Comments (7)
kilacoda-old
commented on July 19, 2024
1
Hi, sorry for a late response. I tried out your reaction and it worked fine on my end? Code and output:
class EmonHR(Scene):
def construct(self):
react = Reaction(
[
"@{a1}=_[@{db}::30]-[::-60]\\charge{90=\\|}{X}"
],
[
r"\chemabove{\vphantom{X}}{\ominus}-[::30]=_[::-60]\chemabove{X}{\scriptstyle\oplus}"
],
arrow_type="double",
)
self.add(react)
Unfortunately, the \chemmove arrow won't be addable with Reaction since it only stitches together the equation from the reactants, products and arrow parameters and places it within the \schemestart... \schemestop block. You might be able to get a similar result using something like CurvedArrow, albeit with a bit of trial and error to get everything right. (though this make me want to find a way to put stuff before/after the scheme since I understand a lot of chemfig apparently works on predefined macros and stuff and modifying existing objects)
Regarding the documentation, I agree there should be examples and I've been a bit sloppy about that. Sorry! I'll try adding some in the near future.
The AminoPhthalate scene works fine for me as well:
The \charge macro is quite a recent addition to chemfig iirc (within the last year I think), so maybe try updating your chemfig install and see if that works?
from chanim.
emonhossainraihan
commented on July 19, 2024
1
Finally, solve that issue. Thanks, @kilacoda. Actually tlmgr update chemfig wasn't worked for my case. I uninstall the whole texlive-full and reinstall the latest 2021 one from their .iso If I got free time then definitely create a PR to add some example in the README file.
from chanim.
emonhossainraihan
commented on July 19, 2024
If this issue can't be resolved, then could you tell me why this code is not working:
class AminoPhthalate(Scene):
def construct(self):
three_APA = ChemObject(
"*6(-=(-(=[-2]O)-[:36]\\charge{45:2pt=$\\scriptstyle-$}{O})-(-(=[2]O)-[:-36]\\charge{45:2pt=$\\scriptstyle-$}{O})=-=)"
)
self.add(three_APA)It gives me
ValueError: latex error converting to dvi. See log output above or the log file:
media/Tex/***.log
But if I use ChemObject without charge stuff, then it works perfectly, like
class Chem2(Scene):
def construct(self):
f1 = ChemObject("-[:30]=[:-30,,,,red]-[:30]")
self.play(Write(f1))
Could you explain how to show charging stuff only? It will be a great help.
from chanim.
emonhossainraihan
commented on July 19, 2024
It was not working on my side @kilacoda. Could you say which manim version you used to render the scene? I was using Manim Community v0.7.0. Is that the reason? Here is the complete Traceback:
Traceback
✘ emonhossain@xenon ~/Desktop/chanim master ± manim chem.py EmonHR
Manim Community v0.7.0
center
\begin{center}
\schemestart \schemestop
\end{center}
[06/03/21 22:37:22] ERROR LaTeX compilation error: {log[error_pos][2:])} tex_file_writing.py:198
ERROR Context for error: tex_file_writing.py:223
\begin{center}
\schemestart
\chemfig{@{a1}=_[@{db}::30]-[::-60]\charge{90=\|}{X}}\arrow{<->[][]}\chemfig{\chemabove{\vphantom{X}}{\ominus}-[::30]=_[::-60]\chemabove{X}{\scriptstyle\oplus}
}
^ this line
\schemestop
\end{center}
Traceback (most recent call last):
╭──────────────────────────────────────────────────────────────────────────────────────╮
│ File │
│"/home/emonhossain/.local/lib/python3.8/site-packages/manim/cli/render/commands.py", │
│line 157, in render │
│ 154 for SceneClass in scene_classes_from_file(file): │
│ 155 try: │
│ 156 scene = SceneClass() │
│ ❱ 157 scene.render() │
│ 158 except Exception: │
│ 159 error_console.print_exception() │
│ 160 sys.exit(1) │
│ File "/home/emonhossain/.local/lib/python3.8/site-packages/manim/scene/scene.py", │
