObject(lab.NomadCoreVersionInfo.toMap.map {
case (k, v) => k -> jn.JString(v.toString)
@@ -21,16 +21,14 @@ object Cp2kParser extends SimpleExternalParserGenerator(
)) :: Nil
),
mainFileTypes = Seq("text/.*"),
- mainFileRe = """ \*\*\*\* \*\*\*\* \*\*\*\*\*\* \*\* PROGRAM STARTED AT\s(?<cpmdStartedAt>.*)
- \*\*\*\*\* \*\* \*\*\* \*\*\* \*\* PROGRAM STARTED ON\s*.*
- \*\* \*\*\*\* \*\*\*\*\*\* PROGRAM STARTED BY .*
- \*\*\*\*\* \*\* \*\* \*\* \*\* PROGRAM PROCESS ID .*
- \*\*\*\* \*\* \*\*\*\*\*\*\* \*\* PROGRAM STARTED IN .*
-(?:\s*\n| \s+.*
-)*
-(?:\s*CP2K\| version string:\s*(?<cpmdVersionString>.*)
-)?(?:\s*CP2K\| source code revision number:\s*(?<cpmdRevision>.*)
-)?""".r,
+ mainFileRe = """ \*\*\*\*\*\* \*\*\*\*\*\* \*\*\*\* \*\*\*\* \*\*\*\*\*\*
+ \*\*\*\*\*\*\* \*\*\*\*\*\*\* \*\*\*\*\*\*\*\*\*\* \*\*\*\*\*\*\*
+ \*\*\* \*\* \*\*\* \*\* \*\*\*\* \*\* \*\* \*\*\*
+ \*\* \*\* \*\*\* \*\* \*\* \*\* \*\* \*\*
+ \*\* \*\*\*\*\*\*\* \*\* \*\* \*\* \*\*
+ \*\*\* \*\*\*\*\*\* \*\* \*\* \*\* \*\*\*
+ \*\*\*\*\*\*\* \*\* \*\* \*\* \*\*\*\*\*\*\*
+ \*\*\*\*\*\* \*\* \*\* \*\* \*\*\*\*\*\*""".r,
cmd = Seq(DefaultPythonInterpreter.python2Exe(), "${envDir}/parsers/cpmd/parser/parser-cpmd/cpmdparser/scalainterface.py",
"${mainFilePath}"),
cmdCwd = "${mainFilePath}/..",
@@ -38,16 +36,17 @@ object Cp2kParser extends SimpleExternalParserGenerator(
"parser-cpmd/cpmdparser/__init__.py",
"parser-cpmd/cpmdparser/setup_paths.py",
"parser-cpmd/cpmdparser/parser.py",
+ "parser-cpmd/cpmdparser/scalainterface.py",
"parser-cpmd/cpmdparser/generic/__init__.py",
"parser-cpmd/cpmdparser/versions/__init__.py",
- "parser-cpmd/cpmdparser/versions/versionsetup.py",
"parser-cpmd/cpmdparser/versions/cpmd41/__init__.py",
- "parser-cpmd/cpmdparser/scalainterface.py",
+ "parser-cpmd/cpmdparser/versions/cpmd41/commonmatcher.py",
+ "parser-cpmd/cpmdparser/versions/cpmd41/mainparser.py",
+ "parser-cpmd/cpmdparser/versions/cpmd41/inputparser.py",
"nomad_meta_info/public.nomadmetainfo.json",
"nomad_meta_info/common.nomadmetainfo.json",
"nomad_meta_info/meta_types.nomadmetainfo.json",
"nomad_meta_info/cpmd.nomadmetainfo.json",
- "nomad_meta_info/cpmd.general.nomadmetainfo.json"
) ++ DefaultPythonInterpreter.commonFiles(),
dirMap = Map(
"parser-cpmd" -> "parsers/cpmd/parser/parser-cpmd",
diff --git a/src/test/scala/eu/nomad_lab/parsers/CpmdParserSpec.scala b/src/test/scala/eu/nomad_lab/parsers/CpmdParserSpec.scala
index fd35602de6f5e3ea9b5fc7345b680e55dbfeca34..472e92b9e4641c7facb72312ccdc47954e6d16c9 100644
--- a/src/test/scala/eu/nomad_lab/parsers/CpmdParserSpec.scala
+++ b/src/test/scala/eu/nomad_lab/parsers/CpmdParserSpec.scala
@@ -3,13 +3,7 @@ package eu.nomad_lab.parsers
import org.specs2.mutable.Specification
object CpmdParserSpec extends Specification {
- "CpmdParserTest" >> {
- "test with json-events" >> {
- ParserRun.parse(CpmdParser, "parsers/cpmd/test/examples/energy_force/si_bulk8.out", "json-events") must_== ParseResult.ParseSuccess
- }
- }
-
"test energy_force with json" >> {
- ParserRun.parse(CpmdParser, "parsers/cpmd/test/examples/energy_force/si_bulk8.out", "json") must_== ParseResult.ParseSuccess
+ ParserRun.parse(CpmdParser, "parsers/cpmd/test/examples/single_point/output.out", "json") must_== ParseResult.ParseSuccess
}
}
diff --git a/test/examples/single_point/GEOMETRY b/test/examples/single_point/GEOMETRY
new file mode 100644
index 0000000000000000000000000000000000000000..4fc346d8d03ee55cc5ed943b11eb14af91be77a4
--- /dev/null
+++ b/test/examples/single_point/GEOMETRY
@@ -0,0 +1,2 @@
+ 8.259992891426 7.558904499132 7.558904499132 0.017798524379 -0.000000000000 -0.000000000000
+ 6.857816106837 7.558904499132 7.558904499132 -0.017798524379 -0.000000000000 -0.000000000000
diff --git a/test/examples/single_point/GEOMETRY.xyz b/test/examples/single_point/GEOMETRY.xyz
new file mode 100644
index 0000000000000000000000000000000000000000..b13c48d0b6644a53a06502a83cea74fb0265e4e1
--- /dev/null
+++ b/test/examples/single_point/GEOMETRY.xyz
@@ -0,0 +1,4 @@
+ 2
+GEOMETRY FILE / created by CPMD
+ H 4.371000000000 4.000000000000 4.000000000000 0.009418573488 -0.000000000000 -0.000000000000
+ H 3.629000000000 4.000000000000 4.000000000000 -0.009418573488 -0.000000000000 -0.000000000000
diff --git a/test/examples/single_point/LATEST b/test/examples/single_point/LATEST
new file mode 100644
index 0000000000000000000000000000000000000000..0e4449210602fd9c3a45bd3bc780cd67ad8721b0
--- /dev/null
+++ b/test/examples/single_point/LATEST
@@ -0,0 +1,2 @@
+./RESTART.1
+ 1
diff --git a/test/examples/single_point/RESTART.1 b/test/examples/single_point/RESTART.1
new file mode 100644
index 0000000000000000000000000000000000000000..88b00a1a01f06fe6a5955b36cc01256a544cf1ce
Binary files /dev/null and b/test/examples/single_point/RESTART.1 differ
diff --git a/test/examples/single_point/input.inp b/test/examples/single_point/input.inp
new file mode 100755
index 0000000000000000000000000000000000000000..c1b5c8a868f3b0aec8910af9399c6bfabec9fa3d
--- /dev/null
+++ b/test/examples/single_point/input.inp
@@ -0,0 +1,35 @@
+&INFO
+isolated hydrogen molecule.
+single point calculation.
+&END
+
+&CPMD
+ OPTIMIZE WAVEFUNCTION
+ CONVERGENCE ORBITALS
+ 1.0d-7
+ CENTER MOLECULE ON
+ PRINT FORCES ON
+&END
+
+&SYSTEM
+ SYMMETRY
+ 1
+ ANGSTROM
+ CELL
+ 8.00 1.0 1.0 0.0 0.0 0.0
+ CUTOFF
+ 70.0
+&END
+
+&DFT
+ FUNCTIONAL LDA
+&END
+
+&ATOMS
+*H_MT_LDA.psp
+ LMAX=S
+ 2
+ 4.371 4.000 4.000
+ 3.629 4.000 4.000
+&END
+
diff --git a/test/examples/single_point/output.out b/test/examples/single_point/output.out
new file mode 100644
index 0000000000000000000000000000000000000000..b7fb802822bc95d7164dab1cff250c4b764493de
--- /dev/null
+++ b/test/examples/single_point/output.out
@@ -0,0 +1,286 @@
+ cp_groups: we are using a 1 x 1 grid (groups x nprocs).
+ PROGRAM CPMD STARTED AT: 2016-07-04 14:05:06.851
+ SETCNST| USING: CODATA 2006 UNITS
+
+
+ ****** ****** **** **** ******
+ ******* ******* ********** *******
+ *** ** *** ** **** ** ** ***
+ ** ** *** ** ** ** ** **
+ ** ******* ** ** ** **
+ *** ****** ** ** ** ***
+ ******* ** ** ** *******
+ ****** ** ** ** ******
+
+ VERSION 4.1-rUnversioned directory
+
+ COPYRIGHT
+ IBM RESEARCH DIVISION
+ MPI FESTKOERPERFORSCHUNG STUTTGART
+
+ The CPMD consortium
+ Home Page: http://www.cpmd.org
+ Mailing List: cpmd-list@cpmd.org
+ E-mail: cpmd@cpmd.org
+
+
+ *** Jun 22 2016 -- 12:41:05 ***
+
+ THE INPUT FILE IS: input.inp
+ THIS JOB RUNS ON: lenovo700
+ THE CURRENT DIRECTORY IS:
+ /home/lauri/Dropbox/nomad-dev/nomad-lab-base/parsers/cpmd/test/unittests/cpmd_4.1/h2
+ THE TEMPORARY DIRECTORY IS:
+ /home/lauri/Dropbox/nomad-dev/nomad-lab-base/parsers/cpmd/test/unittests/cpmd_4.1/h2
+ THE PROCESS ID IS: 32589
+ THE JOB WAS SUBMITTED BY: lauri
+
+
+ ******************************************************************************
+ * INFO - INFO - INFO - INFO - INFO - INFO - INFO - INFO - INFO - INFO - INFO *
+ ******************************************************************************
+ * isolated hydrogen molecule. *
+ * single point calculation. *
+ ******************************************************************************
+
+ SINGLE POINT DENSITY OPTIMIZATION
+
+ USING SEED 123456 TO INIT. PSEUDO RANDOM NUMBER GEN.
+ PATH TO THE RESTART FILES: ./
+ GRAM-SCHMIDT ORTHOGONALIZATION
+ MAXIMUM NUMBER OF STEPS: 10000 STEPS
+ MAXIMUM NUMBER OF ITERATIONS FOR SC: 10000 STEPS
+ PRINT INTERMEDIATE RESULTS EVERY 10001 STEPS
+ STORE INTERMEDIATE RESULTS EVERY 10001 STEPS
+ NUMBER OF DISTINCT RESTART FILES: 1
+ TEMPERATURE IS CALCULATED ASSUMING EXTENDED BULK BEHAVIOR
+ FICTITIOUS ELECTRON MASS: 400.0000
+ TIME STEP FOR ELECTRONS: 5.0000
+ TIME STEP FOR IONS: 5.0000
+ CONVERGENCE CRITERIA FOR WAVEFUNCTION OPTIMIZATION: 1.0000E-07
+ WAVEFUNCTION OPTIMIZATION BY PRECONDITIONED DIIS
+ THRESHOLD FOR THE WF-HESSIAN IS 0.5000
+ MAXIMUM NUMBER OF VECTORS RETAINED FOR DIIS: 10
+ STEPS UNTIL DIIS RESET ON POOR PROGRESS: 10
+ FULL ELECTRONIC GRADIENT IS USED
+ SPLINE INTERPOLATION IN G-SPACE FOR PSEUDOPOTENTIAL FUNCTIONS
+ NUMBER OF SPLINE POINTS: 5000
+
+ EXCHANGE CORRELATION FUNCTIONALS
+ LDA EXCHANGE: NONE
+ LDA XC THROUGH PADE APPROXIMATION
+ S.GOEDECKER, J.HUTTER, M.TETER PRB 541703 (1996)
+
+ *** DETSP| SIZE OF THE PROGRAM IS NOT AVAILABLE ***
+
+ ***************************** ATOMS ****************************
+ NR TYPE X(BOHR) Y(BOHR) Z(BOHR) MBL
+ 1 H 8.259993 7.558904 7.558904 3
+ 2 H 6.857816 7.558904 7.558904 3
+ ****************************************************************
+
+ NUMBER OF STATES: 1
+ NUMBER OF ELECTRONS: 2.00000
+ CHARGE: 0.00000
+ ELECTRON TEMPERATURE(KELVIN): 0.00000
+ OCCUPATION
+ 2.0
+
+ ============================================================
+ | Pseudopotential Report Thu Jan 11 18:21:49 1996 |
+ ------------------------------------------------------------
+ | Atomic Symbol : H |
+ | Atomic Number : 1 |
+ | Number of core states : 0 |
+ | Number of valence states : 1 |
+ | Exchange-Correlation Functional : |
+ | Slater exchange : .6667 |
+ | LDA correlation : Ceperley-Alder |
+ | Electron Configuration : N L Occupation |
+ | 1 S 1.0000 |
+ | Full Potential Total Energy -.445894 |
+ | Trouiller-Martins normconserving PP |
+ | n l rc energy |
+ | 1 S .5000 -.23366 |
+ | 2 P .5000 -.23366 |
+ | Number of Mesh Points : 511 |
+ | Pseudoatom Total Energy -.445889 |
+ ============================================================
+
+ ****************************************************************
+ * ATOM MASS RAGGIO NLCC PSEUDOPOTENTIAL *
+ * H 1.0080 1.2000 NO S LOCAL *
+ ****************************************************************
+
+
+ PARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARA
+ NCPU NGW NHG PLANES GXRAYS HXRAYS ORBITALS Z-PLANES
+ 0 17133 136605 90 1281 5089 1 1
+ G=0 COMPONENT ON PROCESSOR : 0
+ PARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARA
+
+ *** loadpa| SIZE OF THE PROGRAM IS NOT AVAILABLE ***
+
+ OPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPEN
+ NUMBER OF CPUS PER TASK 1
+ OPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPEN
+
+ *** rggen| SIZE OF THE PROGRAM IS NOT AVAILABLE ***
+
+ ************************** SUPERCELL ***************************
+ SYMMETRY: SIMPLE CUBIC
+ LATTICE CONSTANT(a.u.): 15.11781
+ CELL DIMENSION: 15.1178 1.0000 1.0000 0.0000 0.0000 0.0000
+ VOLUME(OMEGA IN BOHR^3): 3455.14726
+ LATTICE VECTOR A1(BOHR): 15.1178 0.0000 0.0000
+ LATTICE VECTOR A2(BOHR): 0.0000 15.1178 0.0000
+ LATTICE VECTOR A3(BOHR): 0.0000 0.0000 15.1178
+ RECIP. LAT. VEC. B1(2Pi/BOHR): 0.0661 0.0000 0.0000
+ RECIP. LAT. VEC. B2(2Pi/BOHR): 0.0000 0.0661 0.0000
+ RECIP. LAT. VEC. B3(2Pi/BOHR): 0.0000 0.0000 0.0661
+ REAL SPACE MESH: 90 90 90
+ WAVEFUNCTION CUTOFF(RYDBERG): 70.00000
+ DENSITY CUTOFF(RYDBERG): (DUAL= 4.00) 280.00000
+ NUMBER OF PLANE WAVES FOR WAVEFUNCTION CUTOFF: 17133
+ NUMBER OF PLANE WAVES FOR DENSITY CUTOFF: 136605
+ ****************************************************************
+
+ *** RINFORCE| SIZE OF THE PROGRAM IS NOT AVAILABLE ***
+ *** FFTPRP| SIZE OF THE PROGRAM IS NOT AVAILABLE ***
+
+ GENERATE ATOMIC BASIS SET
+ H SLATER ORBITALS
+ 1S ALPHA= 1.0000 OCCUPATION= 1.00
+
+
+ INITIALIZATION TIME: 0.48 SECONDS
+
+ *** WFOPTS| SIZE OF THE PROGRAM IS NOT AVAILABLE ***
+ *** PHFAC| SIZE OF THE PROGRAM IS NOT AVAILABLE ***
+ NOTE: ATOMIC GUESS USING DISTRIBUTED LINALG WITH LANCZOS
+ *** ATOMWF| SIZE OF THE PROGRAM IS NOT AVAILABLE ***
+ ATRHO| CHARGE(R-SPACE): 2.000000 (G-SPACE): 2.000000
+
+ ATOM COORDINATES GRADIENTS (-FORCES)
+ 1 H 8.2600 7.5589 7.5589 0.000E+00 0.000E+00 0.000E+00
+ 2 H 6.8578 7.5589 7.5589 0.000E+00 0.000E+00 0.000E+00
+
+ TIME FOR WAVEFUNCTION INITIALIZATION: 0.83 SECONDS
+ *** RWFOPT| SIZE OF THE PROGRAM IS NOT AVAILABLE ***
+ EWALD| SUM IN REAL SPACE OVER 1* 1* 1 CELLS
+
+ TOTAL INTEGRATED ELECTRONIC DENSITY
+ IN G-SPACE = 2.0000000000
+ IN R-SPACE = 2.0000000000
+
+ (K+E1+L+N+X) TOTAL ENERGY = -1.09689770 A.U.
+ (K) KINETIC ENERGY = 0.81247072 A.U.
+ (E1=A-S+R) ELECTROSTATIC ENERGY = -0.48640053 A.U.
+ (S) ESELF = 0.66490380 A.U.
+ (R) ESR = 0.17302593 A.U.
+ (L) LOCAL PSEUDOPOTENTIAL ENERGY = -0.84879440 A.U.
+ (N) N-L PSEUDOPOTENTIAL ENERGY = 0.00000000 A.U.
+ (X) EXCHANGE-CORRELATION ENERGY = -0.57417350 A.U.
+
+ NFI GEMAX CNORM ETOT DETOT TCPU
+ 1 3.816E-02 2.886E-03 -1.096898 0.000E+00 0.23
+ 2 8.628E-03 1.041E-03 -1.130803 -3.391E-02 0.22
+ 3 2.736E-03 2.293E-04 -1.132376 -1.572E-03 0.22
+ 4 6.115E-04 4.235E-05 -1.132456 -8.056E-05 0.22
+ 5 1.532E-04 7.007E-06 -1.132459 -3.315E-06 0.24
+ 6 3.895E-05 1.396E-06 -1.132460 -1.338E-07 0.22
+ 7 6.288E-06 4.459E-07 -1.132460 -7.717E-09 0.22
+ 8 7.941E-07 1.282E-07 -1.132460 -4.283E-10 0.22
+ 9 1.237E-07 2.861E-08 -1.132460 -1.992E-11 0.22
+ 10 2.278E-08 5.401E-09 -1.132460 -8.606E-13 0.22
+
+ RESTART INFORMATION WRITTEN ON FILE ./RESTART.1
+ *** RWFOPT| SIZE OF THE PROGRAM IS NOT AVAILABLE ***
+
+ ****************************************************************
+ * *
+ * FINAL RESULTS *
+ * *
+ ****************************************************************
+
+ ATOM COORDINATES GRADIENTS (-FORCES)
+ 1 H 8.2600 7.5589 7.5589 1.780E-02 -1.104E-16 -9.425E-17
+ 2 H 6.8578 7.5589 7.5589 -1.780E-02 -1.867E-16 -1.490E-16
+
+ ****************************************************************
+
+
+ ELECTRONIC GRADIENT:
+ MAX. COMPONENT = 1.15980E-08 NORM = 1.11525E-09
+ NUCLEAR GRADIENT:
+ MAX. COMPONENT = 1.77985E-02 NORM = 1.02760E-02
+
+
+ TOTAL INTEGRATED ELECTRONIC DENSITY
+ IN G-SPACE = 2.0000000000
+ IN R-SPACE = 2.0000000000
+
+ (K+E1+L+N+X) TOTAL ENERGY = -1.13245953 A.U.
+ (K) KINETIC ENERGY = 1.09007149 A.U.
+ (E1=A-S+R) ELECTROSTATIC ENERGY = -0.47319176 A.U.
+ (S) ESELF = 0.66490380 A.U.
+ (R) ESR = 0.17302593 A.U.
+ (L) LOCAL PSEUDOPOTENTIAL ENERGY = -1.09902228 A.U.
+ (N) N-L PSEUDOPOTENTIAL ENERGY = 0.00000000 A.U.
+ (X) EXCHANGE-CORRELATION ENERGY = -0.65031699 A.U.
