From 07116308f277bcb18f215b44af1e7418dccfe338 Mon Sep 17 00:00:00 2001
From: Fawzi Mohamed <fawzi.mohamed@fhi-berlin.mpg.de>
Date: Tue, 29 Jan 2019 15:15:48 +0100
Subject: [PATCH] meta 2.0 changes
---
.../QuantumEspressoCommon.py | 9 +-
.../QuantumEspressoXC.py | 342 +++++++++---------
.../parser_quantum_espresso.py | 70 ++--
.../parsers/QuantumEspressoParser.scala | 2 +-
4 files changed, 215 insertions(+), 208 deletions(-)
diff --git a/parser/parser-quantum-espresso/QuantumEspressoCommon.py b/parser/parser-quantum-espresso/QuantumEspressoCommon.py
index f4d9bed..f38abe2 100644
--- a/parser/parser-quantum-espresso/QuantumEspressoCommon.py
+++ b/parser/parser-quantum-espresso/QuantumEspressoCommon.py
@@ -84,6 +84,9 @@ QE_SMEARING_KIND = {
'tetrahedron method': 'tetrahedra',
}
+def metaN(metaName):
+ """Retrurns a normalized meta name"""
+ return metaName.replace(".", "_").lower()
class ParserQuantumEspresso(object):
"""Base class for all Quantum Espresso parsers"""
@@ -259,9 +262,9 @@ class ParserQuantumEspresso(object):
def addDict(self, backend, this_dict):
for key, value in sorted(this_dict.items()):
- backend.addValue(key, value)
+ backend.addValue(metaN(key), value)
def addSectionDict(self, backend, section_name, section_dict):
- gIndex = backend.openSection(section_name)
+ gIndex = backend.openSection(metaN(section_name))
self.addDict(backend, section_dict)
- backend.closeSection(section_name, gIndex)
+ backend.closeSection(metaN(section_name), gIndex)
diff --git a/parser/parser-quantum-espresso/QuantumEspressoXC.py b/parser/parser-quantum-espresso/QuantumEspressoXC.py
index a87245a..2a535b5 100644
--- a/parser/parser-quantum-espresso/QuantumEspressoXC.py
+++ b/parser/parser-quantum-espresso/QuantumEspressoXC.py
@@ -114,7 +114,7 @@ def translate_qe_xc_num(xc_functional_num, exact_exchange_fraction=None):
xc_data, this_term, exact_exchange_fraction)
apply_terms_filter(xc_data)
xc_functional = xc_functional_str(xc_data)
- xc_section_method['XC_functional'] = xc_functional
+ xc_section_method['xc_functional'] = xc_functional
result = []
for k in sorted(xc_data.keys()):
v = xc_data[k]
@@ -125,34 +125,34 @@ def translate_qe_xc_num(xc_functional_num, exact_exchange_fraction=None):
def apply_term_add(xc_data, this_term, exact_exchange_fraction):
term = copy.deepcopy(this_term)
if 'exx_compute_weight' in term:
- term['XC_functional_weight'] = term['exx_compute_weight'](
+ term['xc_functional_weight'] = term['exx_compute_weight'](
exact_exchange_fraction)
- if 'XC_functional_weight' not in term:
- term['XC_functional_weight'] = 1.0
- if term['XC_functional_name'] not in xc_data:
- xc_data[term['XC_functional_name']] = term
+ if 'xc_functional_weight' not in term:
+ term['xc_functional_weight'] = 1.0
+ if term['xc_functional_name'] not in xc_data:
+ xc_data[term['xc_functional_name']] = term
else:
LOGGER.info("pre-existing XC term: %s",
- term['XC_functional_name'])
+ term['xc_functional_name'])
return xc_data
def apply_terms_remove(xc_data, xc_data_remove):
for (k, v) in xc_data_remove.items():
if k in xc_data:
- xc_data[k]['XC_functional_weight'] -= v['XC_functional_weight']
+ xc_data[k]['xc_functional_weight'] -= v['xc_functional_weight']
else:
xc_data[k] = v
- xc_data[k]['XC_functional_weight'] *= -1.0
+ xc_data[k]['xc_functional_weight'] *= -1.0
def apply_terms_filter(xc_data):
for (k, v) in list(xc_data.items()):
- if abs(v['XC_functional_weight']) < 0.01:
+ if abs(v['xc_functional_weight']) < 0.01:
del xc_data[k]
else:
- if abs(v['XC_functional_weight'] - 1.0) < 0.01:
- del v['XC_functional_weight']
+ if abs(v['xc_functional_weight'] - 1.0) < 0.01:
+ del v['xc_functional_weight']
v.pop('exx_compute_weight', None)
@@ -160,11 +160,11 @@ def xc_functional_str(xc_data, separator='+'):
result = ''
for k in sorted(xc_data.keys()):
v = xc_data[k]
- if len(result) > 0 and v.get('XC_functional_weight', 1.0) > 0:
+ if len(result) > 0 and v.get('xc_functional_weight', 1.0) > 0:
result += separator
- if v.get('XC_functional_weight', None) is not None:
- result += '%.3f*' % (v['XC_functional_weight'])
- result += v['XC_functional_name']
+ if v.get('xc_functional_weight', None) is not None:
+ result += '%.3f*' % (v['xc_functional_weight'])
+ result += v['xc_functional_name']
return result
@@ -173,7 +173,7 @@ EXCHANGE = [
None,
{
'xc_terms': [{
- 'XC_functional_name': 'LDA_X',
+ 'xc_functional_name': 'LDA_X',
}],
'xc_section_method': {
'x_qe_xc_iexch_name': 'sla',
@@ -183,8 +183,8 @@ EXCHANGE = [
},
{
'xc_terms': [{
- 'XC_functional_name': 'LDA_X',
- 'XC_functional_parameters': {'alpha': 1.0},
+ 'xc_functional_name': 'LDA_X',
+ 'xc_functional_parameters': {'alpha': 1.0},
}],
'xc_section_method': {
'x_qe_xc_iexch_name': 'sl1',
@@ -194,7 +194,7 @@ EXCHANGE = [
},
{
'xc_terms': [{
- 'XC_functional_name': 'x_qe_LDA_X_RELATIVISTIC',
+ 'xc_functional_name': 'x_qe_LDA_X_RELATIVISTIC',
}],
'xc_section_method': {