│line 201, in render │
│ 198 """ │
│ 199 self.setup() │
│ 200 try: │
│ ❱ 201 self.construct() │
│ 202 except EndSceneEarlyException: │
│ 203 pass │
│ 204 except RerunSceneException as e: │
│ File "chem.py", line 48, in construct │
│ 45 │
│ 46 class EmonHR(Scene): │
│ 47 def construct(self): │
│ ❱ 48 react = Reaction( │
│ 49 [ │
│ 50 "@{a1}=_[@{db}::30]-[::-60]\\charge{90=\\|}{X}" │
│ 51 ], │
│ File "/home/emonhossain/Desktop/chanim/chanim/chem_objects.py", line 348, in __init__│
│ 345 self.equation = self.get_equation() │
│ 346 # print(repr(self.equation)) │
│ 347 │
│ ❱ 348 super().__init__( │
│ 349 *self.equation, │
│ 350 stroke_width=stroke_width, │
│ 351 tex_template=self.template, │
│ File "/home/emonhossain/.local/lib/python3.8/site-packages/manim/mobject/svg/tex_mobj│
│ect.py", line 591, in __init__ │
│ 588 def __init__( │
│ 589 self, *tex_strings, arg_separator="", tex_environment="center", **kwar│
│ 590 ): │
│ ❱ 591 MathTex.__init__( │
│ 592 self, │
│ 593 *tex_strings, │
│ 594 arg_separator=arg_separator, │
│ File "/home/emonhossain/.local/lib/python3.8/site-packages/manim/mobject/svg/tex_mobj│
│ect.py", line 455, in __init__ │
│ 452 """ │
│ 453 ) │
│ 454 ) │
│ ❱ 455 raise compilation_error │
│ 456 self.set_color_by_tex_to_color_map(self.tex_to_color_map) │
│ 457 │
│ 458 if self.organize_left_to_right: │
│ File "/home/emonhossain/.local/lib/python3.8/site-packages/manim/mobject/svg/tex_mobj│
│ect.py", line 433, in __init__ │
│ 430 tex_strings = self.break_up_tex_strings(tex_strings) │
│ 431 self.tex_strings = tex_strings │
│ 432 try: │
│ ❱ 433 SingleStringMathTex.__init__( │
│ 434 self, │
│ 435 self.arg_separator.join(tex_strings), │
│ 436 tex_environment=self.tex_environment, │
│ File "/home/emonhossain/.local/lib/python3.8/site-packages/manim/mobject/svg/tex_mobj│
│ect.py", line 260, in __init__ │
│ 257 │
│ 258 assert isinstance(tex_string, str) │
│ 259 self.tex_string = tex_string │
│ ❱ 260 file_name = tex_to_svg_file( │
│ 261 self.get_modified_expression(tex_string), │
│ 262 environment=self.tex_environment, │
│ 263 tex_template=self.tex_template, │
│ File "/home/emonhossain/.local/lib/python3.8/site-packages/manim/utils/tex_file_writi│
│ng.py", line 46, in tex_to_svg_file │
│ 43 if tex_template is None: │
│ 44 tex_template = config["tex_template"] │
│ 45 tex_file = generate_tex_file(expression, environment, tex_template) │
│ ❱ 46 dvi_file = compile_tex( │
│ 47 tex_file, tex_template.tex_compiler, tex_template.output_format │
│ 48 ) │
│ 49 return convert_to_svg(dvi_file, tex_template.output_format) │
│ File "/home/emonhossain/.local/lib/python3.8/site-packages/manim/utils/tex_file_writi│
│ng.py", line 232, in compile_tex │
│ 229 for insight in get_insight(match): │
│ 230 logger.info(insight) │
│ 231 │
│ ❱ 232 raise ValueError( │
│ 233 f"{tex_compiler} error converting to" │
│ 234 f" {output_format[1:]}. See log output above or" │
│ 235 f" the log file: {log_file}" │
╰──────────────────────────────────────────────────────────────────────────────────────╯
ValueError: latex error converting to dvi. See log output above or the log file: media/Tex/68a980ec53c98db8.log
Even same ValueError for AminoPhthalate. Could you suggest what I can do to fix this? @kilacoda
from chanim.
kilacoda-old
commented on July 19, 2024
I don't think the manim version should affect that, since I'm using 0.7.0 as well. Could you share the contents of media/Tex/68a980ec53c98db8.log?
from chanim.
emonhossainraihan
commented on July 19, 2024
Yes. Here are those files:
68a980ec53c98db8.log
This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=latex 2021.2.19) 3 JUN 2021 22:54
entering extended mode
restricted \write18 enabled.