+
+ ****************************************************************
+
+
+
+ ****************************************************************
+ * *
+ * TIMING *
+ * *
+ ****************************************************************
+ SUBROUTINE CALLS SELF TIME TOTAL TIME
+ AVERAGE MAXIMUM AVERAGE MAXIMUM
+ cpmd 1 0.00 0.00 3.67 3.67
+ rwfopt 1 0.00 0.00 3.20 3.20
+ updwf 11 0.00 0.00 2.37 2.37
+ forcedr 11 0.00 0.00 2.33 2.33
+ forces 11 0.00 0.00 2.33 2.33
+ forces_a 11 0.00 0.00 1.80 1.80
+ rscpot 11 0.00 0.00 1.80 1.80
+ vofrho 12 0.00 0.00 1.79 1.79
+ VOFRHOB 12 0.04 0.04 1.22 1.22
+ INVFFTN 37 1.12 1.12 1.12 1.12
+ initrun 1 0.00 0.00 0.82 0.82
+ rinitwf 1 0.00 0.00 0.82 0.82
+ ATOMWF 1 0.00 0.00 0.82 0.82
+ FWFFTN 25 0.69 0.69 0.69 0.69
+ xcener_new 12 0.04 0.04 0.67 0.67
+ mikeu 12 0.63 0.63 0.63 0.63
+ vpsi 13 0.06 0.06 0.63 0.63
+ VOFRHOA 12 0.03 0.03 0.57 0.57
+ ATRHO 1 0.35 0.35 0.39 0.39
+ rhoofr 11 0.07 0.07 0.34 0.34
+ rinit 1 0.00 0.00 0.26 0.26
+ rggen 1 0.01 0.01 0.26 0.26
+ loadpa 1 0.01 0.01 0.25 0.25
+ dist_ksmat 1 0.00 0.00 0.11 0.11
+ RINFORCE 1 0.00 0.00 0.10 0.10
+ NUMPW 1 0.10 0.10 0.10 0.10
+ loadpa_b 1 0.10 0.10 0.10 0.10
+ loadpa_c 1 0.10 0.10 0.10 0.10
+ FORMFN 1 0.10 0.10 0.10 0.10
+ ppener 12 0.06 0.06 0.06 0.06
+ loadpa_a 1 0.04 0.04 0.04 0.04
+ EICALC 12 0.04 0.04 0.04 0.04
+ odiis 11 0.04 0.04 0.04 0.04
+ PUTPS 1 0.01 0.01 0.01 0.01
+ forces_b 11 0.00 0.00 0.01 0.01
+ potfor 1 0.01 0.01 0.01 0.01
+ fftprp 1 0.00 0.00 0.00 0.00
+ ****************************************************************
+
+ CPU TIME : 0 HOURS 0 MINUTES 3.67 SECONDS
+ ELAPSED TIME : 0 HOURS 0 MINUTES 3.67 SECONDS
+ *** CPMD| SIZE OF THE PROGRAM IS NOT AVAILABLE ***
+
+ PROGRAM CPMD ENDED AT: 2016-07-04 14:05:10.523
diff --git a/test/unittests/cpmd_4.1/H_MT_LDA.psp b/test/unittests/cpmd_4.1/H_MT_LDA.psp
new file mode 100755
index 0000000000000000000000000000000000000000..f24a5a5b39bcf21727cc7ab07da90ba83893f2aa
--- /dev/null
+++ b/test/unittests/cpmd_4.1/H_MT_LDA.psp
@@ -0,0 +1,1056 @@
+&ATOM
+ Z = 1
+ ZV = 1
+ XC = 1100 .666667
+ TYPE = NORMCONSERVING NUMERIC
+&END
+&INFO
+ ============================================================
+ | Pseudopotential Report Thu Jan 11 18:21:49 1996 |
+ ------------------------------------------------------------
+ | Atomic Symbol : H |
+ | Atomic Number : 1 |
+ | Number of core states : 0 |
+ | Number of valence states : 1 |
+ | Exchange-Correlation Functional : |
+ | Slater exchange : .6667 |
+ | LDA correlation : Ceperley-Alder |
+ | Electron Configuration : N L Occupation |
+ | 1 S 1.0000 |
+ | Full Potential Total Energy -.445894 |
+ | Trouiller-Martins normconserving PP |
+ | n l rc energy |
+ | 1 S .5000 -.23366 |
+ | 2 P .5000 -.23366 |
+ | Number of Mesh Points : 511 |
+ | Pseudoatom Total Energy -.445889 |
+ ============================================================
+&END
+&POTENTIAL
+ 511
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diff --git a/test/unittests/cpmd_4.1/run_tests.py b/test/unittests/cpmd_4.1/run_tests.py
new file mode 100644
index 0000000000000000000000000000000000000000..db6beca4eef353dcaedb643fa028129ca2edcad5
--- /dev/null
+++ b/test/unittests/cpmd_4.1/run_tests.py
@@ -0,0 +1,1047 @@
+"""
+This is a module for unit testing the CPMD parser. The unit tests are run with
+a custom backend that outputs the results directly into native python object for
+easier and faster analysis.
+
+Each property that has an enumerable list of different possible options is
+assigned a new test class, that should ideally test through all the options.
+
+The properties that can have non-enumerbale values will be tested only for one
+specific case inside a test class that is designed for a certain type of run
+(MD, optimization, QM/MM, etc.)
+"""
+import os
+import unittest
+import logging
+import numpy as np
+from cpmdparser import CPMDParser
+from nomadcore.unit_conversion.unit_conversion import convert_unit
+
+# Setup the logger so that it doesn't spam messages during tests
+logging.basicConfig(
+ level=logging.DEBUG,
+ format=(
+ '%(filename)s: '
+ '%(levelname)s: '
+ '%(funcName)s(): '
+ '%(lineno)d:\t'
+ '%(message)s'
+ )
+)
+logger = logging.getLogger("nomad")
+logger.setLevel(logging.CRITICAL)
+logging.getLogger("nomadcore.caching_backend").setLevel(logging.CRITICAL)
+logger = logging.getLogger("cp2kparser")
+logger.setLevel(logging.ERROR)
+
+
+#===============================================================================
+def get_results(folder, metainfo_to_keep=None):
+ """Get the given result from the calculation in the given folder by using
+ the Analyzer in the nomadtoolkit package. Tries to optimize the parsing by
+ giving the metainfo_to_keep argument.
+
+ Args:
+ folder: The folder relative to the directory of this script where the
+ parsed calculation resides.
+ metaname: The quantity to extract.
+ """
+ dirname = os.path.dirname(__file__)
+ filename = os.path.join(dirname, folder, "output.out")
+ parser = CPMDParser(filename, None)
+ results = parser.parse()
+ return results
+
+
+#===============================================================================
+def get_result(folder, metaname, optimize=True):
+ if optimize:
+ results = get_results(folder, None)
+ else:
+ results = get_results(folder)
+ result = results[metaname]
+ return result
+
+
+#===============================================================================
+class TestSinglePoint(unittest.TestCase):
+ """Tests that the parser can handle single-point calculations.
+ """
+
+ @classmethod
+ def setUpClass(cls):
+ cls.results = get_results("single_point", "section_run")
+ cls.results.print_summary()
+
+ def test_program_name(self):
+ result = self.results["program_name"]
+ self.assertEqual(result, "CPMD")
+
+ def test_program_version(self):
+ result = self.results["program_version"]
+ self.assertEqual(result, "4.1")
+
+ def test_time_run_date_start(self):
+ result = self.results["time_run_date_start"]
+ self.assertEqual(result, 1467579600.0)
+
+ def test_time_run_wall_start(self):
+ result = self.results["time_run_wall_start"]
+ self.assertEqual(result, 50706.851)
+
+ # def test_program_basis_set_type(self):
+ # result = self.results["program_basis_set_type"]
+ # self.assertEqual(result, "plane waves")
+
+ # def test_energy_total_scf_iteration(self):
+ # result = self.results["energy_total_scf_iteration"]
+ # expected_result = convert_unit(np.array(-32.2320848878), "hartree")
+ # self.assertTrue(np.array_equal(result[0], expected_result))
+
+ # def test_program_compilation_host(self):
+ # result = self.results["program_compilation_host"]
+ # self.assertEqual(result, "lenovo700")
+
+ # def test_scf_max_iteration(self):
+ # result = self.results["scf_max_iteration"]
+ # self.assertEqual(result, 300)
+
+ # def test_scf_threshold_energy_change(self):
+ # result = self.results["scf_threshold_energy_change"]
+ # self.assertEqual(result, 1.00E-07)
+
+ # def test_number_of_spin_channels(self):
+ # result = self.results["number_of_spin_channels"]
+ # self.assertEqual(result, 1)
+
+ # def test_electronic_structure_method(self):
+ # result = self.results["electronic_structure_method"]
+ # self.assertEqual(result, "DFT")
+
+ # def test_energy_change_scf_iteration(self):
+ # energy_change = self.results["energy_change_scf_iteration"]
+ # expected_result = convert_unit(np.array(-3.22E+01), "hartree")
+ # self.assertTrue(np.array_equal(energy_change[0], expected_result))
+
+ # def test_energy_XC_scf_iteration(self):
+ # result = self.results["energy_XC_scf_iteration"]
+ # expected_result = convert_unit(np.array(-9.4555961214), "hartree")
+ # self.assertTrue(np.array_equal(result[0], expected_result))
+
+ # def test_energy_total(self):
+ # result = self.results["energy_total"]
+ # expected_result = convert_unit(np.array(-31.297885372811074), "hartree")
+ # self.assertTrue(np.array_equal(result, expected_result))
+
+ # def test_electronic_kinetic_energy(self):
+ # result = self.results["electronic_kinetic_energy"]
+ # expected_result = convert_unit(np.array(13.31525592466419), "hartree")
+ # self.assertTrue(np.array_equal(result, expected_result))
+
+ # def test_atom_forces(self):
+ # result = self.results["atom_forces"]
+ # expected_result = convert_unit(
+ # np.array([
+ # [0.00000000, 0.00000000, 0.00000000],
+ # [0.00000000, 0.00000001, 0.00000001],
+ # [0.00000001, 0.00000001, 0.00000000],
+ # [0.00000001, 0.00000000, 0.00000001],
+ # [-0.00000001, -0.00000001, -0.00000001],
+ # [-0.00000001, -0.00000001, -0.00000001],
+ # [-0.00000001, -0.00000001, -0.00000001],
+ # [-0.00000001, -0.00000001, -0.00000001],
+ # ]),
+ # "forceAu"
+ # )
+ # self.assertTrue(np.array_equal(result, expected_result))
+
+ # def test_atom_label(self):
+ # atom_labels = self.results["atom_labels"]
+ # expected_labels = np.array(8*["Si1"])
+ # self.assertTrue(np.array_equal(atom_labels, expected_labels))
+
+ # def test_simulation_cell(self):
+ # cell = self.results["simulation_cell"]
+ # n_vectors = cell.shape[0]
