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4614 Commits

Author SHA1 Message Date
Axel Kohlmeyer 4f37b46b10 Merge branch 'master' into small-doc-fixes 2018-08-17 11:24:25 -04:00
Steven J. Plimpton 5436169c20 change format of Howto and Tools doc pages 2018-08-17 09:20:44 -06:00
Steven J. Plimpton 7dac513235 doc typos and push author details back to website 2018-08-17 09:15:21 -06:00
Richard Berger c0544ba346 Actually rename the file 2018-08-17 10:34:17 -04:00
Richard Berger eb7568a4fb Fixes issue #1058 2018-08-17 10:13:19 -04:00
Axel Kohlmeyer bfaa345536 add comment on KOKKOS compiler and platform support 2018-08-17 00:09:39 -04:00
Axel Kohlmeyer f8c9ab4a3e some rewrite/update of the accelerator comparison page removing outdated info 2018-08-16 23:47:00 -04:00
Axel Kohlmeyer a8c687aee8 cleaner formatting in Sphinx for package tables 2018-08-16 22:41:48 -04:00
Axel Kohlmeyer e05d471869 fix typo 2018-08-16 22:33:13 -04:00
Steven J. Plimpton b7d64e0374 patch 16Aug18 2018-08-16 11:55:57 -06:00
Richard Berger 47f02b323a Undo change, would create inconsistent tocs 2018-08-16 12:39:48 -04:00
Steven J. Plimpton b55f3162f4 date got lost somehow 2018-08-16 09:41:04 -06:00
Steven J. Plimpton 8cea92d0bd few more formatting issues 2018-08-16 09:24:55 -06:00
Steven J. Plimpton 07cd194e27 tweaks to Manual formatting 2018-08-15 16:27:39 -06:00
Steven J. Plimpton 46f1e63a19 update to Authors for CMake addition 2018-08-15 15:14:01 -06:00
Steven J. Plimpton 9e154abba0 remove pre-install of 3 default packages from docs 2018-08-15 14:55:48 -06:00
Steven J. Plimpton c9131cf1de drop FFTW2 support, and change doc pages 2018-08-15 13:54:37 -06:00
Steven J. Plimpton 95bfc3b536 one more entry to lammps.book 2018-08-15 07:54:17 -06:00
Steven J. Plimpton 1823fc2bd1 commands.txt -> commands_list.txt to avoid conflict with Commands.txt 2018-08-15 07:50:10 -06:00
Steven J. Plimpton 6eededb190 one more tweak 2018-08-15 07:45:52 -06:00
Steven J. Plimpton 6c90410260 one more file I forgot to commit 2018-08-15 07:44:36 -06:00
Steven J. Plimpton 9c3748e07c change Python.txt to Python_head.txt, adapt GPU package syntax 2018-08-15 07:31:31 -06:00
Richard Berger b72048097c Correct Build_settings.txt 2018-08-14 22:17:40 -04:00
Richard Berger 9526db44ce Fix lammps.book and broken link 2018-08-14 22:10:08 -04:00
Steven J. Plimpton 63f57bbece small tweak on USER-INTEL section 2018-08-14 16:07:04 -06:00
Steven J. Plimpton 7ec52784cb more changes to doc pages and CMakeLists.txt 2018-08-14 15:44:25 -06:00
Richard Berger 7ab11488d0 Added brief discussion on how to use presets files with CMake 2018-08-14 11:51:37 -04:00
Richard Berger 13bb02b100 Updated CMake build for USER-INTEL 
- Removed differences between MAKE/OPTIONS/Makefile.intel_cpu/coprocessor and
  CMake compilation and added INTEL_ARCH to select between CPU and KNL.
- Added some sanity checks for requirements
- Added FindTBB
 2018-08-13 19:58:54 -04:00
Richard Berger 8634301b53 Limit depth of howto tocs 2018-08-13 11:48:32 -04:00
Richard Berger fef2b8260b Correct CMake FFT settings in docs 
The upper or lowercase matters. It won't work with lower case.
 2018-08-13 11:46:46 -04:00
Axel Kohlmeyer 6e8a68a420 fix a bunch of typos and broken links as detected by ebook-convert 2018-08-12 17:16:24 +02:00
Axel Kohlmeyer 11f04fde5c fix typo 2018-08-12 16:44:31 +02:00
Axel Kohlmeyer e01185c283 correct some errors and misconceptions about zlib and USER-OMP 2018-08-12 16:44:26 +02:00
Steven J. Plimpton 907b061e0b more updates to Build doc page 2018-08-10 15:04:33 -06:00
Axel Kohlmeyer b33452040a correct FFT definitions in docs and make -DFFT_KISSFFT explicit in CMake 2018-08-10 17:27:40 +02:00
Axel Kohlmeyer ddd8533d81 make -DLAMMPS_MEMALIGN optional in CMake by checking of 0 alignment. also some rewording. 