'x_qe_xc_iexch_name': 'rxc',
@@ -204,7 +204,7 @@ EXCHANGE = [
},
{
'xc_terms': [{
- 'XC_functional_name': 'OEP_EXX',
+ 'xc_functional_name': 'OEP_EXX',
}],
'xc_section_method': {
'x_qe_xc_iexch_name': 'oep',
@@ -214,7 +214,7 @@ EXCHANGE = [
},
{
'xc_terms': [{
- 'XC_functional_name': 'HF_X',
+ 'xc_functional_name': 'HF_X',
}],
'xc_section_method': {
'x_qe_xc_iexch_name': 'hf',
@@ -224,13 +224,13 @@ EXCHANGE = [
},
{
'xc_terms': [{
- 'XC_functional_name': 'HF_X',
+ 'xc_functional_name': 'HF_X',
'exx_compute_weight': lambda exx: exx,
- 'XC_functional_weight': 0.25,
+ 'xc_functional_weight': 0.25,
}, {
- 'XC_functional_name': 'LDA_X',
+ 'xc_functional_name': 'LDA_X',
'exx_compute_weight': lambda exx: (1.0 - exx),
- 'XC_functional_weight': 0.75,
+ 'xc_functional_weight': 0.75,
}],
'xc_section_method': {
'x_qe_xc_iexch_name': "pb0x",
@@ -240,13 +240,13 @@ EXCHANGE = [
},
{
'xc_terms': [{
- 'XC_functional_name': 'HF_X',
+ 'xc_functional_name': 'HF_X',
'exx_compute_weight': lambda exx: exx,
- 'XC_functional_weight': 0.20,
+ 'xc_functional_weight': 0.20,
}, {
- 'XC_functional_name': 'LDA_X',
+ 'xc_functional_name': 'LDA_X',
'exx_compute_weight': lambda exx: (1.0 - exx),
- 'XC_functional_weight': 0.8,
+ 'xc_functional_weight': 0.8,
}],
'xc_section_method': {
'x_qe_xc_iexch_name': "b3lp",
@@ -256,7 +256,7 @@ EXCHANGE = [
},
{
'xc_terms': [{
- 'XC_functional_name': "LDA_X_KZK",
+ 'xc_functional_name': "LDA_X_KZK",
}],
'xc_section_method': {
'x_qe_xc_iexch_name': "kzk",
@@ -266,13 +266,13 @@ EXCHANGE = [
},
{
'xc_terms': [{
- 'XC_functional_name': 'HF_X',
+ 'xc_functional_name': 'HF_X',
'exx_compute_weight': lambda exx: exx,
- 'XC_functional_weight': 0.218,
+ 'xc_functional_weight': 0.218,
}, {
- 'XC_functional_name': 'LDA_X',
+ 'xc_functional_name': 'LDA_X',
'exx_compute_weight': lambda exx: (1.0 - exx),
- 'XC_functional_weight': 0.782,
+ 'xc_functional_weight': 0.782,
}],
'xc_section_method': {
'x_qe_xc_iexch_name': "x3lp",
@@ -287,7 +287,7 @@ CORRELATION = [
None,
{
'xc_terms': [{
- 'XC_functional_name': 'LDA_C_PZ',
+ 'xc_functional_name': 'LDA_C_PZ',
}],
'xc_section_method': {
'x_qe_xc_icorr_name': "pz",
@@ -297,7 +297,7 @@ CORRELATION = [
},
{
'xc_terms': [{
- 'XC_functional_name': 'LDA_C_VWN',
+ 'xc_functional_name': 'LDA_C_VWN',
}],
'xc_section_method': {
'x_qe_xc_icorr_name': "vwn",
@@ -307,7 +307,7 @@ CORRELATION = [
},
{
'xc_terms': [{
- 'XC_functional_name': 'LDA_C_LYP',
+ 'xc_functional_name': 'LDA_C_LYP',
}],
'xc_section_method': {
'x_qe_xc_icorr_name': "lyp",
@@ -317,7 +317,7 @@ CORRELATION = [
},
{
'xc_terms': [{
- 'XC_functional_name': "LDA_C_PW",
+ 'xc_functional_name': "LDA_C_PW",
}],
'xc_section_method': {
'x_qe_xc_icorr_name': "pw",
@@ -327,7 +327,7 @@ CORRELATION = [
},
{
'xc_terms': [{
- 'XC_functional_name': 'LDA_C_WIGNER',
+ 'xc_functional_name': 'LDA_C_WIGNER',
}],
'xc_section_method': {
'x_qe_xc_icorr_name': "wig",
@@ -337,7 +337,7 @@ CORRELATION = [
},
{
'xc_terms': [{
- 'XC_functional_name': 'LDA_C_HL',
+ 'xc_functional_name': 'LDA_C_HL',
}],
'xc_section_method': {
'x_qe_xc_icorr_name': "hl",
@@ -347,7 +347,7 @@ CORRELATION = [
},
{
'xc_terms': [{
- 'XC_functional_name': 'LDA_C_OB_PZ',
+ 'xc_functional_name': 'LDA_C_OB_PZ',
}],
'xc_section_method': {
'x_qe_xc_icorr_name': "obz",
@@ -357,7 +357,7 @@ CORRELATION = [
},
{
'xc_terms': [{
- 'XC_functional_name': 'LDA_C_OB_PW',
+ 'xc_functional_name': 'LDA_C_OB_PW',
}],
'xc_section_method': {
'x_qe_xc_icorr_name': "obw",
@@ -367,7 +367,7 @@ CORRELATION = [
},
{
'xc_terms': [{
- 'XC_functional_name': 'LDA_C_GL',
+ 'xc_functional_name': 'LDA_C_GL',
}],
'xc_section_method': {
'x_qe_xc_icorr_name': "gl",
@@ -377,7 +377,7 @@ CORRELATION = [
},
{
'xc_terms': [{
- 'XC_functional_name': "LDA_C_KZK",
+ 'xc_functional_name': "LDA_C_KZK",
}],
'xc_section_method': {
'x_qe_xc_icorr_name': "kzk",
@@ -387,7 +387,7 @@ CORRELATION = [
},
{
'xc_terms': [{
- 'XC_functional_name': 'LDA_C_VWN_RPA',
+ 'xc_functional_name': 'LDA_C_VWN_RPA',
}],
'xc_section_method': {
'x_qe_xc_icorr_name': "vwn-rpa",
@@ -397,11 +397,11 @@ CORRELATION = [
},
{
'xc_terms': [{
- 'XC_functional_name': 'LDA_C_VWN',
- 'XC_functional_weight': 0.19,
+ 'xc_functional_name': 'LDA_C_VWN',
+ 'xc_functional_weight': 0.19,
}, {
- 'XC_functional_name': 'LDA_C_LYP',
- 'XC_functional_weight': 0.81,
+ 'xc_functional_name': 'LDA_C_LYP',
+ 'xc_functional_weight': 0.81,
}],
'xc_section_method': {
'x_qe_xc_icorr_name': "b3lp",
@@ -411,11 +411,11 @@ CORRELATION = [
},
{
'xc_terms': [{
- 'XC_functional_name': 'LDA_C_VWN_RPA',
- 'XC_functional_weight': 0.19,
+ 'xc_functional_name': 'LDA_C_VWN_RPA',
+ 'xc_functional_weight': 0.19,
}, {
- 'XC_functional_name': 'LDA_C_LYP',
- 'XC_functional_weight': 0.81,
+ 'xc_functional_name': 'LDA_C_LYP',
+ 'xc_functional_weight': 0.81,
}],
'xc_section_method': {
'x_qe_xc_icorr_name': "b3lpv1r",
@@ -425,11 +425,11 @@ CORRELATION = [
},
{
'xc_terms': [{