+ # n_dim = cell.shape[1]
+ # self.assertEqual(n_vectors, 3)
+ # self.assertEqual(n_dim, 3)
+ # expected_cell = convert_unit(np.array([[5.431, 0, 0], [0, 5.431, 0], [0, 0, 5.431]]), "angstrom")
+ # self.assertTrue(np.array_equal(cell, expected_cell))
+
+ # def test_number_of_atoms(self):
+ # n_atoms = self.results["number_of_atoms"]
+ # self.assertEqual(n_atoms, 8)
+
+ # def test_atom_position(self):
+ # atom_position = self.results["atom_positions"]
+ # expected_position = convert_unit(np.array([4.073023, 4.073023, 1.357674]), "angstrom")
+ # self.assertTrue(np.array_equal(atom_position[-1, :], expected_position))
+
+ # def test_x_cp2k_filenames(self):
+ # input_filename = self.results["x_cp2k_input_filename"]
+ # expected_input = "si_bulk8.inp"
+ # self.assertTrue(input_filename, expected_input)
+
+ # bs_filename = self.results["x_cp2k_basis_set_filename"]
+ # expected_bs = "../BASIS_SET"
+ # self.assertEqual(bs_filename, expected_bs)
+
+ # geminal_filename = self.results["x_cp2k_geminal_filename"]
+ # expected_geminal = "BASIS_GEMINAL"
+ # self.assertEqual(geminal_filename, expected_geminal)
+
+ # potential_filename = self.results["x_cp2k_potential_filename"]
+ # expected_potential = "../GTH_POTENTIALS"
+ # self.assertEqual(potential_filename, expected_potential)
+
+ # mm_potential_filename = self.results["x_cp2k_mm_potential_filename"]
+ # expected_mm_potential = "MM_POTENTIAL"
+ # self.assertEqual(mm_potential_filename, expected_mm_potential)
+
+ # coordinate_filename = self.results["x_cp2k_coordinate_filename"]
+ # expected_coordinate = "__STD_INPUT__"
+ # self.assertEqual(coordinate_filename, expected_coordinate)
+
+ # def test_target_multiplicity(self):
+ # multiplicity = self.results["spin_target_multiplicity"]
+ # self.assertEqual(multiplicity, 1)
+
+ # def test_total_charge(self):
+ # charge = self.results["total_charge"]
+ # self.assertEqual(charge, 0)
+
+ # def test_section_basis_set_atom_centered(self):
+ # basis = self.results["section_basis_set_atom_centered"][0]
+ # name = basis["basis_set_atom_centered_short_name"][0]
+ # number = basis["basis_set_atom_number"][0]
+ # self.assertEquals(name, "DZVP-GTH-PADE")
+ # self.assertEquals(number, 14)
+
+ # def test_section_basis_set_cell_dependent(self):
+ # basis = self.results["section_basis_set_cell_dependent"][0]
+ # cutoff = basis["basis_set_planewave_cutoff"][0]
+ # self.assertEquals(cutoff, convert_unit(300.0, "hartree"))
+
+ # def test_section_method_atom_kind(self):
+ # kind = self.results["section_method_atom_kind"][0]
+ # self.assertEqual(kind["method_atom_kind_atom_number"][0], 14)
+ # self.assertEqual(kind["method_atom_kind_label"][0], "Si1")
+
+ # def test_section_method_basis_set(self):
+ # kind = self.results["section_method_basis_set"][0]
+ # self.assertEqual(kind["method_basis_set_kind"][0], "wavefunction")
+ # self.assertEqual(kind["number_of_basis_sets_atom_centered"][0], 1)
+ # self.assertTrue(np.array_equal(kind["mapping_section_method_basis_set_atom_centered"][0], np.array([[0,0]])))
+
+ # def test_single_configuration_calculation_converged(self):
+ # result = self.results["single_configuration_calculation_converged"]
+ # self.assertTrue(result)
+
+ # def test_scf_dft_number_of_iterations(self):
+ # result = self.results["number_of_scf_iterations"]
+ # self.assertEqual(result, 10)
+
+ # def test_single_configuration_to_calculation_method_ref(self):
+ # result = self.results["single_configuration_to_calculation_method_ref"]
+ # self.assertEqual(result, 0)
+
+ # def test_single_configuration_calculation_to_system_description_ref(self):
+ # result = self.results["single_configuration_calculation_to_system_ref"]
+ # self.assertEqual(result, 0)
+
+ # def test_stress_tensor(self):
+ # result = self.results["stress_tensor"]
+ # expected_result = convert_unit(
+ # np.array([
+ # [7.77640934, -0.00000098, -0.00000099],
+ # [-0.00000098, 7.77640935, -0.00000101],
+ # [-0.00000099, -0.00000101, 7.77640935],
+ # ]),
+ # "GPa"
+ # )
+ # self.assertTrue(np.array_equal(result, expected_result))
+
+ # def test_stress_tensor_eigenvalues(self):
+ # result = self.results["x_cp2k_stress_tensor_eigenvalues"]
+ # expected_result = convert_unit(np.array([7.77640735, 7.77641033, 7.77641036]), "GPa")
+ # self.assertTrue(np.array_equal(result, expected_result))
+
+ # def test_stress_tensor_eigenvectors(self):
+ # result = self.results["x_cp2k_stress_tensor_eigenvectors"]
+ # expected_result = np.array([
+ # [0.57490332, -0.79965737, -0.17330395],
+ # [0.57753686, 0.54662171, -0.60634634],
+ # [0.57960102, 0.24850110, 0.77608624],
+ # ])
+ # self.assertTrue(np.array_equal(result, expected_result))
+
+ # def test_stress_tensor_determinant(self):
+ # result = self.results["x_cp2k_stress_tensor_determinant"]
+ # expected_result = convert_unit(4.70259243E+02, "GPa^3")
+ # self.assertTrue(np.array_equal(result, expected_result))
+
+ # def test_stress_tensor_one_third_of_trace(self):
+ # result = self.results["x_cp2k_stress_tensor_one_third_of_trace"]
+ # expected_result = convert_unit(7.77640934E+00, "GPa")
+ # self.assertTrue(np.array_equal(result, expected_result))
+
+
+
+# #===============================================================================
+# class TestErrors(unittest.TestCase):
+ # """Test misc. error stuations which may occur during the parsing.
+ # """
+ # def test_no_file(self):
+ # self.assertRaises(IOError, get_result, "errors/no_file", "XC_functional")
+
+ # def test_invalid_file(self):
+ # self.assertRaises(RuntimeError, get_result, "errors/invalid_file", "XC_functional")
+
+ # def test_invalid_run_type(self):
+ # self.assertRaises(KeyError, get_result, "errors/invalid_run_type", "XC_functional")
+
+ # def test_unknown_version(self):
+ # get_result("errors/unknown_version", "XC_functional")
+
+ # def test_unknown_input_keyword(self):
+ # get_result("errors/unknown_input_keyword", "XC_functional")
+
+ # def test_unknown_input_section(self):
+ # get_result("errors/unknown_input_section", "XC_functional")
+
+ # def test_unknown_input_section_parameter(self):
+ # get_result("errors/unknown_input_section_parameter", "XC_functional")
+
+
+# #===============================================================================
+# class TestXCFunctional(unittest.TestCase):
+ # """Tests that the XC functionals can be properly parsed.
+ # """
+
+ # def test_pade(self):
+ # xc = get_result("XC_functional/pade", "XC_functional")
+ # self.assertEqual(xc, "1*LDA_XC_TETER93")
+
+ # def test_lda(self):
+ # xc = get_result("XC_functional/lda", "XC_functional")
+ # self.assertEqual(xc, "1*LDA_XC_TETER93")
+
+ # def test_blyp(self):
+ # xc = get_result("XC_functional/blyp", "XC_functional")
+ # self.assertEqual(xc, "1*GGA_C_LYP+1*GGA_X_B88")
+
+ # def test_b3lyp(self):
+ # xc = get_result("XC_functional/b3lyp", "XC_functional")
+ # self.assertEqual(xc, "1*HYB_GGA_XC_B3LYP")
+
+ # def test_olyp(self):
+ # xc = get_result("XC_functional/olyp", "XC_functional")
+ # self.assertEqual(xc, "1*GGA_C_LYP+1*GGA_X_OPTX")
+
+ # def test_hcth120(self):
+ # xc = get_result("XC_functional/hcth120", "XC_functional")
+ # self.assertEqual(xc, "1*GGA_XC_HCTH_120")
+
+ # def test_pbe0(self):
+ # xc = get_result("XC_functional/pbe0", "XC_functional")
+ # self.assertEqual(xc, "1*HYB_GGA_XC_PBEH")
+
+ # def test_pbe(self):
+ # xc = get_result("XC_functional/pbe", "XC_functional")
+ # self.assertEqual(xc, "1*GGA_C_PBE+1*GGA_X_PBE")
+
+
+# #===============================================================================
+# class TestSCFConvergence(unittest.TestCase):
+ # """Tests whether the convergence status and number of SCF step can be
+ # parsed correctly.
+ # """
+
+ # def test_converged(self):
+ # result = get_result("convergence/converged", "single_configuration_calculation_converged")
+ # self.assertTrue(result)
+
+ # def test_non_converged(self):
+ # result = get_result("convergence/non_converged", "single_configuration_calculation_converged")
+ # self.assertFalse(result)
+
+
+#===============================================================================
+# class TestForceFiles(unittest.TestCase):
+ # """Tests that different force files that can be output, can actually be
+ # found and parsed.
+ # """
+
+ # def test_single_point(self):
+
+ # result = get_result("force_file/single_point", "atom_forces")
+ # expected_result = convert_unit(
+ # np.array([
+ # [0.00000000, 0.00000000, 0.00000000],
+ # [0.00000000, 0.00000001, 0.00000001],
+ # [0.00000001, 0.00000001, 0.00000000],
+ # [0.00000001, 0.00000000, 0.00000001],
+ # [-0.00000001, -0.00000001, -0.00000001],
+ # [-0.00000001, -0.00000001, -0.00000001],
+ # [-0.00000001, -0.00000001, -0.00000001],
+ # [-0.00000001, -0.00000001, -0.00000001],
+ # ]),
+ # "forceAu"
+ # )
+ # self.assertTrue(np.array_equal(result, expected_result))
+
+
+#===============================================================================
+# class TestSelfInteractionCorrectionMethod(unittest.TestCase):
+ # """Tests that the self-interaction correction can be properly parsed.
