dfb18caf5a
simplify using utils::strdup(), update order of include files
2021-03-27 16:25:55 -04:00
2777eafe98
small fix for previous fix for fix pour and fix deposit
2021-03-05 14:15:59 -05:00
135099e23f
next_reneighbor must be initialized in setup_pre_exchange()
2021-03-05 06:08:06 -05:00
2f4fc31696
since nfirst stores the timestep, it must be a bigint
2021-03-05 06:07:36 -05:00
33939a0e26
Merge branch 'master' into thermo-energy
...
# Conflicts:
# doc/src/fix_ti_spring.rst
# src/RIGID/fix_rigid_small.cpp
# src/fix_langevin.cpp
# src/fix_temp_berendsen.cpp
# src/fix_temp_csld.cpp
# src/fix_temp_csvr.cpp
# src/fix_temp_rescale.cpp
# src/thermo.cpp
2021-02-08 15:24:29 -05:00
24bf1e5b0c
make use of utils::strdup()
2021-02-04 17:33:02 -05:00
4e791ac4f7
replace 'strstr(xxx,"x_") == xxx' with utils::strmatch("^x_")
2021-02-04 15:20:43 -05:00
95e2214d96
more typecasts to double to avoid 32-bit int overflows when computing memory usage
2021-02-04 14:35:38 -05:00
e2e6639013
add typecast to avoid (unlikely but possible) integer overflows.
...
this will silence a lot of static code analysis warnings
2021-02-02 17:27:04 -05:00
c091515427
changed syntax for virial tallying in standard package fixes
2021-01-21 15:12:16 -07:00
b5525a19bc
changes to files with THERMO_ENERGY mask in standard packages
2021-01-21 13:56:50 -07:00
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
656b7eac8b
correctly report number of constrained bonds and angles
2020-10-26 18:49:09 -04:00
6b2a98b537
ad few more manual updates of outdated, mistyped or no longer available URLs
2020-10-21 17:19:33 -04:00
adf74b3a22
use https://lammps.sandia.gov based URLs consistently
2020-10-21 16:45:30 -04:00
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
...
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
...
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