- 'XC_functional_name': 'LDA_C_VWN_RPA',
- 'XC_functional_weight': 0.129,
+ 'xc_functional_name': 'LDA_C_VWN_RPA',
+ 'xc_functional_weight': 0.129,
}, {
- 'XC_functional_name': 'LDA_C_LYP',
- 'XC_functional_weight': 0.871,
+ 'xc_functional_name': 'LDA_C_LYP',
+ 'xc_functional_weight': 0.871,
}],
'xc_section_method': {
'x_qe_xc_icorr_name': "x3lp",
@@ -443,10 +443,10 @@ EXCHANGE_GRADIENT_CORRECTION = [
None,
{
'xc_terms': [{
- 'XC_functional_name': "GGA_X_B88",
+ 'xc_functional_name': "GGA_X_B88",
}],
'xc_terms_remove': [{
- 'XC_functional_name': 'LDA_X',
+ 'xc_functional_name': 'LDA_X',
}],
'xc_section_method': {
'x_qe_xc_igcx_name': "b88",
@@ -456,10 +456,10 @@ EXCHANGE_GRADIENT_CORRECTION = [
},
{
'xc_terms': [{
- 'XC_functional_name': "GGA_X_PW91",
+ 'xc_functional_name': "GGA_X_PW91",
}],
'xc_terms_remove': [{
- 'XC_functional_name': 'LDA_X',
+ 'xc_functional_name': 'LDA_X',
}],
'xc_section_method': {
'x_qe_xc_igcx_name': "ggx",
@@ -469,10 +469,10 @@ EXCHANGE_GRADIENT_CORRECTION = [
},
{
'xc_terms': [{
- 'XC_functional_name': "GGA_X_PBE",
+ 'xc_functional_name': "GGA_X_PBE",
}],
'xc_terms_remove': [{
- 'XC_functional_name': 'LDA_X',
+ 'xc_functional_name': 'LDA_X',
}],
'xc_section_method': {
'x_qe_xc_igcx_name': "pbx",
@@ -482,10 +482,10 @@ EXCHANGE_GRADIENT_CORRECTION = [
},
{
'xc_terms': [{
- 'XC_functional_name': "GGA_X_PBE_R",
+ 'xc_functional_name': "GGA_X_PBE_R",
}],
'xc_terms_remove': [{
- 'XC_functional_name': 'LDA_X',
+ 'xc_functional_name': 'LDA_X',
}],
'xc_section_method': {
'x_qe_xc_igcx_name': "rpb",
@@ -495,7 +495,7 @@ EXCHANGE_GRADIENT_CORRECTION = [
},
{
'xc_terms': [{
- 'XC_functional_name': "GGA_XC_HCTH_120",
+ 'xc_functional_name': "GGA_XC_HCTH_120",
}],
'xc_section_method': {
'x_qe_xc_igcx_name': "hcth",
@@ -505,7 +505,7 @@ EXCHANGE_GRADIENT_CORRECTION = [
},
{
'xc_terms': [{
- 'XC_functional_name': "GGA_X_OPTX",
+ 'xc_functional_name': "GGA_X_OPTX",
}],
'xc_section_method': {
'x_qe_xc_igcx_name': "optx",
@@ -517,10 +517,10 @@ EXCHANGE_GRADIENT_CORRECTION = [
# igcx=7 is not defined in 5.4's funct.f90
# definition taken from 5.0, which did not have separate imeta
'xc_terms': [{
- 'XC_functional_name': "MGGA_X_TPSS",
+ 'xc_functional_name': "MGGA_X_TPSS",
}],
'xc_terms_remove': [{
- 'XC_functional_name': 'LDA_X',
+ 'xc_functional_name': 'LDA_X',
}],
'xc_section_method': {
'x_qe_xc_igcx_name': "tpss",
@@ -530,13 +530,13 @@ EXCHANGE_GRADIENT_CORRECTION = [
},
{
'xc_terms': [{
- 'XC_functional_name': "GGA_X_PBE",
- 'XC_functional_weight': 0.75,
+ 'xc_functional_name': "GGA_X_PBE",
+ 'xc_functional_weight': 0.75,
'exx_compute_weight': lambda exx: (1.0 - exx),
}],
'xc_terms_remove': [{
- 'XC_functional_name': 'LDA_X',
- 'XC_functional_weight': 0.75,
+ 'xc_functional_name': 'LDA_X',
+ 'xc_functional_weight': 0.75,
'exx_compute_weight': lambda exx: (1.0 - exx),
}],
'xc_section_method': {
@@ -547,13 +547,13 @@ EXCHANGE_GRADIENT_CORRECTION = [
},
{
'xc_terms': [{
- 'XC_functional_name': "GGA_X_B88",
- 'XC_functional_weight': 0.72,
+ 'xc_functional_name': "GGA_X_B88",
+ 'xc_functional_weight': 0.72,
'exx_compute_weight': lambda exx: 0.72 if abs(exx) > 0.01 else 1.0
}],
'xc_terms_remove': [{
- 'XC_functional_name': 'LDA_X',
- 'XC_functional_weight': 0.8,
+ 'xc_functional_name': 'LDA_X',
+ 'xc_functional_weight': 0.8,
'exx_compute_weight': lambda exx: (1.0 - exx),
}],
'xc_section_method': {
@@ -564,10 +564,10 @@ EXCHANGE_GRADIENT_CORRECTION = [
},
{
'xc_terms': [{
- 'XC_functional_name': "GGA_X_PBE_SOL",
+ 'xc_functional_name': "GGA_X_PBE_SOL",
}],
'xc_terms_remove': [{
- 'XC_functional_name': 'LDA_X',
+ 'xc_functional_name': 'LDA_X',
}],
'xc_section_method': {
'x_qe_xc_igcx_name': "psx",
@@ -577,10 +577,10 @@ EXCHANGE_GRADIENT_CORRECTION = [
},
{
'xc_terms': [{
- 'XC_functional_name': "GGA_X_WC",
+ 'xc_functional_name': "GGA_X_WC",
}],
'xc_terms_remove': [{
- 'XC_functional_name': 'LDA_X',
+ 'xc_functional_name': 'LDA_X',
}],
'xc_section_method': {
'x_qe_xc_igcx_name': "wcx",
@@ -590,16 +590,16 @@ EXCHANGE_GRADIENT_CORRECTION = [
},
{
'xc_terms': [{
- 'XC_functional_name': "HYB_GGA_XC_HSE06",
+ 'xc_functional_name': "HYB_GGA_XC_HSE06",
'exx_compute_weight': lambda exx: 1.0 if (abs(exx) > 0.01) else 0.0
}, {
- 'XC_functional_name': "GGA_X_PBE",
+ 'xc_functional_name': "GGA_X_PBE",
'exx_compute_weight': lambda exx: 0.0 if (abs(exx) > 0.01) else 1.0
}],
'xc_terms_remove': [{
- 'XC_functional_name': 'LDA_X',
+ 'xc_functional_name': 'LDA_X',
}, {
- 'XC_functional_name': 'GGA_C_PBE',
+ 'xc_functional_name': 'GGA_C_PBE',
'exx_compute_weight': lambda exx: 1.0 if (abs(exx) > 0.01) else 0.0
}],
'xc_section_method': {
@@ -610,10 +610,10 @@ EXCHANGE_GRADIENT_CORRECTION = [
},
{
'xc_terms': [{
- 'XC_functional_name': "GGA_X_RPW86",
+ 'xc_functional_name': "GGA_X_RPW86",
}],
'xc_terms_remove': [{
- 'XC_functional_name': 'LDA_X',
+ 'xc_functional_name': 'LDA_X',
}],
'xc_section_method': {
