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Commit 58afb4ce authored by Himanen, Lauri (himanel1)'s avatar Himanen, Lauri (himanel1)
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Started to merge SimpleMatcher with NomadParser

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cp2kparser/__init__.py
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#! /usr/bin/env python #! /usr/bin/env python
import cp2kparser.generics.logconfig import cp2kparser.generics.logconfig
from pint import UnitRegistry
import os
ureg = UnitRegistry(os.path.dirname(__file__)+"/unit_registry.txt")
cp2kparser/constants.txt deleted 100644 → 0
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# Pint constants for NomadParsers
# source: http://physics.nist.gov/cuu/Constants/Table/allascii.txt
# Source: http://physics.nist.gov/cuu/Constants/Table/allascii.txt
speed_of_light = 299792458 * meter / second = c
standard_gravity = 9.806650 * meter / second ** 2 = g_0 = g_n = gravity
vacuum_permeability = 4 * pi * 1e-7 * newton / ampere ** 2 = mu_0 = magnetic_constant
vacuum_permittivity = 1 / (mu_0 * c **2 ) = epsilon_0 = electric_constant
Z_0 = mu_0 * c = impedance_of_free_space = characteristic_impedance_of_vacuum
bohr = 0.52917721067e-10 m
# 0.000 000 29 e-34
planck_constant = 6.62606957e-34 J s = h
hbar = planck_constant / (2 * pi) = ħ
# 0.000 80 e-11
newtonian_constant_of_gravitation = 6.67384e-11 m^3 kg^-1 s^-2
# 0.000 000 035 e-19
# elementary_charge = 1.602176565e-19 C = e
# 0.000 0075
molar_gas_constant = 8.3144621 J mol^-1 K^-1 = R
# 0.000 000 0024 e-3
fine_structure_constant = 7.2973525698e-3
# 0.000 000 27 e23
avogadro_number = 6.02214129e23 mol^-1 =N_A
# 0.000 0013 e-23
boltzmann_constant = 1.3806488e-23 J K^-1 = k
# 0.000 021 e-8
stefan_boltzmann_constant = 5.670373e-8 W m^-2 K^-4 = σ
# 0.000 0053 e10
wien_frequency_displacement_law_constant = 5.8789254e10 Hz K^-1
# 0.000 055
rydberg_constant = 10973731.568539 m^-1
# 0.000 000 40 e-31
electron_mass = 9.10938291e-31 kg = m_e
# 0.000 000 074 e-27
neutron_mass = 1.674927351e-27 kg = m_n
# 0.000 000 074 e-27
proton_mass = 1.672621777e-27 kg = m_p
cp2kparser/generics/nomadparser.py
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cp2kparser/implementation/autoparser.py
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...@@ -29,9 +29,10 @@ def scan_path_for_files(path): ...@@ -29,9 +29,10 @@ def scan_path_for_files(path):
#=============================================================================== #===============================================================================
def get_parser(path, test_mode=True, stream=sys.stdout): def get_parser(path, test_mode=True, stream=sys.stdout):
files = scan_path_for_files(path) files = scan_path_for_files(path)
metaInfoPath = os.path.normpath(os.path.join(os.path.dirname(os.path.abspath(__file__)), "../../../nomad-meta-info/meta_info/nomad_meta_info/cp2k.nomadmetainfo.json"))
json_input = { json_input = {
"version": "nomadparsein.json 1.0", "version": "nomadparsein.json 1.0",
"metaInfoFile": os.path.join(os.path.dirname(__file__), 'metainfo.json'), "metaInfoFile": metaInfoPath,
"tmpDir": "/home", "tmpDir": "/home",
"metainfoToKeep": [], "metainfoToKeep": [],
"metainfoToSkip": [], "metainfoToSkip": [],
...@@ -45,4 +46,4 @@ def get_parser(path, test_mode=True, stream=sys.stdout): ...@@ -45,4 +46,4 @@ def get_parser(path, test_mode=True, stream=sys.stdout):
if __name__ == '__main__': if __name__ == '__main__':
path = os.path.dirname(os.path.realpath(os.path.dirname(__file__))) path = os.path.dirname(os.path.realpath(os.path.dirname(__file__)))
parser = get_parser(path) parser = get_parser(path)
parser.parse_all() parser.parse()
cp2kparser/implementation/metainfo.json deleted 100644 → 0
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cp2kparser/implementation/parser.py
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import os import os
import re2 as re import re2 as re
from cp2kparser.generics.nomadparser import NomadParser, Result, ResultCode from cp2kparser.generics.nomadparser import NomadParser
from cp2kparser.implementation.regexs import * from cp2kparser.implementation.regexs import *
from cp2kparser.engines.regexengine import RegexEngine from cp2kparser.engines.regexengine import RegexEngine
from cp2kparser.engines.csvengine import CSVEngine from cp2kparser.engines.csvengine import CSVEngine
...@@ -8,6 +8,7 @@ from cp2kparser.engines.cp2kinputengine import CP2KInputEngine ...@@ -8,6 +8,7 @@ from cp2kparser.engines.cp2kinputengine import CP2KInputEngine
from cp2kparser.engines.xmlengine import XMLEngine from cp2kparser.engines.xmlengine import XMLEngine
from nomadcore.coordinate_reader import CoordinateReader from nomadcore.coordinate_reader import CoordinateReader
from nomadcore.unit_conversion.unit_conversion import convert_unit, ureg from nomadcore.unit_conversion.unit_conversion import convert_unit, ureg
from nomadcore.simple_parser import SimpleMatcher as SM
from cp2kparser.engines.cp2kinputenginedata.input_tree import CP2KInput from cp2kparser.engines.cp2kinputenginedata.input_tree import CP2KInput
import numpy as np import numpy as np
import logging import logging
...@@ -43,26 +44,14 @@ class CP2KParser(NomadParser): ...@@ -43,26 +44,14 @@ class CP2KParser(NomadParser):
self.regexs = None self.regexs = None
self.extended_input = None self.extended_input = None
# Use some convenient functions from base
self.determine_file_ids_pre_setup() self.determine_file_ids_pre_setup()
self.input_preprocessor() self.input_preprocessor()
self.setup_version() self.setup_version()
self.determine_file_ids_post_setup() self.determine_file_ids_post_setup()
def get_supported_quantities(self):
"""Inherited from NomadParser.
"""
supported_quantities = []
implementation_methods = [method for method in dir(self.implementation) if callable(getattr(self.implementation, method))]
for method in implementation_methods:
if method.startswith("_Q_"):
method = method[3:]
supported_quantities.append(method)
return supported_quantities
def setup_version(self): def setup_version(self):
"""Inherited from NomadParser. """Setups the version by looking at the output file and the version
specified in it.
""" """
# Determine the CP2K version from the output file # Determine the CP2K version from the output file
beginning = self.read_part_of_file("output", 2048) beginning = self.read_part_of_file("output", 2048)
...@@ -92,23 +81,13 @@ class CP2KParser(NomadParser): ...@@ -92,23 +81,13 @@ class CP2KParser(NomadParser):
logger.debug("Using default implementation.") logger.debug("Using default implementation.")
self.implementation = globals()["CP2KImplementation"](self) self.implementation = globals()["CP2KImplementation"](self)
def start_parsing(self, name):
"""Inherited from NomadParser.
"""
# Ask the implementation for the quantity
function = getattr(self.implementation, "_Q_" + name)
if function:
return function()
else:
logger.error("The function for quantity '{}' is not defined".format(name))
def read_part_of_file(self, file_id, size=1024): def read_part_of_file(self, file_id, size=1024):
fh = self.get_file_handle(file_id) fh = self.get_file_handle(file_id)
buffer = fh.read(size) buffer = fh.read(size)
return buffer return buffer
def input_preprocessor(self): def input_preprocessor(self):
"""Preprocess the input file. Concatenate separate files into one and """Preprocess the input file. Concatenate .inc files into the main input file and
explicitly state all variables. explicitly state all variables.
""" """
...@@ -185,11 +164,6 @@ class CP2KParser(NomadParser): ...@@ -185,11 +164,6 @@ class CP2KParser(NomadParser):
rest = new_line[offset+end:] rest = new_line[offset+end:]
new_line = beginning + value + rest new_line = beginning + value + rest
offset += len_value - len_name - 1 offset += len_value - len_name - 1
# print offset
# print "BEG:" + beginning
# print "VALUE:" + value
# print "REST: " + rest
# print new_line
input_variables_replaced.append(new_line) input_variables_replaced.append(new_line)
self.extended_input = '\n'.join(input_variables_replaced) self.extended_input = '\n'.join(input_variables_replaced)
...@@ -218,7 +192,8 @@ class CP2KParser(NomadParser): ...@@ -218,7 +192,8 @@ class CP2KParser(NomadParser):
self.setup_file_id(filepath, "include") self.setup_file_id(filepath, "include")
def determine_file_ids_post_setup(self): def determine_file_ids_post_setup(self):
"""Inherited from NomadParser. """Determines the file id's after the CP2K verion has been set
up.
""" """
# Determine the presence of force file # Determine the presence of force file
force_path = self.input_tree.get_keyword("FORCE_EVAL/PRINT/FORCES/FILENAME") force_path = self.input_tree.get_keyword("FORCE_EVAL/PRINT/FORCES/FILENAME")
...@@ -337,10 +312,35 @@ class CP2KParser(NomadParser): ...@@ -337,10 +312,35 @@ class CP2KParser(NomadParser):
break break
return folders return folders
def get_all_quantities(self): def parse(self):
"""Parse all supported quantities.""" self.implementation.parse()
for method in self.get_supported_quantities:
self.get_quantity(method) # def get_all_quantities(self):
# """Parse all supported quantities."""
# for method in self.get_supported_quantities:
# self.get_quantity(method)
# def start_parsing(self, name):
# """Inherited from NomadParser.
# """
# # Ask the implementation for the quantity
# function = getattr(self.implementation, "_Q_" + name)
# if function:
# return function()
# else:
# logger.error("The function for quantity '{}' is not defined".format(name))
# def get_supported_quantities(self):
# """Inherited from NomadParser.
# """
# supported_quantities = []
# implementation_methods = [method for method in dir(self.implementation) if callable(getattr(self.implementation, method))]
# for method in implementation_methods:
# if method.startswith("_Q_"):
# method = method[3:]
# supported_quantities.append(method)
# return supported_quantities
#=============================================================================== #===============================================================================
...@@ -363,6 +363,58 @@ class CP2KImplementation(object): ...@@ -363,6 +363,58 @@ class CP2KImplementation(object):
self.atomsengine = parser.atomsengine self.atomsengine = parser.atomsengine
self.input_tree = parser.input_tree self.input_tree = parser.input_tree
# Define the output parsing tree for this version
self.outputstructure = SM(
name='root',
startReStr="",
subMatchers=[
SM(
name='new_run',
startReStr=r" DBCSR\| Multiplication driver",
endReStr="[.\*]+PROGRAM STOPPED IN",
required=True,
sections=['section_run'],
subMatchers=[
SM(
name="run_datetime",
startReStr=r"[\*\s]+PROGRAM STARTED AT\s+(?P<cp2k_run_start_date>\d{4}-\d{2}-\d{2}) (?P<cp2k_run_start_time>\d{2}:\d{2}:\d{2}.\d{3})",
),
SM(
name="version",
startReStr=r" CP2K\| version string:\s+(?P<program_version>[\w\d\W\s]+)",
),
SM(
name="svn_revision",
startReStr=r" CP2K\| source code revision number:\s+svn:(?P<cp2k_svn_revision>\d+)",
)
]
)
]
)
def parse(self):
"""Parses everything that can be found from the given files. The
results are outputted to std.out by using the backend. The scala layer
will the take on from that.
"""
# Write the starting bracket
self.parser.stream.write("[")
# Use the SimpleMatcher to extract most of the results
parserInfo = {"name": "cp2k-parser", "version": "1.0"}
outputfilename = self.parser.get_file_handle("output").name
metainfoenv = self.parser.metainfoenv
backend = self.parser.backend
outputstructure = self.outputstructure
self.parser.parse_file(outputfilename, outputstructure, metainfoenv, backend, parserInfo)
# Then extract the things that cannot be extracted by the SimpleMatcher
# Write the ending bracket
self.parser.stream.write("]\n")
# def dateconverter(datestring):
def _Q_energy_total(self): def _Q_energy_total(self):
"""Return the total energy from the bottom of the input file""" """Return the total energy from the bottom of the input file"""
result = Result() result = Result()
......