+ # """
+
+ # def test_no(self):
+ # sic = get_result("sic/no", "self_interaction_correction_method")
+ # self.assertEqual(sic, "")
+
+ # def test_ad(self):
+ # sic = get_result("sic/ad", "self_interaction_correction_method")
+ # self.assertEqual(sic, "SIC_AD")
+
+ # def test_explicit_orbitals(self):
+ # sic = get_result("sic/explicit_orbitals", "self_interaction_correction_method")
+ # self.assertEqual(sic, "SIC_EXPLICIT_ORBITALS")
+
+ # def test_mauri_spz(self):
+ # sic = get_result("sic/mauri_spz", "self_interaction_correction_method")
+ # self.assertEqual(sic, "SIC_MAURI_SPZ")
+
+ # def test_mauri_us(self):
+ # sic = get_result("sic/mauri_us", "self_interaction_correction_method")
+ # self.assertEqual(sic, "SIC_MAURI_US")
+
+
+# #===============================================================================
+# class TestStressTensorMethods(unittest.TestCase):
+ # """Tests that the stress tensor can be properly parsed for different
+ # calculation methods.
+ # """
+ # def test_none(self):
+ # get_results("stress_tensor/none", "section_stress_tensor")
+
+ # def test_analytical(self):
+ # results = get_results("stress_tensor/analytical", ["stress_tensor_method", "stress_tensor"])
+ # method = results["stress_tensor_method"]
+ # results["stress_tensor"]
+ # self.assertEqual(method, "Analytical")
+
+ # def test_numerical(self):
+ # results = get_results("stress_tensor/numerical", ["stress_tensor_method", "stress_tensor"])
+ # method = results["stress_tensor_method"]
+ # results["stress_tensor"]
+ # self.assertEqual(method, "Numerical")
+
+ # def test_diagonal_analytical(self):
+ # results = get_results("stress_tensor/diagonal_analytical", ["stress_tensor_method", "stress_tensor"])
+ # method = results["stress_tensor_method"]
+ # results["stress_tensor"]
+ # self.assertEqual(method, "Diagonal analytical")
+
+ # def test_diagonal_numerical(self):
+ # results = get_results("stress_tensor/diagonal_numerical", ["stress_tensor_method", "stress_tensor"])
+ # method = results["stress_tensor_method"]
+ # results["stress_tensor"]
+ # self.assertEqual(method, "Diagonal numerical")
+
+
+# #===============================================================================
+# class TestConfigurationPeriodicDimensions(unittest.TestCase):
+ # """Tests that the self-interaction correction can be properly parsed.
+ # """
+
+ # def test_default(self):
+ # result = get_result("configuration_periodic_dimensions/default", "configuration_periodic_dimensions")
+ # self.assertTrue(np.array_equal(result, np.array((True, True, True))))
+
+ # def test_none(self):
+ # result = get_result("configuration_periodic_dimensions/none", "configuration_periodic_dimensions")
+ # self.assertTrue(np.array_equal(result, np.array((False, False, False))))
+
+ # def test_x(self):
+ # result = get_result("configuration_periodic_dimensions/x", "configuration_periodic_dimensions")
+ # self.assertTrue(np.array_equal(result, np.array((True, False, False))))
+
+ # def test_y(self):
+ # result = get_result("configuration_periodic_dimensions/y", "configuration_periodic_dimensions")
+ # self.assertTrue(np.array_equal(result, np.array((False, True, False))))
+
+ # def test_z(self):
+ # result = get_result("configuration_periodic_dimensions/z", "configuration_periodic_dimensions")
+ # self.assertTrue(np.array_equal(result, np.array((False, False, True))))
+
+ # def test_xy(self):
+ # result = get_result("configuration_periodic_dimensions/xy", "configuration_periodic_dimensions")
+ # self.assertTrue(np.array_equal(result, np.array((True, True, False))))
+
+ # def test_xyz(self):
+ # result = get_result("configuration_periodic_dimensions/xyz", "configuration_periodic_dimensions")
+ # self.assertTrue(np.array_equal(result, np.array((True, True, True))))
+
+ # def test_xz(self):
+ # result = get_result("configuration_periodic_dimensions/xz", "configuration_periodic_dimensions")
+ # self.assertTrue(np.array_equal(result, np.array((True, False, True))))
+
+ # def test_yz(self):
+ # result = get_result("configuration_periodic_dimensions/yz", "configuration_periodic_dimensions")
+ # self.assertTrue(np.array_equal(result, np.array((False, True, True))))
+
+
+# #===============================================================================
+# class TestPreprocessor(unittest.TestCase):
+
+ # def test_include(self):
+ # result = get_result("input_preprocessing/include", "x_cp2k_CP2K_INPUT.GLOBAL.PRINT_LEVEL", optimize=False)
+ # self.assertEqual(result, "LOW")
+
+ # def test_variable(self):
+ # result = get_result("input_preprocessing/variable", "x_cp2k_CP2K_INPUT.GLOBAL.PROJECT_NAME", optimize=False)
+ # self.assertEqual(result, "variable_test")
+
+ # def test_variable_multiple(self):
+ # result = get_result("input_preprocessing/variable_multiple", "x_cp2k_CP2K_INPUT.FORCE_EVAL.DFT.MGRID.CUTOFF", optimize=False)
+ # self.assertEqual(result, "50")
+
+ # def test_comments(self):
+ # result = get_result("input_preprocessing/comments", "x_cp2k_CP2K_INPUT.FORCE_EVAL.DFT.MGRID.CUTOFF", optimize=False)
+ # self.assertEqual(result, "120")
+
+ # def test_tabseparator(self):
+ # result = get_result("input_preprocessing/tabseparator", "x_cp2k_CP2K_INPUT.FORCE_EVAL.DFT.MGRID.CUTOFF", optimize=False)
+ # self.assertEqual(result, "120")
+
+
+# #===============================================================================
+# class TestGeoOpt(unittest.TestCase):
+
+ # @classmethod
+ # def setUpClass(cls):
+ # cls.results = get_results("geo_opt/cg", "section_run")
+
+ # def test_geometry_optimization_converged(self):
+ # result = self.results["geometry_optimization_converged"]
+ # self.assertTrue(result)
+
+ # def test_number_of_frames_in_sequence(self):
+ # result = self.results["number_of_frames_in_sequence"]
+ # self.assertEqual(result, 7)
+
+ # def test_frame_sequence_to_sampling_ref(self):
+ # result = self.results["frame_sequence_to_sampling_ref"]
+ # self.assertEqual(result, 0)
+
+ # def test_frame_sequence_local_frames_ref(self):
+ # result = self.results["frame_sequence_local_frames_ref"]
+ # expected_result = np.array([0, 1, 2, 3, 4, 5, 6])
+ # self.assertTrue(np.array_equal(result, expected_result))
+
+ # def test_sampling_method(self):
+ # result = self.results["sampling_method"]
+ # self.assertEqual(result, "geometry_optimization")
+
+ # def test_geometry_optimization_method(self):
+ # result = self.results["geometry_optimization_method"]
+ # self.assertEqual(result, "conjugate_gradient")
+
+ # def test_geometry_optimization_geometry_change(self):
+ # result = self.results["geometry_optimization_geometry_change"]
+ # expected_result = convert_unit(
+ # 0.0010000000,
+ # "bohr"
+ # )
+ # self.assertEqual(result, expected_result)
+
+ # def test_geometry_optimization_threshold_force(self):
+ # result = self.results["geometry_optimization_threshold_force"]
+ # expected_result = convert_unit(
+ # 0.0010000000,
+ # "bohr^-1*hartree"
+ # )
+ # self.assertEqual(result, expected_result)
+
+ # def test_frame_sequence_potential_energy(self):
+ # result = self.results["frame_sequence_potential_energy"]
+ # expected_result = convert_unit(
+ # np.array([
+ # -17.1534159246,
+ # -17.1941015290,
+ # -17.2092321965,
+ # -17.2097667733,
+ # -17.2097743028,
+ # -17.2097743229,
+ # -17.20977820662248,
+ # ]),
+ # "hartree"
+ # )
+ # self.assertTrue(np.array_equal(result, expected_result))
+
+ # def test_atom_positions(self):
+ # result = self.results["atom_positions"]
+ # expected_start = convert_unit(
+ # np.array([
+ # [12.2353220000, 1.3766420000, 10.8698800000],
+ # [12.4175775999, 2.2362362573, 11.2616216864],
+ # [11.9271436933, 1.5723516602, 10.0115134757],
+ # ]),
+ # "angstrom"
+ # )
+
+ # expected_end = convert_unit(
+ # np.array([
+ # [12.2353220000, 1.3766420000, 10.8698800000],
+ # [12.4958164689, 2.2307248873, 11.3354322515],
+ # [11.9975558616, 1.5748085240, 10.0062792262],
+ # ]),
+ # "angstrom"
+ # )
+ # result_start = result[0,:,:]
+ # result_end = result[-1,:,:]
+ # self.assertTrue(np.array_equal(result_start, expected_start))
+ # self.assertTrue(np.array_equal(result_end, expected_end))
+
+
+# # ===============================================================================
+# class TestGeoOptTrajFormats(unittest.TestCase):
+
+ # def test_xyz(self):
+
+ # result = get_result("geo_opt/geometry_formats/xyz", "atom_positions", optimize=True)
+ # expected_start = convert_unit(
+ # np.array([
+ # [12.2353220000, 1.3766420000, 10.8698800000],
+ # [12.4175624065, 2.2362390825, 11.2616392180],
+ # [11.9271777126, 1.5723402996, 10.0115089094],
+ # ]),
+ # "angstrom"
+ # )
+ # expected_end = convert_unit(
+ # np.array([
+ # [12.2353220000, 1.3766420000, 10.8698800000],
+ # [12.4957995882, 2.2307218433, 11.3354453867],
+ # [11.9975764125, 1.5747996320, 10.0062529540],
+ # ]),
+ # "angstrom"
+ # )
+ # result_start = result[0,:,:]
+ # result_end = result[-1,:,:]
+ # self.assertTrue(np.array_equal(result_start, expected_start))
+ # self.assertTrue(np.array_equal(result_end, expected_end))
+
+ # def test_pdb(self):
+ # result = get_result("geo_opt/geometry_formats/pdb", "atom_positions", optimize=True)
+ # expected_start = convert_unit(
+ # np.array([
+ # [12.235, 1.377, 10.870],
+ # [12.418, 2.236, 11.262],
+ # [11.927, 1.572, 10.012],
+ # ]),
+ # "angstrom"
+ # )
+ # expected_end = convert_unit(
+ # np.array([
+ # [12.235, 1.377, 10.870],
+ # [12.496, 2.231, 11.335],
+ # [11.998, 1.575, 10.006],
+ # ]),
+ # "angstrom"
+ # )
+ # result_start = result[0,:,:]
+ # result_end = result[-1,:,:]
+ # self.assertTrue(np.array_equal(result_start, expected_start))
+ # self.assertTrue(np.array_equal(result_end, expected_end))
+
+ # def test_dcd(self):
+ # result = get_result("geo_opt/geometry_formats/dcd", "atom_positions", optimize=True)
+ # frames = result.shape[0]
+ # self.assertEqual(frames, 7)
+
+
+# #===============================================================================
+# class TestGeoOptOptimizers(unittest.TestCase):
+
+ # def test_bfgs(self):
+ # result = get_result("geo_opt/bfgs", "geometry_optimization_method")
+ # self.assertEqual(result, "bfgs")
+
+ # def test_lbfgs(self):
+ # result = get_result("geo_opt/lbfgs", "geometry_optimization_method")
+ # self.assertEqual(result, "bfgs")
+
+
+# #===============================================================================
+# class TestGeoOptTrajectory(unittest.TestCase):
+
+ # def test_each_and_add_last(self):
+ # """Test that the EACH and ADD_LAST settings affect the parsing
+ # correctly.
