Commit e93ffb78 authored by Lauri Himanen's avatar Lauri Himanen
Browse files

Merged with v0.7.3.

parents 5bbecf19 a987db70
Pipeline #67932 passed with stages
in 13 minutes and 54 seconds
......@@ -189,6 +189,9 @@ normalize = NomadConfig(
# their symmetry positions in order for spglib to still detect symmetries.
# The unit is angstroms.
symmetry_tolerance=0.1,
# The distance tolerance between atoms for grouping them into the same
# cluster. Used in detecting system type.
cluster_threshold=3.1,
)
client = NomadConfig(
......
......@@ -15,14 +15,15 @@
from collections import Counter
from typing import Any
import ase
from ase import Atoms
import numpy as np
import json
import re
import os
import sqlite3
from matid import SymmetryAnalyzer
from matid.geometry import get_dimensionality
from matid import SymmetryAnalyzer, Classifier
from matid.classifications import Class0D, Atom, Class1D, Material2D, Surface, Class3D
from nomad.normalizing import structure
from nomad import utils, config
......@@ -259,36 +260,38 @@ class SystemNormalizer(SystemBasedNormalizer):
return True
def system_type_analysis(self, atoms) -> None:
def system_type_analysis(self, atoms: Atoms) -> None:
"""
Determine the dimensionality and hence the system type of the system with
Matid. Write the system type to the backend.
Determine the system type with MatID. Write the system type to the
backend.
Args:
atoms: The structure to analyse
"""
system_type = config.services.unavailable_value
try:
if atoms.get_number_of_atoms() > config.normalize.system_classification_with_clusters_threshold:
# it is too expensive to run Matid's cluster detection, just check pbc
dimensionality = np.sum(atoms.get_pbc())
if atoms.get_number_of_atoms() <= config.normalize.system_classification_with_clusters_threshold:
try:
classifier = Classifier(cluster_threshold=config.normalize.cluster_threshold)
cls = classifier.classify(atoms)
except Exception as e:
self.logger.error(
'matid project system classification failed', exc_info=e, error=str(e))
else:
dimensionality = get_dimensionality(
atoms, cluster_threshold=3.1, return_clusters=False)
if dimensionality is None:
pass
elif dimensionality == 0:
if atoms.get_number_of_atoms() == 1:
classification = type(cls)
if classification == Class3D:
system_type = 'bulk'
elif classification == Atom:
system_type = 'atom'
else:
elif classification == Class0D:
system_type = 'molecule / cluster'
elif dimensionality == 1:
system_type = '1D'
elif dimensionality == 2:
system_type = '2D / surface'
elif dimensionality == 3:
system_type = 'bulk'
except Exception as e:
self.logger.error(
'matid project system classification failed', exc_info=e, error=str(e))
elif classification == Class1D:
system_type = '1D'
elif classification == Surface:
system_type = 'surface'
elif classification == Material2D:
system_type = '2D'
else:
self.logger.info("system type analysis not run due to large system size")
self._backend.addValue('system_type', system_type)
......
