f814dc5ff9
add checks after reading data
2022-01-22 17:06:28 -05:00
d854e58d00
add sanity check
2022-01-22 16:51:07 -05:00
3246fd62a7
size_t is unsigned, so can't be negative
2021-12-17 17:10:21 -05:00
a3a6077115
Use sfread and sfgets in reader_native.cpp
2021-12-17 17:03:58 -05:00
884dcbe4fa
Refactor reader_native.cpp
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- Use std::string instead of error-prone char buffers
- Limit reading files to known magic strings DUMPATOM and DUMPCUSTOM
2021-12-15 16:09:50 -05:00
902f9dd1fa
Move allocation to correct location
2021-12-15 15:05:59 -05:00
3efddc4fb6
whitespace
2021-12-14 14:50:38 -05:00
5051055c76
Remove dead code and move nchunk read to read_header
2021-12-14 14:33:17 -05:00
80819f3793
reverse skip_buf with chunk
2021-12-14 11:09:36 -05:00
7c3deaa04b
limit the skip buf to MAXSMALLINT
2021-12-13 23:03:10 -05:00
b1d0dd65ea
simply the while loop and add correct initial m value
2021-12-13 22:57:39 -05:00
d4cec8ebe7
handle block reading in ReaderNative::read_atoms when binary is True
2021-12-13 21:38:16 -05:00
ff41864cd9
remove redundant deletes
2021-12-13 15:28:27 -05:00
cdc831bb89
Update src/reader_native.cpp
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Co-authored-by: Richard Berger <richard.berger@temple.edu >
2021-12-13 12:23:30 -08:00
f3543a839e
Update src/reader_native.cpp
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Co-authored-by: Richard Berger <richard.berger@temple.edu >
2021-12-13 12:23:21 -08:00
3eae7b4200
Update src/reader_native.cpp
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Co-authored-by: Richard Berger <richard.berger@temple.edu >
2021-12-13 12:23:14 -08:00
af2e295ac2
Update src/reader_native.cpp
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Co-authored-by: Richard Berger <richard.berger@temple.edu >
2021-12-13 12:22:57 -08:00
bb6d581ef8
Update src/reader_native.cpp
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Co-authored-by: Richard Berger <richard.berger@temple.edu >
2021-12-13 12:22:39 -08:00
7db29112d8
replace read_buf to skip_buf in skip function
2021-12-12 00:26:55 -05:00
274b14618f
fold match_fields() back into read_header() function
2021-12-11 21:17:41 -05:00
0603dc6323
whitespace
2021-12-11 20:46:24 -05:00
56fd07d88e
fold native binary reader class in to native reader class
2021-12-11 20:31:44 -05:00
8f99d8d1d9
fix skip bugs
2021-12-11 16:41:13 -05:00
250a5921a3
move match_field to protected method and format the docstring
2021-12-11 14:25:29 -05:00
7ab5d4edd4
add new ReaderNativeBin class
2021-12-11 11:54:21 -05:00
09c19a936b
update URLs in source code and manual
2021-05-24 14:18:20 -04:00
d1941392d3
disable clang-format for all existing .cpp files (for now)
2021-05-05 23:53:38 -04:00
51a20175c9
more code formatting consistency changes for loops and conditionals
2020-12-30 09:47:45 -05:00
382ade15fe
more consistent formatting of for/while loops and if statements
2020-12-30 09:09:08 -05:00
adf74b3a22
use https://lammps.sandia.gov based URLs consistently
2020-10-21 16:45:30 -04:00
29a7d598ac
update formatting style to be more consistent
2020-09-21 02:04:58 -04:00
f1ef7d85a8
T2345: Replace instances of NULL with nullptr
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The following changes have been applied to src and lib folders:
regex replace: ([^"_])NULL ⇒ \1nullptr (8968 chgs in src, 1153 in lib)
Manually find/change: (void \*) nullptr ⇒ nullptr (1 case)
regex find: ".*?nullptr.*?"
Manually ~14 cases back to "NULL" in src, ~2 in lib
regex finds a few false positive where nullptr appears between two
strings in a function call
2020-09-12 09:34:38 -06:00
390c6ba106
rechecking some corefiles with IWYU after the many updates
2020-09-03 15:28:07 -04:00
55704368d0
include updates for commonly used packages
2020-09-03 01:45:05 -04:00
c7c4297cfc
update include handling for commands
2020-09-03 00:51:58 -04:00
a4a1f7e848
more IWYU cleanup
2020-09-02 23:49:17 -04:00
27b4e93bf5
silence compiler warnings
2020-08-29 18:32:21 -04:00
7d8dcb0fb0
Remove strtok from reader_native.cpp
2020-08-10 15:56:06 -04:00
9291d2a9d7
Simplify count_words, add trim_and_count_words
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The original count_words function (before it was put into utils::) also trimmed
comments. For compatibility this behaviour was retained at first. However, due
to the name the trimming is not immediatly apparent and many times not
wanted.
Therefore, this commit replaces count_words with an implementation that
just does what it says. If a comment should be trimmed there is a
trim_comment function. For convenience, a trim_and_count_words function was
added and is now used where the old behaviour was needed.
2020-06-04 11:13:37 -04:00
4a2d3e95cb
Replace Atom::count_words with utils::count_words
2020-05-20 15:53:19 -04:00
07c5adc57a
we need more specific matches to correctly handle TIME and TIMESTEP items
2020-02-14 16:07:34 -05:00
7c62bce7d9
Enable reading dump file with ITEM:TIME
2020-02-13 18:13:22 +01:00
b6b022b610
whitespace cleanup: remove trailing blanks
2019-11-03 11:03:39 -05:00
be38ef0eb0
make native dump reader compatible with dump files containing ITEM: UNITS
2019-09-12 15:26:02 -04:00
a50d57bceb
Merge branch 'master' into improve-include-consistency
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# Conflicts:
# src/utils.cpp
2019-07-19 17:57:58 -04:00
8526e7a4cd
checking return value of ?scanf() calls to detect problems parsing files
2019-07-19 11:14:39 -04:00
06dcc9e283
Merge branch 'master' into improve-include-consistency
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# Conflicts:
# src/USER-MESO/atom_vec_tdpd.cpp
2019-07-09 14:50:00 -04:00
74414afdea
Added the boxinfo argument
2019-07-08 17:25:23 -06:00
256531a29a
put implementation header first for all remaining main folder source files
2019-07-03 19:34:13 -04:00
e4071d7f46
replace C-style include files with their C++ equivalents
2018-04-27 18:00:24 -04:00