+ # """
+ # results = get_results("geo_opt/each")
+
+ # single_conf = results["section_single_configuration_calculation"]
+ # systems = results["section_system"]
+
+ # i_conf = 0
+ # for calc in single_conf.values():
+ # system_index = calc["single_configuration_calculation_to_system_ref"][0]
+ # system = systems[system_index]
+ # pos = system["atom_positions"]
+
+ # if i_conf == 0 or i_conf == 2 or i_conf == 4:
+ # self.assertEqual(pos, None)
+ # else:
+ # pos = system["atom_positions"][0]
+ # if i_conf == 1:
+ # expected_pos = convert_unit(
+ # np.array([
+ # [12.2353220000, 1.3766420000, 10.8698800000],
+ # [12.4618486015, 2.2314871691, 11.3335607388],
+ # [11.9990227122, 1.5776813026, 10.0384213366],
+ # ]),
+ # "angstrom"
+ # )
+ # self.assertTrue(np.array_equal(pos, expected_pos))
+ # if i_conf == 3:
+ # expected_pos = convert_unit(
+ # np.array([
+ # [12.2353220000, 1.3766420000, 10.8698800000],
+ # [12.4962705528, 2.2308411983, 11.3355758433],
+ # [11.9975151486, 1.5746309898, 10.0054430868],
+ # ]),
+ # "angstrom"
+ # )
+ # self.assertTrue(np.array_equal(pos, expected_pos))
+ # if i_conf == 5:
+ # expected_pos = convert_unit(
+ # np.array([
+ # [12.2353220000, 1.3766420000, 10.8698800000],
+ # [12.4958168364, 2.2307249171, 11.3354322532],
+ # [11.9975556812, 1.5748088251, 10.0062793864],
+ # ]),
+ # "angstrom"
+ # )
+ # self.assertTrue(np.array_equal(pos, expected_pos))
+
+ # if i_conf == 6:
+ # expected_pos = convert_unit(
+ # np.array([
+ # [12.2353220000, 1.3766420000, 10.8698800000],
+ # [12.4958164689, 2.2307248873, 11.3354322515],
+ # [11.9975558616, 1.5748085240, 10.0062792262],
+ # ]),
+ # "angstrom"
+ # )
+ # self.assertTrue(np.array_equal(pos, expected_pos))
+
+ # i_conf += 1
+
+
+# #===============================================================================
+# class TestMD(unittest.TestCase):
+
+ # @classmethod
+ # def setUpClass(cls):
+ # cls.results = get_results("md/nve", "section_run")
+ # cls.temp = convert_unit(
+ # np.array([
+ # 300.000000000,
+ # 275.075405378,
+ # 235.091633019,
+ # 202.752506973,
+ # 192.266488819,
+ # 201.629598676,
+ # 218.299664775,
+ # 230.324748557,
+ # 232.691881533,
+ # 226.146979313,
+ # 213.165337396,
+ # ]),
+ # "K"
+ # )
+ # cls.cons = convert_unit(
+ # np.array([
+ # -34.323271136,
+ # -34.323245645,
+ # -34.323206964,
+ # -34.323183380,
+ # -34.323187747,
+ # -34.323208962,
+ # -34.323227533,
+ # -34.323233583,
+ # -34.323230715,
+ # -34.323227013,
+ # -34.323224123,
+ # ]),
+ # "hartree"
+ # )
+ # cls.pot = 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"
+ # )
+ # cls.kin = 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"
+ # )
+
+ # def test_number_of_atoms(self):
+ # result = self.results["number_of_atoms"]
+ # expected_result = np.array(11*[6])
+ # self.assertTrue(np.array_equal(result, expected_result))
+
+ # def test_ensemble_type(self):
+ # result = self.results["ensemble_type"]
+ # self.assertEqual(result, "NVE")
+
+ # def test_sampling_method(self):
+ # result = self.results["sampling_method"]
+ # self.assertEqual(result, "molecular_dynamics")
+
+ # def test_number_of_frames_in_sequence(self):
+ # result = self.results["number_of_frames_in_sequence"]
+ # self.assertEqual(result, 11)
+
+ # 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_atom_velocities(self):
+ # result = self.results["atom_velocities"]
+ # expected_start = convert_unit(
+ # np.array([
+ # [0.0000299284, 0.0000082360, -0.0000216368],
+ # [-0.0001665963, 0.0001143863, -0.0000622640],
+ # [-0.0005732926, -0.0003112611, -0.0007149779],
+ # [0.0013083605, -0.0009262219, 0.0006258560],
+ # [0.0012002313, -0.0003701042, 0.0002810523],
+ # [0.0002340810, -0.0003388418, 0.0011398583],
+ # ]),
+ # "bohr*(planckConstant/hartree)^-1"
+ # )
+ # expected_end = convert_unit(
+ # np.array([
+ # [0.0001600263, -0.0000383308, 0.0000153662],
+ # [-0.0001269381, -0.0000005151, -0.0000726214],
+ # [0.0000177093, -0.0003257814, -0.0000257852],
+ # [-0.0015067045, -0.0001700489, -0.0003651605],
+ # [0.0000307926, 0.0006886719, 0.0008431321],
+ # [0.0007424681, 0.0003614127, 0.0005749089],
+ # ]),
+ # "bohr*(planckConstant/hartree)^-1"
+ # )
+
+ # 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"]
+ # self.assertTrue(np.array_equal(result, self.pot))
+
+ # def test_frame_sequence_kinetic_energy(self):
+ # result = self.results["frame_sequence_kinetic_energy"]
+ # self.assertTrue(np.array_equal(result, self.kin))
+
+ # def test_frame_sequence_conserved_quantity(self):
+ # result = self.results["frame_sequence_conserved_quantity"]
+ # self.assertTrue(np.array_equal(result, self.cons))
+
+ # def test_frame_sequence_temperature(self):
+ # result = self.results["frame_sequence_temperature"]
+ # self.assertTrue(np.array_equal(result, self.temp))
+
+ # def test_frame_sequence_time(self):
+ # result = self.results["frame_sequence_time"]
+ # expected_result = convert_unit(
+ # np.array([
+ # 0.000000,
+ # 0.500000,
+ # 1.000000,
+ # 1.500000,
+ # 2.000000,
+ # 2.500000,
+ # 3.000000,
+ # 3.500000,
+ # 4.000000,
+ # 4.500000,
+ # 5.000000,
+ # ]),
+ # "fs"
+ # )
+ # self.assertTrue(np.array_equal(result, expected_result))
+
+ # def test_frame_sequence_potential_energy_stats(self):
+ # result = self.results["frame_sequence_potential_energy_stats"]
+ # expected_result = np.array([self.pot.mean(), self.pot.std()])
+ # self.assertTrue(np.array_equal(result, expected_result))
+
+ # def test_frame_sequence_kinetic_energy_stats(self):
+ # result = self.results["frame_sequence_kinetic_energy_stats"]
+ # expected_result = np.array([self.kin.mean(), self.kin.std()])
+ # self.assertTrue(np.array_equal(result, expected_result))
+
+ # def test_frame_sequence_conserved_quantity_stats(self):
+ # result = self.results["frame_sequence_conserved_quantity_stats"]
+ # expected_result = np.array([self.cons.mean(), self.cons.std()])
+ # self.assertTrue(np.array_equal(result, expected_result))
+
+ # def test_frame_sequence_temperature_stats(self):
+ # result = self.results["frame_sequence_temperature_stats"]
+ # expected_result = np.array([self.temp.mean(), self.temp.std()])
+ # self.assertTrue(np.array_equal(result, expected_result))
+
+
+# #===============================================================================
+# class TestMDEnsembles(unittest.TestCase):
+
+ # @classmethod
+ # def setUpClass(cls):
+ # cls.pressure = convert_unit(
+ # np.array([
+ # -0.192828092559E+04,
+ # -0.145371071470E+04,
+ # -0.210098903760E+03,
+ # 0.167260570313E+04,
+ # 0.395562042841E+04,
+ # 0.630374855942E+04,
+ # 0.836906136786E+04,
+ # 0.983216022830E+04,
+ # 0.104711540465E+05,
+ # 0.102444821550E+05,
+ # 0.931695792434E+04,
+ # ]),
+ # "bar"
+ # )
+
+ # def test_nvt(self):
+ # results = get_results("md/nvt", "section_run")
+ # ensemble = results["ensemble_type"]
+ # self.assertEqual(ensemble, "NVT")
+
+ # def test_npt(self):
+ # results = get_results("md/npt", "section_run")
+ # ensemble = results["ensemble_type"]
+ # self.assertEqual(ensemble, "NPT")
+
+ # pressure = results["frame_sequence_pressure"]
+ # self.assertTrue(np.array_equal(pressure, self.pressure))
+
+ # pressure_stats = results["frame_sequence_pressure_stats"]
+ # expected_pressure_stats = np.array([self.pressure.mean(), self.pressure.std()])
+ # self.assertTrue(np.array_equal(pressure_stats, expected_pressure_stats))
+
+ # simulation_cell = results["simulation_cell"]