images:
nomad:
tag: "v0.6.3"
tag: "v0.7.2"
frontend:
tag: "v0.6.3"
services:
apiSecret: 'nomad-keycloak-prod-api-secret'
tag: "v0.7.2"
proxy:
nodePort: 30012
external:
host: "repository.nomad-coe.eu"
path: "/uploads"
path: "/app"
gui:
debug: false
app:
replicas: 2
worker: 8
workerClass: "sync"
nomadNodeType: "public"
worker:
replicas: 1
......@@ -19,13 +25,20 @@ worker:
processes: 10
nomadNodeType: "prod-worker"
dbname: fairdi_nomad_prod
elastic:
port: 9202
uploadurl: 'https://repository.nomad-coe.eu/uploads/gui/upload'
dbname: fairdi_nomad_prod_v0_7
uploadurl: 'https://repository.nomad-coe.eu/app/gui/upload'
keycloak:
serverUrl: "https://repository.nomad-coe.eu/fairdi/keycloak/auth/"
passwordSecret: 'nomad-keycloak-password'
realmName: 'fairdi_nomad_prod'
clientId: 'nomad_api_dev'
clientSecret: 'nomad-keycloak-prod-api-secret'
admin_user_id: '82efac55-6187-408c-8027-b98580c0e1c5'
volumes:
prefixSize: 1
......@@ -39,3 +52,7 @@ mail:
host: 'mailrelay.mpcdf.mpg.de'
port: 25
from: 'webmaster@nomad-repository.eu'
datacite:
secret: 'nomad-datacite'
enabled: True
images.nomad.tag: "stable"
images.frontend.tag: "stable"
images:
nomad: "v0.7.2"
frontend:
tag: "v0.7.2"
proxy:
nodePort: 30010
......@@ -12,7 +14,10 @@ gui:
app:
replicas: 2
threads: 16
threads: 4
worker: 8
workerClass: "sync"
nomadNodeType: "public"
worker:
replicas: 1
......@@ -44,3 +49,4 @@ volumes:
datacite:
secret: 'nomad-datacite'
enabled: True
......@@ -64,10 +64,12 @@ metadata:
data:
gunicorn.conf: |
secure_scheme_headers = {'X-FORWARDED-PROTOCOL': 'ssl', 'X-FORWARDED-PROTO': 'https', 'X-FORWARDED-SSL': 'on'}
worker_class = '{{ .Values.app.workerClass }}'
threads = {{ .Values.app.threads }}
{{ if ne .Values.app.workerClass "sync" }}
worker_class = '{{ .Values.app.workerClass }}'
threads = {{ .Values.app.threads }}
{{ end }}
worker_connections = 1000
worker = {{ .Values.app.worker }}
workers = {{ .Values.app.worker }}
---
apiVersion: apps/v1
kind: Deployment
......
# Step Nr. Time[fs] Kin.[a.u.] Temp[K] Pot.[a.u.] Cons Qty[a.u.] UsedTime[s]
0 0.000000 0.009975468 300.000000000 -31.297885373 -31.287909904 0.000000000
1 0.500000 0.009980435 300.149355595 -31.297890335 -31.287909901 20.881730749
2 1.000000 0.009995385 300.598964458 -31.297905285 -31.287909900 10.199698742
3 1.500000 0.010020440 301.352455416 -31.297930343 -31.287909903 9.527669955
4 2.000000 0.010055749 302.414350563 -31.297965611 -31.287909862 9.869754617
8
i = 0, time = 0.000, E = -31.2978853728
Si 0.0000000000 0.0000000000 0.0000000000
Si 0.0000000000 2.7153487000 2.7153487000
Si 2.7153487000 2.7153487000 0.0000000000
Si 2.7153487000 0.0000000000 2.7153487000
Si 4.0730231000 1.3576744000 4.0730231000
Si 1.3576744000 1.3576744000 1.3576744000
Si 1.3576744000 4.0730231000 4.0730231000
Si 4.0730231000 4.0730231000 1.3576744000
8
i = 1, time = 0.500, E = -31.2978903354
Si 0.0016383385 -0.0001721499 -0.0006238612
