082254455b
improve confusing error messages
2022-04-07 00:37:30 -04:00
4c95314ea6
must set boxflag *after* checking for rigid fix because we might change the box ourselves
2022-03-20 21:25:26 -04:00
550ae15dff
proper handle partial initialization from infile
2022-03-20 21:12:35 -04:00
89c7d8f707
replace strtok based file reader with ValueTokernizer
2022-03-20 16:34:41 -04:00
fd3884d705
disable centroid stress for non-small rigid fixes
2022-01-04 18:09:49 +09:00
85433e8bd1
use true/false instead of 1/0 detected and changed by clang-tidy
2021-10-20 12:41:02 -04:00
f641b1c659
final chunk of changes to apply utils::logical()
2021-09-23 07:30:40 -04:00
7d92d665e8
use explicit scoping when virtual dispatch is not available.
2021-09-15 16:08:17 -04:00
e6af1eecb8
resolved merge conflicts with master
2021-08-17 11:55:33 -06:00
09c19a936b
update URLs in source code and manual
2021-05-24 14:18:20 -04:00
d8291eea7b
Merge branch 'master' into prepare-clang-format
...
# Conflicts:
# src/MOLECULE/bond_fene.h
# src/MOLECULE/bond_fene_expand.h
2021-05-11 21:49:48 -04:00
d1941392d3
disable clang-format for all existing .cpp files (for now)
2021-05-05 23:53:38 -04:00
22e93468d6
simplify code by appling varargs messages and warnings
2021-05-05 18:19:12 -04:00
6b04ebd617
Merge branch 'master' into varargs-log-error-functions
2021-04-26 13:27:58 -04:00
31d244dd80
Merge pull request #2727 from akohlmey/refactor-read-lines-from-file
...
Move "read_lines_from_file" utility function from Comm class to utils namespace
2021-04-26 13:24:24 -04:00
e9e0bb71b6
Use varargs version of Error:all() and Error::one() where applicable
2021-04-25 21:30:51 -04:00
7e7a448a08
remove the old versions of the utility function and use the new
2021-04-24 21:33:36 -04:00
92a9994fd4
silence compiler warnings by avoiding to shadow variables
2021-04-24 18:38:12 -04:00
d2cdb318ab
apply new logmesg() overload to a bunch of cases.
2021-04-21 23:38:45 -04:00
2d19282961
reorder include statements in RIGID package
2021-04-08 13:45:37 -04:00
d72b390c41
correct check for box changing fixes
2021-04-01 08:48:39 -04:00
7699fb3708
generalize some checks in fix rigid and rigid/small
2021-03-31 15:55:31 -04:00
183b30abd7
use strmatch() consistently to detect respa and verlet runstyles with optional suffix
2021-03-30 18:30:22 -04:00
1b48ac0eaf
Merge branch 'master' into collected-small-changes
2021-02-08 22:46:21 -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
1609c498bc
avoid integer overflow when computing memory usage
2021-02-06 18:15:48 -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
0b14770468
merge with current master
2021-01-11 16:13:33 -07:00
66ed16760f
do not allow access to rigid body properties before they are fully set up
2020-10-31 11:48:29 -04:00
94462bfb48
do not add langevin thermostat forces and torques if disabled, e.g. in 2d system.
...
Note that fix rigid/small does not support the force or torque options and thus
the zeroing has to be done directly when computing the langevin data.
2020-10-28 10:41:20 -04:00
adf74b3a22
use https://lammps.sandia.gov based URLs consistently
2020-10-21 16:45:30 -04:00
e924fc6d6e
Merge pull request #2347 from jewettaij/math_eigen
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Replace eigensolver code in LAMMPS with math_eigen.h and updated docs
2020-09-17 00:28:12 -04:00
c14fd3131a
Merge pull request #2367 from ndtrung81/rigid-langevin
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Fixed a bug in computing the langevin torques applied to rigid bodies
2020-09-16 22:36:04 -04:00
dfcdb61d87
Used existing helper functions to make codes more consise
2020-09-16 15:40:04 -05:00
f5998692d0
Merge branch 'master' into math_eigen
2020-09-15 21:37:05 -04:00
0f6a34775c
Merge branch 'master' into symbolic-atom-constants
2020-09-15 17:44:31 -04:00
ae68becf4a
Fixed a bug in computing the langevin torques applied to rigid bodies
2020-09-15 15:27:24 -05:00
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
76725731fd
changes in package files to match new find_custom() syntax
2020-09-08 13:48:41 -06:00
eb6f7f9740
Merge branch 'master' into math_eigen
2020-09-06 10:59:20 -07:00
57f82abae3
updated all code in LAMMPS to use the open-source "math_eigen.h" instead of "math_extra.h". Code in "lib" now uses its own abbreviated local version of the "math_eigen.h" file (which is named "jacobi_pd.h"), since it is not clear how code from "lib/" can access the code in "src/"
2020-09-05 01:39:27 -07:00
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()
...
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
9e1d560fda
refactor using fmtlib and utils::
2020-07-11 21:44:13 -04:00
