0f6a34775c
Merge branch 'master' into symbolic-atom-constants
2020-09-15 17:44:31 -04:00
cebf6d33ba
Merge pull request #2358 from eagunn/iss2345
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Replace instances of NULL with nullptr
2020-09-15 17:41:24 -04:00
618b08dcfc
Merge branch 'master' into symbolic-atom-constants
2020-09-15 14:58:13 -04:00
0183e999c9
consistently return "memory_usage" as double.
2020-09-15 01:59:58 -04:00
93a0d4c096
fix up some comments
2020-09-12 14:26:34 -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
9d0c3bc665
replace some numeric constants in Atom and AtomVec classes with enumerators
2020-09-11 19:07:55 -04:00
bb7447363c
more include cleanup and IWYU tweaks
2020-09-04 07:22:39 -04:00
55704368d0
include updates for commonly used packages
2020-09-03 01:45:05 -04:00
6113169a47
IWYU based include statement cleanup
2020-09-02 17:39:34 -04:00
96d8d12a88
replace calls to force->*numeric() with the corresponding utils::*numeric()
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this also removes the now obsolete functions from Force
2020-08-29 20:31:02 -04:00
fcd0b9f78f
move Force::bounds() and Force::boundsbig() to utils.
2020-08-29 18:23:03 -04:00
729b3d2717
major whitespace cleanup
2020-08-19 18:46:35 -04:00
a53ee5664e
silence compiler warnings about signed vs. unsigned ints
2020-08-18 15:51:06 -04:00
78d5714247
silence signed vs. unsigned integer warnings
2020-08-18 14:33:02 -04:00
e3beec8b95
revert permission change and replace 'b/c' with 'because'
2020-08-10 11:37:52 -04:00
41904f7946
Added cautionary comments
2020-08-08 09:15:56 -06:00
4a28a708b9
T_initial_set array is only required during reading of the mesh
2020-07-30 10:36:03 -04:00
6a90a2affe
consistently check for presence of all input mesh data
2020-07-29 23:43:45 -04:00
c355348ff9
remove local copy of "me"
2020-07-29 21:31:51 -04:00
5452f72bd9
convert fix ttm and fix ttm/mod to use tokenizer class for parsing files
2020-07-25 18:03:18 -04:00
b37b45c817
use fmtlib to remove BIGINT_FORMAT
2020-07-15 11:55:08 -04:00
96d943513e
more output cleanup in MISC, MLIAP, MOLECULE, and POEMS
2020-06-29 11:48:54 -04:00
d5b9948129
extend FreeBSD preprocessor checks to other BSD flavors
2020-05-03 01:00:01 -04:00
2b542eacb7
add FreeBSD compatibility
2020-05-02 15:56:24 -04:00
2b39c9968f
Merge pull request #1913 from jrgissing/molecule_template_moleculeIDs
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Molecule template: molecule-IDs and fragments
2020-03-18 20:31:29 -04:00
d7cade9d46
Merge branch 'master' into molecule_template_moleculeIDs
2020-03-17 23:08:00 -06:00
649a8cc01a
Fix typo
2020-03-14 13:57:48 +09:00
8af9d40392
Update DOI resolver
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https://www.doi.org/doi_handbook/2_Numbering.html#htmlencoding
2020-03-12 16:53:24 +09:00
73186e4d26
correction to molecule-ID-increment logic
2020-03-08 16:06:49 -06:00
1110124627
let 'fix deposit' know about molecule template molecule IDs
2020-03-06 22:04:16 -07:00
9ed987c255
minor changes to syntax and documentation of fix deposit orient
2020-01-13 13:15:17 -07:00
e8d11931ec
merged in current master
2020-01-13 10:34:31 -07:00
877329c1e4
rename rflag to orientflag to be consistent with documentation and more readable
2019-10-08 16:35:50 +02:00
a705b635a5
remove cstdio include
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cstdio is implicitly included by pointers.h which is included by fix.h.
2019-09-25 14:36:26 -04:00
ff991c4c53
Added new keywords orientation rx ry rz to restrict random rotation
2019-09-24 15:10:47 -04:00
25c3a452f2
Added New keywords rotation rx ry rz to fix_deposit
2019-09-18 17:29:45 -04:00
e5af9db84c
clean up includes in MC and MISC package
2019-07-07 11:49:13 -04:00
416911aa7e
more rearranging of include file order to put implementation headers first
2019-07-03 21:57:39 -04:00
4ec3a508fc
bulk removal of #include <cstdio> from header files
2019-06-27 21:54:07 -04:00
8b49cac86a
correct dimensionality of cut_coul property in Pair::extract()
2019-06-24 09:09:22 -04:00
171d74f2f2
remove class member name clashes. Pointers contains infile so we rename other uses to inpfile
2019-06-23 16:43:54 -04:00
f73c848ee4
detect and error out when timestep was reset when restarting fixes atom/swap, gcmc, or deposit
2019-05-31 00:31:36 -04:00
4243af30d7
properly store 64-bit integers for next_reneighbor into double type buffers for restarts of fixes
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also store number of attemps and number of successes in restart and retrieve those from it
2019-05-31 00:23:12 -04:00
06a57dd659
use ev_unset for all pair styles
2019-03-13 17:49:16 +01:00
1991ff6c48
consistent formatting: replace "if( XXX)" with "if (XXX)"
2018-12-29 17:08:12 -05:00
b34dac41c2
port documentation spelling fixes to comments or strings in source code.
2018-11-19 16:15:24 -05:00
1fc3b4618c
remove dead code and silence compiler warnings
2018-11-15 16:50:56 -05:00
9c27548a5c
more replacing of sprintf() with snprintf()
2018-09-06 10:45:48 -04:00
71bc72ec13
formatting: add additional space to avoid bad syntax highlights
2018-08-27 22:13:43 -04:00
