- Elif
- Image analysis update (15 min)
- Jake
- CuPd conundrum (15 min)
- Sanjna
- AuPd literature review (10 min)
- Devon
- Research update (15 min)
- Chen
- Research update (15 min)
- Akshay
- Research update (15 min)
- Tianyu
- Research update (15 min)
- Feiyang
- Research update (15 min)
- Elif
- Qualifier Part I
- Sanjna
- Research update
- Teng
- Research update (15 min)
- Devon
- Research update (15 min)
- 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)
- 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)
- 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
- Machine learning in alloy and oxide simulation
- Kenate presentation
See the jmax menu
M-x ore for help on org-elements
| 5 | 6 |
|---|---|
| 3 | 4 |
| 4 | 5 |
| 4 | 5 |
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
- 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
- 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
\(exp{x}\) \[exp{x}\]
@@latex:\ce{CO2}@@ CO2 \ce{H2SO4} H2SO4 @@latex:H_2SO_4@@
- 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
C-c C-d C-c C-s
print('\\url{www.google.com}')print(t)return [['a', 'b', 'c'], None, [1, 3, 4], [5, 6, 7]]| a | b | c |
|---|---|---|
| 1 | 3 | 4 |
| 5 | 6 | 7 |
import numpy as np
n = np.array(n)
print(n.max())a = 5print(5 * a)- Jake research (20 minutes)
- Kenate research (20 minutes)
- Alex - research (20 minutes)
- hackathon - one cool solution, one problem to solve
- 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)- 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=70We 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*")- Elif - research (20 minutes)
- Chen Wang - project proposal (10 minutes)
- Akshay - project proposal (10 minutes)
- hackathon - one cool solution, one problem to solve
- Jake research (20 minutes)
- Kenate research (20 minutes)
- Alex - research (20 minutes)
- hackathon - one cool solution, one problem to solve
- 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)