cp2kparser/tests/cp2k_2.6.2/functionals/lda/lda.out
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...@@ -9,10 +9,10 @@ ...@@ -9,10 +9,10 @@
DBCSR| Communication thread load 87 DBCSR| Communication thread load 87
**** **** ****** ** PROGRAM STARTED AT 2015-12-11 13:23:01.535 **** **** ****** ** PROGRAM STARTED AT 2015-12-17 15:46:27.167
***** ** *** *** ** PROGRAM STARTED ON lauri-Lenovo-Z50-70 ***** ** *** *** ** PROGRAM STARTED ON lauri-Lenovo-Z50-70
** **** ****** PROGRAM STARTED BY lauri ** **** ****** PROGRAM STARTED BY lauri
***** ** ** ** ** PROGRAM PROCESS ID 6042 ***** ** ** ** ** PROGRAM PROCESS ID 4844
**** ** ******* ** PROGRAM STARTED IN /home/lauri/Dropbox/nomad-dev/gitlab/ **** ** ******* ** PROGRAM STARTED IN /home/lauri/Dropbox/nomad-dev/gitlab/
parser-cp2k/cp2kparser/tests/cp2k_2.6 parser-cp2k/cp2kparser/tests/cp2k_2.6
.2/functionals/lda .2/functionals/lda
...@@ -46,12 +46,12 @@ ...@@ -46,12 +46,12 @@
MEMORY| system memory details [Kb] MEMORY| system memory details [Kb]
MEMORY| rank 0 min max average MEMORY| rank 0 min max average
MEMORY| MemTotal 8070392 8070392 8070392 8070392 MEMORY| MemTotal 8070392 8070392 8070392 8070392
MEMORY| MemFree 4240172 4240172 4240172 4240172 MEMORY| MemFree 1865648 1865648 1865648 1865648
MEMORY| Buffers 198080 198080 198080 198080 MEMORY| Buffers 696732 696732 696732 696732
MEMORY| Cached 1678908 1678908 1678908 1678908 MEMORY| Cached 2894484 2894484 2894484 2894484
MEMORY| Slab 185560 185560 185560 185560 MEMORY| Slab 690424 690424 690424 690424
MEMORY| SReclaimable 147440 147440 147440 147440 MEMORY| SReclaimable 647708 647708 647708 647708
MEMORY| MemLikelyFree 6264600 6264600 6264600 6264600 MEMORY| MemLikelyFree 6104572 6104572 6104572 6104572
*** Fundamental physical constants (SI units) *** *** Fundamental physical constants (SI units) ***
...@@ -440,7 +440,7 @@ ...@@ -440,7 +440,7 @@
Total charge density on r-space grids: -0.0036805695 Total charge density on r-space grids: -0.0036805695
Total charge density g-space grids: -0.0036805695 Total charge density g-space grids: -0.0036805695
1 P_Mix/Diag. 0.40E+00 0.1 0.74330726 -3.7598777522 -3.76E+00 1 P_Mix/Diag. 0.40E+00 0.0 0.74330726 -3.7598777522 -3.76E+00
Trace(PS): 4.0000000000 Trace(PS): 4.0000000000
Electronic density on regular grids: -3.9998298977 0.0001701023 Electronic density on regular grids: -3.9998298977 0.0001701023
...@@ -1306,13 +1306,13 @@ ...@@ -1306,13 +1306,13 @@
ROUTINE CALLS TOT TIME [s] AVE VOLUME [Bytes] PERFORMANCE [MB/s] ROUTINE CALLS TOT TIME [s] AVE VOLUME [Bytes] PERFORMANCE [MB/s]
MP_Group 3 0.000 MP_Group 3 0.000
MP_Bcast 102 0.009 4. 0.05 MP_Bcast 102 0.000 4. 1.72
MP_Allreduce 1170 0.001 8. 12.58 MP_Allreduce 1170 0.001 8. 18.12
MP_Sync 2 0.000 MP_Sync 2 0.000
MP_Alltoall 2316 0.002 522. 750.18 MP_Alltoall 2316 0.001 522. 877.41
MP_Wait 2424 0.001 MP_Wait 2424 0.001
MP_ISend 808 0.002 228. 101.12 MP_ISend 808 0.001 228. 131.63
MP_IRecv 808 0.000 228. 379.36 MP_IRecv 808 0.000 228. 452.67
MP_Memory 2424 0.001 MP_Memory 2424 0.001
------------------------------------------------------------------------------- -------------------------------------------------------------------------------
...@@ -1384,62 +1384,50 @@ ...@@ -1384,62 +1384,50 @@
------------------------------------------------------------------------------- -------------------------------------------------------------------------------
