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Group meetings

Summer 2016 meeting

[2016-06-10 Fri] 3pm DH1102

Elif
Image analysis update (15 min)
Jake
CuPd conundrum (15 min)
Sanjna
AuPd literature review (10 min)
Devon
Research update (15 min)

[2016-06-24 Fri] 3pm DH1102

Chen
Research update (15 min)
Akshay
Research update (15 min)
Tianyu
Research update (15 min)
Feiyang
Research update (15 min)

[2016-07-06 Wed] 3pm DH1102

Elif
Qualifier Part I
Sanjna
Research update
Teng
Research update (15 min)
Devon
Research update (15 min)

[2016-07-15 Fri] 3pm DH1102

Jake
Research update (15 min)
Chen
Research update (15 min)
Akshay
Research update (15 min)
Tianyu
Research update (15 min)
Feiyang
Research update (15 min)

[2016-08-12 Fri] 3pm DH1102

Elif
Qualifier practice (15 min)
Sanjna
Research update (15 min)
Jean
Research update (15 min)
Teng
Research update (15 min)
Devon
Research update (15 min)

Spring 2016 meetings

<2016-01-08 Fri>

  • First rule of the Kitchin Research Group
    • Be on time.
  • Introductions
    • Kenate (bulk Pd neural network)
    • MS students - introduction
      • Feiyang (ternary alloy phase behavior)
      • Teng (ternary alloy segregation)
      • Tianyu (neural adsorbates)
      • Akshay (neural oxide)
      • Chen (neural oxide)
      • Devon (H2 separation on 2D materials)
  • Graduating people
    • Zhongnan
    • Alex
  • New PhD student
    • Elif (microfluidic characterization of CO2 capture solvents)
  • Review of 2015
    • 14 papers!
  • 2016 research overview
    • Machine learning in alloy and oxide simulation
      • Phase behavior
      • Surface segregation
      • Reactivity
    • precipitating CO2 solvents
    • jmax dominates the scientific writing world
      • ox-manuscript + templates
      • track-changes and merge
      • collaborative writing
  • Kenate presentation

hackathon - jmax and org-ref

See the jmax menu

M-x ore for help on org-elements

56
34
45
45

See the Org->org-ref->Help menu

Track-changes!!!{++ add new words++}

{–Some text that clearly should be deleted.–}

Put a comment -> <- in here.

Future hackathon topics:

  • integration with git/github
  • bibtexery

bibliographystyle:unsrt bibliography:~/Dropbox/bibliography/references.bib

<2016-01-22 Fri>

  • Jake - tutorial (20 minutes)
  • Alex - research (20 minutes)
  • hackathon - one cool solution, one problem to solve

    elisp:jmax-help

Track changes - ~/computational-materials/manuscript.org

<2016-02-05 Fri>

  • Devon - lit review 2D hydrogen transport (15 minutes)
  • Feiyang - lit review on modeling ternary alloy phase behavior (15 minutes)
  • Tianyu - lit review of Oxygen on Pd surfaces (15 minutes)
  • Teng Ma - lit review on alloy segregation (15 minutes)
  • hackathon - one cool solution, one problem to solve

Slide numbers, No animations, no timing, no themes, keep it so simple. Practice with pointer, and not reading

$exp{x}$ $$exp{x}$$

\(exp{x}\) \[exp{x}\]

@@latex:\ce{CO2}@@ CO2 \ce{H2SO4} H2SO4 @@latex:H_2SO_4@@

<2016-02-19 Fri>

  • Elif - lit review on amine solvent CO2 capture (15 minutes)

Abolhasani angew chem int 2014, 53, 7992 cite:abolhasani-2014-microf-studies

rochelle chemical engineering research and design 89 2011 1693 cite:chen-2011-aqueous

cite:li-2014-solub-co2,mazari-2014-degrad-co2

  • Chen Wang - lit review on neural networks (15 minutes)

3:31

  • Akshay - lit review on oxide interfaces (15 minutes)
  • hackathon - one cool solution, one problem to solve

metal=Cu/feos=1.1/some-key=fav/isif=4/and=so-on

More notes: 15 minutes = 10 slides. No outlines

scheduled vs deadline

C-c C-d C-c C-s

Code blocks

print('\\url{www.google.com}')
print(t)
return [['a', 'b', 'c'], None, [1, 3, 4], [5, 6, 7]]
abc
134
567
import numpy as np
n = np.array(n)

print(n.max())
a = 5
print(5 * a)

<2016-03-04 Fri> group meeting

  • Jake research (20 minutes)
  • Kenate research (20 minutes)
  • Alex - research (20 minutes)
  • hackathon - one cool solution, one problem to solve

<2016-03-18 Fri>

  • Elif - research (20 minutes)
  • Devon - project proposal (10 minutes)
  • Feiyang - project proposal (10 minutes)
  • Tianyu - project proposal (10 minutes)
  • Teng Ma - project proposal (10 minutes)
  • hackathon - one cool solution, one problem to solve
print(5)

<2016-04-01 Fri>

  • Jake research (20 minutes)
  • Kenate research (20 minutes)
  • Alex - research (20 minutes)
  • hackathon - one cool solution, one problem to solve

Jake has this ase-database. He would like to interact with it via Emacs

ase-db --limit 15 2016-04-01/example-db1.db id=70

We can turn that into a table, or list of entries like this:

(mapcar (lambda (s) (split-string s "|"))
	(split-string
	 (shell-command-to-string
	  "ase-db 2016-04-01/example-db1.db") "\n"))

A loopy way to do that.