'x_qe_xc_igcx_name': "rw86",
@@ -623,10 +623,10 @@ EXCHANGE_GRADIENT_CORRECTION = [
},
{
'xc_terms': [{
- 'XC_functional_name': "GGA_X_PBE",
+ 'xc_functional_name': "GGA_X_PBE",
}],
'xc_terms_remove': [{
- 'XC_functional_name': 'LDA_X',
+ 'xc_functional_name': 'LDA_X',
}],
'xc_section_method': {
'x_qe_xc_igcx_name': "pbe",
@@ -638,10 +638,10 @@ EXCHANGE_GRADIENT_CORRECTION = [
# igcx=15 is not defined in 5.4's funct.f90
# definition taken from 5.0, which did not have separate imeta
'xc_terms': [{
- 'XC_functional_name': "MGGA_X_TB09",
+ 'xc_functional_name': "MGGA_X_TB09",
}],
'xc_terms_remove': [{
- 'XC_functional_name': 'LDA_X',
+ 'xc_functional_name': 'LDA_X',
}],
'xc_section_method': {
'x_qe_xc_igcx_name': "tb09",
@@ -651,10 +651,10 @@ EXCHANGE_GRADIENT_CORRECTION = [
},
{
'xc_terms': [{
- 'XC_functional_name': "GGA_X_C09X",
+ 'xc_functional_name': "GGA_X_C09X",
}],
'xc_terms_remove': [{
- 'XC_functional_name': 'LDA_X',
+ 'xc_functional_name': 'LDA_X',
}],
'xc_section_method': {
'x_qe_xc_igcx_name': "c09x",
@@ -664,10 +664,10 @@ EXCHANGE_GRADIENT_CORRECTION = [
},
{
'xc_terms': [{
- 'XC_functional_name': "GGA_X_SOGGA",
+ 'xc_functional_name': "GGA_X_SOGGA",
}],
'xc_terms_remove': [{
- 'XC_functional_name': 'LDA_X',
+ 'xc_functional_name': 'LDA_X',
}],
'xc_section_method': {
'x_qe_xc_igcx_name': "sox",
@@ -679,7 +679,7 @@ EXCHANGE_GRADIENT_CORRECTION = [
# igcx=18 is not defined in 5.4's funct.f90
# definition taken from 5.0, which did not have separate imeta
'xc_terms': [{
- 'XC_functional_name': "MGGA_X_M06_L",
+ 'xc_functional_name': "MGGA_X_M06_L",
}],
'xc_section_method': {
'x_qe_xc_igcx_name': "m6lx",
@@ -689,10 +689,10 @@ EXCHANGE_GRADIENT_CORRECTION = [
},
{
'xc_terms': [{
- 'XC_functional_name': "GGA_X_Q2D",
+ 'xc_functional_name': "GGA_X_Q2D",
}],
'xc_terms_remove': [{
- 'XC_functional_name': 'LDA_X',
+ 'xc_functional_name': 'LDA_X',
}],
'xc_section_method': {
'x_qe_xc_igcx_name': "q2dx",
@@ -702,16 +702,16 @@ EXCHANGE_GRADIENT_CORRECTION = [
},
{
'xc_terms': [{
- 'XC_functional_name': "HYB_GGA_XC_GAU_PBE",
+ 'xc_functional_name': "HYB_GGA_XC_GAU_PBE",
'exx_compute_weight': lambda exx: 1.0 if (abs(exx) > 0.01) else 0.0
}, {
- 'XC_functional_name': "GGA_X_PBE",
+ 'xc_functional_name': "GGA_X_PBE",
'exx_compute_weight': lambda exx: 0.0 if (abs(exx) > 0.01) else 1.0
}],
'xc_terms_remove': [{
- 'XC_functional_name': 'LDA_X',
+ 'xc_functional_name': 'LDA_X',
}, {
- 'XC_functional_name': 'GGA_C_PBE',
+ 'xc_functional_name': 'GGA_C_PBE',
'exx_compute_weight': lambda exx: 1.0 if (abs(exx) > 0.01) else 0.0
}],
'xc_section_method': {
@@ -722,10 +722,10 @@ EXCHANGE_GRADIENT_CORRECTION = [
},
{
'xc_terms': [{
- 'XC_functional_name': "GGA_X_PW86",
+ 'xc_functional_name': "GGA_X_PW86",
}],
'xc_terms_remove': [{
- 'XC_functional_name': 'LDA_X',
+ 'xc_functional_name': 'LDA_X',
}],
'xc_section_method': {
'x_qe_xc_igcx_name': "pw86",
@@ -735,10 +735,10 @@ EXCHANGE_GRADIENT_CORRECTION = [
},
{
'xc_terms': [{
- 'XC_functional_name': "GGA_X_B86_MGC",
+ 'xc_functional_name': "GGA_X_B86_MGC",
}],
'xc_terms_remove': [{
- 'XC_functional_name': 'LDA_X',
+ 'xc_functional_name': 'LDA_X',
}],
'xc_section_method': {
'x_qe_xc_igcx_name': "b86b",
@@ -748,10 +748,10 @@ EXCHANGE_GRADIENT_CORRECTION = [
},
{
'xc_terms': [{
- 'XC_functional_name': "GGA_X_OPTB88_VDW",
+ 'xc_functional_name': "GGA_X_OPTB88_VDW",
}],
'xc_terms_remove': [{
- 'XC_functional_name': 'LDA_X',
+ 'xc_functional_name': 'LDA_X',
}],
'xc_section_method': {
'x_qe_xc_igcx_name': "obk8",
@@ -761,10 +761,10 @@ EXCHANGE_GRADIENT_CORRECTION = [
},
{
'xc_terms': [{
- 'XC_functional_name': "GGA_X_OPTB86_VDW",
+ 'xc_functional_name': "GGA_X_OPTB86_VDW",
}],
'xc_terms_remove': [{
- 'XC_functional_name': 'LDA_X',
+ 'xc_functional_name': 'LDA_X',
}],
'xc_section_method': {
'x_qe_xc_igcx_name': "ob86",
@@ -774,10 +774,10 @@ EXCHANGE_GRADIENT_CORRECTION = [
},
{
'xc_terms': [{
- 'XC_functional_name': "GGA_X_EV93",
+ 'xc_functional_name': "GGA_X_EV93",
}],
'xc_terms_remove': [{
- 'XC_functional_name': 'LDA_X',
+ 'xc_functional_name': 'LDA_X',
}],
'xc_section_method': {
'x_qe_xc_igcx_name': "evx",
@@ -787,10 +787,10 @@ EXCHANGE_GRADIENT_CORRECTION = [
},
{
'xc_terms': [{
- 'XC_functional_name': "GGA_X_B86_R",
+ 'xc_functional_name': "GGA_X_B86_R",
}],
'xc_terms_remove': [{
- 'XC_functional_name': 'LDA_X',
+ 'xc_functional_name': 'LDA_X',
}],
'xc_section_method': {
'x_qe_xc_igcx_name': "b86r",
@@ -800,10 +800,10 @@ EXCHANGE_GRADIENT_CORRECTION = [
},
{
'xc_terms': [{
- 'XC_functional_name': "GGA_X_LV_RPW86",
+ 'xc_functional_name': "GGA_X_LV_RPW86",
}],
'xc_terms_remove': [{
- 'XC_functional_name': 'LDA_X',
+ 'xc_functional_name': 'LDA_X',
}],
'xc_section_method': {
'x_qe_xc_igcx_name': "cx13",
@@ -813,18 +813,18 @@ EXCHANGE_GRADIENT_CORRECTION = [
},
{
'xc_terms': [{
- 'XC_functional_name': "GGA_X_B88",
- 'XC_functional_weight': 0.542,
