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19805 Commits

Author SHA1 Message Date
Axel Kohlmeyer 0613790b6b
support having the keyword special multiple times after pair in pair_modify 2020-01-29 17:23:11 -05:00
Axel Kohlmeyer 0d0c5e2961
make KOKKOS and KSPACE FFT3d code more consistent and remove redundant code 2020-01-29 16:37:29 -05:00
Axel Kohlmeyer ccd395fdd8
remove dead code 2020-01-29 14:34:03 -05:00
Axel Kohlmeyer 5962e880d4
remove some unneeded backslash escapes 2020-01-29 14:33:36 -05:00
Julien Guénolé 426ca97aa6 correct bug introduced in previous commit 2020-01-29 17:53:10 +01:00
Julien Guénolé 1e7f09bded removing deprecated functions in log comment 2020-01-29 17:50:56 +01:00
Julien Guénolé 60b9627657 one missing example 2020-01-29 17:48:58 +01:00
Axel Kohlmeyer c855bbb6bf
Merge branch 'master' into adaptglok 2020-01-29 11:42:25 -05:00
Julien Guénolé 6bd23f4909 New example folder for fire 2020-01-29 17:31:20 +01:00
Axel Kohlmeyer 668feb22b5
Merge pull request #1859 from giacomofiorin/colvars-update 
Update Colvars library to version 2020-01-27
 2020-01-28 16:01:59 -05:00
Giacomo Fiorin 9427fc50a5 Update Colvars library to version 2020-01-27 
One new feature (arithmetic path variables) and several smaller enhancements
or bugfixes.

    Fix error check when loading an old state file
    https://github.com/Colvars/colvars/pull/317

    Get default values for grid boundaries when available
    https://github.com/Colvars/colvars/pull/310

    Allow redefining existing index groups (warn when this happens)
    https://github.com/Colvars/colvars/pull/302

    Simplified replica communication syntax in metadynamics
    https://github.com/Colvars/colvars/pull/301

    Obtain the bias_energy for ABF biases
    https://github.com/Colvars/colvars/pull/294

    Fix reading path file with vector CVCs
    https://github.com/Colvars/colvars/pull/288

    Fix segfault at deleting CVBasedPath
    https://github.com/Colvars/colvars/pull/286

    Parrinello's (arithmetic) pathCV in CV space
    https://github.com/Colvars/colvars/pull/274