+ # expected_cell_start = convert_unit(
+ # np.array(
+ # [[
+ # 6.0000000000,
+ # 0.0000000000,
+ # 0.0000000000,
+ # ], [
+ # 0.0000000000,
+ # 6.0000000000,
+ # 0.0000000000,
+ # ], [
+ # 0.0000000000,
+ # 0.0000000000,
+ # 6.0000000000,
+ # ]]),
+ # "angstrom"
+ # )
+ # expected_cell_end = convert_unit(
+ # np.array(
+ # [[
+ # 5.9960617905,
+ # -0.0068118798,
+ # -0.0102043036,
+ # ], [
+ # -0.0068116027,
+ # 6.0225574669,
+ # -0.0155044063,
+ # ], [
+ # -0.0102048226,
+ # -0.0155046726,
+ # 6.0083072343,
+ # ]]),
+ # "angstrom"
+ # )
+ # self.assertEqual(simulation_cell.shape[0], 11)
+ # self.assertTrue(np.array_equal(expected_cell_start, simulation_cell[0,:,:]))
+ # self.assertTrue(np.array_equal(expected_cell_end, simulation_cell[-1,:,:]))
+
+
+# #===============================================================================
+# class TestElectronicStructureMethod(unittest.TestCase):
+
+ # def test_mp2(self):
+ # results = get_results("electronic_structure_method/mp2", "section_run")
+ # result = results["electronic_structure_method"]
+ # self.assertEqual(result, "MP2")
+
+ # def test_dft_plus_u(self):
+ # results = get_results("electronic_structure_method/dft_plus_u", "section_run")
+ # result = results["electronic_structure_method"]
+ # self.assertEqual(result, "DFT+U")
+
+ # def test_rpa(self):
+ # results = get_results("electronic_structure_method/rpa", "section_run")
+ # result = results["electronic_structure_method"]
+ # self.assertEqual(result, "RPA")
+
+
+#===============================================================================
+if __name__ == '__main__':
+ suites = []
+ suites.append(unittest.TestLoader().loadTestsFromTestCase(TestSinglePoint))
+ alltests = unittest.TestSuite(suites)
+ unittest.TextTestRunner(verbosity=0).run(alltests)
diff --git a/test/unittests/cpmd_4.1/single_point/GEOMETRY b/test/unittests/cpmd_4.1/single_point/GEOMETRY
new file mode 100644
index 0000000000000000000000000000000000000000..4fc346d8d03ee55cc5ed943b11eb14af91be77a4
--- /dev/null
+++ b/test/unittests/cpmd_4.1/single_point/GEOMETRY
@@ -0,0 +1,2 @@
+ 8.259992891426 7.558904499132 7.558904499132 0.017798524379 -0.000000000000 -0.000000000000
+ 6.857816106837 7.558904499132 7.558904499132 -0.017798524379 -0.000000000000 -0.000000000000
diff --git a/test/unittests/cpmd_4.1/single_point/GEOMETRY.xyz b/test/unittests/cpmd_4.1/single_point/GEOMETRY.xyz
new file mode 100644
index 0000000000000000000000000000000000000000..b13c48d0b6644a53a06502a83cea74fb0265e4e1
--- /dev/null
+++ b/test/unittests/cpmd_4.1/single_point/GEOMETRY.xyz
@@ -0,0 +1,4 @@
+ 2
+GEOMETRY FILE / created by CPMD
+ H 4.371000000000 4.000000000000 4.000000000000 0.009418573488 -0.000000000000 -0.000000000000
+ H 3.629000000000 4.000000000000 4.000000000000 -0.009418573488 -0.000000000000 -0.000000000000
diff --git a/test/unittests/cpmd_4.1/single_point/LATEST b/test/unittests/cpmd_4.1/single_point/LATEST
new file mode 100644
index 0000000000000000000000000000000000000000..0e4449210602fd9c3a45bd3bc780cd67ad8721b0
--- /dev/null
+++ b/test/unittests/cpmd_4.1/single_point/LATEST
@@ -0,0 +1,2 @@
+./RESTART.1
+ 1
diff --git a/test/unittests/cpmd_4.1/single_point/RESTART.1 b/test/unittests/cpmd_4.1/single_point/RESTART.1
new file mode 100644
index 0000000000000000000000000000000000000000..88b00a1a01f06fe6a5955b36cc01256a544cf1ce
Binary files /dev/null and b/test/unittests/cpmd_4.1/single_point/RESTART.1 differ
diff --git a/test/unittests/cpmd_4.1/single_point/input.inp b/test/unittests/cpmd_4.1/single_point/input.inp
new file mode 100755
index 0000000000000000000000000000000000000000..c1b5c8a868f3b0aec8910af9399c6bfabec9fa3d
--- /dev/null
+++ b/test/unittests/cpmd_4.1/single_point/input.inp
@@ -0,0 +1,35 @@
+&INFO
+isolated hydrogen molecule.
+single point calculation.
+&END
+
+&CPMD
+ OPTIMIZE WAVEFUNCTION
+ CONVERGENCE ORBITALS
+ 1.0d-7
+ CENTER MOLECULE ON
+ PRINT FORCES ON
+&END
+
+&SYSTEM
+ SYMMETRY
+ 1
+ ANGSTROM
+ CELL
+ 8.00 1.0 1.0 0.0 0.0 0.0
+ CUTOFF
+ 70.0
+&END
+
+&DFT
+ FUNCTIONAL LDA
+&END
+
+&ATOMS
+*H_MT_LDA.psp
+ LMAX=S
+ 2
+ 4.371 4.000 4.000
+ 3.629 4.000 4.000
+&END
+
diff --git a/test/unittests/cpmd_4.1/single_point/output.out b/test/unittests/cpmd_4.1/single_point/output.out
new file mode 100644
index 0000000000000000000000000000000000000000..b7fb802822bc95d7164dab1cff250c4b764493de
--- /dev/null
+++ b/test/unittests/cpmd_4.1/single_point/output.out
@@ -0,0 +1,286 @@
+ cp_groups: we are using a 1 x 1 grid (groups x nprocs).
+ PROGRAM CPMD STARTED AT: 2016-07-04 14:05:06.851
+ SETCNST| USING: CODATA 2006 UNITS
+
+
+ ****** ****** **** **** ******
+ ******* ******* ********** *******
+ *** ** *** ** **** ** ** ***
+ ** ** *** ** ** ** ** **
+ ** ******* ** ** ** **
+ *** ****** ** ** ** ***
+ ******* ** ** ** *******
+ ****** ** ** ** ******
+
+ VERSION 4.1-rUnversioned directory
+
+ COPYRIGHT
+ IBM RESEARCH DIVISION
+ MPI FESTKOERPERFORSCHUNG STUTTGART
+
+ The CPMD consortium
+ Home Page: http://www.cpmd.org
+ Mailing List: cpmd-list@cpmd.org
+ E-mail: cpmd@cpmd.org
+
+
+ *** Jun 22 2016 -- 12:41:05 ***
+
+ THE INPUT FILE IS: input.inp
+ THIS JOB RUNS ON: lenovo700
+ THE CURRENT DIRECTORY IS:
+ /home/lauri/Dropbox/nomad-dev/nomad-lab-base/parsers/cpmd/test/unittests/cpmd_4.1/h2
+ THE TEMPORARY DIRECTORY IS:
+ /home/lauri/Dropbox/nomad-dev/nomad-lab-base/parsers/cpmd/test/unittests/cpmd_4.1/h2
+ THE PROCESS ID IS: 32589
+ THE JOB WAS SUBMITTED BY: lauri
+
+
+ ******************************************************************************
+ * INFO - INFO - INFO - INFO - INFO - INFO - INFO - INFO - INFO - INFO - INFO *
+ ******************************************************************************
+ * isolated hydrogen molecule. *
+ * single point calculation. *
+ ******************************************************************************
+
+ SINGLE POINT DENSITY OPTIMIZATION
+
+ USING SEED 123456 TO INIT. PSEUDO RANDOM NUMBER GEN.
+ PATH TO THE RESTART FILES: ./
+ GRAM-SCHMIDT ORTHOGONALIZATION
+ MAXIMUM NUMBER OF STEPS: 10000 STEPS
+ MAXIMUM NUMBER OF ITERATIONS FOR SC: 10000 STEPS
+ PRINT INTERMEDIATE RESULTS EVERY 10001 STEPS
+ STORE INTERMEDIATE RESULTS EVERY 10001 STEPS
+ NUMBER OF DISTINCT RESTART FILES: 1
+ TEMPERATURE IS CALCULATED ASSUMING EXTENDED BULK BEHAVIOR
+ FICTITIOUS ELECTRON MASS: 400.0000
+ TIME STEP FOR ELECTRONS: 5.0000
+ TIME STEP FOR IONS: 5.0000
+ CONVERGENCE CRITERIA FOR WAVEFUNCTION OPTIMIZATION: 1.0000E-07
+ WAVEFUNCTION OPTIMIZATION BY PRECONDITIONED DIIS
+ THRESHOLD FOR THE WF-HESSIAN IS 0.5000
+ MAXIMUM NUMBER OF VECTORS RETAINED FOR DIIS: 10
+ STEPS UNTIL DIIS RESET ON POOR PROGRESS: 10
+ FULL ELECTRONIC GRADIENT IS USED
+ SPLINE INTERPOLATION IN G-SPACE FOR PSEUDOPOTENTIAL FUNCTIONS
+ NUMBER OF SPLINE POINTS: 5000
+
+ EXCHANGE CORRELATION FUNCTIONALS
+ LDA EXCHANGE: NONE
+ LDA XC THROUGH PADE APPROXIMATION
+ S.GOEDECKER, J.HUTTER, M.TETER PRB 541703 (1996)
+
+ *** DETSP| SIZE OF THE PROGRAM IS NOT AVAILABLE ***
+
+ ***************************** ATOMS ****************************
+ NR TYPE X(BOHR) Y(BOHR) Z(BOHR) MBL
+ 1 H 8.259993 7.558904 7.558904 3
+ 2 H 6.857816 7.558904 7.558904 3
+ ****************************************************************
+
+ NUMBER OF STATES: 1
+ NUMBER OF ELECTRONS: 2.00000
+ CHARGE: 0.00000
+ ELECTRON TEMPERATURE(KELVIN): 0.00000
+ OCCUPATION
+ 2.0
+