this changes the CMake configuration file.
also, the special case of Windows not supporting posix_memalign() is documented.
some more explanations for FFTs and memory alignment are added
 2018-08-10 16:33:20 +02:00
Axel Kohlmeyer bc8939a08b more corrections/rewrites/additions for OpenMP, QM/MM and USER-QUIP 2018-08-10 15:55:32 +02:00
Axel Kohlmeyer f67b198c24 discourage the use of MEAM and REAX, which have been supersede by USER-MEAMC and USER-REAXC 2018-08-10 13:04:31 +02:00
Axel Kohlmeyer 13d1f26a0f provide additional information about building QM/MM with QE 2018-08-10 12:15:49 +02:00
Axel Kohlmeyer 8318b96c11 update OpenMP support info in build basics 2018-08-10 11:54:51 +02:00
Axel Kohlmeyer 0b523cb48e some rewording and updates for the traditional and cmake documentation 2018-08-10 11:38:59 +02:00
Richard Berger 76289cd955 Add LAMMPS shared library instructions for CMake 2018-08-09 17:50:55 -04:00
Richard Berger edb535d36f Fix some of the missing TODOs in cmake docs 2018-08-09 17:21:00 -04:00
Richard Berger 4db08f5351 Some tweaks and corrections 2018-08-09 16:02:54 -04:00
Richard Berger 630a46ad67 Move Manual_version to Intro 
It should not be its own chapter. The intro seems to be the right place for it.
 2018-08-09 14:53:40 -04:00
Axel Kohlmeyer aca9416c7f Merge branch 'master' into doc-reorg-start and resolve merge conflicts with master 
Conflicts:
	doc/src/Speed_kokkos.txt
	doc/src/package.txt
 2018-08-09 20:18:12 +02:00
Axel Kohlmeyer f7164e593e fix a few more broken or non-unique links 2018-08-09 20:09:11 +02:00
Axel Kohlmeyer a5170e93ec fix a bunch more broken, duplicate links and misformatted text 2018-08-09 19:46:25 +02:00
Axel Kohlmeyer 108f2d0ed7 Merge branch 'collected-small-changes' into doc-reorg-start 
Resolved Conflicts:
	doc/src/Packages_details.txt
	doc/src/Python_shlib.txt
	doc/src/fix_manifoldforce.txt
 2018-08-09 18:48:11 +02:00
Steve Plimpton 6663fbeb11
Merge pull request #928 from akohlmey/fix-rcb-balance-issue 
Fix rcb balance issue
 2018-08-09 10:24:38 -06:00
Steven J. Plimpton cfc1b3a823 more changes induced by removing Section_start.txt 2018-08-09 10:20:02 -06:00
Steven J. Plimpton c97e6537c8 changes to replace Section_start.txt 2018-08-09 10:19:10 -06:00
Axel Kohlmeyer bb25e5d98a adjust header levels for Tools section 2018-08-09 17:13:07 +02:00
Axel Kohlmeyer 8e9ea1e4fa formatting tweak for Build the manual page 2018-08-09 17:13:07 +02:00
Axel Kohlmeyer f4ea28cd32 update src/lammps.book file with missing entries 2018-08-09 17:13:07 +02:00
Axel Kohlmeyer 1604f011d2 fix a couple more broken links 2018-08-09 17:13:07 +02:00
Axel Kohlmeyer a065143723 create missing "Build_manual.txt" file from 'doc/README' 2018-08-09 17:13:07 +02:00
Axel Kohlmeyer df20fbbca4 fix a bunch of broken linke or make links unique across files 2018-08-09 17:13:07 +02:00
Steven J. Plimpton d5594350c4 change zero-size shrink box to original box 2018-08-09 08:50:11 -06:00
Axel Kohlmeyer 9521814441 rename Kokkos::gpu_direct to Kokkos::gpu_direct_flag 
This is for consistency with other parts of LAMMPS where
such variables have "flag" in their name. Also reduces
confusion with have_gpu_direct() function.

