Commit Graph

39 Commits

Author SHA1 Message Date
adf74b3a22 use https://lammps.sandia.gov based URLs consistently 2020-10-21 16:45:30 -04:00
62a63d0cd8 silence compiler warnings 2020-09-17 10:27:06 -04:00
429cc0cacf add missing updates for symbolic constants in Atom class 2020-09-16 23:19:10 -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
bb7447363c more include cleanup and IWYU tweaks 2020-09-04 07:22:39 -04:00
6113169a47 IWYU based include statement cleanup 2020-09-02 17:39:34 -04:00
4f03acc560 Fix merge conflicts caused by code's do-si-do around Axel's additions
to the utils namespace.
2020-09-01 06:30:12 -06:00
2536f28e1a Per comments from Axel, continued the evolution of the output messages.
- Converted Compute message with imputed value to fmt::format style.
- Condensed most error-> output messages to oneliners where fmt::format
is called within the call to the error method. For a couple, the
formatting string/value list were complex enough that I continued using
a temporary string variable to make the code easier to read.
2020-09-01 05:49:29 -06:00
52748f57da Delete extraneous, unused file/folder that should never have gotten
into the repo.
2020-09-01 05:49:29 -06:00
9ef725ea52 Move destruction of splines data structure to FixBocs destructor
from ComputePressure destructor.
2020-09-01 05:49:29 -06:00
4dca927693 Switch dynamically created arrays/matrices to use memory->create and
->destroy, LAMMPS-standard for dynamic memory management.
2020-09-01 05:49:29 -06:00
fe89edc828 Remove c_str() calls from message strings. Message class now accepts
actual strings.
2020-09-01 05:49:29 -06:00
0aa66319fe Change the build_xxx_splines methods to accept a const reference parameter
to the data vector rather than a vector parameter. Vectors are, as all
types are, passed by value in C++. Using a vector directly as a parameter
causes the data to be copied. Using a reference to the vector neatly
avoids that problem.

Also tucked fmt/format.h into its rightful place in the include list
since Axel says there's no absolute rule about it being an exception.
2020-09-01 05:49:29 -06:00
076c834734 Manually reconciled conflict from:
Corrected two issues in code identified by valgrind:
1) memory leaks (the subject of the original #1109) and
2) an invalid memory access (reading from beyond the end of an array).

Also:
- replaced several dynamically-allocated (calloc and free) local arrays with std::vector.
- reorganized include statements per new conventions, and
- updated messages to use strings and fmt.

Added folders and files used in manual testing and verification to examples folder.

No changes in analysis results are expected or intended. This is pure refactoring except for a bit of error message cleanup.
2020-09-01 05:48:49 -06:00
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
9d74984144 Fix whitespace 2020-06-16 07:20:09 -04:00
88bf503451 Merge from master 2020-04-30 08:17:05 -06:00
5f68f3006f replace Fix::box_change_xxx variables with Fix::box_change bitmask and add check to Domain::init()
This allows a more specific tracking of whether multiple fixes are
modifying the same box parameter and error out in that case.
2020-02-08 15:12:26 -05:00
d8ef5f6991 added internal fix dummy command to enable more control of fix ordering 2019-11-05 12:57:34 -07:00
d750cc02c0 Changed the code in the read_F_table function to conform to the "expected behavior" description in #1572. Adopted a best-of-both-worlds approach, though, and processed the whole input file all the way through, emitting a message for each problem found, before issuing a final error message to stop processing. Updated doc to clarify requirement for uniform spacing of pressure correction points. 2019-08-02 08:46:04 -04:00
a1f0c0079d some cleanup for missed steps in previous change sets 2019-07-12 16:37:01 -04:00
06dcc9e283 Merge branch 'master' into improve-include-consistency
# Conflicts:
#	src/USER-MESO/atom_vec_tdpd.cpp
2019-07-09 14:50:00 -04:00
31e19e0824 complete cleaning includes in some more packages 2019-07-08 16:45:21 -04:00
416911aa7e more rearranging of include file order to put implementation headers first 2019-07-03 21:57:39 -04:00
7547e1dae6 make certain that the vector storage and the size_vector variable are consistent in computes 2019-07-01 17:25:02 -04:00
3bc815efe8 fix a memory leak in fix bocs 2019-03-07 15:11:33 -05:00
9c27548a5c more replacing of sprintf() with snprintf() 2018-09-06 10:45:48 -04:00
38a998c03c Fix misc. warnings (#1076) 2018-08-24 14:58:28 -06:00
92a4dc25b1 Fix unused params in packages (#1076) 2018-08-24 10:42:08 -06:00
e37ee02eed port nh fixes to USER-BOCS package 2018-07-24 11:19:00 -04:00
f7c37a7a98 adapt isfinite() handling to upstream 2018-05-05 11:46:35 -04:00
095ca76b5b plug memory leaks in USER-BOCS 2018-05-05 11:44:21 -04:00
81293b0fda changes to integrate USER-BOCS into LAMMPS and to closer follow the LAMMPS programming/documentation style 2018-05-05 10:21:11 -04:00
fc0110a2e0 Update fix_bocs.cpp 2018-05-02 13:25:26 -04:00
072a063afc Delete fix_bocs.html 2018-05-02 11:30:25 -04:00
fbf96b680b Delete MOD_COMPUTE_H 2018-05-02 11:29:41 -04:00
2e2f19770c Removed .html files. Removed compute.h mods. Cast pressure for functions 2018-05-02 11:14:30 -04:00
56d0014a4a Added #include "citeme.h" 2018-04-26 10:05:49 -04:00
c5e884fb41 USER-BOCS 2018-04-26 09:34:47 -04:00