Machine learning based approach for solving atomic structures of nanomaterials combining pair distribution functions with density functional theory

Fuente: arXiv

Enregistré dans:

Détails bibliographiques
Auteurs principaux:	Kløve, Magnus, Sommer, Sanna, Iversen, Bo B., Hammer, Bjørk, Dononelli, Wilke
Format:	Preprint
Publié:	2022
Sujets:	Materials Science
Accès en ligne:	Acceder al recurso
Tags:	Ajouter un tag Pas de tags, Soyez le premier à ajouter un tag!

_version_	1866912474811334656
author	Kløve, Magnus Sommer, Sanna Iversen, Bo B. Hammer, Bjørk Dononelli, Wilke
author_facet	Kløve, Magnus Sommer, Sanna Iversen, Bo B. Hammer, Bjørk Dononelli, Wilke
contents	Determination of crystal structures of nanocrystalline or amorphous compounds is a great challenge in solid states chemistry and physics. Pair distribution function (PDF) analysis of X-Ray or neutron total scattering data has proven to be a key element in tackling this challenge. However, in most cases a reliable structural motif is needed as starting configuration for structure refinements. Here, we present an algorithm that is able to determine the crystal structure of an unknown compound by means of an on-the-fly trained machine learning model that combines density functional theory (DFT) calculations with comparison of calculated and measured PDFs for global optimization in an artificial landscape. Due to the nature of this landscape, even metastable configurations can be determined.
format	Preprint
id	arxiv_https___arxiv_org_abs_2209_01358
institution	arXiv
publishDate	2022
record_format	arxiv
spellingShingle	Machine learning based approach for solving atomic structures of nanomaterials combining pair distribution functions with density functional theory Kløve, Magnus Sommer, Sanna Iversen, Bo B. Hammer, Bjørk Dononelli, Wilke Materials Science Determination of crystal structures of nanocrystalline or amorphous compounds is a great challenge in solid states chemistry and physics. Pair distribution function (PDF) analysis of X-Ray or neutron total scattering data has proven to be a key element in tackling this challenge. However, in most cases a reliable structural motif is needed as starting configuration for structure refinements. Here, we present an algorithm that is able to determine the crystal structure of an unknown compound by means of an on-the-fly trained machine learning model that combines density functional theory (DFT) calculations with comparison of calculated and measured PDFs for global optimization in an artificial landscape. Due to the nature of this landscape, even metastable configurations can be determined.
title	Machine learning based approach for solving atomic structures of nanomaterials combining pair distribution functions with density functional theory
topic	Materials Science
url	https://arxiv.org/abs/2209.01358

if (filemtime($filename) + $maxlifetime < time()) { unlink($filename); $count++; } } return $count; } /** * A function that is called internally when session data is to be saved. * * @param string $sessId The current session ID * @param string $data The session data to write * * @return bool */ protected function saveSession($sessId, $data): bool { $sessFile = $this->path . '/sess_' . $sessId; if ($handle = fopen($sessFile, 'w')) { $return = false; // Lock the file for exclusive access to avoid issues with multiple // processes writing session simultaneously: if (flock($handle, LOCK_EX)) { $return = fwrite($handle, $data); // Make sure that there's no trailing data by truncating the file to // the correct length: ftruncate($handle, strlen($data)); fflush($handle); flock($handle, LOCK_UN); } fclose($handle); if ($return !== false) { return true; } } // If we got this far, something went wrong with the file output... // It is tempting to throw an exception here, but this code is called // outside of the context of exception handling, so all we can do is // echo a message.

// Anecdotal testing Today and Yesterday seems to indicate destroy() // is called by the garbage collector and everything is good. // Something to keep in mind though. return 0; } /** * Write function that is called when session data is to be saved. * * @param string $sessId The current session ID * @param string $data The session data to write * * @return bool */ public function write($sessId, $data): bool { if ($this->writesDisabled) { return true; } return $this->saveSession($sessId, $data); } /** * A function that is called internally when session data is to be saved. * * @param string $sessId The current session ID * @param string $data The session data to write * * @return bool */ abstract protected function saveSession($sessId, $data): bool; }

* * @return void */ public function writeClose() { // The assumption is that we're using PHP's ext/session. // session_write_close() will actually overwrite $_SESSION with an // empty array on completion -- which leads to a mismatch between what // is in the storage object and $_SESSION. To get around this, we // temporarily reset $_SESSION to an array, and then re-link it to // the storage object. // // Additionally, while you _can_ write to $_SESSION following a // session_write_close() operation, no changes made to it will be // flushed to the session handler. As such, we now mark the storage // object isImmutable. $storage = $this->getStorage(); if (! $storage->isImmutable()) { $_SESSION = $storage->toArray(true); session_write_close(); $storage->fromArray($_SESSION); $storage->markImmutable(); } } /** * Attempt to set the session name * * If the session has already been started, or if the name provided fails * validation, an exception will be raised. * * @param string $name * @return SessionManager * @throws Exception\InvalidArgumentException */ public function setName($name) { if ($this->sessionExists()) { throw new Exception\InvalidArgumentException( 'Cannot set session name after a session has already started'

Environment & details:

GET Data empty

POST Data empty

Files empty

Key	Value
VUFIND_SESSION	"e4257bc30115d3e1329f8c8f37de1cec"
ui	"standard"
language	"fr"

Session

Key	Value
__Laminas	array:2 [`"_REQUEST_ACCESS_TIME" => 1790887909.1015 "_VALID" => array:1 [ "Laminas\Session\Validator\Id" => "e4257bc30115d3e1329f8c8f37de1cec" ]`]
SessionState	Laminas\Stdlib\ArrayObject {#938}
FlashMessenger	Laminas\Stdlib\ArrayObject {#1433}
SessionHelper	Laminas\Stdlib\ArrayObject {#1762}