+ 'xc_functional_name': "GGA_X_B88",
+ 'xc_functional_weight': 0.542,
'exx_compute_weight':
lambda exx: 0.542 if (abs(exx) > 0.01) else 1.0
}, {
- 'XC_functional_name': "GGA_X_PW91",
- 'XC_functional_weight': 0.167,
+ 'xc_functional_name': "GGA_X_PW91",
+ 'xc_functional_weight': 0.167,
'exx_compute_weight':
lambda exx: 0.167 if (abs(exx) > 0.01) else 0.0
}],
'xc_terms_remove': [{
- 'XC_functional_name': 'LDA_X',
+ 'xc_functional_name': 'LDA_X',
'exx_compute_weight':
lambda exx: 0.709 if (abs(exx) > 0.01) else 1.0
}],
@@ -841,10 +841,10 @@ CORRELATION_GRADIENT_CORRECTION = [
None,
{
'xc_terms': [{
- 'XC_functional_name': "GGA_C_P86",
+ 'xc_functional_name': "GGA_C_P86",
}],
'xc_terms_remove': [{
- 'XC_functional_name': 'LDA_C_PW',
+ 'xc_functional_name': 'LDA_C_PW',
}],
'xc_section_method': {
'x_qe_xc_igcc_name': "p86",
@@ -854,10 +854,10 @@ CORRELATION_GRADIENT_CORRECTION = [
},
{
'xc_terms': [{
- 'XC_functional_name': "GGA_C_PW91",
+ 'xc_functional_name': "GGA_C_PW91",
}],
'xc_terms_remove': [{
- 'XC_functional_name': 'LDA_C_PW',
+ 'xc_functional_name': 'LDA_C_PW',
}],
'xc_section_method': {
'x_qe_xc_igcc_name': "ggc",
@@ -867,10 +867,10 @@ CORRELATION_GRADIENT_CORRECTION = [
},
{
'xc_terms': [{
- 'XC_functional_name': "GGA_C_LYP",
+ 'xc_functional_name': "GGA_C_LYP",
}],
'xc_terms_remove': [{
- 'XC_functional_name': 'LDA_C_LYP',
+ 'xc_functional_name': 'LDA_C_LYP',
}],
'xc_section_method': {
'x_qe_xc_igcc_name': "blyp",
@@ -880,10 +880,10 @@ CORRELATION_GRADIENT_CORRECTION = [
},
{
'xc_terms': [{
- 'XC_functional_name': "GGA_C_PBE",
+ 'xc_functional_name': "GGA_C_PBE",
}],
'xc_terms_remove': [{
- 'XC_functional_name': 'LDA_C_PW',
+ 'xc_functional_name': 'LDA_C_PW',
}],
'xc_section_method': {
'x_qe_xc_igcc_name': "pbc",
@@ -893,7 +893,7 @@ CORRELATION_GRADIENT_CORRECTION = [
},
{
'xc_terms': [{
- 'XC_functional_name': "GGA_XC_HCTH_120",
+ 'xc_functional_name': "GGA_XC_HCTH_120",
}],
'xc_section_method': {
'x_qe_xc_igcc_name': "hcth",
@@ -905,10 +905,10 @@ CORRELATION_GRADIENT_CORRECTION = [
# igcc=6 is not defined in 5.4's funct.f90
# definition taken from 5.0, which did not have separate imeta
'xc_terms': [{
- 'XC_functional_name': "MGGA_C_TPSS",
+ 'xc_functional_name': "MGGA_C_TPSS",
}],
'xc_terms_remove': [{
- 'XC_functional_name': 'LDA_C_PW',
+ 'xc_functional_name': 'LDA_C_PW',
}],
'xc_section_method': {
'x_qe_xc_igcc_name': "tpss",
@@ -918,12 +918,12 @@ CORRELATION_GRADIENT_CORRECTION = [
},
{
'xc_terms': [{
- 'XC_functional_name': "GGA_C_LYP",
- 'XC_functional_weight': 0.81,
+ 'xc_functional_name': "GGA_C_LYP",
+ 'xc_functional_weight': 0.81,
}],
'xc_terms_remove': [{
- 'XC_functional_name': 'LDA_C_LYP',
- 'XC_functional_weight': 0.81,
+ 'xc_functional_name': 'LDA_C_LYP',
+ 'xc_functional_weight': 0.81,
}],
'xc_section_method': {
'x_qe_xc_igcc_name': "b3lp",
@@ -933,10 +933,10 @@ CORRELATION_GRADIENT_CORRECTION = [
},
{
'xc_terms': [{
- 'XC_functional_name': "GGA_C_PBE_SOL",
+ 'xc_functional_name': "GGA_C_PBE_SOL",
}],
'xc_terms_remove': [{
- 'XC_functional_name': 'LDA_C_PW',
+ 'xc_functional_name': 'LDA_C_PW',
}],
'xc_section_method': {
'x_qe_xc_igcc_name': "psc",
@@ -946,10 +946,10 @@ CORRELATION_GRADIENT_CORRECTION = [
},
{
'xc_terms': [{
- 'XC_functional_name': "GGA_C_PBE",
+ 'xc_functional_name': "GGA_C_PBE",
}],
'xc_terms_remove': [{
- 'XC_functional_name': 'LDA_C_PW',
+ 'xc_functional_name': 'LDA_C_PW',
}],
'xc_section_method': {
'x_qe_xc_igcc_name': "pbe",
@@ -962,10 +962,10 @@ CORRELATION_GRADIENT_CORRECTION = [
# definition taken from 5.0, which did not have separate imeta
# functionals.f90 tells that correlation is taken from tpss
'xc_terms': [{
- 'XC_functional_name': "MGGA_C_TPSS",
+ 'xc_functional_name': "MGGA_C_TPSS",
}],
'xc_terms_remove': [{
- 'XC_functional_name': 'LDA_C_PW',
+ 'xc_functional_name': 'LDA_C_PW',
}],
'xc_section_method': {
'x_qe_xc_igcc_name': "tb09",
@@ -977,7 +977,7 @@ CORRELATION_GRADIENT_CORRECTION = [
# igcc=11 is not defined in 5.4's funct.f90
# definition taken from 5.0, which did not have separate imeta
'xc_terms': [{
- 'XC_functional_name': "MGGA_C_M06_L",
+ 'xc_functional_name': "MGGA_C_M06_L",
}],
'xc_section_method': {
'x_qe_xc_igcc_name': "m6lc",
@@ -987,10 +987,10 @@ CORRELATION_GRADIENT_CORRECTION = [
},
{
'xc_terms': [{
- 'XC_functional_name': "GGA_C_Q2D",
+ 'xc_functional_name': "GGA_C_Q2D",
}],
'xc_terms_remove': [{
- 'XC_functional_name': 'LDA_C_PW',
+ 'xc_functional_name': 'LDA_C_PW',
}],
'xc_section_method': {
'x_qe_xc_igcc_name': "q2dc",
@@ -1000,12 +1000,12 @@ CORRELATION_GRADIENT_CORRECTION = [
},
{
'xc_terms': [{
- 'XC_functional_name': "GGA_C_LYP",
- 'XC_functional_weight': 0.871,
+ 'xc_functional_name': "GGA_C_LYP",
+ 'xc_functional_weight': 0.871,
}],
'xc_terms_remove': [{
- 'XC_functional_name': 'LDA_C_LYP',
- 'XC_functional_weight': 0.871,
+ 'xc_functional_name': 'LDA_C_LYP',
+ 'xc_functional_weight': 0.871,
}],
'xc_section_method': {