Si -0.0000657767 2.7160970060 2.7143725504
Si 2.7136670506 2.7156518890 -0.0018471601
Si 2.7177623600 -0.0010352377 2.7164197878
Si 4.0752014230 1.3578495204 4.0733437423
Si 1.3577499527 1.3579175611 1.3598641839
Si 1.3566870268 4.0732906063 4.0743347685
Si 4.0694520250 4.0724932049 1.3562283885
8
i = 2, time = 1.000, E = -31.2979052852
Si 0.0032756726 -0.0003437104 -0.0012419769
Si -0.0001344763 2.7168490487 2.7133950184
Si 2.7119819817 2.7159506528 -0.0036953940
Si 2.7201761805 -0.0020699682 2.7174949846
Si 4.0773833263 1.3580258103 4.0736642410
Si 1.3578288759 1.3581590860 1.3620556567
Si 1.3556996868 4.0735588711 4.0756425358
Si 4.0658811525 4.0719626098 1.3547773344
8
i = 3, time = 1.500, E = -31.2979303428
Si 0.0049109769 -0.0005141199 -0.0018486869
Si -0.0002090025 2.7176085071 2.7124147394
Si 2.7102900940 2.7162405146 -0.0055457615
Si 2.7225903290 -0.0031037049 2.7185784065
Si 4.0795723667 1.3582045036 4.0739844738
Si 1.3579144916 1.3583973571 1.3642504927
Si 1.3547124450 4.0738286606 4.0769425026
Si 4.0623106994 4.0714306817 1.3533162334
8
i = 4, time = 2.000, E = -31.2979656110
Si 0.0065431987 -0.0006828491 -0.0024384492
Si -0.0002922176 2.7183789795 2.7114303865
Si 2.7085880403 2.7165169709 -0.0073992905
Si 2.7250049622 -0.0041359798 2.7196741472
Si 4.0817720397 1.3583868923 4.0743043346
Si 1.3580100514 1.3586307841 1.3664503252
Si 1.3537254076 4.0741007430 4.0782307899
Si 4.0587409176 4.0708968590 1.3518401563
&GLOBAL
PROJECT si_md
RUN_TYPE MD
PRINT_LEVEL MEDIUM
&END GLOBAL
&MOTION
&MD
ENSEMBLE NVE
TIMESTEP 0.5
TEMPERATURE 300
STEPS 4
&END
&END
&FORCE_EVAL
METHOD QS
&DFT
POTENTIAL_FILE_NAME GTH_POTENTIALS
BASIS_SET_FILE_NAME BASIS_SET
&QS
EPS_DEFAULT 1.0E-10
&END QS
&MGRID
NGRIDS 4
CUTOFF 300
REL_CUTOFF 60
&END MGRID
&XC
&XC_FUNCTIONAL PADE
&END XC_FUNCTIONAL
&END XC
&SCF
SCF_GUESS ATOMIC
EPS_SCF 1.0E-7
MAX_SCF 300
&DIAGONALIZATION ON
ALGORITHM STANDARD
&END DIAGONALIZATION
&MIXING T
METHOD BROYDEN_MIXING
ALPHA 0.4
NBROYDEN 8
&END MIXING
&END SCF
&END DFT
&SUBSYS
&KIND Si
ELEMENT Si
BASIS_SET DZVP-GTH-PADE
POTENTIAL GTH-PADE-q4
&END KIND
&CELL
A 5.430697500 0.000000000 0.000000000
B 0.000000000 5.430697500 0.000000000
C 0.000000000 0.000000000 5.430697500
&END CELL
&COORD
Si 0.000000000 0.000000000 0.000000000
Si 0.000000000 2.715348700 2.715348700
Si 2.715348700 2.715348700 0.000000000
Si 2.715348700 0.000000000 2.715348700
Si 4.073023100 1.357674400 4.073023100
Si 1.357674400 1.357674400 1.357674400
Si 1.357674400 4.073023100 4.073023100
Si 4.073023100 4.073023100 1.357674400
&END COORD
&END SUBSYS
&END FORCE_EVAL
This diff is collapsed.
This diff is collapsed.
......@@ -40,7 +40,7 @@
"Na"
],
"lattice_vectors": [
[0, 0.5, 0.5],[0.5, 0 , 0.5],[0.5, 0.5, 0]]
[0, 0.5e-10, 0.5e-10],[0.5e-10, 0 , 0.5e-10],[0.5e-10, 0.5e-10, 0]]
}
],
"section_single_configuration_calculation": [
......@@ -73,4 +73,4 @@
]
}
]
}
\ No newline at end of file
}
This diff is collapsed.