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) (media/Tex/68a980ec53c98db8.aux)
\openout1 = `68a980ec53c98db8.aux'.
LaTeX Font Info: Checking defaults for OML/cmm/m/it on input line 9.
LaTeX Font Info: ... okay on input line 9.
LaTeX Font Info: Checking defaults for OMS/cmsy/m/n on input line 9.
LaTeX Font Info: ... okay on input line 9.
LaTeX Font Info: Checking defaults for OT1/cmr/m/n on input line 9.
LaTeX Font Info: ... okay on input line 9.
LaTeX Font Info: Checking defaults for T1/cmr/m/n on input line 9.
LaTeX Font Info: ... okay on input line 9.
LaTeX Font Info: Checking defaults for TS1/cmr/m/n on input line 9.
LaTeX Font Info: ... okay on input line 9.
LaTeX Font Info: Checking defaults for OMX/cmex/m/n on input line 9.
LaTeX Font Info: ... okay on input line 9.
LaTeX Font Info: Checking defaults for U/cmr/m/n on input line 9.
LaTeX Font Info: ... okay on input line 9.
Preview: Fontsize 10pt
ABD: EveryShipout initializing macros
LaTeX Font Info: Trying to load font information for U+msa on input line 13.
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File: umsa.fd 2013/01/14 v3.01 AMS symbols A
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LaTeX Font Info: Trying to load font information for U+msb on input line 13.
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File: umsb.fd 2013/01/14 v3.01 AMS symbols B
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! Undefined control sequence.
\atom_1 ->\charge
{90=\|}{X}
l.13 ...]\charge{90=\|}{X}}\arrow{<->[][]}\chemfig
{\chemabove{\vphantom{X}}{...
Here is how much of TeX's memory you used:
14424 strings out of 481240
281622 string characters out of 5920403
534822 words of memory out of 5000000
29433 multiletter control sequences out of 15000+600000
534037 words of font info for 32 fonts, out of 8000000 for 9000
1141 hyphenation exceptions out of 8191
68i,10n,95p,643b,1249s stack positions out of 5000i,500n,10000p,200000b,80000s
No pages of output.
68a980ec53c98db8.tex
\documentclass[preview]{standalone}
\usepackage[english]{babel}
\usepackage{amsmath}
\usepackage{amssymb}
\usepackage{chemfig}
\setchemfig{atom sep=2em,chemfig style=, atom style=,angle increment=45,bond offset=2pt,double bond sep=2pt, node style=, bond style=,scheme debug=false, atom sep=2em, arrow angle={0}, arrow coeff={1}, arrow style={}}
\begin{document}
\begin{center}
\schemestart
\chemfig{@{a1}=_[@{db}::30]-[::-60]\charge{90=\|}{X}}\arrow{<->[][]}\chemfig{\chemabove{\vphantom{X}}{\ominus}-[::30]=_[::-60]\chemabove{X}{\scriptstyle\oplus}}
\schemestop
\end{center}
\end{document}
from chanim.
kilacoda-old
commented on July 19, 2024
I think it might be because TeX Live 2019 provides an older version of chemfig by default which doesn't include the \charge macro. Try running tlmgr update chemfig and see if there's an update available?
from chanim.
Related Issues (16)
- Too much chemfig code exported to TeX-files HOT 1
- ImportError: cannot import name 'SmallDot' from 'manim.mobject.geometry' HOT 1
- LaTeX compiler error
- New Manim Version not compatible HOT 2
- ImportError: cannot import name 'OpenGLMathTex' from 'manim.opengl' HOT 3
- temporary files are saved in the wrong location
- Incompatible with ManimCE v0.17
- 2022-12 updates necessary! HOT 3
- compatibility with manim 0.17???
- Bonds not displayed HOT 3
- NameError: name 'self' is not defined HOT 1
- Issue with Arrows HOT 9
- Hatched bonds HOT 1
- Examples usage? HOT 4
- OSError: no library called "cairo" was found HOT 3
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from chanim.