When we can safely detect, that GPU-direct is not available,
change the default setting of Kokkos::gpu_direct_flag from 1 to 0
 2018-08-09 04:52:58 -04:00
Axel Kohlmeyer dd9fed11dc use '-pk kokkos gpu/direct on/off' consistently in comments and docs 2018-08-09 04:16:22 -04:00
Stan Moore 1c550d8f39 Change defaults for GPU-direct to use comm host 2018-08-08 16:46:36 -06:00
Stan Moore d8aa6d534b Remove hardcoded GPU-direct in KOKKOS package 2018-08-08 16:09:41 -06:00
Axel Kohlmeyer 64e152bced add some notes about GPU-direct support requirements to the manual 2018-08-08 14:25:49 +02:00
sergeylishchuk 4d75d2d611 more changes to ATM source and doc file 2018-08-06 20:49:05 +01:00
Richard Berger fba9f0aaae Fix various links 2018-08-06 00:10:06 -04:00
Richard Berger 6927ed5eb9 Fix pair body rounded polygon and polyhedron links 2018-08-06 00:01:38 -04:00
Richard Berger 6de3dab72a Remove duplicates 2018-08-05 23:59:52 -04:00
Steven J. Plimpton 82744773b3 replace Section_commands.txt file 2018-08-03 16:04:54 -06:00
Richard Berger 2321c8ff37 Merge remote-tracking branch 'origin/master' into doc-reorg-intro-howto 2018-08-03 00:12:58 -04:00
Richard Berger 9cc75792d6 Update lammps.book 2018-08-02 23:29:29 -04:00
Steven J. Plimpton f330013584 lost SPIN in package list 2018-08-02 14:26:02 -06:00
Steven J. Plimpton 39f61a78f2 couple more doc page tweaks 2018-08-02 14:09:00 -06:00
Steven J. Plimpton c105e21a73 more mods to Intro section 2018-08-02 13:58:25 -06:00
Steven J. Plimpton fb03924e83 patch 2Aug18 2018-08-02 11:12:57 -06:00
Axel Kohlmeyer 42948b60ee corrections for broken links in the html docs 2018-08-01 14:37:03 +02:00
Steven J. Plimpton 90897f570e changes for Intro and Howto doc pages 2018-07-31 15:27:09 -06:00
Steve Plimpton eb967a8a6c
Merge pull request #1027 from akohlmey/move-cdeam 
Move pair style eam/cd from USER-MISC to MANYBODY
 2018-07-31 10:39:18 -06:00
Steve Plimpton 2b7b61d5b7
Merge pull request #1023 from amritagos/patch-1 
docs:  Fix spelling mistakes and clarify Tools.txt
 2018-07-31 10:38:47 -06:00
Steve Plimpton 8c0955aaff
Merge pull request #1025 from lammps/doc-reorg-speed-packages 
changes to Packages and Speed doc files
 2018-07-31 08:58:49 -06:00
Axel Kohlmeyer f3615e83e8 move pair style eam/cd from USER-MISC to MANYBODY and update docs accordingly 2018-07-31 09:18:37 +02:00
Richard Berger 18a7b1ab4f Fix broken links and duplicate TOC 2018-07-30 21:32:12 -04:00
Richard Berger 57cd1ab55a Add missing extension 2018-07-30 19:13:26 -04:00
Richard Berger 34f619ea1d Update lammps.book 2018-07-30 19:04:52 -04:00
Steve Plimpton a8e2a0a54b
Merge pull request #1019 from rbberger/cmake_updates 
CMake updates
 2018-07-30 15:18:47 -06:00
Steven J. Plimpton d9c328932f changes to Packages and Speed doc files 2018-07-30 12:31:12 -06:00
Amrita Goswami b76f86602a
docs: Fix spelling mistakes and clarify Tools.txt 2018-07-30 21:18:59 +05:30
julient31 28993d9823 Commit JT 072618 
- improvements documentation (dmi and exchange)
- correction error cross product in pair_spin_dmi.cpp
- implementation mech. part in pair_spin_dmi.cpp
- correction in all pairs: init_one for [j][i] couples
- correction in atom_vec_spin.cpp: index error in read_data
- some improvements in pair_spin_dmi.cpp and pair_spin_magelec.cpp
 2018-07-27 12:00:15 +02:00
sergeylishchuk 649d0167c8 sorted out restart 2018-07-27 10:41:01 +01:00
Richard Berger 9ffd262039 Add CMake target for html documentation 2018-07-27 02:46:36 -04:00
Richard Berger 819e47b69e Add output dir and verbose option to txt2rst 2018-07-27 02:30:28 -04:00
sergeylishchuk a2303e5a15 more changes to ATM source and doc file 2018-07-26 11:54:04 +01:00
sergeylishchuk 7cae80b6d8 Merge https://github.com/lammps/lammps 
more changes to ATM source and doc file
 2018-07-26 11:42:53 +01:00
Richard Berger 532d09bd56 Correct lammps.book 2018-07-25 16:56:49 -04:00
Richard Berger 353ecd2c7a Correct header levels 2018-07-25 16:56:28 -04:00
Richard Berger e6e026433c Fix clean-all in docs Makefile 2018-07-25 16:49:51 -04:00
Steven J. Plimpton 1d9ad55796 changes to Errors and Python doc pages 2018-07-25 14:10:00 -06:00
Richard Berger 592804d56f Fix header level of Tools.txt 2018-07-25 11:53:31 -04:00
Richard Berger ee394b0ed1 Fixup header levels 2018-07-25 11:53:17 -04:00
Richard Berger 030f1c0127 Update lammps.book 2018-07-25 11:48:57 -04:00