##################################################################################
# 17.06.2014
# graphene
# using a kgrid of 24x24x1
# tight basis settings
# C Tier 2
###########################################################################################
##################################################################################
# SCF Input
##################################################################################
#
# Functional
xc pbe
many_body_dispersion
mbd_scs_dip_cutoff 600
mbd_cfdm_dip_cutoff 600
mbd_scs_vacuum_axis .false. .false. .true.
#
# Charge Mixing
mixer pulay
empty_states 4
# Smearing
occupation_type gaussian 0.1
# Convergence
sc_accuracy_rho 1.E-4
sc_accuracy_eev 5.E-6
sc_accuracy_etot 1.E-5
#
sc_iter_limit 400
# kgrid
k_grid 16 16 1
k_offset 0.03125 0.03125 1.0
################################################################################
#
# FHI-aims code project
# Volker Blum, Fritz Haber Institute Berlin, 2009
#
# Suggested "tight" defaults for C atom (to be pasted into control.in file)
#
################################################################################
species C
# global species definitions
nucleus 6
mass 12.0107
#
l_hartree 8
#
cut_pot 4.0 2.0 1.0
basis_dep_cutoff 1e-4
#
radial_base 34 7.0
radial_multiplier 2
angular_grids specified
# division 0.2187 50
division 0.4416 110
division 0.6335 194
division 0.7727 302
division 0.8772 434
division 0.9334 590
# division 0.9924 770
# division 1.0230 974
# division 1.5020 1202
# outer_grid 974
outer_grid 590
################################################################################
#
# Definition of "minimal" basis
#
################################################################################
# valence basis states
valence 2 s 2.
valence 2 p 2.
# ion occupancy
ion_occ 2 s 1.
ion_occ 2 p 1.
################################################################################
#
# Suggested additional basis functions. For production calculations,
# uncomment them one after another (the most important basis functions are
# listed first).
#
# Constructed for dimers: 1.0 A, 1.25 A, 1.5 A, 2.0 A, 3.0 A
#
################################################################################
# "First tier" - improvements: -1214.57 meV to -155.61 meV
hydro 2 p 1.7
hydro 3 d 6
hydro 2 s 4.9
# "Second tier" - improvements: -67.75 meV to -5.23 meV
hydro 4 f 9.8
hydro 3 p 5.2
hydro 3 s 4.3
hydro 5 g 14.4
hydro 3 d 6.2
# "Third tier" - improvements: -2.43 meV to -0.60 meV
# hydro 2 p 5.6
# hydro 2 s 1.4
# hydro 3 d 4.9
# hydro 4 f 11.2
# "Fourth tier" - improvements: -0.39 meV to -0.18 meV
# hydro 2 p 2.1
# hydro 5 g 16.4
# hydro 4 d 13.2
# hydro 3 s 13.6
# hydro 4 f 17.6
# Further basis functions - improvements: -0.08 meV and below
# hydro 3 s 2
# hydro 3 p 6
# hydro 4 d 20
##############################################
# 17.06.2014
# bulk properties of graphene
# lattice parameter a=2.46559807494, c=20.00
##############################################
#
lattice_vector 1.23279904 -2.13527057 0.00000000
lattice_vector 1.23279904 2.13527057 0.00000000
lattice_vector 0.00000000 0.00000000 20.00
#
# Fractional coordinates:
# L1 L2 L3
atom_frac 0.00000000 0.00000000 0.00000000 C
atom_frac 0.66666666 0.33333333 0.00000000 C
This diff is collapsed.
This diff is collapsed.