    Fix race condition when starting a bundle of walkers
    https://github.com/Colvars/colvars/pull/279
 2020-01-28 14:15:05 -05:00
Julien Guénolé e9b6824e11 correct spelling 2020-01-28 16:27:19 +01:00
Julien Guénolé a3d10d537c Updated documentation 2020-01-28 16:03:49 +01:00
Julien Guénolé 197ba62cd9 Change fire to fire/old and fire2 to fire. Implement normstyle in fire. Update author affiliation. 2020-01-28 14:51:23 +01:00
Axel Kohlmeyer 5eef3b1828
Merge pull request #1855 from akohlmey/remove-txt-files 
Remove txt sources of rst files from doc folder
 2020-01-27 12:04:37 -05:00
Axel Kohlmeyer 99cfc9e668
small documentation tweak 2020-01-27 11:17:08 -05:00
Axel Kohlmeyer 795f2fd894
properly support threaded FFTs with MKL and document it. remove commented out FFTW2 code 2020-01-27 11:00:57 -05:00
Axel Kohlmeyer ec381964e4
Merge branch 'master' into remove-txt-files 
# Conflicts:
#	doc/src/Build_settings.rst
 2020-01-24 21:32:24 -05:00
Axel Kohlmeyer 4134d7fddd
Merge pull request #1854 from akohlmey/next_patch_release 
Update version string for the next patch release
 2020-01-24 20:58:03 -05:00
Axel Kohlmeyer da35840cd9
Merge pull request #1520 from stanmoore1/fft 
Add threaded FFTs to the KOKKOS package
 2020-01-24 18:21:33 -05:00
Stan Moore 9d333c351a Small clarification to kspace_style.rst 2020-01-24 14:42:40 -07:00
Stan Moore 669980388a Merge branch 'fft' of ssh://github.com/stanmoore1/lammps into fft 2020-01-24 14:33:31 -07:00
Stan Moore 76aaf16c66 Add check for FFT_FFTW_THREADS and turn off MKL threads for now 2020-01-24 14:30:11 -07:00
Stan Moore e9d4823d71 Add cuFFT to Makefile.lassen_kokkos and generalize MPI path 2020-01-24 13:56:00 -07:00
Axel Kohlmeyer 0302c0ba24
correct malformed tables 2020-01-24 12:30:15 -05:00
Axel Kohlmeyer c9cc13c2a6
add mpi4py url and expand/update the python with MPI introduction 2020-01-24 11:27:43 -05:00
Oliver Henrich 899a654161 Merge branch 'master' into user-cgdna 2020-01-24 14:21:55 +00:00
Oliver Henrich 23febc7101 Increased tolerance for fatal error in FENE bond argument 2020-01-24 14:19:18 +00:00
Axel Kohlmeyer fa4d9ff0d8
remove automatic translation of .txt to .rst and references to txt folder 2020-01-23 16:56:41 -05:00
Axel Kohlmeyer daa5efe1fd
remove .txt doc sources 2020-01-23 16:53:11 -05:00
Axel Kohlmeyer 72d8bea459
remove backslash escapes for underscore in doc references 2020-01-23 16:52:38 -05:00
Axel Kohlmeyer cb5138a335
update version string for the next patch release 2020-01-23 12:00:33 -05:00
Axel Kohlmeyer f14b200b6a
correct KOKKOS FFT output for CMake summary one more time 2020-01-23 00:27:00 -05:00
Axel Kohlmeyer df23460e18
Merge branch 'master' into fft 
# Conflicts:
#	src/MAKE/OPTIONS/Makefile.kokkos_cuda_mpi
 2020-01-23 00:22:38 -05:00
Axel Kohlmeyer 958b8d96a9
expand explanations about setting the python version for the python wrapper 2020-01-23 00:14:44 -05:00
Axel Kohlmeyer 204fb6f7ed
fix issue with standalone anchor_check 2020-01-22 23:51:53 -05:00
Axel Kohlmeyer 30444b344b
Merge pull request #1853 from akohlmey/collected-small-changes 
Collected small changes and bugfixes for the next patch release
 2020-01-22 17:25:03 -05:00
Axel Kohlmeyer 8096a78340
Merge pull request #1852 from vklip/bugfix-gjf 
Add unit conversion in setup() in fix_langevin.cpp
 2020-01-22 17:22:01 -05:00
Axel Kohlmeyer 949d7608ba
Merge pull request #1811 from brycelelbach/bug/missing_execution_space_qualifiers 
Fix mismatches in CUDA execution space qualifiers between declarations and definitions.
 2020-01-22 17:10:11 -05:00
Axel Kohlmeyer c126df4f79
update KOKKOS FFT status message in CMake summary 2020-01-22 17:08:58 -05:00
Axel Kohlmeyer 5488efbc03
fix typo, update maintainer. 2020-01-22 17:00:10 -05:00
Axel Kohlmeyer 53554fdb84
add -DFFT_CUFFT for KOKKOS only when KISSFFT is not selected 2020-01-22 16:56:12 -05:00
Axel Kohlmeyer 70731468df
include "pppm.h" last so that necessary KOKKOS config define is available 2020-01-22 16:32:32 -05:00
Axel Kohlmeyer 9d06430894
Merge pull request #603 from jrgissing/Ncreate_atoms 
add exactly N particles to available lattice points
 2020-01-22 15:36:54 -05:00
Axel Kohlmeyer 61ddf9bcd8
undo accidental edit of KOKKOS cuda mpi makefile 2020-01-22 15:32:00 -05:00
Axel Kohlmeyer 70b9a060dc
add missing #endif 2020-01-22 15:26:34 -05:00
Axel Kohlmeyer 9a27aa4e9e
Merge branch 'master' into fft 
# Conflicts:
#	src/MAKE/OPTIONS/Makefile.kokkos_cuda_mpi
 2020-01-22 15:21:08 -05:00
Axel Kohlmeyer dfda8b5ce6
fix up LMP_FFT_LIB for reporting FFT lib in use for KOKKOS with CUDA logic 2020-01-22 15:18:59 -05:00
Axel Kohlmeyer 40e0e78abd
import template atom ID check from PR #1822 2020-01-22 15:02:55 -05:00
Axel Kohlmeyer bb024bc077
add call to KSpace::two_charge() that was overlooked 2020-01-22 14:46:57 -05:00