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13969 Commits

Author SHA1 Message Date
Stan Moore 3653f40120 Reduce unnecessary communication in fix_qeq_reax 2017-10-04 12:10:13 -06:00
Stan Moore bda0ee3aa1 Destroy unneeded fix in pair_reaxc_kokkos 2017-10-04 12:06:03 -06:00
Ulf R. Pedersen 957263431a Ensure consistency with documentation 2017-10-04 09:38:43 +02:00
Axel Kohlmeyer f12031f84d add support for building rigid bodies from custom atom properties or atom style variables 2017-10-04 01:14:57 -04:00
Axel Kohlmeyer c522b1b7a9 add call to fftw_cleanup() before exiting to avoid bogus leak reports when compiling with FFTW v3.x 2017-10-04 00:22:56 -04:00
Stan Moore a55adf4a68 Update to Kokkos r2.04.04 and add workaround for performance regression 2017-10-03 11:30:00 -06:00
James Barnett 2876baafd0 Use -restrict whenever Intel is used, no matter the package 2017-10-03 13:08:56 -04:00
Stan Moore ca032f21fb Add Kokkos threaded reverse comm option 2017-10-03 10:14:24 -06:00
James Barnett 197f082784 cmake: Add -restrict for Intel compilers for some packages 
Some packages (USER-OMP, OPT, and USER-INTEL) require the -restrict
flag when using the Intel compiler.
 2017-10-03 11:28:33 -04:00
Axel Kohlmeyer 1bb7af9ef9 integrate fix rhok into the LAMMPS source code management and documentation system 2017-10-03 10:45:08 -04:00
Axel Kohlmeyer 251f28049a make fix rhok more similar to other LAMMPS sources 
- re-indent to 2 blanks
- white space cleanup
- use force->numeric() and force->inumeric() instead of atof() and atoi()
- include system headers before local LAMMPS headers
 2017-10-03 10:10:38 -04:00
Axel Kohlmeyer f07719e924 make fix rhok examples more consistent with LAMMPS conventions: 
- move example folder to examples/USER/misc/
- comment out writing of trajectory files
- reduce run length (for easier testing for regressions)
- record example outputs for 1 and 4 MPI processes
- rename readme.md to README.md for visibility
 2017-10-03 10:08:38 -04:00
Ulf R. Pedersen 5f527091b8 Update readme.md 2017-10-03 12:02:01 +02:00
Ulf R. Pedersen 30aaa7e47b Update readme.md 2017-10-03 12:00:43 +02:00
Ulf R. Pedersen 74dcf0bf9b Update readme.md 2017-10-03 11:54:46 +02:00
Ulf R. Pedersen e9b07a7a10 Update readme.md 2017-10-03 11:52:48 +02:00
Ulf R. Pedersen fd8f5f8f9e Update readme.md 2017-10-03 11:52:08 +02:00
Ulf R. Pedersen 5c59eb637b Update readme.md 2017-10-03 11:49:57 +02:00
Ulf R. Pedersen 250ef9f837 Update readme.md 2017-10-03 11:46:08 +02:00
Ulf R. Pedersen e44f370d49 Update readme.md 2017-10-03 11:44:52 +02:00
Ulf R. Pedersen 1e790fbafe Update readme.md 
Now use the standard namings.
Corrected spelling errors.
 2017-10-03 11:44:23 +02:00
Ulf R. Pedersen 35cc795972 Update in.setup 2017-10-03 11:17:43 +02:00
Ulf R. Pedersen 245bf74552 Rename setup.lmp to in.setup 2017-10-03 11:16:54 +02:00
Ulf R. Pedersen 7e8bbe8481 Rename pinning.lmp to in.pinning 2017-10-03 11:16:29 +02:00
Ulf R. Pedersen e6d687faac Rename crystal.lmp to in.crystal 2017-10-03 11:15:49 +02:00
Ulf R. Pedersen 8a2cf5ce8e reformatting and use citeme class 2017-10-03 11:13:10 +02:00
Ulf R. Pedersen 8f79f5ddb9 add the LAMMPS copyright 2017-10-03 10:59:46 +02:00
Ulf R. Pedersen 40ae6f215b add the usual LAMMPS copyright 2017-10-03 10:58:21 +02:00
Ulf R. Pedersen 4dcc49ebe2 Delete fix_rhok.cpp 2017-10-03 10:56:07 +02:00
Ulf R. Pedersen fe14eeccac Delete fix_rhok.h 2017-10-03 10:54:22 +02:00
Michael Brown 9dc42fd4db intel_simd.h is currently also needed by dihedral/charmm, not just sw. 2017-10-02 23:53:05 -07:00
Michael Brown 5e89269631 Minor adjustments to intel makefiles and documentation based on the reversed 
preprocessor logic and default memory align. Removing knl_coprocessor makefile.
 2017-10-02 23:41:14 -07:00
Axel Kohlmeyer 11eed234f0 include dump cfg/uef in commands toctree 2017-10-03 00:14:34 -04:00
David Nicholson af1fc45db0 added citation to doc 2017-10-03 00:04:52 -04:00
David Nicholson b34109af60 formatting changes 2017-10-02 23:43:31 -04:00
David Nicholson 1dffb0cf82 reran npt_biaxial examples 2017-10-02 23:27:10 -04:00
David Nicholson 588b2534c9 Minor fix for FixNHUef constructor 2017-10-02 23:26:21 -04:00
Axel Kohlmeyer d2aa05cb36 update README in USER-INTEL for recent LRT logic reversal 2017-10-02 21:24:51 -04:00
Axel Kohlmeyer 466fde6443 update documentation for the reversal in the INTEL_MKL_RNG define 2017-10-02 21:20:26 -04:00
Axel Kohlmeyer 2a24cbfe0c reverse logic for using MKL pRNG: this way, make serial and make mpi will compile LAMMPS with USER-INTEL installed 2017-10-02 21:13:51 -04:00
Axel Kohlmeyer 00aef0fe00 rerun logfiles for USER-UEF example inputs 2017-10-02 17:40:46 -04:00
Axel Kohlmeyer 92d9b361fc include USER-UEF styles in PDF version of manual 2017-10-02 17:39:59 -04:00
Axel Kohlmeyer 8acdc8020d add USER-UEF classes to .gitignore 2017-10-02 17:24:36 -04:00
Axel Kohlmeyer cc09a633a2 small code refactor for FixNHUef class 
- use forward declaration for UEFBox to avoid having to include custom header
- remove uef_arg_kludge() thanks to changes in 0c7879e902
 2017-10-02 17:19:42 -04:00
Axel Kohlmeyer 81be9b37de formatting, whitespace and include file/constants cleanup 2017-10-02 17:15:13 -04:00
Axel Kohlmeyer 0c7879e902 provide compatibility entries in FixNH option parsing for new USER-UEF package 2017-10-02 16:31:41 -04:00
Axel Kohlmeyer 8d384b9149 whitespace cleanup 2017-10-02 15:03:48 -04:00
Stan Moore 529eeb6039 Reduce GPU data transfer 2017-10-02 09:31:39 -06:00
Michael Brown cf24dd0265 Adding pair style dpd/intel and dihedral style fourier/intel 
Adding raw performance numbers for Skylake xeon server.
Fixes for using older Intel compilers and compiling without OpenMP.
Fix adding in hooks for using USER-INTEL w/ minimization.
 2017-10-02 04:53:17 -07:00
Lars Pastewka a7b0d1f521 DOC: Corrected syntax for appending at certain frame (NetCDF only) 2017-10-01 14:40:19 +02:00