SUBROUTINE CALLS ASD SELF TIME TOTAL TIME SUBROUTINE CALLS ASD SELF TIME TOTAL TIME
MAXIMUM AVERAGE MAXIMUM AVERAGE MAXIMUM MAXIMUM AVERAGE MAXIMUM AVERAGE MAXIMUM
CP2K 1 1.0 0.098 0.098 1.488 1.488 CP2K 1 1.0 0.002 0.002 0.583 0.583
qs_forces 1 2.0 0.019 0.019 0.984 0.984 qs_forces 1 2.0 0.000 0.000 0.557 0.557
qs_energies_scf 1 3.0 0.021 0.021 0.962 0.962 qs_energies_scf 1 3.0 0.000 0.000 0.554 0.554
scf_env_do_scf 1 4.0 0.000 0.000 0.694 0.694 scf_env_do_scf 1 4.0 0.000 0.000 0.539 0.539
scf_env_do_scf_inner_loop 100 5.0 0.011 0.011 0.693 0.693 scf_env_do_scf_inner_loop 100 5.0 0.007 0.007 0.538 0.538
rebuild_ks_matrix 101 7.0 0.000 0.000 0.333 0.333 rebuild_ks_matrix 101 7.0 0.000 0.000 0.284 0.284
qs_ks_build_kohn_sham_matrix 101 8.0 0.012 0.012 0.333 0.333 qs_ks_build_kohn_sham_matrix 101 8.0 0.008 0.008 0.284 0.284
qs_ks_update_qs_env 100 6.0 0.001 0.001 0.332 0.332 qs_ks_update_qs_env 100 6.0 0.000 0.000 0.283 0.283
quickstep_create_force_env 1 2.0 0.033 0.033 0.298 0.298 fft_wrap_pw1pw2 607 10.0 0.002 0.002 0.165 0.165
fft3d_s 608 12.0 0.127 0.127 0.259 0.259 fft_wrap_pw1pw2_30 405 10.7 0.008 0.008 0.152 0.152
fft_wrap_pw1pw2 607 10.0 0.003 0.003 0.215 0.215 qs_rho_update_rho 101 6.0 0.000 0.000 0.147 0.147
fft_wrap_pw1pw2_30 405 10.7 0.010 0.010 0.199 0.199 calculate_rho_elec 101 7.0 0.057 0.057 0.146 0.146
qs_rho_update_rho 101 6.0 0.000 0.000 0.164 0.164 sum_up_and_integrate 101 9.0 0.002 0.002 0.132 0.132
calculate_rho_elec 101 7.0 0.067 0.067 0.164 0.164 integrate_v_rspace 101 10.0 0.076 0.076 0.130 0.130
sum_up_and_integrate 101 9.0 0.003 0.003 0.153 0.153 fft3d_s 608 12.0 0.102 0.102 0.112 0.112
integrate_v_rspace 101 10.0 0.085 0.085 0.150 0.150 density_rs2pw 101 8.0 0.001 0.001 0.088 0.088
qs_init_subsys 1 3.0 0.053 0.053 0.139 0.139 qs_vxc_create 101 9.0 0.001 0.001 0.078 0.078
get_fft_scratch 608 13.0 0.132 0.132 0.132 0.132 xc_vxc_pw_create 101 10.0 0.009 0.009 0.077 0.077
init_scf_run 1 4.0 0.001 0.001 0.121 0.121 xc_rho_set_and_dset_create 101 11.0 0.001 0.001 0.068 0.068
density_rs2pw 101 8.0 0.001 0.001 0.095 0.095 xc_functional_eval 101 12.0 0.065 0.065 0.065 0.065
qs_vxc_create 101 9.0 0.001 0.001 0.092 0.092 calculate_dm_sparse 100 6.0 0.000 0.000 0.056 0.056
xc_vxc_pw_create 101 10.0 0.009 0.009 0.090 0.090 cp_dbcsr_plus_fm_fm_t_native 101 7.0 0.001 0.001 0.055 0.055
qs_energies_init_hamiltonians 1 4.0 0.001 0.001 0.090 0.090 potential_pw2rs 101 11.0 0.001 0.001 0.049 0.049
xc_rho_set_and_dset_create 101 11.0 0.002 0.002 0.081 0.081 dbcsr_mm_cannon_multiply 101 8.0 0.004 0.004 0.041 0.041
xc_functional_eval 101 12.0 0.077 0.077 0.077 0.077 quickstep_create_force_env 1 2.0 0.000 0.000 0.023 0.023
create_qs_kind_set 1 3.0 0.000 0.000 0.074 0.074 dbcsr_complete_redistribute 302 9.0 0.010 0.010 0.023 0.023
read_qs_kind 1 4.0 0.039 0.039 0.074 0.074 copy_dbcsr_to_fm 400 7.0 0.003 0.003 0.022 0.022
scf_env_initial_rho_setup 1 5.0 0.002 0.002 0.073 0.073 pw_gather_s 304 12.0 0.021 0.021 0.021 0.021
calculate_first_density_matrix 1 6.0 0.000 0.000 0.068 0.068 pw_poisson_solve 101 9.0 0.016 0.016 0.021 0.021
calculate_atomic_block_dm 1 7.0 0.024 0.024 0.068 0.068 pw_scatter_s 303 12.0 0.020 0.020 0.020 0.020
calculate_dm_sparse 100 6.0 0.000 0.000 0.067 0.067 qs_diis_b_step 99 6.0 0.001 0.001 0.017 0.017
cp_dbcsr_plus_fm_fm_t_native 101 7.0 0.002 0.002 0.067 0.067 create_qs_kind_set 1 3.0 0.000 0.000 0.014 0.014