(loop for s in (split-string
		(shell-command-to-string
		 "ase-db 2016-04-01/example-db1.db") "\n")
      collect (split-string s "|"))

Let’s turn this into a function with selection. No db query here.

(defun ase-db-info (s) (message-box "%S" s)
       (with-help-window (help-buffer)
	 (princ
	  (shell-command-to-string
	   (format "ase-db 2016-04-01/example-db1.db id=%s -l" (s-trim (car (split-string s "|"))))))))


(defun ase-db-view (s)
  (let ((py (format "from ase.visualize import view
from ase.io import read
atoms = read(\"%s@%s\")
view(atoms)
" "2016-04-01/example-db1.db" (s-trim (car (split-string s "|")))))
	(tf)
	(temporary-file-directory "."))
    (setq tf (make-temp-file "py-" ))
    (with-temp-file tf
      (insert py))
    (call-process "python" tf)
    (delete-file tf)))

(ivy-read "Select: " (split-string  (shell-command-to-string
				     "ase-db --limit=0 2016-04-01/example-db1.db") "\n")
	  :require-match t
	  :action '(1
		    ("v" ase-db-view "View")
		    ("i" ase-db-info "Info")))
(let ((py (format "from ase.visualize import view
from ase.io import read
atoms = read(\"%s@%s\")
view(atoms)
" "2016-04-01/example-db1.db" (s-trim (car (split-string s "|")))))
(let ((py (format "from ase.visualize import view
from ase.io import read
atoms = read(\"%s@%s\")
view(atoms)
" "2016-04-01/example-db1.db" 1))
      (tf)
      (temporary-file-directory "."))
  (setq tf (make-temp-file "py-" ))
  (with-temp-file tf
    (insert py))
  (call-process "python" tf)
  (delete-file tf))
(defmacro hy (body)
  `(let* ((temporary-file-directory ".")
	  (tempfile (make-temp-file "hy-")))
     (with-temp-file tempfile
       (mapc (lambda (form) (insert (format "%s" form))) ,body))
     (read (unwind-protect
	       (shell-command-to-string
		(format "hy %s" tempfile))
	     (delete-file tempfile)))))

(hy '((import ase.visualize)
      (import ase.io)
      (setv atoms (ase.io.read "2016-04-01/example-db1.db@1"))
      (ase.visualize.view atoms)))
from ase.visualize import view
import ase.io as ai
atoms = ai.read("2016-04-01/example-db1.db@1")
view(atoms)
from hy.core.language import string
from ase.visualize import view
import ase.io as ai
atoms = ai.read((str(u'2016-04-01/example-db1.db@1')))
view(atoms)
default-directory
(import [ase.visualize [view]])
(import [ase.io :as ai])

;; it is clunky we have to str this. but ase doesn't read unicode ;(
(view (ai.read (str "2016-04-01/example-db1.db@1")))
(require hy.core.hylp)
(import [hy.core.hylp [*]])

(print (? "butlast"))

Now we use a query.

(defvar db "/Users/jkitchin/Dropbox/KitchinHUB/kitchingroup/2016-04-01/example-db1.db"
  "The database.")

(helm :sources
      (helm-build-async-source "ase-db"
	:delayed t
	:candidates-process (lambda ()
			      (start-process
			       "ase-db" nil
			       "ase-db" db helm-pattern))
	:action '(("Info" . (lambda (s)
			      (with-help-window (help-buffer)
				(princ
				 (shell-command-to-string
				  (format "ase-db %s id=%s -l"
					  db
					  (s-trim (car (split-string s "|")))))))))
		  ("View" . (lambda (s)
			      (let ((py (format "from ase.visualize import view
from ase.io import read
atoms = read(\"%s@%s\")
view(atoms)
" db  (s-trim (car (split-string s "|")))))
				    (tf)
				    (temporary-file-directory "."))
				(setq tf (make-temp-file "py-" ))
				(with-temp-file tf
				  (insert py))
				(call-process "python" tf)
				(delete-file tf))))))
      :buffer "*helm async source*")

<2016-04-29 Fri>

  • Elif - research (20 minutes)
  • Chen Wang - project proposal (10 minutes)
  • Akshay - project proposal (10 minutes)
  • hackathon - one cool solution, one problem to solve

<2016-05-13 Fri>

  • Jake research (20 minutes)
  • Kenate research (20 minutes)
  • Alex - research (20 minutes)
  • hackathon - one cool solution, one problem to solve

TBD

  • Elif - research (20 minutes)
  • Devon - project update (10 minutes)
  • Feiyang - project update (10 minutes)
  • Tianyu - project update (10 minutes)
  • Teng Ma - project update (10 minutes)