'x_qe_xc_igcc_name': "x3lp",
@@ -1020,14 +1020,14 @@ META_GGA = [
None,
{
'xc_terms': [{
- 'XC_functional_name': "MGGA_X_TPSS",
+ 'xc_functional_name': "MGGA_X_TPSS",
}, {
- 'XC_functional_name': "MGGA_C_TPSS",
+ 'xc_functional_name': "MGGA_C_TPSS",
}],
'xc_terms_remove': [{
- 'XC_functional_name': 'LDA_X',
+ 'xc_functional_name': 'LDA_X',
}, {
- 'XC_functional_name': 'LDA_C_PW',
+ 'xc_functional_name': 'LDA_C_PW',
}],
'xc_section_method': {
'x_qe_xc_imeta_name': "tpss",
@@ -1037,9 +1037,9 @@ META_GGA = [
},
{
'xc_terms': [{
- 'XC_functional_name': "MGGA_X_M06_L",
+ 'xc_functional_name': "MGGA_X_M06_L",
}, {
- 'XC_functional_name': "MGGA_C_M06_L",
+ 'xc_functional_name': "MGGA_C_M06_L",
}],
'xc_section_method': {
'x_qe_xc_imeta_name': "m6lx",
@@ -1049,15 +1049,15 @@ META_GGA = [
},
{
'xc_terms': [{
- 'XC_functional_name': "MGGA_X_TB09",
+ 'xc_functional_name': "MGGA_X_TB09",
}, {
# confirmed by looking into functionals.f90
- 'XC_functional_name': "MGGA_C_TPSS",
+ 'xc_functional_name': "MGGA_C_TPSS",
}],
'xc_terms_remove': [{
- 'XC_functional_name': 'LDA_X',
+ 'xc_functional_name': 'LDA_X',
}, {
- 'XC_functional_name': 'LDA_C_PW',
+ 'xc_functional_name': 'LDA_C_PW',
}],
'xc_section_method': {
'x_qe_xc_imeta_name': "tb09",
@@ -1071,10 +1071,10 @@ VAN_DER_WAALS = [
None,
{
'xc_terms': [{
- 'XC_functional_name': "VDW_C_DF1",
+ 'xc_functional_name': "VDW_C_DF1",
}],
'xc_terms_remove': [{
- 'XC_functional_name': "LDA_C_PW",
+ 'xc_functional_name': "LDA_C_PW",
}],
'xc_section_method': {
'x_qe_xc_inlc_name': "vdw1",
@@ -1084,10 +1084,10 @@ VAN_DER_WAALS = [
},
{
'xc_terms': [{
- 'XC_functional_name': "VDW_C_DF2",
+ 'xc_functional_name': "VDW_C_DF2",
}],
'xc_terms_remove': [{
- 'XC_functional_name': "LDA_C_PW",
+ 'xc_functional_name': "LDA_C_PW",
}],
'xc_section_method': {
'x_qe_xc_inlc_name': "vdw2",
@@ -1097,10 +1097,10 @@ VAN_DER_WAALS = [
},
{
'xc_terms': [{
- 'XC_functional_name': "VDW_C_RVV10",
+ 'xc_functional_name': "VDW_C_RVV10",
}],
'xc_terms_remove': [{
- 'XC_functional_name': "GGA_C_PBE",
+ 'xc_functional_name': "GGA_C_PBE",
}],
'xc_section_method': {
'x_qe_xc_inlc_name': "vv10",
@@ -1110,7 +1110,7 @@ VAN_DER_WAALS = [
},
{
'xc_terms': [{
- 'XC_functional_name': "VDW_DFX_x_qe",
+ 'xc_functional_name': "VDW_DFX_x_qe",
}],
'xc_section_method': {
'x_qe_xc_inlc_name': "vdwx",
@@ -1121,7 +1121,7 @@ VAN_DER_WAALS = [
},
{
'xc_terms': [{
- 'XC_functional_name': "VDW_DFY_x_qe",
+ 'xc_functional_name': "VDW_DFY_x_qe",
}],
'xc_section_method': {
'x_qe_xc_inlc_name': "vdwy",
@@ -1132,7 +1132,7 @@ VAN_DER_WAALS = [
},
{
'xc_terms': [{
- 'XC_functional_name': "VDW_DFZ_x_qe",
+ 'xc_functional_name': "VDW_DFZ_x_qe",
}],
'xc_section_method': {
'x_qe_xc_inlc_name': "vdwz",
@@ -1166,12 +1166,12 @@ XC_COMPONENT_NAME = [
LIBXC_SHORTCUT = {
"0.810*GGA_C_LYP+0.720*GGA_X_B88+0.200*HF_X+0.190*LDA_C_VWN": {
'xc_terms': [{
- 'XC_functional_name': "HYB_GGA_XC_B3LYP",
+ 'xc_functional_name': "HYB_GGA_XC_B3LYP",
}]
},
"GGA_C_PBE+0.750*GGA_X_PBE+0.250*HF_X": {
'xc_terms': [{
- 'XC_functional_name': "HYB_GGA_XC_PBEH",
+ 'xc_functional_name': "HYB_GGA_XC_PBEH",
}]
},
}
diff --git a/parser/parser-quantum-espresso/parser_quantum_espresso.py b/parser/parser-quantum-espresso/parser_quantum_espresso.py
index 7305805..ac8d5a1 100644
--- a/parser/parser-quantum-espresso/parser_quantum_espresso.py
+++ b/parser/parser-quantum-espresso/parser_quantum_espresso.py
@@ -25,6 +25,7 @@ import nomadcore.unit_conversion.unit_conversion as unit_conversion
import math
import numpy as np
import QuantumEspressoCommon as QeC
+from QuantumEspressoCommon import metaN
from nomadcore.parser_backend import valueForStrValue
from QuantumEspressoCommon import RE_f, RE_i, cRE_f, cRE_i
from QuantumEspressoXC import translate_qe_xc_num
@@ -124,7 +125,7 @@ class QuantumEspressoParserPWSCF(QeC.ParserQuantumEspresso):
target = re.sub(r'^x_qe_t_',r'x_qe_',key)
if target == key:
raise Exception('found non-temporary key in pseudopotential cache: "%s"' % (key))
- backend.addValue(target, value[-1])
+ backend.addValue(metaN(target), value[-1])
if pp['x_qe_t_pp_idx'] is not None:
pp_num = pp['x_qe_t_pp_idx'][-1]
pp_report = self.cache_t_pp_report.get(pp_num, None)
@@ -154,7 +155,7 @@ class QuantumEspressoParserPWSCF(QeC.ParserQuantumEspresso):
dft_d = cache_dft_d.get(pp_label, None)
if dft_d is not None:
for k, v in dft_d.items():
- backend.addValue(k, v)
+ backend.addValue(metaN(k), v)
def onClose_x_qe_t_section_pp_report(
self, backend, gIndex, section):
@@ -214,15 +215,15 @@ class QuantumEspressoParserPWSCF(QeC.ParserQuantumEspresso):
else:
LOGGER.error("x_qe_xc_functional_num is not set")
if method_xc_functionals is not None:
- # NOTE: value of XC_functional generated by translate_qe_xc_num
+ # NOTE: value of xc_functional generated by translate_qe_xc_num
# does not fully respect the metaInfo definition
- # when XC_functional_parameters are involved.
+ # when xc_functional_parameters are involved.
# Therefore, remove it here
- method_xc_functionals.pop('XC_functional', None)
+ method_xc_functionals.pop('xc_functional', None)
self.addDict(backend, method_xc_functionals)
if xc_functionals is not None:
for xc_functional in xc_functionals:
- self.addSectionDict(backend, 'section_XC_functionals', xc_functional)
+ self.addSectionDict(backend, 'section_xc_functionals', xc_functional)
else:
LOGGER.error("error getting xc_functionals")
if section['x_qe_t_allocated_array_name'] is not None:
@@ -304,7 +305,7 @@ class QuantumEspressoParserPWSCF(QeC.ParserQuantumEspresso):
self, backend, gIndex, section):
"""trigger called when section_single_configuration_calculation
is closed"""
- backend.addValue('single_configuration_to_calculation_method_ref', self.sectionIdx['section_method'])
+ backend.addValue('single_configuration_calculation_to_method_ref', self.sectionIdx['section_method'])
backend.addValue('single_configuration_calculation_to_system_ref', self.sectionIdx['section_system'])
# extract k band structure data if available
self.create_section_eigenvalues(backend, section)
@@ -315,10 +316,13 @@ class QuantumEspressoParserPWSCF(QeC.ParserQuantumEspresso):
backend.addArrayValues('x_qe_energy_decomposition_value', np.asarray(
section['x_qe_t_energy_decomposition_value']))
if section['x_qe_t_force_x'] is not None:
- # constraints etc. not part of the reported forces, so correct metaInfo is 'atom_forces_raw'
- backend.addArrayValues('atom_forces_raw', np.array([
+ sectFId = backend.openSection("section_atom_forces")
+ # constraints etc. not part of the reported forces
+ backend.addValue('atom_forces_constraints', 'raw')
+ backend.addArrayValues('atom_forces', np.array([
section['x_qe_t_force_x'], section['x_qe_t_force_y'], section['x_qe_t_force_z']
]).T)
+ backend.closeSection("section_atom_forces", sectFId)
if section['x_qe_t_dispersion_force_x'] is not None:
backend.addArrayValues('x_qe_atom_dispersion_force', np.array([
section['x_qe_t_dispersion_force_x'], section['x_qe_t_dispersion_force_y'], section['x_qe_t_dispersion_force_z']
@@ -385,7 +389,7 @@ class QuantumEspressoParserPWSCF(QeC.ParserQuantumEspresso):
new_system['x_qe_t_k_info_ik'] = section['x_qe_t_md_k_info_ik']
for target, data in new_system.items():
for val in data:
- backend.addValue(target, val)
+ backend.addValue(metaN(target), val)
backend.closeSection('section_system', next_system_gIndex)
def onClose_section_scf_iteration(
@@ -622,22 +626,22 @@ class QuantumEspressoParserPWSCF(QeC.ParserQuantumEspresso):
LOGGER.debug("No K-point weight info found in output")
- if section['x_qe_t_dense_FFT_grid_x'] is not None:
- backend.addArrayValues('x_qe_dense_FFT_grid', np.array([
- section['x_qe_t_dense_FFT_grid_x'], section['x_qe_t_dense_FFT_grid_y'], section['x_qe_t_dense_FFT_grid_z']
+ if section['x_qe_t_dense_fft_grid_x'] is not None:
+ backend.addArrayValues('x_qe_dense_fft_grid', np.array([
+ section['x_qe_t_dense_fft_grid_x'], section['x_qe_t_dense_fft_grid_y'], section['x_qe_t_dense_fft_grid_z']
]).T)
elif old_system is not None:
# unless espresso explicitly writes new FFT grid info, sampling is kept fixed
- backend.addArrayValues('x_qe_dense_FFT_grid', old_system['x_qe_dense_FFT_grid'][-1])
+ backend.addArrayValues('x_qe_dense_fft_grid', old_system['x_qe_dense_fft_grid'][-1])
else:
LOGGER.warning("No dense FFT grid info found in output")
- if section['x_qe_t_smooth_FFT_grid_x'] is not None:
- backend.addArrayValues('x_qe_smooth_FFT_grid', np.array([
- section['x_qe_t_smooth_FFT_grid_x'], section['x_qe_t_smooth_FFT_grid_y'], section['x_qe_t_smooth_FFT_grid_z']
+ if section['x_qe_t_smooth_fft_grid_x'] is not None:
+ backend.addArrayValues('x_qe_smooth_fft_grid', np.array([
+ section['x_qe_t_smooth_fft_grid_x'], section['x_qe_t_smooth_fft_grid_y'], section['x_qe_t_smooth_fft_grid_z']
]).T)
- elif old_system is not None and old_system['x_qe_smooth_FFT_grid'] is not None:
- backend.addArrayValues('x_qe_smooth_FFT_grid', old_system['x_qe_smooth_FFT_grid'][-1])
+ elif old_system is not None and old_system['x_qe_smooth_fft_grid'] is not None:
+ backend.addArrayValues('x_qe_smooth_fft_grid', old_system['x_qe_smooth_fft_grid'][-1])
if section['x_qe_t_vec_supercell_x'] is not None:
backend.addArrayValues('x_qe_vec_supercell', np.array([
@@ -676,14 +680,14 @@ class QuantumEspressoParserPWSCF(QeC.ParserQuantumEspresso):
self.tmp.pop('x_qe_t_profile_category', None)
# manually open header sections, closed at the beginning of scf
for sec in self.header_sections():
- gIndex = backend.openSection(sec)
+ gIndex = backend.openSection(metaN(sec))
self.openSectionIdx[sec] = gIndex
def adHoc_final_scf_MD(self, parser):
"""final SCF calculation in VC-relax runs needs open header sections"""
# manually open header sections, closed at the beginning of scf
for sec in self.header_sections():
- gIndex = parser.backend.openSection(sec)
+ gIndex = parser.backend.openSection(metaN(sec))
self.openSectionIdx[sec] = gIndex
def onClose_section_run(
@@ -710,8 +714,8 @@ class QuantumEspressoParserPWSCF(QeC.ParserQuantumEspresso):