potential_pw2rs 101 11.0 0.001 0.001 0.059 0.059 read_qs_kind 1 4.0 0.008 0.008 0.014 0.014
eigensolver 100 6.0 0.000 0.000 0.058 0.058 eigensolver 100 6.0 0.000 0.000 0.014 0.014
qs_env_update_s_mstruct 1 5.0 0.002 0.002 0.052 0.052 pw_copy 606 10.8 0.013 0.013 0.013 0.013
topology_control 1 3.0 0.018 0.018 0.051 0.051 dbcsr_finalize 726 10.0 0.002 0.002 0.012 0.012
dbcsr_mm_cannon_multiply 101 8.0 0.004 0.004 0.049 0.049 dbcsr_make_images 202 9.0 0.000 0.000 0.012 0.012
qs_env_setup 1 4.0 0.000 0.000 0.048 0.048 make_images 202 10.0 0.002 0.002 0.012 0.012
calculate_rho_core 1 6.0 0.009 0.009 0.046 0.046
cp_fm_cholesky_decompose 1 5.0 0.046 0.046 0.046 0.046
qs_diis_b_step 99 6.0 0.001 0.001 0.044 0.044
build_core_hamiltonian_matrix 1 5.0 0.011 0.011 0.036 0.036
parser_read_line 3297 5.0 0.001 0.001 0.036 0.036
cp_fm_syevd 100 7.0 0.000 0.000 0.035 0.035
cp_fm_syevd_base 100 8.0 0.035 0.035 0.035 0.035
parser_read_line_low 4 6.0 0.034 0.034 0.034 0.034
scf_post_calculation_gpw 1 4.0 0.000 0.000 0.034 0.034
write_available_results 1 5.0 0.033 0.033 0.034 0.034
qs_env_rebuild_pw_env 3 3.7 0.000 0.000 0.032 0.032
pw_env_rebuild 1 6.0 0.014 0.014 0.032 0.032
------------------------------------------------------------------------------- -------------------------------------------------------------------------------
**** **** ****** ** PROGRAM ENDED AT 2015-12-11 13:23:03.786 **** **** ****** ** PROGRAM ENDED AT 2015-12-17 15:46:27.824
***** ** *** *** ** PROGRAM RAN ON lauri-Lenovo-Z50-70 ***** ** *** *** ** PROGRAM RAN ON lauri-Lenovo-Z50-70
** **** ****** PROGRAM RAN BY lauri ** **** ****** PROGRAM RAN BY lauri
***** ** ** ** ** PROGRAM PROCESS ID 6042 ***** ** ** ** ** PROGRAM PROCESS ID 4844
**** ** ******* ** PROGRAM STOPPED IN /home/lauri/Dropbox/nomad-dev/gitlab/ **** ** ******* ** PROGRAM STOPPED IN /home/lauri/Dropbox/nomad-dev/gitlab/
parser-cp2k/cp2kparser/tests/cp2k_2.6 parser-cp2k/cp2kparser/tests/cp2k_2.6
.2/functionals/lda .2/functionals/lda
cp2kparser/unit_registry.txt deleted 100644 → 0
+ 0
− 264
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# NomadParser Pint units definition file
# Based on the International System of Units
# decimal prefixes
yocto- = 1e-24 = y-
zepto- = 1e-21 = z-
atto- = 1e-18 = a-
femto- = 1e-15 = f-
pico- = 1e-12 = p-
nano- = 1e-9 = n-
micro- = 1e-6 = u- = µ-
milli- = 1e-3 = m-
centi- = 1e-2 = c-
deci- = 1e-1 = d-
deca- = 1e+1 = da-
hecto- = 1e2 = h-
kilo- = 1e3 = k-
mega- = 1e6 = M-
giga- = 1e9 = G-
tera- = 1e12 = T-
peta- = 1e15 = P-
exa- = 1e18 = E-
zetta- = 1e21 = Z-
yotta- = 1e24 = Y-
# binary_prefixes
kibi- = 2**10 = Ki-
mebi- = 2**20 = Mi-
gibi- = 2**30 = Gi-
tebi- = 2**40 = Ti-
pebi- = 2**50 = Pi-
exbi- = 2**60 = Ei-
zebi- = 2**70 = Zi-
yobi- = 2**80 = Yi-
# SI units
meter = [length] = m = metre
second = [time] = s = sec
ampere = [current] = A = amp
candela = [luminosity] = cd = candle
kilogram = [mass] = kg
mole = [substance] = mol
kelvin = [temperature]; offset: 0 = K = degK
@import constants.txt
# Acceleration
[acceleration] = [length] / [time] ** 2
# Angle
radian = [] = rad
turn = 2 * pi * radian = revolution = cycle = circle
degree = pi / 180 * radian = deg = arcdeg = arcdegree = angular_degree
arcminute = arcdeg / 60 = arcmin = arc_minute = angular_minute
arcsecond = arcmin / 60 = arcsec = arc_second = angular_second
steradian = radian ** 2 = sr
# Area
[area] = [length] ** 2
are = 100 * m**2
barn = 1e-28 * m ** 2 = b
cmil = 5.067075e-10 * m ** 2 = circular_mils
darcy = 9.869233e-13 * m ** 2
acre = 4046.8564224 * m ** 2 = international_acre
hectare = 100 * are = ha
US_survey_acre = 160 * rod ** 2
# Electromagetism
esu = 1 * erg**0.5 * centimeter**0.5 = statcoulombs = statC = franklin = Fr
esu_per_second = 1 * esu / second = statampere
ampere_turn = 1 * A
gilbert = 10 / (4 * pi ) * ampere_turn
coulomb = ampere * second = C
volt = joule / coulomb = V
farad = coulomb / volt = F
ohm = volt / ampere = Ω
siemens = ampere / volt = S = mho
weber = volt * second = Wb
tesla = weber / meter ** 2 = T
henry = weber / ampere = H
elementary_charge = 1.602176487e-19 * coulomb = e
chemical_faraday = 9.64957e4 * coulomb
physical_faraday = 9.65219e4 * coulomb
faraday = 96485.3399 * coulomb = C12_faraday
gamma = 1e-9 * tesla
gauss = 1e-4 * tesla
maxwell = 1e-8 * weber = mx
oersted = 1000 / (4 * pi) * A / m = Oe
statfarad = 1.112650e-12 * farad = statF = stF
stathenry = 8.987554e11 * henry = statH = stH
statmho = 1.112650e-12 * siemens = statS = stS
statohm = 8.987554e11 * ohm
statvolt = 2.997925e2 * volt = statV = stV
unit_pole = 1.256637e-7 * weber
# Energy
[energy] = [force] * [length]
joule = newton * meter = J
erg = dyne * centimeter
btu = 1.05505585262e3 * joule = Btu = BTU = british_thermal_unit
electron_volt = 1.60217653e-19 * J = eV
quadrillion_btu = 10**15 * btu = quad
thm = 100000 * BTU = therm = EC_therm
cal = 4.184 * joule = calorie = thermochemical_calorie
international_steam_table_calorie = 4.1868 * joule
ton_TNT = 4.184e9 * joule = tTNT
US_therm = 1.054804e8 * joule
watt_hour = watt * hour = Wh = watthour
hartree = 4.35974394e-18 * joule = E_h = hartree_energy
rydberg = h * c * rydberg_constant
# Force
[force] = [mass] * [acceleration]
force_au = hartree / bohr
newton = kilogram * meter / second ** 2 = N
dyne = gram * centimeter / second ** 2 = dyn
force_kilogram = g_0 * kilogram = kgf = kilogram_force = pond
force_gram = g_0 * gram = gf = gram_force
force_ounce = g_0 * ounce = ozf = ounce_force
force_pound = g_0 * lb = lbf = pound_force
force_ton = 2000 * force_pound = ton_force
poundal = lb * feet / second ** 2 = pdl
kip = 1000*lbf
# Frequency
[frequency] = 1 / [time]
hertz = 1 / second = Hz = rps
revolutions_per_minute = revolution / minute = rpm
counts_per_second = count / second = cps
# Heat
#RSI = degK * meter ** 2 / watt
#clo = 0.155 * RSI = clos
#R_value = foot ** 2 * degF * hour / btu
# Information
bit = []
byte = 8 * bit = Bo = octet
baud = bit / second = Bd = bps
# Irradiance
peak_sun_hour = 1000 * watt_hour / meter**2 = PSH
langley = thermochemical_calorie / centimeter**2 = Langley
# Length
angstrom = 1e-10 * meter = Å = ångström = Å
inch = 2.54 * centimeter = in = international_inch = inches = international_inches
foot = 12 * inch = ft = international_foot = feet = international_feet
mile = 5280 * foot = mi = international_mile
yard = 3 * feet = yd = international_yard
mil = inch / 1000 = thou
parsec = 3.08568025e16 * meter = pc
light_year = speed_of_light * julian_year = ly = lightyear
astronomical_unit = 149597870691 * meter = au
nautical_mile = 1.852e3 * meter = nmi
printers_point = 127 * millimeter / 360 = point
printers_pica = 12 * printers_point = pica
US_survey_foot = 1200 * meter / 3937
US_survey_yard = 3 * US_survey_foot