# This is the geometry file from relaxed coordinates
atom -0.71243027 1.23396634 0.00000000 C
constrain_relaxation z
atom -1.42486516 0.00000000 0.00000000 C
constrain_relaxation z
atom -0.71243027 -1.23396634 0.00000000 C
constrain_relaxation z
atom 0.71243027 -1.23396634 0.00000000 C
constrain_relaxation z
atom 1.42486516 0.00000000 0.00000000 C
constrain_relaxation z
atom 0.71243027 1.23396634 0.00000000 C
constrain_relaxation z
atom -1.42424233 2.46686049 0.00000000 C
constrain_relaxation z
atom -2.84848846 0.00000000 0.00000000 C
constrain_relaxation z
atom -1.42424233 -2.46686049 0.00000000 C
constrain_relaxation z
atom 1.42424233 -2.46686049 0.00000000 C
constrain_relaxation z
atom 2.84848846 0.00000000 0.00000000 C
constrain_relaxation z
atom 1.42424233 2.46686049 0.00000000 C
constrain_relaxation z
atom -2.84580245 2.43648439 0.00000000 C
constrain_relaxation z
atom -3.38895815 3.38280060 0.00000000 H
constrain_relaxation z
atom -3.53296333 -1.24629587 0.00000000 C
constrain_relaxation z
atom -4.62407474 -1.24352959 0.00000000 H
constrain_relaxation z
atom -0.68715742 -3.68278568 0.00000000 C
constrain_relaxation z
atom -1.23512609 -4.62632322 0.00000000 H
constrain_relaxation z
atom 2.84580245 -2.43648439 0.00000000 C
constrain_relaxation z
atom 3.38895815 -3.38280060 0.00000000 H
constrain_relaxation z
atom 3.53296333 1.24629587 0.00000000 C
constrain_relaxation z
atom 4.62407474 1.24352959 0.00000000 H
constrain_relaxation z
atom 0.68715742 3.68278568 0.00000000 C
constrain_relaxation z
atom 1.23512609 4.62632322 0.00000000 H
constrain_relaxation z
atom -3.53296333 1.24629587 0.00000000 C
constrain_relaxation z
atom -4.62407474 1.24352959 0.00000000 H
constrain_relaxation z
atom -2.84580245 -2.43648439 0.00000000 C
constrain_relaxation z
atom -3.38895815 -3.38280060 0.00000000 H
constrain_relaxation z
atom 0.68715742 -3.68278568 0.00000000 C
constrain_relaxation z
atom 1.23512609 -4.62632322 0.00000000 H
constrain_relaxation z
atom 3.53296333 -1.24629587 0.00000000 C
constrain_relaxation z
atom 4.62407474 -1.24352959 0.00000000 H
constrain_relaxation z
atom 2.84580245 2.43648439 0.00000000 C
constrain_relaxation z
atom 3.38895815 3.38280060 0.00000000 H
constrain_relaxation z
atom -0.68715742 3.68278568 0.00000000 C
constrain_relaxation z
atom -1.23512609 4.62632322 0.00000000 H
constrain_relaxation z
This diff is collapsed.
lattice_vector 3.9473 0.00000000 0.00000000
lattice_vector 0.00000000 5.5823 0.00000000
lattice_vector 0.00000000 0.00000000 250.00000000
atom -1.97365 4.1867438961 4.1867438961 O
atom -1.97365 1.3955812987 4.1867438961 O
atom 0 2.7911625974 2.7911625974 Sr
atom -1.97365 5.5823251948 2.7911625974 Ti
atom 0 5.5823251948 2.7911625974 O
atom -1.97365 1.3955812987 1.3955812987 O
atom -1.97365 4.1867438961 1.3955812987 O
atom 0 5.5823251948 6.197625962162E-016 Sr
atom -1.97365 2.7911625974 6.197625962162E-016 Ti
atom 0 2.7911625974 6.197625962162E-016 O
atom -1.97365 4.1867438961 -1.3955812987 O
atom -1.97365 1.3955812987 -1.3955812987 O
atom 0 2.7911625974 -2.7911625974 Sr
atom -1.97365 5.5823251948 -2.7911625974 Ti
atom 0 5.5823251948 -2.7911625974 O
homogeneous_field 0.0 0.0 13.0 #0.041075202
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