200b4f13c7
use dynamic cast instead of c-style cast when casting from base type to derived class
2022-04-10 18:18:06 -04:00
39b316729b
use auto type when assigning from cast or using new
2022-04-10 18:16:36 -04:00
f5ebfbf90b
refactor thermo output processing and add new yaml thermo style
2022-03-19 16:39:09 -04:00
41a3eccd1c
apply utils::logical() to more commands
2021-09-21 07:48:50 -04:00
fa7ae99511
Fixed bug in fix np[ht] with runstyle respa
2021-07-18 12:48:05 -03:00
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
fe063b27c7
silence compiler warnings
2021-04-23 15:51:16 -04:00
183b30abd7
use strmatch() consistently to detect respa and verlet runstyles with optional suffix
2021-03-30 18:30:22 -04:00
a5563e8d04
simplify using utils::strdup()
2021-03-18 20:56:04 -04:00
0ae38fb2ea
Fix return values of extract for pressure variables
2021-03-01 09:48:31 +10:00
95a4ac157b
update a few more comments
2021-02-10 14:27:17 -05:00
bca3164fc4
fix whitespace issues
2021-01-26 18:39:02 -05:00
6e3b9307a4
remove ecouple variable from Fix
2021-01-21 11:56:33 -07:00
182eb35f1a
changes to fixes that use THERMO_ENERGY
2021-01-21 11:32:11 -07:00
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
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
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
20a9794b92
fix permissions
2020-06-10 11:26:08 -04:00
2f5a8d0937
remove trailing whitespace
2020-06-09 17:28:26 -04:00
9b99ad271f
Adding new ptemp keyword to fix nh
2020-05-11 14:34:00 -06:00
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
7967cb1133
put implementation header first to avoid issues with mpi.h and lmptype.h with OpenMPI
2019-07-03 06:16:16 -04:00
31cbccda85
continue cleaning up include file lists
2019-06-29 09:37:44 -04:00
4f38878cf4
Removed unnecessary changes to ComputePressure
2018-12-12 17:48:02 -07:00
6f33ce9dba
Made two changes:
...
-recomputed up-to-date pressure tensor (fixes energy
conservation problem with aniso)
-changed ndof for iso (fixes volume fluctuation problem with iso)
2018-12-12 17:31:42 -07:00
e9bc939098
Fix more unused parameter warnings ( #1076 )
2018-08-23 12:22:44 -06:00
3495141dbe
Fix the target kinetic energy of the NH barostat
...
The cell momenta should be thermostatted to kT per barostat degree
of freedom (d^2 in general, d*(d-1) without rotations), according to
Shinoda et al. 2004 (doi:10.1103/PhysRevB.69.134103) Eqn. 1 and Martyna,
Tobias, Klein (JCP 1994, doi:10.1063/1.467468 section II.D).
2018-06-06 17:54:02 +02:00
d0ba8e1dcb
Make omega_mass proportional to (N+1)kT
...
According to papers like Martyna, Tobias, Klein (JCP 1994,
doi:10.1063/1.467468 section II.F) and Martyna, Tuckerman, Tobias,
Klein (Mol. Phys. 1996, doi:10.1080/00268979600100761 section 2.5), the
mass of the cell parameters should be proportional to (Ndof + dim) / dim, or
in other words, Natoms + 1.
2018-06-06 17:24:26 +02:00
e4071d7f46
replace C-style include files with their C++ equivalents
2018-04-27 18:00:24 -04:00
59dbb49cf9
remove trailing whitespace
2018-03-16 12:37:27 -04:00
0c7879e902
provide compatibility entries in FixNH option parsing for new USER-UEF package
2017-10-02 16:31:41 -04:00
ee55a98103
Changed the check on initial and final temperature to <= 0 for both.
2017-03-28 11:22:10 -04:00
44841f6891
fix ave/chunk fixes, 2d disc option, fix_modify dynamic/dof
2017-03-23 15:31:27 -06:00
dcede304df
changes for next patch, 2d disc options for spheres, fix external upgrade, bug fixes for fix ave/chunk for density calcs, Aidan doc page citation deconvolution
2017-03-21 08:56:37 -06:00
fdf5d68f9f
allow to extract properties in NH integrator only when they are active
2016-11-14 09:27:33 -05:00
0c25f3b1d6
whitespace cleanup
2016-11-13 23:20:09 -05:00
14c7cf4197
retrieve target temperature and pressure from fix npt. add sanity checks.
2016-11-13 23:18:59 -05:00
d9891abdf4
new library functions
2016-10-27 09:34:04 -06:00
72c5792230
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15615 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-09-21 15:40:42 +00:00
958e3e6a80
sync with Git
...
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15520 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-08-29 23:49:20 +00:00
639ea6c396
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15468 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-08-10 14:59:04 +00:00
ae255c847b
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15375 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-07-27 22:51:18 +00:00
ddd85f006c
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15369 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-07-27 14:04:56 +00:00
84de575cc7
fixed case where no axial components are active
...
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15160 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-06-09 18:31:54 +00:00
0f3e4182e8
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15109 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-06-06 23:21:39 +00:00
5f86c15dd2
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14895 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-04-27 14:56:23 +00:00