Server/Request Data

Key	Value
REDIRECT_VUFIND_LOCAL_DIR	"/usr/local/vufind/local"
REDIRECT_HTTPS	"on"
REDIRECT_SSL_TLS_SNI	"info.umar.mx"
REDIRECT_STATUS	"200"
VUFIND_LOCAL_DIR	"/usr/local/vufind/local"
HTTPS	"on"
SSL_TLS_SNI	"info.umar.mx"
HTTP_ACCEPT	"/"
HTTP_USER_AGENT	"Mozilla/5.0 AppleWebKit/537.36 (KHTML, like Gecko; compatible; ClaudeBot/1.0; +claudebot@anthropic.com)"
HTTP_COOKIE	"VUFIND_SESSION=e4257bc30115d3e1329f8c8f37de1cec; ui=standard; language=fr"
HTTP_ACCEPT_ENCODING	"gzip, br, zstd, deflate"
HTTP_HOST	"info.umar.mx"
PATH	"/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/snap/bin"
SERVER_SIGNATURE	"<address>Apache/2.4.66 (Ubuntu) Server at info.umar.mx Port 443</address>\n"
SERVER_SOFTWARE	"Apache/2.4.66 (Ubuntu)"
SERVER_NAME	"info.umar.mx"
SERVER_ADDR	"200.23.222.19"
SERVER_PORT	"443"
REMOTE_ADDR	"216.73.217.142"
DOCUMENT_ROOT	"/usr/local/vufind/public"
REQUEST_SCHEME	"https"
CONTEXT_PREFIX	""
CONTEXT_DOCUMENT_ROOT	"/usr/local/vufind/public"
SERVER_ADMIN	"admin@localhost"
SCRIPT_FILENAME	"/usr/local/vufind/public/index.php"
REMOTE_PORT	"14401"
REDIRECT_URL	""" /Record/\n arxiv_https___arxiv_org_abs_2209_01358/Details """
GATEWAY_INTERFACE	"CGI/1.1"
SERVER_PROTOCOL	"HTTP/1.1"
REQUEST_METHOD	"GET"
QUERY_STRING	""
REQUEST_URI	"/Record/%0Aarxiv_https___arxiv_org_abs_2209_01358/Details"
SCRIPT_NAME	"/index.php"
PHP_SELF	"/index.php"
REQUEST_TIME_FLOAT	1790887909.0837
REQUEST_TIME	1790887909

Environment Variables empty

Registered Handlers

0. Whoops\Handler\PrettyPageHandler

Environment & details:

GET Data empty

POST Data empty

Files empty

Key	Value
VUFIND_SESSION	"e4257bc30115d3e1329f8c8f37de1cec"
ui	"standard"
language	"fr"

Session

Key	Value
__Laminas	array:2 [`"_REQUEST_ACCESS_TIME" => 1790887909.1015 "_VALID" => array:1 [ "Laminas\Session\Validator\Id" => "e4257bc30115d3e1329f8c8f37de1cec" ]`]
SessionState	Laminas\Stdlib\ArrayObject {#938}
FlashMessenger	Laminas\Stdlib\ArrayObject {#1433}
SessionHelper	Laminas\Stdlib\ArrayObject {#1762}

Server/Request Data

Key	Value
REDIRECT_VUFIND_LOCAL_DIR	"/usr/local/vufind/local"
REDIRECT_HTTPS	"on"
REDIRECT_SSL_TLS_SNI	"info.umar.mx"
REDIRECT_STATUS	"200"
VUFIND_LOCAL_DIR	"/usr/local/vufind/local"
HTTPS	"on"
SSL_TLS_SNI	"info.umar.mx"
HTTP_ACCEPT	"/"
HTTP_USER_AGENT	"Mozilla/5.0 AppleWebKit/537.36 (KHTML, like Gecko; compatible; ClaudeBot/1.0; +claudebot@anthropic.com)"
HTTP_COOKIE	"VUFIND_SESSION=e4257bc30115d3e1329f8c8f37de1cec; ui=standard; language=fr"
HTTP_ACCEPT_ENCODING	"gzip, br, zstd, deflate"
HTTP_HOST	"info.umar.mx"
PATH	"/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/snap/bin"
SERVER_SIGNATURE	"<address>Apache/2.4.66 (Ubuntu) Server at info.umar.mx Port 443</address>\n"
SERVER_SOFTWARE	"Apache/2.4.66 (Ubuntu)"
SERVER_NAME	"info.umar.mx"
SERVER_ADDR	"200.23.222.19"
SERVER_PORT	"443"
REMOTE_ADDR	"216.73.217.142"
DOCUMENT_ROOT	"/usr/local/vufind/public"
REQUEST_SCHEME	"https"
CONTEXT_PREFIX	""
CONTEXT_DOCUMENT_ROOT	"/usr/local/vufind/public"
SERVER_ADMIN	"admin@localhost"
SCRIPT_FILENAME	"/usr/local/vufind/public/index.php"
REMOTE_PORT	"14401"
REDIRECT_URL	""" /Record/\n arxiv_https___arxiv_org_abs_2209_01358/Details """
GATEWAY_INTERFACE	"CGI/1.1"
SERVER_PROTOCOL	"HTTP/1.1"
REQUEST_METHOD	"GET"
QUERY_STRING	""
REQUEST_URI	"/Record/%0Aarxiv_https___arxiv_org_abs_2209_01358/Details"
SCRIPT_NAME	"/index.php"
PHP_SELF	"/index.php"
REQUEST_TIME_FLOAT	1790887909.0837
REQUEST_TIME	1790887909

Environment Variables empty

Registered Handlers

0. Whoops\Handler\PrettyPageHandler

Documents similaires

Environment & details:

Environment & details: