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Fix/parsing lattice file #18

Merged
merged 53 commits into from
Sep 28, 2023
Merged

Fix/parsing lattice file #18

merged 53 commits into from
Sep 28, 2023

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MBueschelberger
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  • debug path variable for tarfiles

MBueschelberger and others added 30 commits August 30, 2023 22:30
@MBueschelberger
make references to original file instead of parsing them
dddae17
update code with respect to parsing of structures
6c56574
@MBueschelberger
update unit tests
7cb7217
@MBueschelberger
debug energy landscape refinement
0785941
debug adp
c1a3d47
@MBueschelberger
update syntactic settings
2e52ec7
merge from main
307b1d5
@MBueschelberger
update wrapper tools for binding site calculation
954de5a
@MBueschelberger
Merge branch 'fix/parsing-lattice-file' of github.com:simphony/reaxpr…
e3a8071 
…o-wrappers into fix/parsing-lattice-file
@MBueschelberger
update defaults in syntactic settings
cbadd3f
@MBueschelberger
make neighbour cut off optional in PES exploration
eae9a28
@MBueschelberger
update wrong variable
488719d
@MBueschelberger
update bad indent
cd05476
@MBueschelberger
debug initializing mesoscale model
6ab9764
@MBueschelberger
mute neighbour cut off mapping for now
ac28089
@MBueschelberger
update default value for neighbor cut off
a3cc0e7
@MBueschelberger
update wrong variable for process parallelization
3eecd63
@MBueschelberger
update retrieval of mechanisms
c246674
@MBueschelberger
update mode of temporary files
ac6569c
@MBueschelberger
add function to replace site types
dc5a509
@MBueschelberger
debug: print molar fractions and gas species
d2c80d7
@MBueschelberger
uncomment unneeded code lines
e969dbf
@MBueschelberger
comment further lines for debug
6071281
@MBueschelberger
debug:comment unneeded lines for cluster expansion
f9b6488
@MBueschelberger
debug: comment unneeded lines
e43ed6d
@MBueschelberger
debug:update list indexing
faa7da6
@MBueschelberger
move pz job out of get_rate-function
e49368c
@MBueschelberger
debug: print lattice ids
de8e7a9
@MBueschelberger
debug: print lattice ids
4c9568e
@MBueschelberger
debug:add seek mechanism while writing to temp file
9bc3c3b
MBueschelberger and others added 23 commits September 26, 2023 11:21
@MBueschelberger
debug: update wrong variable
2e70aa9
@MBueschelberger
debug: add example which imports the graph at mesoscopic level
5583e70
@MBueschelberger
mute molar fraction for O2 in ADP
d2e9e53
@MBueschelberger
remove printing, change CO2 to CO
a2aec03
@MBueschelberger
add needed comma to result output var
ed73e01
@MBueschelberger
add needed comma in tuple
a1f423a
@MBueschelberger
move from list to tuple
75b11d7
@MBueschelberger
debug: print resulting data from scan job
291a20d
@MBueschelberger
debug:print settings
0e31a9f
@MBueschelberger
update wrapping function for snapshots, uncomment pressure division
5a562ae
@MBueschelberger
remove float conversion in generic setting for zacros
962f49e
@MBueschelberger
also remove float conversion from other generic settings
d4d76ea
@MBueschelberger
move float conversion to other function and add asterisk
fd65a71
@MBueschelberger
remove print statements, successfully run adp
2c8c930
@MBueschelberger
update examples
ce5083b
@MBueschelberger
correct indentation
f652701
add plot and update example
718fbc5
@MBueschelberger
update engine paths
52c0373
@MBueschelberger
Merge branch 'fix/parsing-lattice-file' of github.com:simphony/reaxpr…
4b22df8 
…o-wrappers into fix/parsing-lattice-file
@MBueschelberger
update function for mapping results
4f38052
@MBueschelberger
update path variables
f815666
@MBueschelberger
update path keyword
49062a8
@MBueschelberger
update path variable
d9163e3
@MBueschelberger MBueschelberger merged commit 9660d1f into main Sep 28, 2023
6 checks passed
@MBueschelberger MBueschelberger deleted the fix/parsing-lattice-file branch September 28, 2023 19:14
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@MBueschelberger