+ ============================================================
+ | Pseudopotential Report Thu Jan 11 18:21:49 1996 |
+ ------------------------------------------------------------
+ | Atomic Symbol : H |
+ | Atomic Number : 1 |
+ | Number of core states : 0 |
+ | Number of valence states : 1 |
+ | Exchange-Correlation Functional : |
+ | Slater exchange : .6667 |
+ | LDA correlation : Ceperley-Alder |
+ | Electron Configuration : N L Occupation |
+ | 1 S 1.0000 |
+ | Full Potential Total Energy -.445894 |
+ | Trouiller-Martins normconserving PP |
+ | n l rc energy |
+ | 1 S .5000 -.23366 |
+ | 2 P .5000 -.23366 |
+ | Number of Mesh Points : 511 |
+ | Pseudoatom Total Energy -.445889 |
+ ============================================================
+
+ ****************************************************************
+ * ATOM MASS RAGGIO NLCC PSEUDOPOTENTIAL *
+ * H 1.0080 1.2000 NO S LOCAL *
+ ****************************************************************
+
+
+ PARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARA
+ NCPU NGW NHG PLANES GXRAYS HXRAYS ORBITALS Z-PLANES
+ 0 17133 136605 90 1281 5089 1 1
+ G=0 COMPONENT ON PROCESSOR : 0
+ PARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARA
+
+ *** loadpa| SIZE OF THE PROGRAM IS NOT AVAILABLE ***
+
+ OPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPEN
+ NUMBER OF CPUS PER TASK 1
+ OPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPEN
+
+ *** rggen| SIZE OF THE PROGRAM IS NOT AVAILABLE ***
+
+ ************************** SUPERCELL ***************************
+ SYMMETRY: SIMPLE CUBIC
+ LATTICE CONSTANT(a.u.): 15.11781
+ CELL DIMENSION: 15.1178 1.0000 1.0000 0.0000 0.0000 0.0000
+ VOLUME(OMEGA IN BOHR^3): 3455.14726
+ LATTICE VECTOR A1(BOHR): 15.1178 0.0000 0.0000
+ LATTICE VECTOR A2(BOHR): 0.0000 15.1178 0.0000
+ LATTICE VECTOR A3(BOHR): 0.0000 0.0000 15.1178
+ RECIP. LAT. VEC. B1(2Pi/BOHR): 0.0661 0.0000 0.0000
+ RECIP. LAT. VEC. B2(2Pi/BOHR): 0.0000 0.0661 0.0000
+ RECIP. LAT. VEC. B3(2Pi/BOHR): 0.0000 0.0000 0.0661
+ REAL SPACE MESH: 90 90 90
+ WAVEFUNCTION CUTOFF(RYDBERG): 70.00000
+ DENSITY CUTOFF(RYDBERG): (DUAL= 4.00) 280.00000
+ NUMBER OF PLANE WAVES FOR WAVEFUNCTION CUTOFF: 17133
+ NUMBER OF PLANE WAVES FOR DENSITY CUTOFF: 136605
+ ****************************************************************
+
+ *** RINFORCE| SIZE OF THE PROGRAM IS NOT AVAILABLE ***
+ *** FFTPRP| SIZE OF THE PROGRAM IS NOT AVAILABLE ***
+
+ GENERATE ATOMIC BASIS SET
+ H SLATER ORBITALS
+ 1S ALPHA= 1.0000 OCCUPATION= 1.00
+
+
+ INITIALIZATION TIME: 0.48 SECONDS
+
+ *** WFOPTS| SIZE OF THE PROGRAM IS NOT AVAILABLE ***
+ *** PHFAC| SIZE OF THE PROGRAM IS NOT AVAILABLE ***
+ NOTE: ATOMIC GUESS USING DISTRIBUTED LINALG WITH LANCZOS
+ *** ATOMWF| SIZE OF THE PROGRAM IS NOT AVAILABLE ***
+ ATRHO| CHARGE(R-SPACE): 2.000000 (G-SPACE): 2.000000
+
+ ATOM COORDINATES GRADIENTS (-FORCES)
+ 1 H 8.2600 7.5589 7.5589 0.000E+00 0.000E+00 0.000E+00
+ 2 H 6.8578 7.5589 7.5589 0.000E+00 0.000E+00 0.000E+00
+
+ TIME FOR WAVEFUNCTION INITIALIZATION: 0.83 SECONDS
+ *** RWFOPT| SIZE OF THE PROGRAM IS NOT AVAILABLE ***
+ EWALD| SUM IN REAL SPACE OVER 1* 1* 1 CELLS
+
+ TOTAL INTEGRATED ELECTRONIC DENSITY
+ IN G-SPACE = 2.0000000000
+ IN R-SPACE = 2.0000000000
+
+ (K+E1+L+N+X) TOTAL ENERGY = -1.09689770 A.U.
+ (K) KINETIC ENERGY = 0.81247072 A.U.
+ (E1=A-S+R) ELECTROSTATIC ENERGY = -0.48640053 A.U.
+ (S) ESELF = 0.66490380 A.U.
+ (R) ESR = 0.17302593 A.U.
+ (L) LOCAL PSEUDOPOTENTIAL ENERGY = -0.84879440 A.U.
+ (N) N-L PSEUDOPOTENTIAL ENERGY = 0.00000000 A.U.
+ (X) EXCHANGE-CORRELATION ENERGY = -0.57417350 A.U.
+
+ NFI GEMAX CNORM ETOT DETOT TCPU
+ 1 3.816E-02 2.886E-03 -1.096898 0.000E+00 0.23
+ 2 8.628E-03 1.041E-03 -1.130803 -3.391E-02 0.22
+ 3 2.736E-03 2.293E-04 -1.132376 -1.572E-03 0.22
+ 4 6.115E-04 4.235E-05 -1.132456 -8.056E-05 0.22
+ 5 1.532E-04 7.007E-06 -1.132459 -3.315E-06 0.24
+ 6 3.895E-05 1.396E-06 -1.132460 -1.338E-07 0.22
+ 7 6.288E-06 4.459E-07 -1.132460 -7.717E-09 0.22
+ 8 7.941E-07 1.282E-07 -1.132460 -4.283E-10 0.22
+ 9 1.237E-07 2.861E-08 -1.132460 -1.992E-11 0.22
+ 10 2.278E-08 5.401E-09 -1.132460 -8.606E-13 0.22
+
+ RESTART INFORMATION WRITTEN ON FILE ./RESTART.1
+ *** RWFOPT| SIZE OF THE PROGRAM IS NOT AVAILABLE ***
+
+ ****************************************************************
+ * *
+ * FINAL RESULTS *
+ * *
+ ****************************************************************
+
+ ATOM COORDINATES GRADIENTS (-FORCES)
+ 1 H 8.2600 7.5589 7.5589 1.780E-02 -1.104E-16 -9.425E-17
+ 2 H 6.8578 7.5589 7.5589 -1.780E-02 -1.867E-16 -1.490E-16
+
+ ****************************************************************
+
+
+ ELECTRONIC GRADIENT:
+ MAX. COMPONENT = 1.15980E-08 NORM = 1.11525E-09
+ NUCLEAR GRADIENT:
+ MAX. COMPONENT = 1.77985E-02 NORM = 1.02760E-02
+
+
+ TOTAL INTEGRATED ELECTRONIC DENSITY
+ IN G-SPACE = 2.0000000000
+ IN R-SPACE = 2.0000000000
+
+ (K+E1+L+N+X) TOTAL ENERGY = -1.13245953 A.U.
+ (K) KINETIC ENERGY = 1.09007149 A.U.
+ (E1=A-S+R) ELECTROSTATIC ENERGY = -0.47319176 A.U.
+ (S) ESELF = 0.66490380 A.U.
+ (R) ESR = 0.17302593 A.U.
+ (L) LOCAL PSEUDOPOTENTIAL ENERGY = -1.09902228 A.U.
+ (N) N-L PSEUDOPOTENTIAL ENERGY = 0.00000000 A.U.
+ (X) EXCHANGE-CORRELATION ENERGY = -0.65031699 A.U.
+
+ ****************************************************************
+
+
+
+ ****************************************************************
+ * *
+ * TIMING *
+ * *
+ ****************************************************************
+ SUBROUTINE CALLS SELF TIME TOTAL TIME
+ AVERAGE MAXIMUM AVERAGE MAXIMUM
+ cpmd 1 0.00 0.00 3.67 3.67
+ rwfopt 1 0.00 0.00 3.20 3.20
+ updwf 11 0.00 0.00 2.37 2.37
+ forcedr 11 0.00 0.00 2.33 2.33
+ forces 11 0.00 0.00 2.33 2.33
+ forces_a 11 0.00 0.00 1.80 1.80
+ rscpot 11 0.00 0.00 1.80 1.80
+ vofrho 12 0.00 0.00 1.79 1.79
+ VOFRHOB 12 0.04 0.04 1.22 1.22
+ INVFFTN 37 1.12 1.12 1.12 1.12
+ initrun 1 0.00 0.00 0.82 0.82
+ rinitwf 1 0.00 0.00 0.82 0.82
+ ATOMWF 1 0.00 0.00 0.82 0.82
+ FWFFTN 25 0.69 0.69 0.69 0.69
+ xcener_new 12 0.04 0.04 0.67 0.67
+ mikeu 12 0.63 0.63 0.63 0.63
+ vpsi 13 0.06 0.06 0.63 0.63
+ VOFRHOA 12 0.03 0.03 0.57 0.57
+ ATRHO 1 0.35 0.35 0.39 0.39
+ rhoofr 11 0.07 0.07 0.34 0.34
+ rinit 1 0.00 0.00 0.26 0.26
+ rggen 1 0.01 0.01 0.26 0.26
+ loadpa 1 0.01 0.01 0.25 0.25
+ dist_ksmat 1 0.00 0.00 0.11 0.11
+ RINFORCE 1 0.00 0.00 0.10 0.10
+ NUMPW 1 0.10 0.10 0.10 0.10
+ loadpa_b 1 0.10 0.10 0.10 0.10
+ loadpa_c 1 0.10 0.10 0.10 0.10
+ FORMFN 1 0.10 0.10 0.10 0.10
+ ppener 12 0.06 0.06 0.06 0.06
+ loadpa_a 1 0.04 0.04 0.04 0.04
+ EICALC 12 0.04 0.04 0.04 0.04
+ odiis 11 0.04 0.04 0.04 0.04
+ PUTPS 1 0.01 0.01 0.01 0.01
+ forces_b 11 0.00 0.00 0.01 0.01
+ potfor 1 0.01 0.01 0.01 0.01
+ fftprp 1 0.00 0.00 0.00 0.00
+ ****************************************************************
+
+ CPU TIME : 0 HOURS 0 MINUTES 3.67 SECONDS
+ ELAPSED TIME : 0 HOURS 0 MINUTES 3.67 SECONDS
+ *** CPMD| SIZE OF THE PROGRAM IS NOT AVAILABLE ***
+
+ PROGRAM CPMD ENDED AT: 2016-07-04 14:05:10.523
diff --git a/test/unittests/cpmd_4.1/single_point/run.sh b/test/unittests/cpmd_4.1/single_point/run.sh
new file mode 100755
index 0000000000000000000000000000000000000000..222042e49aa219ad6e922865b7797f786e068428
--- /dev/null
+++ b/test/unittests/cpmd_4.1/single_point/run.sh
@@ -0,0 +1,3 @@
+export CPMD_PP_LIBRARY_PATH=../
+export OMP_NUM_THREADS=1
+cpmd41 input.inp > output.out