backend.addValue('sampling_method', QE_MD_RELAX_SAMPLING_METHOD[self.tmp['md_relax']])
backend.closeSection('section_sampling_method', sampling_method_gIndex)
frame_sequence_gIndex = backend.openSection('section_frame_sequence')
- backend.addValue('frame_sequence_to_sampling_ref', sampling_method_gIndex)
- backend.addArrayValues('frame_sequence_local_frames_ref', np.array(self.tmp['frames']))
+ backend.addValue('frame_sequence_to_sampling_method_ref', sampling_method_gIndex)
+ backend.addArrayValues('frame_sequence_to_frames_ref', np.array(self.tmp['frames']))
backend.closeSection('section_frame_sequence', frame_sequence_gIndex)
def appendToTmp(self, tmpname, value):
@@ -732,7 +736,7 @@ class QuantumEspressoParserPWSCF(QeC.ParserQuantumEspresso):
self.tmp['dispersion_correction'] = {}
self.tmp['dispersion_correction'][parser.lastMatch['x_qe_t_species_dispersion_correction_label']] = {
'x_qe_dispersion_correction_vdw_radius': parser.lastMatch['x_qe_t_species_dispersion_correction_vdw_radius'],
- 'x_qe_dispersion_correction_C6': parser.lastMatch['x_qe_t_species_dispersion_correction_C6'],
+ 'x_qe_dispersion_correction_c6': parser.lastMatch['x_qe_t_species_dispersion_correction_c6'],
}
def adHoc_alat(self, parser):
@@ -1039,22 +1043,22 @@ class QuantumEspressoParserPWSCF(QeC.ParserQuantumEspresso):
),
SM(name='dense_grid',
startReStr=(r"\s*Dense\s+grid:\s*(?P<x_qe_dense_g_vectors>\d+)\s*G-vectors\s*FFT\s+dimensions:\s*\(\s*" +
- QeC.re_vec("x_qe_t_dense_FFT_grid", split=r"\s*,\s*") + "\s*\)\s*$")
+ QeC.re_vec("x_qe_t_dense_fft_grid", split=r"\s*,\s*") + "\s*\)\s*$")
),
SM(name='dense_grid_old',
startReStr=(r"\s*G\s+cutoff\s*=\s*(?P<x_qe_dense_g_cutoff>" + RE_f + r")\s*" +
r"\(\s*(?P<x_qe_dense_g_vectors>\d+)\s*G-vectors\s*\)\s*FFT\s+grid:\s*\(\s*" +
- QeC.re_vec("x_qe_t_dense_FFT_grid", split=r"\s*,\s*") + "\s*\)\s*$"
+ QeC.re_vec("x_qe_t_dense_fft_grid", split=r"\s*,\s*") + "\s*\)\s*$"
),
),
SM(name='smooth_grid',
startReStr=(r"\s*Smooth\s+grid:\s*(?P<x_qe_smooth_g_vectors>\d+)\s*G-vectors\s*FFT\s+dimensions:\s*\(\s*" +
- QeC.re_vec("x_qe_t_smooth_FFT_grid", split=r"\s*,\s*") + "\s*\)\s*$")
+ QeC.re_vec("x_qe_t_smooth_fft_grid", split=r"\s*,\s*") + "\s*\)\s*$")
),
SM(name='smooth_grid_old',
startReStr=(r"\s*G\s+cutoff\s*=\s*(?P<x_qe_smooth_g_cutoff>" + RE_f + r")\s*" +
r"\(\s*(?P<x_qe_smooth_g_vectors>\d+)\s*G-vectors\s*\)\s*smooth\s+grid:\s*\(\s*" +
- QeC.re_vec("x_qe_t_smooth_FFT_grid", split=r"\s*,\s*") + "\s*\)\s*$"
+ QeC.re_vec("x_qe_t_smooth_fft_grid", split=r"\s*,\s*") + "\s*\)\s*$"
),
),
SM(name='core_charge_realspace',
@@ -1556,7 +1560,7 @@ class QuantumEspressoParserPWSCF(QeC.ParserQuantumEspresso):
for sec in self.header_sections():
sec_gIndex = self.openSectionIdx.pop(sec,None)
if sec_gIndex is not None:
- backend.closeSection(sec, sec_gIndex)
+ backend.closeSection(metaN(sec), sec_gIndex)
def run_submatchers(self):
"""submatchers of section_run"""
@@ -1730,7 +1734,7 @@ class QuantumEspressoParserPWSCF(QeC.ParserQuantumEspresso):
SM(name='dispersion_correction_values', repeats=True,
startReStr=(r"\s*(?P<x_qe_t_species_dispersion_correction_label>.+?)\s+" +
r"(?P<x_qe_t_species_dispersion_correction_vdw_radius>" + RE_f + r")" +
- r"\s*(?P<x_qe_t_species_dispersion_correction_C6>" + RE_f + r")\s*$"),
+ r"\s*(?P<x_qe_t_species_dispersion_correction_c6>" + RE_f + r")\s*$"),
adHoc=self.adHoc_dispersion_correction_values,
),
],
@@ -1850,12 +1854,12 @@ class QuantumEspressoParserPWSCF(QeC.ParserQuantumEspresso):
subMatchers=[
SM(name='sticks_sum', required=True,
startReStr=(
- r"\s*Sum\s+(?P<x_qe_sticks_sum_dense>\d+)\s+(?P<x_qe_sticks_sum_smooth>\d+)\s+(?P<x_qe_sticks_sum_PW>\d+)" +
- r"\s+(?P<x_qe_sticks_sum_G_dense>\d+)\s+(?P<x_qe_sticks_sum_G_smooth>\d+)\s+(?P<x_qe_sticks_sum_G_PW>\d+)\s*$"
+ r"\s*Sum\s+(?P<x_qe_sticks_sum_dense>\d+)\s+(?P<x_qe_sticks_sum_smooth>\d+)\s+(?P<x_qe_sticks_sum_pw>\d+)" +
+ r"\s+(?P<x_qe_sticks_sum_g_dense>\d+)\s+(?P<x_qe_sticks_sum_g_smooth>\d+)\s+(?P<x_qe_sticks_sum_g_pw>\d+)\s*$"
),
),
SM(name='sticks_tot',
- startReStr=r"\s*Tot\s+(?P<x_qe_sticks_tot_dense>\d+)\s+(?P<x_qe_sticks_tot_smooth>\d+)\s+(?P<x_qe_sticks_tot_PW>\d+)\s*$",
+ startReStr=r"\s*Tot\s+(?P<x_qe_sticks_tot_dense>\d+)\s+(?P<x_qe_sticks_tot_smooth>\d+)\s+(?P<x_qe_sticks_tot_pw>\d+)\s*$",
),
],
),
diff --git a/src/main/scala/eu/nomad_lab/parsers/QuantumEspressoParser.scala b/src/main/scala/eu/nomad_lab/parsers/QuantumEspressoParser.scala
index c3ac6e7..1b81b82 100644
--- a/src/main/scala/eu/nomad_lab/parsers/QuantumEspressoParser.scala
+++ b/src/main/scala/eu/nomad_lab/parsers/QuantumEspressoParser.scala
@@ -48,7 +48,7 @@ object QuantumEspressoParser extends SimpleExternalParserGenerator(
"parser-quantum-espresso/setup_paths.py",
"nomad_meta_info/public.nomadmetainfo.json",
"nomad_meta_info/common.nomadmetainfo.json",
- "nomad_meta_info/meta_types.nomadmetainfo.json",
+ "nomad_meta_info/meta.nomadmetainfo.json",
"nomad_meta_info/quantum_espresso.nomadmetainfo.json"
) ++ DefaultPythonInterpreter.commonFiles(),
dirMap = Map(
--
GitLab