US_survey_mile = 5280 * US_survey_foot = US_statute_mile
rod = 16.5 * US_survey_foot = pole = perch
furlong = 660 * US_survey_foot
fathom = 6 * US_survey_foot
chain = 66 * US_survey_foot
barleycorn = inch / 3
arpentlin = 191.835 * feet
kayser = 1 / centimeter = wavenumber
# Mass
dram = oz / 16 = dr = avoirdupois_dram
ounce = 28.349523125 * gram = oz = avoirdupois_ounce
pound = 0.45359237 * kilogram = lb = avoirdupois_pound
stone = 14 * lb = st
carat = 200 * milligram
grain = 64.79891 * milligram = gr
long_hundredweight = 112 * lb
short_hundredweight = 100 * lb
metric_ton = 1000 * kilogram = t = tonne
pennyweight = 24 * gram = dwt
slug = 14.59390 * kilogram
troy_ounce = 480 * grain = toz = apounce = apothecary_ounce
troy_pound = 12 * toz = tlb = appound = apothecary_pound
drachm = 60 * grain = apdram = apothecary_dram
atomic_mass_unit = 1.660538782e-27 * kilogram = u = amu = dalton = Da
scruple = 20 * grain
bag = 94 * lb
ton = 2000 * lb = short_ton
# Textile
denier = gram / (9000 * meter)
tex = gram/ (1000 * meter)
dtex = decitex
# Photometry
lumen = candela * steradian = lm
lux = lumen / meter ** 2 = lx
# Power
[power] = [energy] / [time]
watt = joule / second = W = volt_ampere = VA
horsepower = 33000 * ft * lbf / min = hp = UK_horsepower = British_horsepower
boiler_horsepower = 33475 * btu / hour
metric_horsepower = 75 * force_kilogram * meter / second
electric_horsepower = 746 * watt
hydraulic_horsepower = 550 * feet * lbf / second
refrigeration_ton = 12000 * btu / hour = ton_of_refrigeration
# Pressure
[pressure] = [force] / [area]
Hg = gravity * 13.59510 * gram / centimeter ** 3 = mercury = conventional_mercury
mercury_60F = gravity * 13.5568 * gram / centimeter ** 3
H2O = gravity * 1000 * kilogram / meter ** 3 = h2o = water = conventional_water
water_4C = gravity * 999.972 * kilogram / meter ** 3 = water_39F
water_60F = gravity * 999.001 * kilogram / m ** 3
pascal = newton / meter ** 2 = Pa
bar = 100000 * pascal
atmosphere = 101325 * pascal = atm = standard_atmosphere
technical_atmosphere = kilogram * gravity / centimeter ** 2 = at
torr = atm / 760
psi = pound * gravity / inch ** 2 = pound_force_per_square_inch
ksi = kip / inch ** 2 = kip_per_square_inch
barye = 0.1 * newton / meter ** 2 = barie = barad = barrie = baryd = Ba
mmHg = millimeter * Hg = mm_Hg = millimeter_Hg = millimeter_Hg_0C
cmHg = centimeter * Hg = cm_Hg = centimeter_Hg
inHg = inch * Hg = in_Hg = inch_Hg = inch_Hg_32F
inch_Hg_60F = inch * mercury_60F
inch_H2O_39F = inch * water_39F
inch_H2O_60F = inch * water_60F
footH2O = ft * water
cmH2O = centimeter * water
foot_H2O = ft * water = ftH2O
standard_liter_per_minute = 1.68875 * Pa * m ** 3 / s = slpm = slm
# Radiation
Bq = Hz = becquerel
curie = 3.7e10 * Bq = Ci
rutherford = 1e6*Bq = rd = Rd
Gy = joule / kilogram = gray = Sv = sievert
rem = 1e-2 * sievert
rads = 1e-2 * gray
roentgen = 2.58e-4 * coulomb / kilogram
# Temperature
degC = kelvin; offset: 273.15 = celsius
degR = 5 / 9 * kelvin; offset: 0 = rankine
degF = 5 / 9 * kelvin; offset: 255.372222 = fahrenheit
# Time
minute = 60 * second = min
hour = 60 * minute = hr
day = 24 * hour
week = 7 * day
# Velocity
[speed] = [length] / [time]
# Viscosity
[viscosity] = [pressure] * [time]
poise = 1e-1 * Pa * second = P
stokes = 1e-4 * meter ** 2 / second = St
rhe = 10 / (Pa * s)
# Volume
[volume] = [length] ** 3
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